Query psy17720
Match_columns 80
No_of_seqs 105 out of 191
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 21:17:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17720.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17720hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1541|consensus 100.0 3.8E-32 8.2E-37 207.8 7.2 68 2-71 148-215 (270)
2 PLN02535 glycolate oxidase 85.2 2.2 4.8E-05 34.1 5.1 42 7-48 123-166 (364)
3 PRK11197 lldD L-lactate dehydr 82.4 3.2 7E-05 33.4 5.1 40 7-46 121-162 (381)
4 TIGR02708 L_lactate_ox L-lacta 79.1 4.4 9.4E-05 32.6 4.8 41 6-46 131-173 (367)
5 cd02922 FCB2_FMN Flavocytochro 78.0 5.6 0.00012 31.3 5.0 42 6-47 116-159 (344)
6 PLN02493 probable peroxisomal 77.6 5.4 0.00012 32.1 4.9 42 7-48 121-164 (367)
7 PLN02979 glycolate oxidase 71.4 10 0.00023 30.7 5.1 42 7-48 120-163 (366)
8 TIGR03534 RF_mod_PrmC protein- 70.4 6.2 0.00013 27.5 3.2 31 2-35 205-235 (251)
9 TIGR00438 rrmJ cell division p 69.4 14 0.00031 25.3 4.9 15 2-16 134-148 (188)
10 TIGR00138 gidB 16S rRNA methyl 67.1 8.8 0.00019 27.0 3.5 33 2-34 130-162 (181)
11 PRK00517 prmA ribosomal protei 65.2 9.9 0.00021 27.6 3.5 32 2-35 201-232 (250)
12 PF12323 HTH_OrfB_IS605: Helix 65.2 8.7 0.00019 21.4 2.6 20 11-31 6-25 (46)
13 PF11232 Med25: Mediator compl 62.9 40 0.00086 24.5 6.2 50 6-57 72-121 (152)
14 cd04736 MDH_FMN Mandelate dehy 62.2 19 0.00041 28.9 4.9 42 7-48 115-157 (361)
15 PRK09328 N5-glutamine S-adenos 60.4 44 0.00096 23.8 6.1 35 2-40 226-260 (275)
16 COG2519 GCD14 tRNA(1-methylade 59.4 13 0.00027 29.1 3.4 32 2-35 183-214 (256)
17 PRK00377 cbiT cobalt-precorrin 59.3 18 0.00039 25.1 3.9 32 2-35 133-164 (198)
18 COG4911 Uncharacterized conser 56.1 19 0.0004 25.6 3.5 40 19-58 50-93 (123)
19 PF01565 FAD_binding_4: FAD bi 55.0 14 0.00031 23.8 2.6 21 14-34 5-25 (139)
20 cd03332 LMO_FMN L-Lactate 2-mo 54.5 30 0.00066 27.9 4.9 41 7-47 137-179 (383)
21 PF08306 Glyco_hydro_98M: Glyc 51.6 8.1 0.00018 31.2 1.2 23 23-45 271-293 (324)
22 PF14307 Glyco_tran_WbsX: Glyc 51.2 22 0.00048 27.4 3.5 35 2-36 152-191 (345)
23 PRK04266 fibrillarin; Provisio 50.5 67 0.0015 23.5 5.8 52 2-55 164-222 (226)
24 PF08704 GCD14: tRNA methyltra 49.6 14 0.0003 28.0 2.1 33 2-36 133-166 (247)
25 PF14794 DUF4479: Domain of un 46.0 20 0.00044 22.7 2.2 24 18-41 49-72 (73)
26 TIGR00537 hemK_rel_arch HemK-r 45.1 42 0.00091 22.7 3.8 39 2-42 128-166 (179)
27 COG3554 Uncharacterized protei 39.9 14 0.0003 28.0 0.8 10 36-45 177-186 (190)
28 smart00828 PKS_MT Methyltransf 39.5 53 0.0011 22.7 3.7 44 2-45 92-148 (224)
29 cd04737 LOX_like_FMN L-Lactate 38.6 71 0.0015 25.4 4.7 40 7-46 124-165 (351)
30 PF02244 Propep_M14: Carboxype 36.4 58 0.0012 19.1 3.1 22 13-34 2-23 (74)
31 TIGR03704 PrmC_rel_meth putati 35.8 80 0.0017 23.2 4.3 36 2-40 204-239 (251)
32 PRK08287 cobalt-precorrin-6Y C 35.4 62 0.0013 22.0 3.5 38 2-42 119-157 (187)
33 PLN02805 D-lactate dehydrogena 35.2 58 0.0013 27.4 3.8 33 11-43 135-185 (555)
34 KOG4730|consensus 35.0 50 0.0011 28.4 3.5 41 14-59 54-94 (518)
35 PRK07402 precorrin-6B methylas 34.2 93 0.002 21.4 4.2 37 2-40 130-166 (196)
36 PHA01753 Holliday junction res 34.1 39 0.00085 23.6 2.3 28 18-45 65-95 (121)
37 PF03456 uDENN: uDENN domain; 34.1 77 0.0017 18.5 3.3 49 10-58 3-52 (65)
38 PF01070 FMN_dh: FMN-dependent 34.1 66 0.0014 25.4 3.8 41 7-47 109-151 (356)
