use cases

Logo

In this repo, we present a full example of the metaGOflow pipeline using actual EMO BON sequence data.

View the Project on GitHub hariszaf/metaGOflow-use-case

Water column

Quality control

metaGOflow invokes fastp that automatically returns a .html report like the one below for the case of this water column sample:

Taxonomic inventory

metaGOflow uses the mapSEQ to extract taxa present on the community based on the ribosomal RNA sequences.

Here is the krona plot metaGOflow returns as a visual component of the community structure.

Functional annotation

metaGOflow supports a functional annotation step that uses the filtered reads and a series of tools and databases to return several types of annotations.

InterProScan (IPS)

On the first column we get the number of hits an id had among the reads, on the second the IPS id and on the third its description.

119800 IPR003439 ABC transporter-like, ATP-binding domain
71034 IPR015590 Aldehyde dehydrogenase domain
48578 IPR002347 Short-chain dehydrogenase/reductase SDR
47497 IPR002300 Aminoacyl-tRNA synthetase, class Ia
46261 IPR000515 ABC transporter type 1, transmembrane domain MetI-like
43537 IPR000873 AMP-dependent synthetase/ligase
35359 IPR003959 ATPase, AAA-type, core
34864 IPR004839 Aminotransferase, class I/classII
34450 IPR000795 Translational (tr)-type GTP-binding domain
34101 IPR017932 Glutamine amidotransferase type 2 domain
32180 IPR001789 Signal transduction response regulator, receiver domain
32062 IPR013126 Heat shock protein 70 family
32003 IPR006222 Aminomethyltransferase, folate-binding domain
30885 IPR001036 Acriflavin resistance protein
29955 IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
28212 IPR001030 Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
27613 IPR001509 NAD-dependent epimerase/dehydratase
27286 IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit
26488 IPR005814 Aminotransferase class-III
25975 IPR005479 Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain
25833 IPR017926 Glutamine amidotransferase
25325 IPR010656 TRAP C4-dicarboxylate transport system permease DctM subunit
25254 IPR000581 Dihydroxy-acid/6-phosphogluconate dehydratase
23899 IPR000788 Ribonucleotide reductase large subunit, C-terminal
23650 IPR024084 Isopropylmalate dehydrogenase-like domain
23099 IPR000917 Sulfatase, N-terminal
22712 IPR000192 Aminotransferase class V domain
22588 IPR016040 NAD(P)-binding domain
22186 IPR014018 SecA motor DEAD
21773 IPR003953 FAD-dependent oxidoreductase 2, FAD binding domain
21759 IPR011527 ABC transporter type 1, transmembrane domain
21342 IPR020846 Major facilitator superfamily domain
21098 IPR008146 Glutamine synthetase, catalytic domain
21091 IPR024041 Ammonium transporter AmtB-like domain
20964 IPR003029 S1 domain
20864 IPR006073 GTP binding domain
20676 IPR022761 Fumarate lyase, N-terminal
20408 IPR005475 Transketolase-like, pyrimidine-binding domain
20363 IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
20123 IPR001460 Penicillin-binding protein, transpeptidase
20021 IPR001986 Enolpyruvate transferase domain
19980 IPR000620 EamA domain
19801 IPR006076 FAD dependent oxidoreductase
19783 IPR000194 ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
19732 IPR002205 DNA topoisomerase, type IIA, domain A
19670 IPR040131 MnmG, N-terminal domain
19310 IPR001753 Enoyl-CoA hydratase/isomerase
18941 IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
18799 IPR023616 Cytochrome c oxidase-like, subunit I domain
18748 IPR023753 FAD/NAD(P)-binding domain
18568 IPR001650 Helicase, C-terminal
18504 IPR007120 DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
18298 IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
18265 IPR023631 Amidase signature domain
18033 IPR004131 Pyrophosphate-energised proton pump
17976 IPR018164 Alanyl-tRNA synthetase, class IIc, N-terminal
17858 IPR000883 Cytochrome c oxidase subunit I
17828 IPR001734 Sodium/solute symporter
17555 IPR002932 Glutamate synthase domain
17449 IPR001173 Glycosyltransferase 2-like
17344 IPR003594 Histidine kinase/HSP90-like ATPase
17311 IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)
17209 IPR002305 Aminoacyl-tRNA synthetase, class Ic
17200 IPR006171 TOPRIM domain
17059 IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal
16902 IPR019734 Tetratricopeptide repeat
16892 IPR012131 Histidinol dehydrogenase
16875 IPR001078 2-oxoacid dehydrogenase acyltransferase, catalytic domain
16662 IPR001851 ABC transporter, permease
16490 IPR001926 Pyridoxal-phosphate dependent enzyme
16470 IPR006062 Histidine biosynthesis protein
16372 IPR003673 CoA-transferase family III
16256 IPR001763 Rhodanese-like domain
16238 IPR014001 Helicase superfamily 1/2, ATP-binding domain
16133 IPR005835 Nucleotidyl transferase domain
16076 IPR000994 Peptidase M24
15779 IPR001182 Probable peptidoglycan glycosyltransferase FtsW/RodA
15703 IPR000891 Pyruvate carboxyltransferase
15686 IPR020058 Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain
15178 IPR002078 RNA polymerase sigma factor 54 interaction domain
15126 IPR001451 Hexapeptide repeat
15062 IPR001114 Adenylosuccinate synthetase
14937 IPR039429 Serine hydroxymethyltransferase-like domain
14837 IPR015413 Methionyl/Leucyl tRNA synthetase
14833 IPR023210 NADP-dependent oxidoreductase domain
14734 IPR000897 Signal recognition particle, SRP54 subunit, GTPase domain
14710 IPR012910 TonB-dependent receptor, plug domain
14623 IPR001279 Metallo-beta-lactamase
14544 IPR001296 Glycosyl transferase, family 1
14504 IPR001098 DNA-directed DNA polymerase, family A, palm domain
14413 IPR000089 Biotin/lipoyl attachment
14309 IPR001048 Aspartate/glutamate/uridylate kinase
14028 IPR015890 Chorismate-utilising enzyme, C-terminal
13924 IPR011764 Biotin carboxylation domain
13871 IPR013221 Mur ligase, central
13719 IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
13561 IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
13457 IPR020616 Thiolase, N-terminal
13439 IPR011763 Acetyl-coenzyme A carboxyltransferase, C-terminal
13379 IPR002823 Protein of unknown function DUF112, transmembrane
13321 IPR011545 DEAD/DEAH box helicase domain
13315 IPR001017 Dehydrogenase, E1 component
13254 IPR001867 OmpR/PhoB-type DNA-binding domain
13205 IPR002020 Citrate synthase
13199 IPR005474 Transketolase, N-terminal
13155 IPR000043 Adenosylhomocysteinase-like
13112 IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
13070 IPR034733 Acetyl-CoA carboxylase
13019 IPR001347 SIS domain
13018 IPR000092 Polyprenyl synthetase
12979 IPR011762 Acetyl-coenzyme A carboxyltransferase, N-terminal
12920 IPR000262 FMN-dependent dehydrogenase
12893 IPR001576 Phosphoglycerate kinase
12703 IPR007197 Radical SAM
12661 IPR003010 Carbon-nitrogen hydrolase
12604 IPR000489 Pterin-binding domain
12548 IPR001518 Argininosuccinate synthase
12471 IPR001093 IMP dehydrogenase/GMP reductase
12388 IPR034300 NADP transhydrogenase beta-like domain
12241 IPR000760 Inositol monophosphatase-like
12225 IPR011761 ATP-grasp fold
12198 IPR002912 ACT domain


GO-slim

GO slim is a cut-down version of the GO ontologies that contain only a subset of terms from the GO resource. metaGOflow provides both a full GO annotation which is not displayed here as it is rather long and a slim version like the one shown here for the water column case. On the first column there is the GO id, on the second its description, on the third its the GO ontology it belogs to (biological process, cellular component, molecular function) and on the fourth one we have the number of hits of the annotation on the reads.

GO:0008150 biological process biological_process 38851
GO:0071973 bacterial-type flagellar cell motility biological_process 5498
GO:0071840 cellular component organization or biogenesis biological_process 67937
GO:0071103 DNA conformation change biological_process 58455
GO:0045454 cell redox homeostasis biological_process 7694
GO:0065003 macromolecular complex assembly biological_process 6748
GO:0016226 iron-sulfur cluster assembly biological_process 19524
GO:0017004 cytochrome complex assembly biological_process 14779
GO:0008152 metabolic process biological_process 133615
GO:0008218 bioluminescence biological_process 415
GO:0009058 biosynthetic process biological_process 864532
GO:0017000 antibiotic biosynthetic process biological_process 4181
GO:0009403 toxin biosynthetic process biological_process 2096
GO:0006259 DNA metabolic process biological_process 260310
GO:0016070 RNA metabolic process biological_process 305843
GO:0006351 transcription, DNA-templated biological_process 117124
GO:0005975 carbohydrate metabolic process biological_process 259282
GO:0048500 signal recognition particle cellular_component 4049
GO:0009288 bacterial type flagellum cellular_component 6493
GO:0005840 ribosome cellular_component 175503
GO:0005694 chromosome cellular_component 1952
GO:0005727 extrachromosomal circular DNA cellular_component 0
GO:0005634 nucleus cellular_component 1706
GO:0009579 thylakoid cellular_component 37866
GO:0019012 virion cellular_component 133
GO:0003674 molecular function molecular_function 62834
GO:0016209 antioxidant activity molecular_function 15983
GO:0004601 peroxidase activity molecular_function 11672
GO:0003824 catalytic activity molecular_function 237894
GO:0016787 hydrolase activity molecular_function 358668
GO:0008233 peptidase activity molecular_function 148778
GO:0016791 phosphatase activity molecular_function 15709
GO:0017111 nucleoside-triphosphatase activity molecular_function 196092
GO:0009055 electron carrier activity molecular_function 83927
GO:0016853 isomerase activity molecular_function 188067
GO:0016874 ligase activity molecular_function 411168
GO:0016829 lyase activity molecular_function 234978
GO:0016491 oxidoreductase activity molecular_function 720889


KEGG terms (KOs)

Similar to the IPS case, on the first column we get the number of hits an id had among the reads, on the second the KO and on the third its description.