39 PRK00107 gidB 16S rRNA methylt 33.7 50 0.0011 23.5 2.9 30 2-34 133-162 (187)
40 PHA03323 nuclear egress membra 33.7 26 0.00057 27.8 1.5 15 5-19 40-54 (272)
41 PRK11230 glycolate oxidase sub 33.4 61 0.0013 26.6 3.6 20 14-33 60-79 (499)
42 PF06475 Glycolipid_bind: Puta 32.2 19 0.0004 26.2 0.5 10 36-45 166-175 (179)
43 PRK14532 adenylate kinase; Pro 31.7 1.1E+02 0.0023 20.7 4.1 27 7-33 78-104 (188)
44 PF00012 HSP70: Hsp70 protein; 31.7 1.7E+02 0.0037 23.4 5.8 42 18-59 147-197 (602)
45 PRK14968 putative methyltransf 31.5 1.5E+02 0.0033 19.4 5.0 34 2-37 136-169 (188)
46 PF02676 TYW3: Methyltransfera 30.3 2.2E+02 0.0049 20.9 6.1 42 12-58 113-155 (205)
47 PRK10901 16S rRNA methyltransf 29.3 2E+02 0.0042 22.8 5.8 26 2-27 360-389 (427)
48 cd03707 EFTU_III Domain III of 29.1 49 0.0011 20.2 2.0 17 3-19 51-67 (90)
49 PRK09502 iscA iron-sulfur clus 28.9 48 0.0011 21.5 2.0 14 33-46 83-96 (107)
50 PF05078 DUF679: Protein of un 28.9 71 0.0015 23.6 3.1 35 13-47 130-166 (170)
51 PF15337 Vasculin: Vascular pr 28.7 47 0.001 22.8 1.9 25 12-36 21-56 (97)
52 PRK00121 trmB tRNA (guanine-N( 28.3 90 0.002 21.9 3.4 31 2-34 144-174 (202)
53 cd04747 OYE_like_5_FMN Old yel 27.6 1.4E+02 0.0031 23.6 4.7 25 28-52 152-186 (361)
54 KOG3201|consensus 26.9 61 0.0013 24.8 2.4 41 2-43 128-168 (201)
55 cd07361 MEMO_like Memo (mediat 26.8 52 0.0011 24.3 2.0 21 12-32 6-26 (266)
56 TIGR00452 methyltransferase, p 26.8 70 0.0015 24.9 2.9 35 2-36 213-268 (314)
57 PRK04235 hypothetical protein; 26.8 1.7E+02 0.0037 21.6 4.8 46 15-65 106-152 (196)
58 COG3413 Predicted DNA binding 25.8 67 0.0015 22.9 2.4 31 13-49 151-182 (215)
59 PRK14967 putative methyltransf 25.8 65 0.0014 22.7 2.3 38 2-41 147-184 (223)
60 PRK08317 hypothetical protein; 25.5 1.2E+02 0.0025 20.4 3.4 13 2-14 112-124 (241)
61 PF02353 CMAS: Mycolic acid cy 25.1 34 0.00074 25.9 0.8 15 2-16 154-168 (273)
62 PRK09372 ribonuclease activity 24.7 65 0.0014 22.9 2.2 18 23-41 76-93 (159)
63 TIGR01935 NOT-MenG RraA famliy 24.5 70 0.0015 22.6 2.3 18 23-41 72-89 (150)
64 COG2226 UbiE Methylase involve 24.5 36 0.00078 25.8 0.9 15 2-16 144-159 (238)
65 PRK08245 hypothetical protein; 24.5 67 0.0015 23.9 2.3 37 4-41 85-123 (240)
66 TIGR02011 IscA iron-sulfur clu 24.3 65 0.0014 20.7 1.9 12 35-46 83-94 (105)
67 TIGR02752 MenG_heptapren 2-hep 24.1 1.2E+02 0.0025 21.1 3.3 13 2-14 139-151 (231)
68 TIGR00563 rsmB ribosomal RNA s 23.8 2.4E+02 0.0053 22.2 5.4 26 2-27 356-385 (426)
69 PLN02244 tocopherol O-methyltr 23.7 91 0.002 23.9 2.9 44 2-45 211-282 (340)
70 PF09969 DUF2203: Uncharacteri 23.4 2.1E+02 0.0045 19.5 4.4 39 20-58 57-99 (120)
71 cd01305 archeal_chlorohydrolas 22.3 2E+02 0.0044 20.5 4.3 44 2-45 60-103 (263)
72 PRK01683 trans-aconitate 2-met 22.2 56 0.0012 23.2 1.4 13 2-14 118-130 (258)
73 COG2819 Predicted hydrolase of 21.9 57 0.0012 25.5 1.5 25 6-31 229-253 (264)
74 PRK11036 putative S-adenosyl-L 21.8 1E+02 0.0022 22.2 2.7 18 2-19 137-154 (255)
75 TIGR00091 tRNA (guanine-N(7)-) 21.7 1.5E+02 0.0033 20.5 3.6 30 2-33 120-149 (194)
76 TIGR01997 sufA_proteo FeS asse 21.6 78 0.0017 20.4 1.9 14 33-46 83-96 (107)
77 PF03737 Methyltransf_6: Demet 21.4 1.1E+02 0.0025 21.1 2.8 18 23-41 77-94 (154)
78 PRK00782 hypothetical protein; 21.4 78 0.0017 23.7 2.1 21 11-31 8-28 (267)
79 PRK11188 rrmJ 23S rRNA methylt 21.3 3.1E+02 0.0068 19.5 5.3 49 2-55 153-204 (209)