</tr>
15983 K01915 glutamine synthetase [EC:6.3.1.2]
15586 K00789 S-adenosylmethionine synthetase [EC:2.5.1.6]
15296 K01251 adenosylhomocysteinase [EC:3.3.1.1]
12811 K02600 transcription termination/antitermination protein NusA
12588 K00626 acetyl-CoA C-acetyltransferase [EC:2.3.1.9]
12054 K00600 glycine hydroxymethyltransferase [EC:2.1.2.1]
11382 K03466 DNA segregation ATPase FtsK/SpoIIIE, S-DNA-T family
11140 K01937 CTP synthase [EC:6.3.4.2]
10805 K01689 enolase [EC:4.2.1.11]
10584 K00134 glyceraldehyde 3-phosphate dehydrogenase [EC:1.2.1.12]
9419 K00602 phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase [EC:2.1.2.3 3.5.4.10]
8882 K00873 pyruvate kinase [EC:2.7.1.40]
8613 K00948 ribose-phosphate pyrophosphokinase [EC:2.7.6.1]
8264 K01698 porphobilinogen synthase [EC:4.2.1.24]
7818 K01358 ATP-dependent Clp protease, protease subunit [EC:3.4.21.92]
7774 K03040 DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
7420 K01939 adenylosuccinate synthase [EC:6.3.4.4]
7376 K03553 recombination protein RecA
7370 K07304 peptide-methionine (S)-S-oxide reductase [EC:1.8.4.11]
7282 K04077 chaperonin GroEL
7186 K03527 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase [EC:1.17.7.4]
7136 K02338 DNA polymerase III subunit beta [EC:2.7.7.7]
7067 K01626 3-deoxy-7-phosphoheptulonate synthase [EC:2.5.1.54]
7062 K00228 coproporphyrinogen III oxidase [EC:1.3.3.3]
6970 K03310 alanine or glycine:cation symporter, AGCS family
6683 K03118 sec-independent protein translocase protein TatC
6589 K02838 ribosome recycling factor
6154 K01803 triosephosphate isomerase (TIM) [EC:5.3.1.1]
6019 K03687 molecular chaperone GrpE
5856 K03701 excinuclease ABC subunit A
5614 K04079 molecular chaperone HtpG
5532 K01918 pantoate--beta-alanine ligase [EC:6.3.2.1]
5513 K03664 SsrA-binding protein
5503 K03111 single-strand DNA-binding protein
5419 K01462 peptide deformylase [EC:3.5.1.88]
5313 K07462 single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
5305 K03522 electron transfer flavoprotein alpha subunit
5302 K03521 electron transfer flavoprotein beta subunit
5229 K03497 ParB family transcriptional regulator, chromosome partitioning protein
5222 K01875 seryl-tRNA synthetase [EC:6.1.1.11]
5208 K02520 translation initiation factor IF-3
5141 K02935 large subunit ribosomal protein L7/L12
5131 K00606 3-methyl-2-oxobutanoate hydroxymethyltransferase [EC:2.1.2.11]
5089 K00275 pyridoxamine 5'-phosphate oxidase [EC:1.4.3.5]
5076 K01940 argininosuccinate synthase [EC:6.3.4.5]
5063 K02897 large subunit ribosomal protein L25
4960 K02879 large subunit ribosomal protein L17
4934 K06153 undecaprenyl-diphosphatase [EC:3.6.1.27]
4847 K01595 phosphoenolpyruvate carboxylase [EC:4.1.1.31]
4835 K04078 chaperonin GroES
4818 K02884 large subunit ribosomal protein L19
4755 K06911 uncharacterized protein
4666 K03526 (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase [EC:1.17.7.1 1.17.7.3]
4637 K09125 uncharacterized protein
4516 K00432 glutathione peroxidase [EC:1.11.1.9]
4509 K03092 RNA polymerase sigma-54 factor
4340 K02888 large subunit ribosomal protein L21
4282 K03101 signal peptidase II [EC:3.4.23.36]
4270 K01056 peptidyl-tRNA hydrolase, PTH1 family [EC:3.1.1.29]
4258 K03313 Na+:H+ antiporter, NhaA family
4256 K00765 ATP phosphoribosyltransferase [EC:2.4.2.17]
4237 K03559 biopolymer transport protein ExbD
4179 K00937 polyphosphate kinase [EC:2.7.4.1]
4157 K06941 23S rRNA (adenine2503-C2)-methyltransferase [EC:2.1.1.192]
4129 K02959 small subunit ribosomal protein S16
4093 K01887 arginyl-tRNA synthetase [EC:6.1.1.19]
3994 K08973 putative membrane protein
3941 K03782 catalase-peroxidase [EC:1.11.1.21]
3934 K01409 N6-L-threonylcarbamoyladenine synthase [EC:2.3.1.234]
3896 K03465 thymidylate synthase (FAD) [EC:2.1.1.148]
3884 K00858 NAD+ kinase [EC:2.7.1.23]
3849 K07738 transcriptional repressor NrdR
3792 K03702 excinuclease ABC subunit B
3741 K02437 glycine cleavage system H protein
3702 K02887 large subunit ribosomal protein L20
3684 K04564 superoxide dismutase, Fe-Mn family [EC:1.15.1.1]
3670 K00793 riboflavin synthase [EC:2.5.1.9]
3652 K01623 fructose-bisphosphate aldolase, class I [EC:4.1.2.13]
3608 K01495 GTP cyclohydrolase IA [EC:3.5.4.16]
3570 K02878 large subunit ribosomal protein L16
3560 K01610 phosphoenolpyruvate carboxykinase (ATP) [EC:4.1.1.49]
3556 K02909 large subunit ribosomal protein L31
3555 K02876 large subunit ribosomal protein L15
3543 K09710 ribosome-associated protein
3490 K02834 ribosome-binding factor A
3428 K03801 lipoyl(octanoyl) transferase [EC:2.3.1.181]
3421 K02950 small subunit ribosomal protein S12
3412 K02899 large subunit ribosomal protein L27
3409 K02954 small subunit ribosomal protein S14
3404 K02867 large subunit ribosomal protein L11
3401 K03621 phosphate acyltransferase [EC:2.3.1.274]
3356 K09919 uncharacterized protein
3342 K01448 N-acetylmuramoyl-L-alanine amidase [EC:3.5.1.28]
3334 K06024 segregation and condensation protein B
3320 K01724 4a-hydroxytetrahydrobiopterin dehydratase [EC:4.2.1.96]
3307 K03070 preprotein translocase subunit SecA [EC:7.4.2.8]
3208 K02078 acyl carrier protein
3204 K01790 dTDP-4-dehydrorhamnose 3,5-epimerase [EC:5.1.3.13]
3193 K06997 PLP dependent protein
3186 K03601 exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
3177 K04066 primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:3.6.4.-]
3176 K01695 tryptophan synthase alpha chain [EC:4.2.1.20]
3144 K01737 6-pyruvoyltetrahydropterin/6-carboxytetrahydropterin synthase [EC:4.2.3.12 4.1.2.50]
3141 K01972 DNA ligase (NAD+) [EC:6.5.1.2]
3117 K02956 small subunit ribosomal protein S15
3107 K02990 small subunit ribosomal protein S6
3106 K00163 pyruvate dehydrogenase E1 component [EC:1.2.4.1]
3070 K06187 recombination protein RecR
3059 K00794 6,7-dimethyl-8-ribityllumazine synthase [EC:2.5.1.78]
3054 K03561 biopolymer transport protein ExbB
3040 K00688 glycogen phosphorylase [EC:2.4.1.1]
3028 K03569 rod shape-determining protein MreB and related proteins
2984 K01736 chorismate synthase [EC:4.2.3.5]


Pfam

Like in the IPS and the KEGG cases.