80 TIGR02350 prok_dnaK chaperone 21.3 2.5E+02 0.0053 23.1 5.1 42 18-59 142-192 (595)
81 TIGR01565 homeo_ZF_HD homeobox 21.2 96 0.0021 18.9 2.1 17 18-34 9-25 (58)
82 PHA02324 hypothetical protein 21.0 29 0.00063 20.9 -0.2 14 29-42 2-15 (47)
83 cd02930 DCR_FMN 2,4-dienoyl-Co 20.5 1.6E+02 0.0035 22.7 3.7 10 5-14 88-97 (353)
84 TIGR01991 HscA Fe-S protein as 20.2 1.5E+02 0.0033 24.7 3.8 42 18-59 141-190 (599)
No 1
>KOG1541|consensus
Probab=99.97 E-value=3.8e-32 Score=207.83 Aligned_cols=68 Identities=63% Similarity=0.997 Sum_probs=63.1
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEeeCCCCCCcceEEEEEEecCCCCCCCcccCCC
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVDYPHSTKAKKFFLVLMTGGDLPLPPALGEGE 71 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvVD~P~S~kaKK~yLvL~~G~~~~lp~~l~~~~ 71 (80)
.||+||+||||||||||++|+|||+++||+|||+||||||||+|+|+|||||||++|+. +|+.++.++
T Consensus 148 ~~l~rg~raV~QfYpen~~q~d~i~~~a~~aGF~GGlvVd~Pes~k~kK~yLVL~~g~~--~~~~l~~~~ 215 (270)
T KOG1541|consen 148 SCLKRGARAVLQFYPENEAQIDMIMQQAMKAGFGGGLVVDWPESTKNKKYYLVLMTGGV--VPRALTAGG 215 (270)
T ss_pred hhhccCceeEEEecccchHHHHHHHHHHHhhccCCceeeecccccccceeEEEEecCCc--ccccccCCc
Confidence 68999999999999999999999999999999999999999999999999999999976 666665443
No 2
>PLN02535 glycolate oxidase
Probab=85.16 E-value=2.2 Score=34.15 Aligned_cols=42 Identities=19% Similarity=0.301 Sum_probs=34.4
Q ss_pred CceEEEEEcc-CChHHHHHHHHHHHHccccc-eEEeeCCCCCCc
Q psy17720 7 TARAVFQFYP-ENSAQIELVTSQAMRAGFYG-GLVVDYPHSTKA 48 (80)
Q Consensus 7 GaRAV~QfYP-en~~Q~emI~~~A~kaGF~G-GlvVD~P~S~ka 48 (80)
++..-||+|+ .+.+-.+-+.+.|-++||.+ .|-||-|.+.+.
T Consensus 123 ~~~~wfQlY~~~dr~~~~~ll~RA~~aG~~alvlTvD~p~~g~R 166 (364)
T PLN02535 123 NAVRFLQLYVYKRRDIAAQLVQRAEKNGYKAIVLTADVPRLGRR 166 (364)
T ss_pred CCCeEEEEeccCCHHHHHHHHHHHHHcCCCEEEEeecCCCCCCc
Confidence 4678999997 55677888889999999987 888999876543
No 3
>PRK11197 lldD L-lactate dehydrogenase; Provisional
Probab=82.37 E-value=3.2 Score=33.44 Aligned_cols=40 Identities=23% Similarity=0.254 Sum_probs=32.6
Q ss_pred CceEEEEEc-cCChHHHHHHHHHHHHccccc-eEEeeCCCCC
Q psy17720 7 TARAVFQFY-PENSAQIELVTSQAMRAGFYG-GLVVDYPHST 46 (80)
Q Consensus 7 GaRAV~QfY-Pen~~Q~emI~~~A~kaGF~G-GlvVD~P~S~ 46 (80)
++..-||+| |.+.+-.+.+.+.|.++||.+ .|-||=|-..
T Consensus 121 ~~~~wfQlY~~~Dr~~~~~li~RA~~aG~~alvlTVD~pv~G 162 (381)
T PRK11197 121 KRPMWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPVPG 162 (381)
T ss_pred CCCeEEEEEecCCHHHHHHHHHHHHHcCCCEEEEecCCCCCC
Confidence 456899999 666677888889999999987 8889987543
No 4
>TIGR02708 L_lactate_ox L-lactate oxidase. Members of this protein oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence.
Probab=79.13 E-value=4.4 Score=32.57 Aligned_cols=41 Identities=20% Similarity=0.196 Sum_probs=32.7
Q ss_pred CCceEEEEEccCChHHH-HHHHHHHHHccccc-eEEeeCCCCC
Q psy17720 6 RTARAVFQFYPENSAQI-ELVTSQAMRAGFYG-GLVVDYPHST 46 (80)
Q Consensus 6 rGaRAV~QfYPen~~Q~-emI~~~A~kaGF~G-GlvVD~P~S~ 46 (80)
.++..-||+|.-.+..+ +-+...|.++||.+ .|-||-|...
T Consensus 131 ~~~~~wfQlY~~~dr~~~~~li~RA~~aG~~alvlTvD~p~~g 173 (367)
T TIGR02708 131 NGTPHWFQFYMSKDDGINRDIMDRVKADGAKAIVLTADATVGG 173 (367)
T ss_pred CCCceEEEEeccCCHHHHHHHHHHHHHcCCCEEEEecCCCCCC
Confidence 35678999999666554 88889999999987 8889987554
No 5
>cd02922 FCB2_FMN Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.
Probab=78.03 E-value=5.6 Score=31.34 Aligned_cols=42 Identities=26% Similarity=0.303 Sum_probs=33.9
Q ss_pred CCceEEEEEc-cCChHHHHHHHHHHHHccccc-eEEeeCCCCCC
Q psy17720 6 RTARAVFQFY-PENSAQIELVTSQAMRAGFYG-GLVVDYPHSTK 47 (80)
Q Consensus 6 rGaRAV~QfY-Pen~~Q~emI~~~A~kaGF~G-GlvVD~P~S~k 47 (80)
+++...||+| |.+.+-++-+...|.++||.. .|-||-|...+
T Consensus 116 ~~~~~w~Qly~~~d~~~~~~l~~ra~~ag~~alvltvD~p~~g~ 159 (344)
T cd02922 116 PDQPLFFQLYVNKDRTKTEELLKRAEKLGAKAIFLTVDAPVLGK 159 (344)
T ss_pred CCCcEEEEEeecCCHHHHHHHHHHHHHcCCCEEEEECCCCCcCc
Confidence 3567789999 567777888889999999987 88889996643
No 6
>PLN02493 probable peroxisomal (S)-2-hydroxy-acid oxidase
Probab=77.64 E-value=5.4 Score=32.09 Aligned_cols=42 Identities=33% Similarity=0.508 Sum_probs=33.2
Q ss_pred CceEEEEEcc-CChHHHHHHHHHHHHccccc-eEEeeCCCCCCc
Q psy17720 7 TARAVFQFYP-ENSAQIELVTSQAMRAGFYG-GLVVDYPHSTKA 48 (80)
Q Consensus 7 GaRAV~QfYP-en~~Q~emI~~~A~kaGF~G-GlvVD~P~S~ka 48 (80)
++..-||+|. .+.+-.+-+.+.|.++||.. .|-||-|...+.
T Consensus 121 ~~~~wfQlY~~~Dr~~~~~li~RA~~aG~~alvlTvD~p~~G~R 164 (367)
T PLN02493 121 PGIRFFQLYVYKNRNVVEQLVRRAERAGFKAIALTVDTPRLGRR 164 (367)
T ss_pred CCCcEEEEeecCCHHHHHHHHHHHHHcCCCEEEEEcCCCCCCcc
Confidence 3567899994 56666778889999999987 788999988433
No 7
>PLN02979 glycolate oxidase
Probab=71.40 E-value=10 Score=30.70 Aligned_cols=42 Identities=33% Similarity=0.508 Sum_probs=33.5
Q ss_pred CceEEEEEcc-CChHHHHHHHHHHHHccccc-eEEeeCCCCCCc
Q psy17720 7 TARAVFQFYP-ENSAQIELVTSQAMRAGFYG-GLVVDYPHSTKA 48 (80)
Q Consensus 7 GaRAV~QfYP-en~~Q~emI~~~A~kaGF~G-GlvVD~P~S~ka 48 (80)
++..-||+|. .+.+-.+-+.+.|.++||.+ .|-||=|.+.+.
T Consensus 120 ~~~~wfQLY~~~Dr~~~~~ll~RA~~aG~~AlvlTVD~pv~G~R 163 (366)
T PLN02979 120 PGIRFFQLYVYKNRNVVEQLVRRAERAGFKAIALTVDTPRLGRR 163 (366)
T ss_pred CCCeEEEEeecCCHHHHHHHHHHHHHcCCCEEEEEecCCCCCCc
Confidence 4578899995 55566788889999999987 888999988443
No 8
>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.
Probab=70.38 E-value=6.2 Score=27.52 Aligned_cols=31 Identities=23% Similarity=0.173 Sum_probs=25.6
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHcccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFY 35 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~ 35 (80)
++|++||+.++-. +..|.+.+.+...++||.
T Consensus 205 ~~L~~gG~~~~~~---~~~~~~~~~~~l~~~gf~ 235 (251)
T TIGR03534 205 RLLKPGGWLLLEI---GYDQGEAVRALFEAAGFA 235 (251)
T ss_pred HhcccCCEEEEEE---CccHHHHHHHHHHhCCCC
Confidence 5789999999976 446778888888999995
No 9
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=69.38 E-value=14 Score=25.26 Aligned_cols=15 Identities=7% Similarity=0.126 Sum_probs=12.6
Q ss_pred CcccCCceEEEEEcc
Q psy17720 2 RYCSRTARAVFQFYP 16 (80)
Q Consensus 2 ~~~~rGaRAV~QfYP 16 (80)
++|++||+.++..+.
T Consensus 134 ~~LkpgG~lvi~~~~ 148 (188)
T TIGR00438 134 EVLKPKGNFVVKVFQ 148 (188)
T ss_pred HHccCCCEEEEEEcc
Confidence 579999999997654
No 10
>TIGR00138 gidB 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.
Probab=67.09 E-value=8.8 Score=26.96 Aligned_cols=33 Identities=9% Similarity=-0.093 Sum_probs=26.8
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGF 34 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF 34 (80)
++|++||+.++.+-|....+++-+...+...||
T Consensus 130 ~~LkpgG~lvi~~~~~~~~~~~~~~e~~~~~~~ 162 (181)
T TIGR00138 130 NLLKVGGYFLAYKGKKYLDEIEEAKRKCQVLGV 162 (181)
T ss_pred HhcCCCCEEEEEcCCCcHHHHHHHHHhhhhcCc
Confidence 579999999999988888888887766666665
No 11
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=65.19 E-value=9.9 Score=27.61 Aligned_cols=32 Identities=22% Similarity=0.177 Sum_probs=26.3
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHcccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFY 35 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~ 35 (80)
++|++||+.+++-.- .++.+.+.+...+.||.