119800 PF00005 ABC transporter
71034 PF00171 Aldehyde dehydrogenase family
48578 PF00106 short chain dehydrogenase
47497 PF00133 tRNA synthetases class I (I, L, M and V)
43537 PF00501 AMP-binding enzyme
34864 PF00155 Aminotransferase class I and II
34360 PF00009 Elongation factor Tu GTP binding domain
33461 PF13561 Enoyl-(Acyl carrier protein) reductase
32062 PF00012 Hsp70 protein
32003 PF01571 Aminomethyltransferase folate-binding domain
30885 PF00873 AcrB/AcrD/AcrF family
29953 PF01053 Cys/Met metabolism PLP-dependent enzyme
29378 PF00528 Binding-protein-dependent transport system inner membrane component
28212 PF00330 Aconitase family (aconitate hydratase)
27613 PF01370 NAD dependent epimerase/dehydratase family
27286 PF00361 Proton-conducting membrane transporter
26483 PF00202 Aminotransferase class-III
25833 PF00117 Glutamine amidotransferase class-I
25624 PF02786 Carbamoyl-phosphate synthase L chain, ATP binding domain
25325 PF06808 Tripartite ATP-independent periplasmic transporter, DctM component
25254 PF00920 Dehydratase family
23896 PF02867 Ribonucleotide reductase, barrel domain
23650 PF00180 Isocitrate/isopropylmalate dehydrogenase
23099 PF00884 Sulfatase
22712 PF00266 Aminotransferase class-V
21773 PF00890 FAD binding domain
21206 PF16363 GDP-mannose 4,6 dehydratase
21091 PF00909 Ammonium Transporter Family
20864 PF01926 50S ribosome-binding GTPase
20676 PF00206 Lyase
20408 PF02779 Transketolase, pyrimidine binding domain
20363 PF01041 DegT/DnrJ/EryC1/StrS aminotransferase family
20123 PF00905 Penicillin binding protein transpeptidase domain
20021 PF00275 EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
19980 PF00892 EamA-like transporter family
19801 PF01266 FAD dependent oxidoreductase
19783 PF00006 ATP synthase alpha/beta family, nucleotide-binding domain
19732 PF00521 DNA gyrase/topoisomerase IV, subunit A
19670 PF01134 Glucose inhibited division protein A
19310 PF00378 Enoyl-CoA hydratase/isomerase
18941 PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
18881 PF00120 Glutamine synthetase, catalytic domain
18748 PF07992 Pyridine nucleotide-disulphide oxidoreductase
18639 PF00004 ATPase family associated with various cellular activities (AAA)
18504 PF00562 RNA polymerase Rpb2, domain 6
18449 PF00072 Response regulator receiver domain
18265 PF01425 Amidase
18033 PF03030 Inorganic H+ pyrophosphatase
17976 PF01411 tRNA synthetases class II (A)
17858 PF00115 Cytochrome C and Quinol oxidase polypeptide I
17588 PF00271 Helicase conserved C-terminal domain
17555 PF01645 Conserved region in glutamate synthase
17311 PF00152 tRNA synthetases class II (D, K and N)
17209 PF00579 tRNA synthetases class I (W and Y)
17059 PF00441 Acyl-CoA dehydrogenase, C-terminal domain
16968 PF00535 Glycosyl transferase family 2
16912 PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
16892 PF00815 Histidinol dehydrogenase
16875 PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
16856 PF00575 S1 RNA binding domain
16662 PF02653 Branched-chain amino acid transport system / permease component
16490 PF00291 Pyridoxal-phosphate dependent enzyme
16470 PF00977 Histidine biosynthesis protein
16372 PF02515 CoA-transferase family III
16133 PF00483 Nucleotidyl transferase
16076 PF00557 Metallopeptidase family M24
15779 PF01098 Cell cycle protein
15686 PF00749 tRNA synthetases class I (E and Q), catalytic domain
15603 PF00310 Glutamine amidotransferases class-II
15307 PF07724 AAA domain (Cdc48 subfamily)
15062 PF00709 Adenylosuccinate synthetase
14937 PF00464 Serine hydroxymethyltransferase
14837 PF09334 tRNA synthetases class I (M)
14833 PF00248 Aldo/keto reductase family
14710 PF07715 TonB-dependent Receptor Plug Domain
14683 PF00448 SRP54-type protein, GTPase domain
14544 PF00534 Glycosyl transferases group 1
14504 PF00476 DNA polymerase family A
14309 PF00696 Amino acid kinase family
14028 PF00425 chorismate binding enzyme
13871 PF08245 Mur ligase middle domain
13719 PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
13457 PF00108 Thiolase, N-terminal domain
13379 PF01970 Tripartite tricarboxylate transporter TctA family
13321 PF00270 DEAD/DEAH box helicase
13315 PF00676 Dehydrogenase E1 component
13205 PF00285 Citrate synthase, C-terminal domain
13155 PF05221 S-adenosyl-L-homocysteine hydrolase
13070 PF01039 Carboxyl transferase domain
13018 PF00348 Polyprenyl synthetase
12920 PF01070 FMN-dependent dehydrogenase
12893 PF00162 Phosphoglycerate kinase
12850 PF00682 HMGL-like
12831 PF06723 MreB/Mbl protein
12738 PF00364 Biotin-requiring enzyme
12548 PF00764 Arginosuccinate synthase
12471 PF00478 IMP dehydrogenase / GMP reductase domain
12388 PF02233 NAD(P) transhydrogenase beta subunit
12250 PF01019 Gamma-glutamyltranspeptidase
12241 PF00459 Inositol monophosphatase family
12150 PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
12087 PF00456 Transketolase, thiamine diphosphate binding domain
12047 PF00132 Bacterial transferase hexapeptide (six repeats)
11987 PF00109 Beta-ketoacyl synthase, N-terminal domain
11854 PF00580 UvrD/REP helicase N-terminal domain
11848 PF00344 SecY
11830 PF07517 SecA DEAD-like domain
11764 PF01264 Chorismate synthase
11729 PF03462 PCRF domain
11697 PF03441 FAD binding domain of DNA photolyase
11686 PF00311 Phosphoenolpyruvate carboxylase
11679 PF02771 Acyl-CoA dehydrogenase, N-terminal domain
11635 PF00154 recA bacterial DNA recombination protein
11598 PF00701 Dihydrodipicolinate synthetase family
11518 PF00474 Sodium:solute symporter family
11455 PF00814 tRNA N6-adenosine threonylcarbamoyltransferase
11430 PF01702 Queuine tRNA-ribosyltransferase
11426 PF01262 Alanine dehydrogenase/PNT, C-terminal domain
11391 PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase
11390 PF01458 SUF system FeS cluster assembly, SufBD
11290 PF00793 DAHP synthetase I family
11170 PF02562 PhoH-like protein
11149 PF00294 pfkB family carbohydrate kinase
11141 PF00574 Clp protease