T Consensus 201 ~~LkpgG~lilsgi~--~~~~~~v~~~l~~~Gf~ 232 (250)
T PRK00517 201 RLLKPGGRLILSGIL--EEQADEVLEAYEEAGFT 232 (250)
T ss_pred HhcCCCcEEEEEECc--HhhHHHHHHHHHHCCCE
Confidence 679999999998554 45778888899999985
No 12
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=65.18 E-value=8.7 Score=21.44 Aligned_cols=20 Identities=20% Similarity=0.282 Sum_probs=15.5
Q ss_pred EEEEccCChHHHHHHHHHHHH
Q psy17720 11 VFQFYPENSAQIELVTSQAMR 31 (80)
Q Consensus 11 V~QfYPen~~Q~emI~~~A~k 31 (80)
-+.+|| |++|.+.|...+--
T Consensus 6 k~rl~P-t~~Q~~~L~~~~~~ 25 (46)
T PF12323_consen 6 KYRLYP-TKEQEEKLERWFGA 25 (46)
T ss_pred EEEEec-CHHHHHHHHHHHHH
Confidence 367999 89999988776543
No 13
>PF11232 Med25: Mediator complex subunit 25 PTOV activation and synapsin 2; InterPro: IPR021394 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear []. ; PDB: 2KY6_A 2L23_A 2XNF_A 2L6U_A.
Probab=62.94 E-value=40 Score=24.46 Aligned_cols=50 Identities=16% Similarity=0.221 Sum_probs=28.0
Q ss_pred CCceEEEEEccCChHHHHHHHHHHHHccccceEEeeCCCCCCcceEEEEEEe
Q psy17720 6 RTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVDYPHSTKAKKFFLVLMT 57 (80)
Q Consensus 6 rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvVD~P~S~kaKK~yLvL~~ 57 (80)
+++|. ++|-+.++.+.---....|..||.|.+-+.. +....=|.++.|++
T Consensus 72 kns~~-v~f~~~~~~E~l~~L~~im~ng~~GcvhF~~-~p~c~iKvL~LlYs 121 (152)
T PF11232_consen 72 KNSRS-VVFHFTTDCESLKSLYRIMSNGFAGCVHFSS-NPPCEIKVLMLLYS 121 (152)
T ss_dssp SSEEE-EEEEESS-HHHHHHHHHHHHCCEEEEEE--S-TSSSS-SEEEEEEE
T ss_pred hcCeE-EEEEcCCChHHHHHHHHHhcCCeEEEEEcCC-CCCCceEEEEEEEc
Confidence 56776 5666654554444446788999988877732 23333455555554
No 14
>cd04736 MDH_FMN Mandelate dehydrogenase (MDH)-like FMN-binding domain. MDH is part of a widespread family of homologous FMN-dependent a-hydroxy acid oxidizing enzymes that oxidizes (S)-mandelate to phenylglyoxalate. MDH is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).
Probab=62.16 E-value=19 Score=28.90 Aligned_cols=42 Identities=24% Similarity=0.297 Sum_probs=34.4
Q ss_pred CceEEEEEccCChHHHHHHHHHHHHccccc-eEEeeCCCCCCc
Q psy17720 7 TARAVFQFYPENSAQIELVTSQAMRAGFYG-GLVVDYPHSTKA 48 (80)
Q Consensus 7 GaRAV~QfYPen~~Q~emI~~~A~kaGF~G-GlvVD~P~S~ka 48 (80)
++..-||+|.-+.+-.+-+.+.|.++||.+ =|-||=|-..+.
T Consensus 115 ~~~~wfQLY~~~r~~~~~ll~RA~~aG~~alvlTvD~pv~g~R 157 (361)
T cd04736 115 DGDLWFQLYVVHRELAELLVKRALAAGYTTLVLTTDVAVNGYR 157 (361)
T ss_pred CCCeEEEEEecCHHHHHHHHHHHHHcCCCEEEEecCCCCCCCc
Confidence 357899999987777888999999999987 666888877543
No 15
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=60.36 E-value=44 Score=23.76 Aligned_cols=35 Identities=23% Similarity=0.250 Sum_probs=26.6
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEe
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVV 40 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvV 40 (80)
++|++||+.++.+ +..|.+.+.....+.||. .+.+
T Consensus 226 ~~Lk~gG~l~~e~---g~~~~~~~~~~l~~~gf~-~v~~ 260 (275)
T PRK09328 226 RYLKPGGWLLLEI---GYDQGEAVRALLAAAGFA-DVET 260 (275)
T ss_pred HhcccCCEEEEEE---CchHHHHHHHHHHhCCCc-eeEE
Confidence 5799999999966 446777777777889997 4433
No 16
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=59.41 E-value=13 Score=29.07 Aligned_cols=32 Identities=19% Similarity=0.211 Sum_probs=27.4
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHcccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFY 35 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~ 35 (80)
+.|++||++|+ |--+.+|++-+..+..+.||.
T Consensus 183 ~~Lkpgg~~~~--y~P~veQv~kt~~~l~~~g~~ 214 (256)
T COG2519 183 DALKPGGVVVV--YSPTVEQVEKTVEALRERGFV 214 (256)
T ss_pred HHhCCCcEEEE--EcCCHHHHHHHHHHHHhcCcc
Confidence 46899987775 766999999999999999885
No 17
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=59.31 E-value=18 Score=25.14 Aligned_cols=32 Identities=16% Similarity=0.108 Sum_probs=26.0
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHcccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFY 35 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~ 35 (80)
++|++||+.|+.+ -+.++.+.+.....+.||.
T Consensus 133 ~~LkpgG~lv~~~--~~~~~~~~~~~~l~~~g~~ 164 (198)
T PRK00377 133 EIIKKGGRIVIDA--ILLETVNNALSALENIGFN 164 (198)
T ss_pred HHcCCCcEEEEEe--ecHHHHHHHHHHHHHcCCC
Confidence 5789999999744 4678888888888899994
No 18
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=56.06 E-value=19 Score=25.61 Aligned_cols=40 Identities=20% Similarity=0.299 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHcccc----ceEEeeCCCCCCcceEEEEEEec
Q psy17720 19 SAQIELVTSQAMRAGFY----GGLVVDYPHSTKAKKFFLVLMTG 58 (80)
Q Consensus 19 ~~Q~emI~~~A~kaGF~----GGlvVD~P~S~kaKK~yLvL~~G 58 (80)
..|++-|..++..-||. --.+||||--...|-.|||--..
T Consensus 50 e~q~k~~l~~i~e~G~iird~d~glVDFpa~~Ng~~~~lCWK~D 93 (123)
T COG4911 50 ESQTKKILDEIIEKGIIIRDIDIGLVDFPAIINGKPAFLCWKID 93 (123)
T ss_pred HHHHHHHHHHHHHcCceeeccccccccchhhhCCceEEEEEecC
Confidence 56889999999999985 23468999998888889997555
No 19
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=54.99 E-value=14 Score=23.79 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=18.6
Q ss_pred EccCChHHHHHHHHHHHHccc
Q psy17720 14 FYPENSAQIELVTSQAMRAGF 34 (80)
Q Consensus 14 fYPen~~Q~emI~~~A~kaGF 34 (80)
+||++.+|+..|.+.|.+.+.
T Consensus 5 v~P~s~~ev~~~v~~a~~~~~ 25 (139)
T PF01565_consen 5 VRPKSVEEVQAIVKFANENGV 25 (139)
T ss_dssp EEESSHHHHHHHHHHHHHTTS
T ss_pred EEeCCHHHHHHHHHHHHHcCC
Confidence 689999999999999997653
No 20
>cd03332 LMO_FMN L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases. It is thought to be a homooctamer with two- and four- fold axes in the center of the octamer.
Probab=54.51 E-value=30 Score=27.93 Aligned_cols=41 Identities=22% Similarity=0.157 Sum_probs=31.6
Q ss_pred CceEEEEEccC-ChHHHHHHHHHHHHccccc-eEEeeCCCCCC
Q psy17720 7 TARAVFQFYPE-NSAQIELVTSQAMRAGFYG-GLVVDYPHSTK 47 (80)
Q Consensus 7 GaRAV~QfYPe-n~~Q~emI~~~A~kaGF~G-GlvVD~P~S~k 47 (80)
.+..-||+|.- +.+-.+-+...|-++||.+ .|-||=|-..+
T Consensus 137 ~~~~wfQlY~~~dr~~~~~ll~RA~~aG~~alvlTVD~pv~g~ 179 (383)
T cd03332 137 DAPRWFQLYWPKDDDLTESLLRRAEKAGYRVLVVTLDTWSLGW 179 (383)
T ss_pred CCCcEEEeeCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCCCCC
Confidence 46789999986 5566778889999999987 77777776543
No 21
>PF08306 Glyco_hydro_98M: Glycosyl hydrolase family 98; InterPro: IPR013191 This domain is the putative catalytic domain of glycosyl hydrolase family 98 proteins.; PDB: 2VNO_B 2VNR_A 2VNG_B 2WMH_A 2WMG_A 2WMF_A 2WMK_A 2WMJ_B 2WMI_B.
Probab=51.65 E-value=8.1 Score=31.17 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=18.2
Q ss_pred HHHHHHHHHccccceEEeeCCCC
Q psy17720 23 ELVTSQAMRAGFYGGLVVDYPHS 45 (80)
Q Consensus 23 emI~~~A~kaGF~GGlvVD~P~S 45 (80)
-||.-.||+..|.||.|.|+|+-
T Consensus 271 a~~~~E~~~v~l~G~tvyd~~~~ 293 (324)
T PF08306_consen 271 AMIGMEMMHVYLNGGTVYDGPEL 293 (324)
T ss_dssp HHHHHHHHHHHTTT--EEEEESH
T ss_pred chhHHhhhheeecCeeEecCCcc
Confidence 46777899999999999999974
No 22
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=51.17 E-value=22 Score=27.39 Aligned_cols=35 Identities=31% Similarity=0.469 Sum_probs=28.5
Q ss_pred CcccCCceEEEEEccCC-----hHHHHHHHHHHHHccccc
Q psy17720 2 RYCSRTARAVFQFYPEN-----SAQIELVTSQAMRAGFYG 36 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen-----~~Q~emI~~~A~kaGF~G 36 (80)
|++|=+||-||-+|.-. .+-++.+-+.|.++||.|
T Consensus 152 rYikVdGKPv~~Iy~p~~~pd~~~~~~~wr~~a~~~G~~g 191 (345)
T PF14307_consen 152 RYIKVDGKPVFLIYRPGDIPDIKEMIERWREEAKEAGLPG 191 (345)
T ss_pred CceeECCEEEEEEECcccccCHHHHHHHHHHHHHHcCCCc
Confidence 67888999999999644 345677789999999986
No 23
>PRK04266 fibrillarin; Provisional
Probab=50.48 E-value=67 Score=23.55 Aligned_cols=52 Identities=13% Similarity=0.052 Sum_probs=31.7
Q ss_pred CcccCCceEEEEEccCCh------HH-HHHHHHHHHHccccceEEeeCCCCCCcceEEEEE
Q psy17720 2 RYCSRTARAVFQFYPENS------AQ-IELVTSQAMRAGFYGGLVVDYPHSTKAKKFFLVL 55 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~------~Q-~emI~~~A~kaGF~GGlvVD~P~S~kaKK~yLvL 55 (80)
++||+||+.|+.++-.+. .+ .+-..+....+||.---++|.+.- .+-+|+++
T Consensus 164 r~LKpGG~lvI~v~~~~~d~~~~~~~~~~~~~~~l~~aGF~~i~~~~l~p~--~~~h~~~v 222 (226)
T PRK04266 164 FFLKDGGYLLLAIKARSIDVTKDPKEIFKEEIRKLEEGGFEILEVVDLEPY--HKDHAAVV 222 (226)
T ss_pred HhcCCCcEEEEEEecccccCcCCHHHHHHHHHHHHHHcCCeEEEEEcCCCC--cCCeEEEE
Confidence 589999999997662211 11 111237777889997777776332 23455444
No 24
>PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []. ; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A.