11102 PF00587 tRNA synthetase class II core domain (G, H, P, S and T)
11090 PF01131 DNA topoisomerase
11025 PF13193 AMP-binding enzyme C-terminal domain
10980 PF00113 Enolase, C-terminal TIM barrel domain
10957 PF00732 GMC oxidoreductase
10832 PF02347 Glycine cleavage system P-protein
10776 PF07733 Bacterial DNA polymerase III alpha NTPase domain
10739 PF03796 DnaB-like helicase C terminal domain
10736 PF01808 AICARFT/IMPCHase bienzyme
10708 PF00158 Sigma-54 interaction domain
10663 PF02514 CobN/Magnesium Chelatase
10634 PF04542 Sigma-70 region 2
10632 PF01207 Dihydrouridine synthase (Dus)
10562 PF00571 CBS domain
10547 PF04898 Glutamate synthase central domain
10465 PF00883 Cytosol aminopeptidase family, catalytic domain
10433 PF03480 Bacterial extracellular solute-binding protein, family 7
10417 PF00664 ABC transporter transmembrane region
10415 PF00916 Sulfate permease family
10412 PF00490 Delta-aminolevulinic acid dehydratase
10347 PF00679 Elongation factor G C-terminus
10342 PF00588 SpoU rRNA Methylase family
10340 PF03109 ABC1 atypical kinase-like domain
10325 PF03989 DNA gyrase C-terminal domain, beta-propeller
10295 PF00124 Photosynthetic reaction centre protein
10114 PF01406 tRNA synthetases class I (C) catalytic domain
10048 PF00849 RNA pseudouridylate synthase
10034 PF06418 CTP synthase N-terminus
10030 PF00118 TCP-1/cpn60 chaperonin family
10024 PF00753 Metallo-beta-lactamase superfamily
9985 PF02163 Peptidase family M50
9984 PF01409 tRNA synthetases class II core domain (F)
9969 PF10150 Ribonuclease E/G family
9955 PF01208 Uroporphyrinogen decarboxylase (URO-D)
9905 PF13450 NAD(P)-binding Rossmann-like domain
9902 PF00561 alpha/beta hydrolase fold
9889 PF00762 Ferrochelatase
9882 PF01434 Peptidase family M41
9875 PF00160 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
9839 PF01625 Peptide methionine sulfoxide reductase
9766 PF01274 Malate synthase
9756 PF01408 Oxidoreductase family, NAD-binding Rossmann fold
9659 PF04551 GcpE protein
9607 PF01380 SIS domain
9505 PF13361 UvrD-like helicase C-terminal domain
9492 PF00593 TonB dependent receptor
9473 PF02321 Outer membrane efflux protein
9460 PF01551 Peptidase family M23
9455 PF01653 NAD-dependent DNA ligase adenylation domain
9397 PF01268 Formate--tetrahydrofolate ligase
9397 PF00224 Pyruvate kinase, barrel domain
9369 PF02934 GatB/GatE catalytic domain
9358 PF00486 Transcriptional regulatory protein, C terminal
9339 PF00809 Pterin binding enzyme
9304 PF01040 UbiA prenyltransferase family
9249 PF06253 Trimethylamine methyltransferase (MTTB)
9183 PF01751 Toprim domain
9162 PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
9107 PF08264 Anticodon-binding domain of tRNA ligase
9100 PF00205 Thiamine pyrophosphate enzyme, central domain
9069 PF00551 Formyl transferase
9038 PF00268 Ribonucleotide reductase, small chain
9029 PF02355 Protein export membrane protein
9027 PF00308 Bacterial dnaA protein
9012 PF02878 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
9010 PF00491 Arginase family
8979 PF10609 NUBPL iron-transfer P-loop NTPase
8972 PF02780 Transketolase, C-terminal domain
8964 PF01565 FAD binding domain
8937 PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain
8934 PF02548 Ketopantoate hydroxymethyltransferase
8931 PF00384 Molybdopterin oxidoreductase
8893 PF04998 RNA polymerase Rpb1, domain 5
8875 PF00326 Prolyl oligopeptidase family
8855 PF00293 NUDIX domain
8787 PF01612 3'-5' exonuclease
8773 PF13292 1-deoxy-D-xylulose-5-phosphate synthase
8772 PF00589 Phage integrase family
8755 PF00318 Ribosomal protein S2
8746 PF02769 AIR synthase related protein, C-terminal domain
8691 PF02540 NAD synthase
8690 PF02092 Glycyl-tRNA synthetase beta subunit
8687 PF00578 AhpC/TSA family
8642 PF02729 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
8635 PF00231 ATP synthase
8601 PF00586 AIR synthase related protein, N-terminal domain
8598 PF01546 Peptidase family M20/M25/M40
8575 PF01474 Class-II DAHP synthetase family
8516 PF03572 Peptidase family S41
8486 PF08669 Glycine cleavage T-protein C-terminal barrel domain
8472 PF00795 Carbon-nitrogen hydrolase
8452 PF01235 Sodium:alanine symporter family
8449 PF01515 Phosphate acetyl/butaryl transferase
8383 PF03023 Lipid II flippase MurJ
8382 PF01795 MraW methylase family
8375 PF02913 FAD linked oxidases, C-terminal domain
8331 PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
8327 PF02353 Mycolic acid cyclopropane synthetase
8301 PF03054 tRNA methyl transferase HUP domain
8298 PF01180 Dihydroorotate dehydrogenase
8251 PF03721 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
8243 PF00204 DNA gyrase B
8184 PF00512 His Kinase A (phospho-acceptor) domain
8137 PF07995 Glucose / Sorbosone dehydrogenase
8121 PF03331 UDP-3-O-acyl N-acetylglycosamine deacetylase
8076 PF01145 SPFH domain / Band 7 family
8044 PF04166 Pyridoxal phosphate biosynthetic protein PdxA
8019 PF00146 NADH dehydrogenase
8018 PF02874 ATP synthase alpha/beta family, beta-barrel domain
7999 PF00510 Cytochrome c oxidase subunit III
7975 PF02770 Acyl-CoA dehydrogenase, middle domain
7971 PF00834 Ribulose-phosphate 3 epimerase family
7949 PF13177 DNA polymerase III, delta subunit
7942 PF00924 Mechanosensitive ion channel
7937 PF00933 Glycosyl hydrolase family 3 N terminal domain
7920 PF03129 Anticodon binding domain
7907 PF00342 Phosphoglucose isomerase
7895 PF01218 Coproporphyrinogen III oxidase
7885 PF01259 SAICAR synthetase
7884 PF01761 3-dehydroquinate synthase
7840 PF00472 RF-1 domain
7830 PF02401 LytB protein
7816 PF00226 DnaJ domain
7807 PF00670 S-adenosyl-L-homocysteine hydrolase, NAD binding domain
7805 PF01063 Amino-transferase class IV
7745 PF00353 RTX calcium-binding nonapeptide repeat (4 copies)
7694 PF00733 Asparagine synthase
7671 PF01979 Amidohydrolase family
7657 PF03740 Pyridoxal phosphate biosynthesis protein PdxJ
7650 PF01209 ubiE/COQ5 methyltransferase family
7636 PF04997 RNA polymerase Rpb1, domain 1
7630 PF00128 Alpha amylase, catalytic domain
7626 PF00121 Triosephosphate isomerase
7608 PF19289 PmbA/TldA metallopeptidase C-terminal domain
7586 PF03382 Mycoplasma protein of unknown function, DUF285
7581 PF13419 Haloacid dehalogenase-like hydrolase
7564 PF08241 Methyltransferase domain
7555 PF02875 Mur ligase family, glutamate ligase domain
7505 PF00300 Histidine phosphatase superfamily (branch 1)
7503 PF02896 PEP-utilising enzyme, PEP-binding domain
7489 PF02852 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
7484 PF01557 Fumarylacetoacetate (FAA) hydrolase family
7466 PF03102 NeuB family
7459 PF01554 MatE
7456 PF08240 Alcohol dehydrogenase GroES-like domain
7442 PF01715 IPP transferase
7428 PF17657 Bacterial DNA polymerase III alpha subunit finger domain
7423 PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus
7421 PF02574 Homocysteine S-methyltransferase
7416 PF00085 Thioredoxin
7408 PF00370 FGGY family of carbohydrate kinases, N-terminal domain
7383 PF02684 Lipid-A-disaccharide synthetase
7383 PF00289 Biotin carboxylase, N-terminal domain
7376 PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit
7364 PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
7347 PF01479 S4 domain
7313 PF07991 Acetohydroxy acid isomeroreductase, NADPH-binding domain
7301 PF02569 Pantoate-beta-alanine ligase
7260 PF01790 Prolipoprotein diacylglyceryl transferase
7240 PF01960 ArgJ family
7209 PF01642 Methylmalonyl-CoA mutase
7196 PF02547 Queuosine biosynthesis protein
7123 PF05362 Lon protease (S16) C-terminal proteolytic domain
7112 PF13932 tRNA modifying enzyme MnmG/GidA C-terminal domain
7108 PF00694 Aconitase C-terminal domain
7100 PF01327 Polypeptide deformylase
7099 PF01379 Porphobilinogen deaminase, dipyromethane cofactor binding domain
7099 PF00216 Bacterial DNA-binding protein
7074 PF10502 Signal peptidase, peptidase S26
7074 PF00465 Iron-containing alcohol dehydrogenase
7052 PF00926 3,4-dihydroxy-2-butanone 4-phosphate synthase
7035 PF01071 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
7020 PF00583 Acetyltransferase (GNAT) family
7017 PF04545 Sigma-70, region 4
7003 PF01227 GTP cyclohydrolase I
6988 PF02774 Semialdehyde dehydrogenase, dimerisation domain
6986 PF01925 Sulfite exporter TauE/SafE
6983 PF10431 C-terminal, D2-small domain, of ClpB protein
6963 PF00581 Rhodanese-like domain
6943 PF00889 Elongation factor TS
6942 PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
6925 PF02348 Cytidylyltransferase
6884 PF02801 Beta-ketoacyl synthase, C-terminal domain
6881 PF02719 Polysaccharide biosynthesis protein
6856 PF02897 Prolyl oligopeptidase, N-terminal beta-propeller domain
6849 PF02803 Thiolase, C-terminal domain
6842 PF00223 Photosystem I psaA/psaB protein
6832 PF02254 TrkA-N domain
6804 PF04127 DNA / pantothenate metabolism flavoprotein
6781 PF13365 Trypsin-like peptidase domain
6776 PF00290 Tryptophan synthase alpha chain
6766 PF01493 GXGXG motif
6761 PF03144 Elongation factor Tu domain 2
6758 PF02445 Quinolinate synthetase A protein
6745 PF07687 Peptidase dimerisation domain
6739 PF01255 Putative undecaprenyl diphosphate synthase
6738 PF00850 Histone deacetylase domain
6737 PF00591 Glycosyl transferase family, a/b domain
6735 PF00912 Transglycosylase
6729 PF00177 Ribosomal protein S7p/S5e
6726 PF04055 Radical SAM superfamily
6699 PF03781 Sulfatase-modifying factor enzyme 1
6662 PF02646 RmuC family
6653 PF01467 Cytidylyltransferase-like
6649 PF01746 tRNA (Guanine-1)-methyltransferase
6641 PF03702 Anhydro-N-acetylmuramic acid kinase
6613 PF00218 Indole-3-glycerol phosphate synthase
6604 PF13614 AAA domain
6589 PF01725 Ham1 family
6583 PF00156 Phosphoribosyl transferase domain
6567 PF01012 Electron transfer flavoprotein domain
6560 PF01578 Cytochrome C assembly protein
6557 PF00070 Pyridine nucleotide-disulphide oxidoreductase
6548 PF02880 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
6537 PF00950 ABC 3 transport family
6518 PF00902 Sec-independent protein translocase protein (TatC)
6514 PF01709 Transcriptional regulator
6512 PF02615 Malate/L-lactate dehydrogenase
6508 PF01921 tRNA synthetases class I (K)
6507 PF01026 TatD related DNase
6505 PF00773 RNB domain
6501 PF05199 GMC oxidoreductase
6471 PF02091 Glycyl-tRNA synthetase alpha subunit
6467 PF00037 4Fe-4S binding domain
6448 PF08442 ATP-grasp domain
6446 PF01580 FtsK/SpoIIIE family
6443 PF07977 FabA-like domain
6430 PF00623 RNA polymerase Rpb1, domain 2
6409 PF01618 MotA/TolQ/ExbB proton channel family
6393 PF13393 Histidyl-tRNA synthetase
6393 PF00502 Phycobilisome protein
6391 PF04244 Deoxyribodipyrimidine photo-lyase-related protein
6383 PF02910 Fumarate reductase flavoprotein C-term
6382 PF07516 SecA Wing and Scaffold domain
6349 PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
6310 PF13603 Leucyl-tRNA synthetase, Domain 2
6307 PF00923 Transaldolase/Fructose-6-phosphate aldolase
6304 PF03466 LysR substrate binding domain
6302 PF01018 GTP1/OBG
6299 PF01138 3' exoribonuclease family, domain 1
6293 PF05222 Alanine dehydrogenase/PNT, N-terminal domain
6278 PF07690 Major Facilitator Superfamily
6270 PF02696 Protein adenylyltransferase SelO
6264 PF00119 ATP synthase A chain
6248 PF00111 2Fe-2S iron-sulfur cluster binding domain
6237 PF02668 Taurine catabolism dioxygenase TauD, TfdA family
6222 PF00107 Zinc-binding dehydrogenase
6197 PF02773 S-adenosylmethionine synthetase, C-terminal domain
6175 PF01118 Semialdehyde dehydrogenase, NAD binding domain
6175 PF00033 Cytochrome b/b6/petB
6148 PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
6142 PF01556 DnaJ C terminal domain
6121 PF01641 SelR domain
6094 PF08459 UvrC RNAse H endonuclease domain
6079 PF00953 Glycosyl transferase family 4
6072 PF05721 Phytanoyl-CoA dioxygenase (PhyH)
6049 PF03483 B3/4 domain
6047 PF02504 Fatty acid synthesis protein
6020 PF00497 Bacterial extracellular solute-binding proteins, family 3
6009 PF01195 Peptidyl-tRNA hydrolase
5995 PF13715 CarboxypepD_reg-like domain