Probab=49.64 E-value=14 Score=28.03 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=26.6
Q ss_pred Ccc-cCCceEEEEEccCChHHHHHHHHHHHHccccc
Q psy17720 2 RYC-SRTARAVFQFYPENSAQIELVTSQAMRAGFYG 36 (80)
Q Consensus 2 ~~~-~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~G 36 (80)
++| ++||+.|+ |=| +-+|++....+..+.||.-
T Consensus 133 ~~L~~~gG~i~~-fsP-~ieQv~~~~~~L~~~gf~~ 166 (247)
T PF08704_consen 133 RALKKPGGRICC-FSP-CIEQVQKTVEALREHGFTD 166 (247)
T ss_dssp HHE-EEEEEEEE-EES-SHHHHHHHHHHHHHTTEEE
T ss_pred HHHhcCCceEEE-ECC-CHHHHHHHHHHHHHCCCee
Confidence 467 78887765 445 9999999999999999963
No 25
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=46.01 E-value=20 Score=22.67 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=14.4
Q ss_pred ChHHHHHHHHHHHHccccceEEee
Q psy17720 18 NSAQIELVTSQAMRAGFYGGLVVD 41 (80)
Q Consensus 18 n~~Q~emI~~~A~kaGF~GGlvVD 41 (80)
+++|++.|-.+=.++||..-|.+|
T Consensus 49 t~eqv~~LN~~l~~~Gf~~~L~~D 72 (73)
T PF14794_consen 49 TEEQVAKLNQALQKAGFDEELEAD 72 (73)
T ss_dssp -HHHHHHHHHHHHHTT--------
T ss_pred CHHHHHHHHHHHHHcCCCceeccC
Confidence 789999999999999999988877
No 26
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=45.15 E-value=42 Score=22.70 Aligned_cols=39 Identities=10% Similarity=-0.028 Sum_probs=26.9
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEeeC
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVDY 42 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvVD~ 42 (80)
++|++||+.++-... ..|.+.+.....++||.--++-++
T Consensus 128 ~~Lk~gG~~~~~~~~--~~~~~~~~~~l~~~gf~~~~~~~~ 166 (179)
T TIGR00537 128 EILKEGGRVQLIQSS--LNGEPDTFDKLDERGFRYEIVAER 166 (179)
T ss_pred HhhCCCCEEEEEEec--cCChHHHHHHHHhCCCeEEEEEEe
Confidence 579999998885433 234556667778889976655544
No 27
>COG3554 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.93 E-value=14 Score=28.01 Aligned_cols=10 Identities=70% Similarity=1.135 Sum_probs=8.3
Q ss_pred ceEEeeCCCC
Q psy17720 36 GGLVVDYPHS 45 (80)
Q Consensus 36 GGlvVD~P~S 45 (80)
-|+|||||.=
T Consensus 177 dGlVvDYPgL 186 (190)
T COG3554 177 DGLVVDYPGL 186 (190)
T ss_pred CceEEeCcch
Confidence 4899999963
No 28
>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes.
Probab=39.45 E-value=53 Score=22.70 Aligned_cols=44 Identities=14% Similarity=-0.046 Sum_probs=29.0
Q ss_pred CcccCCceEEEEEccC------ChH-------HHHHHHHHHHHccccceEEeeCCCC
Q psy17720 2 RYCSRTARAVFQFYPE------NSA-------QIELVTSQAMRAGFYGGLVVDYPHS 45 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPe------n~~-------Q~emI~~~A~kaGF~GGlvVD~P~S 45 (80)
++|++||+.+++-... +.+ -.+-+.+...++||.-.-.+|...+
T Consensus 92 ~~LkpgG~l~i~~~~~~~~~~~~~~~~~~~~~s~~~~~~~l~~~Gf~~~~~~~~~~~ 148 (224)
T smart00828 92 RHLKDGGHLVLADFIANLLSAIEHEETTSYLVTREEWAELLARNNLRVVEGVDASLE 148 (224)
T ss_pred HHcCCCCEEEEEEcccccCccccccccccccCCHHHHHHHHHHCCCeEEEeEECcHh
Confidence 5799999999985421 110 0234556778899988777776444
No 29
>cd04737 LOX_like_FMN L-Lactate oxidase (LOX) FMN-binding domain. LOX is a member of the family of FMN-containing alpha-hydroxyacid oxidases and catalyzes the oxidation of l-lactate using molecular oxygen to generate pyruvate and H2O2. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).
Probab=38.61 E-value=71 Score=25.42 Aligned_cols=40 Identities=20% Similarity=0.127 Sum_probs=29.0
Q ss_pred CceEEEEEccCCh-HHHHHHHHHHHHccccc-eEEeeCCCCC
Q psy17720 7 TARAVFQFYPENS-AQIELVTSQAMRAGFYG-GLVVDYPHST 46 (80)
Q Consensus 7 GaRAV~QfYPen~-~Q~emI~~~A~kaGF~G-GlvVD~P~S~ 46 (80)
++...||+|+-.+ +=.+-+...|-++||.. .+-||=|...