5948 PF01066 CDP-alcohol phosphatidyltransferase
5948 PF00984 UDP-glucose/GDP-mannose dehydrogenase family, central domain
5917 PF00437 Type II/IV secretion system protein
5898 PF04851 Type III restriction enzyme, res subunit
5887 PF00355 Rieske [2Fe-2S] domain
5884 PF00213 ATP synthase delta (OSCP) subunit
5881 PF01494 FAD binding domain
5869 PF01475 Ferric uptake regulator family
5859 PF03764 Elongation factor G, domain IV
5855 PF02739 5'-3' exonuclease, N-terminal resolvase-like domain
5854 PF01450 Acetohydroxy acid isomeroreductase, catalytic domain
5846 PF00238 Ribosomal protein L14p/L23e
5838 PF14849 YidC periplasmic domain
5823 PF13537 Glutamine amidotransferase domain
5820 PF01025 GrpE
5818 PF01168 Alanine racemase, N-terminal domain
5811 PF02628 Cytochrome oxidase assembly protein
5777 PF02545 Maf-like protein
5774 PF01432 Peptidase family M3
5749 PF00691 OmpA family
5742 PF00817 impB/mucB/samB family
5741 PF01765 Ribosome recycling factor
5735 PF02386 Cation transport protein
5733 PF13368 Topoisomerase C-terminal repeat
5731 PF03143 Elongation factor Tu C-terminal domain
5726 PF02511 Thymidylate synthase complementing protein
5721 PF07676 WD40-like Beta Propeller Repeat
5716 PF00185 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
5713 PF13507 CobB/CobQ-like glutamine amidotransferase domain
5703 PF00475 Imidazoleglycerol-phosphate dehydratase
5697 PF02785 Biotin carboxylase C-terminal domain
5678 PF04069 Substrate binding domain of ABC-type glycine betaine transport system
5665 PF13378 Enolase C-terminal domain-like
5660 PF02606 Tetraacyldisaccharide-1-P 4'-kinase
5653 PF00303 Thymidylate synthase
5639 PF02222 ATP-grasp domain
5636 PF07230 Bacteriophage T4-like portal protein (Gp20)
5630 PF00573 Ribosomal protein L4/L1 family
5623 PF01225 Mur ligase family, catalytic domain
5596 PF00919 Uncharacterized protein family UPF0004
5591 PF00590 Tetrapyrrole (Corrin/Porphyrin) Methylases
5583 PF00994 Probable molybdopterin binding domain
5577 PF01036 Bacteriorhodopsin-like protein
5549 PF02673 Bacitracin resistance protein BacA
5544 PF00875 DNA photolyase
5530 PF00717 Peptidase S24-like
5507 PF02441 Flavoprotein
5497 PF00144 Beta-lactamase
5490 PF00306 ATP synthase alpha/beta chain, C terminal domain
5489 PF00141 Peroxidase
5487 PF03717 Penicillin-binding Protein dimerisation domain
5479 PF00742 Homoserine dehydrogenase
5473 PF02142 MGS-like domain
5470 PF17941 Polyphosphate kinase C-terminal domain 1
5463 PF12228 Protein of unknown function (DUF3604)
5462 PF00410 Ribosomal protein S8
5456 PF03061 Thioesterase superfamily
5455 PF01293 Phosphoenolpyruvate carboxykinase
5435 PF17757 UvrB interaction domain
5431 PF00768 D-alanyl-D-alanine carboxypeptidase
5417 PF07244 Surface antigen variable number repeat
5412 PF11775 Cobalamin biosynthesis protein CobT VWA domain
5409 PF00800 Prephenate dehydratase
5400 PF00183 Hsp90 protein
5367 PF14833 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
5361 PF05992 SbmA/BacA-like family
5354 PF03739 Lipopolysaccharide export system permease LptF/LptG
5342 PF02350 UDP-N-acetylglucosamine 2-epimerase
5338 PF01300 Telomere recombination
5337 PF00549 CoA-ligase
5332 PF04539 Sigma-70 region 3
5328 PF03725 3' exoribonuclease family, domain 2
5327 PF02687 FtsX-like permease family
5322 PF01245 Ribosomal protein L19
5308 PF13328 HD domain
5307 PF18962 Secretion system C-terminal sorting domain
5305 PF01668 SmpB protein
5284 PF00925 GTP cyclohydrolase II
5245 PF01103 Omp85 superfamily domain
5244 PF02224 Cytidylate kinase
5235 PF02096 60Kd inner membrane protein
5216 PF01636 Phosphotransferase enzyme family
5178 PF00427 Phycobilisome Linker polypeptide
5168 PF01842 ACT domain
5129 PF00252 Ribosomal protein L16p/L10e
5126 PF07973 Threonyl and Alanyl tRNA synthetase second additional domain
5114 PF01116 Fructose-bisphosphate aldolase class-II
5110 PF01202 Shikimate kinase
5101 PF01435 Peptidase family M48
5094 PF03255 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
5091 PF04452 RNA methyltransferase domain
5091 PF02190 ATP-dependent protease La (LON) substrate-binding domain
5088 PF00731 AIR carboxylase
5085 PF00687 Ribosomal protein L1p/L10e family
5084 PF00596 Class II Aldolase and Adducin N-terminal domain
5078 PF00406 Adenylate kinase
5076 PF08529 NusA N-terminal domain
5066 PF01676 Metalloenzyme superfamily
5062 PF01343 Peptidase family S49
5041 PF00274 Fructose-bisphosphate aldolase class-I
5040 PF01171 PP-loop family
5035 PF00334 Nucleoside diphosphate kinase
5025 PF01966 HD domain
5020 PF00140 Sigma-70 factor, region 1.2
5004 PF00116 Cytochrome C oxidase subunit II, periplasmic domain
5003 PF03947 Ribosomal Proteins L2, C-terminal domain
5001 PF00398 Ribosomal RNA adenine dimethylase
4996 PF00929 Exonuclease
4996 PF00069 Protein kinase domain
4995 PF08502 LeuA allosteric (dimerisation) domain
4995 PF03320 Bacterial fructose-1,6-bisphosphatase, glpX-encoded
4979 PF01220 Dehydroquinase class II
4950 PF00494 Squalene/phytoene synthase
4943 PF00462 Glutaredoxin
4928 PF07478 D-ala D-ala ligase C-terminus
4918 PF02503 Polyphosphate kinase middle domain
4916 PF01553 Acyltransferase
4914 PF02151 UvrB/uvrC motif
4912 PF00166 Chaperonin 10 Kd subunit
4909 PF13347 MFS/sugar transport protein
4904 PF13406 Transglycosylase SLT domain
4885 PF02028 BCCT, betaine/carnitine/choline family transporter
4879 PF07650 KH domain
4875 PF01244 Membrane dipeptidase (Peptidase family M19)
4872 PF00488 MutS domain V
4867 PF04561 RNA polymerase Rpb2, domain 2
4861 PF00988 Carbamoyl-phosphate synthase small chain, CPSase domain
4857 PF00380 Ribosomal protein S9/S16
4853 PF00625 Guanylate kinase
4850 PF06421 GTP-binding protein LepA C-terminus
4838 PF13662 Toprim domain
4838 PF00436 Single-strand binding protein family
4818 PF02738 Molybdopterin cofactor-binding domain
4817 PF02772 S-adenosylmethionine synthetase, central domain
4807 PF17759 Phenylalanyl tRNA synthetase beta chain CLM domain
4800 PF00075 RNase H
4789 PF02508 Rnf-Nqr subunit, membrane protein
4787 PF01043 SecA preprotein cross-linking domain
4779 PF05690 Thiazole biosynthesis protein ThiG
4744 PF02167 Cytochrome C1 family
4743 PF03952 Enolase, N-terminal domain
4737 PF00677 Lumazine binding domain
4728 PF02492 CobW/HypB/UreG, nucleotide-binding domain
4721 PF00861 Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
4715 PF04339 Peptidogalycan biosysnthesis/recognition
4711 PF01555 DNA methylase
4683 PF11987 Translation-initiation factor 2
4680 PF13793 N-terminal domain of ribose phosphate pyrophosphokinase
4679 PF17871 AAA lid domain
4678 PF02955 Prokaryotic glutathione synthetase, ATP-grasp domain
4668 PF00254 FKBP-type peptidyl-prolyl cis-trans isomerase
4657 PF00421 Photosystem II protein
4643 PF01687 Riboflavin kinase
4641 PF02879 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
4640 PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
4637 PF13090 Polyphosphate kinase C-terminal domain 2
4632 PF01230 HIT domain
4628 PF17760 UvrA interaction domain
4608 PF14492 Elongation Factor G, domain III
4608 PF00313 'Cold-shock' DNA-binding domain
4594 PF20256 Molybdopterin cofactor-binding domain
4588 PF06965 Na+/H+ antiporter 1
4587 PF12706 Beta-lactamase superfamily domain
4584 PF07045 Domain of unknown function (DUF1330)
4584 PF04290 Tripartite ATP-independent periplasmic transporters, DctQ component
4574 PF02782 FGGY family of carbohydrate kinases, C-terminal domain
4572 PF13517 FG-GAP-like repeat
4565 PF02472 Biopolymer transport protein ExbD/TolR
4555 PF00572 Ribosomal protein L13
4533 PF04107 Glutamate-cysteine ligase family 2(GCS2)
4523 PF04565 RNA polymerase Rpb2, domain 3
4501 PF11751 Type IX secretion system membrane protein PorP/SprF
4490 PF00164 Ribosomal protein S12/S23
4464 PF00416 Ribosomal protein S13/S18
4454 PF02541 Ppx/GppA phosphatase family
4453 PF00375 Sodium:dicarboxylate symporter family
4444 PF01743 Poly A polymerase head domain
4429 PF03486 HI0933-like protein
4418 PF01196 Ribosomal protein L17
4417 PF02357 Transcription termination factor nusG
4415 PF13759 Putative 2OG-Fe(II) oxygenase
4399 PF00296 Luciferase-like monooxygenase
4398 PF03321 GH3 auxin-responsive promoter
4390 PF17803 Bacterial cadherin-like domain
4390 PF00805 Pentapeptide repeats (8 copies)
4378 PF14403 Circularly permuted ATP-grasp type 2
4377 PF03819 MazG nucleotide pyrophosphohydrolase domain
4365 PF17963 Bacterial Ig domain
4365 PF01588 Putative tRNA binding domain
4351 PF13510 2Fe-2S iron-sulfur cluster binding domain
4348 PF09424 Yqey-like protein
4348 PF04321 RmlD substrate binding domain
4329 PF00828 Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
4316 PF01351 Ribonuclease HII
4314 PF16870 2-oxoglutarate dehydrogenase C-terminal
4314 PF05173 Dihydrodipicolinate reductase, C-terminus
4305 PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region
4297 PF17755 UvrA DNA-binding domain
4282 PF00411 Ribosomal protein S11
4272 PF03741 Integral membrane protein TerC family
4270 PF02881 SRP54-type protein, helical bundle domain
4265 PF03116 NQR2, RnfD, RnfE family
4261 PF01512 Respiratory-chain NADH dehydrogenase 51 Kd subunit
4255 PF03971 Monomeric isocitrate dehydrogenase
4246 PF01050 Mannose-6-phosphate isomerase
4246 PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
4230 PF08275 DNA primase catalytic core, N-terminal domain
4227 PF03972 MmgE/PrpD N-terminal domain
4223 PF00829 Ribosomal prokaryotic L21 protein
4220 PF16177 Acetyl-coenzyme A synthetase N-terminus
4215 PF01464 Transglycosylase SLT domain
4204 PF00453 Ribosomal protein L20
4204 PF00365 Phosphofructokinase
4202 PF00082 Subtilase family
4192 PF00750 tRNA synthetases class I (R)
4189 PF00673 ribosomal L5P family C-terminus
4188 PF02464 Competence-damaged protein
4181 PF13277 YmdB-like protein
4181 PF01804 Penicillin amidase
4179 PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
4168 PF00347 Ribosomal protein L6
4161 PF01699 Sodium/calcium exchanger protein
4158 PF00237 Ribosomal protein L22p/L17e
4145 PF02811 PHP domain
4142 PF00338 Ribosomal protein S10p/S20e
4139 PF03969 AFG1-like ATPase
4138 PF13522 Glutamine amidotransferase domain
4131 PF06574 FAD synthetase
4130 PF16327 Cytochrome c-type biogenesis protein CcmF C-terminal
4120 PF02637 GatB domain
4099 PF02817 e3 binding domain
4098 PF02578 Multi-copper polyphenol oxidoreductase laccase
4077 PF01476 LysM domain
4069 PF00487 Fatty acid desaturase
4062 PF01048 Phosphorylase superfamily
4050 PF00550 Phosphopantetheine attachment site
4047 PF03602 Conserved hypothetical protein 95
4047 PF01297 Zinc-uptake complex component A periplasmic
4044 PF02861 Clp amino terminal domain, pathogenicity island component
4031 PF13649 Methyltransferase domain
4031 PF00986 DNA gyrase B subunit, carboxyl terminus
4023 PF01193 RNA polymerase Rpb3/Rpb11 dimerisation domain
4022 PF02978 Signal peptide binding domain
4019 PF06071 Protein of unknown function (DUF933)
4008 PF04413 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase)
4000 PF01729 Quinolinate phosphoribosyl transferase, C-terminal domain
3992 PF00543 Nitrogen regulatory protein P-II
3985 PF07068 Major capsid protein Gp23
3983 PF17820 PDZ domain
3983 PF00463 Isocitrate lyase family
3980 PF02824 TGS domain
3977 PF01728 FtsJ-like methyltransferase
3972 PF00211 Adenylate and Guanylate cyclase catalytic domain
3961 PF02527 rRNA small subunit methyltransferase G
3960 PF03328 HpcH/HpaI aldolase/citrate lyase family
3958 PF05861 Bacterial phosphonate metabolism protein (PhnI)
3950 PF01509 TruB family pseudouridylate synthase (N terminal domain)
3940 PF00011 Hsp20/alpha crystallin family
3938 PF02405 Permease MlaE
3933 PF04607 Region found in RelA / SpoT proteins
3932 PF01016 Ribosomal L27 protein
3929 PF03232 Ubiquinone biosynthesis protein COQ7
3925 PF00885 6,7-dimethyl-8-ribityllumazine synthase
3923 PF00480 ROK family


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