T Consensus 124 ~~~~wfQlY~~~d~~~~~~ll~rA~~aG~~alvlTvD~p~~g 165 (351)
T cd04737 124 GGPKWFQLYMSKDDGFNRSLLDRAKAAGAKAIILTADATVGG 165 (351)
T ss_pred CCCeEEEEeecCCHHHHHHHHHHHHHcCCCEEEEecCCCCCC
Confidence 5678999997444 44666678888999976 6667765544
No 30
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=36.36 E-value=58 Score=19.14 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=17.7
Q ss_pred EEccCChHHHHHHHHHHHHccc
Q psy17720 13 QFYPENSAQIELVTSQAMRAGF 34 (80)
Q Consensus 13 QfYPen~~Q~emI~~~A~kaGF 34 (80)
.+.|+|.+|+++|.+-....++
T Consensus 2 rv~p~t~~q~~~L~~L~~~~~~ 23 (74)
T PF02244_consen 2 RVTPKTEEQLELLQELEQSNEL 23 (74)
T ss_dssp EEEESSHHHHHHHHHHHHHSTE
T ss_pred EEEeCCHHHHHHHHHHhcccce
Confidence 5789999999999988855443
No 31
>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.
Probab=35.83 E-value=80 Score=23.24 Aligned_cols=36 Identities=14% Similarity=0.171 Sum_probs=28.6
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEe
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVV 40 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvV 40 (80)
+.|++||+.++=.= .+|.+.+.+...+.||...++.
T Consensus 204 ~~L~~gG~l~l~~~---~~~~~~v~~~l~~~g~~~~~~~ 239 (251)
T TIGR03704 204 DWLAPGGHLLVETS---ERQAPLAVEAFARAGLIARVAS 239 (251)
T ss_pred HhcCCCCEEEEEEC---cchHHHHHHHHHHCCCCceeeE
Confidence 57899999998754 4577788888888999887765
No 32
>PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated
Probab=35.35 E-value=62 Score=22.01 Aligned_cols=38 Identities=18% Similarity=0.152 Sum_probs=25.4
Q ss_pred CcccCCceEEEEE-ccCChHHHHHHHHHHHHccccceEEeeC
Q psy17720 2 RYCSRTARAVFQF-YPENSAQIELVTSQAMRAGFYGGLVVDY 42 (80)
Q Consensus 2 ~~~~rGaRAV~Qf-YPen~~Q~emI~~~A~kaGF~GGlvVD~ 42 (80)
++|++||+.++.+ -+++ .+.+.....+.||.---+..+
T Consensus 119 ~~Lk~gG~lv~~~~~~~~---~~~~~~~l~~~g~~~~~~~~~ 157 (187)
T PRK08287 119 AHLHPGGRLVLTFILLEN---LHSALAHLEKCGVSELDCVQL 157 (187)
T ss_pred HhcCCCeEEEEEEecHhh---HHHHHHHHHHCCCCcceEEEE
Confidence 5799999999975 3333 344556778899965444333
No 33
>PLN02805 D-lactate dehydrogenase [cytochrome]
Probab=35.16 E-value=58 Score=27.36 Aligned_cols=33 Identities=12% Similarity=0.354 Sum_probs=25.8
Q ss_pred EEEEccCChHHHHHHHHHHHHccc------------------cceEEeeCC
Q psy17720 11 VFQFYPENSAQIELVTSQAMRAGF------------------YGGLVVDYP 43 (80)
Q Consensus 11 V~QfYPen~~Q~emI~~~A~kaGF------------------~GGlvVD~P 43 (80)
-.=++|+|.+|+..|.+.|.+.|. .||++||.-
T Consensus 135 ~~Vv~P~s~eeV~~ivk~a~~~~ipv~prGgGts~~G~~~~~~ggivIdl~ 185 (555)
T PLN02805 135 DVVVFPRSEEEVSKIVKSCNKYKVPIVPYGGATSIEGHTLAPHGGVCIDMS 185 (555)
T ss_pred CEEEEcCCHHHHHHHHHHHHHCCCcEEEECCCCCCCCCccCCCCEEEEEcc
Confidence 334689999999999999987642 368888874
No 34
>KOG4730|consensus
Probab=34.99 E-value=50 Score=28.39 Aligned_cols=41 Identities=29% Similarity=0.272 Sum_probs=31.3
Q ss_pred EccCChHHHHHHHHHHHHccccceEEeeCCCCCCcceEEEEEEecC
Q psy17720 14 FYPENSAQIELVTSQAMRAGFYGGLVVDYPHSTKAKKFFLVLMTGG 59 (80)
Q Consensus 14 fYPen~~Q~emI~~~A~kaGF~GGlvVD~P~S~kaKK~yLvL~~G~ 59 (80)
-||++.++++-|..+|.++|-.==+|- |-||--. ||+..|.
T Consensus 54 ~yP~teaeL~~lVa~A~~a~~kirvVg-~gHSp~~----l~ctdg~ 94 (518)
T KOG4730|consen 54 NYPKTEAELVELVAAATEAGKKIRVVG-SGHSPSK----LVCTDGL 94 (518)
T ss_pred CCCCCHHHHHHHHHHHHHcCceEEEec-ccCCCCc----ceecccc
Confidence 499999999999999999998765555 8777422 4555553
No 35
>PRK07402 precorrin-6B methylase; Provisional
Probab=34.21 E-value=93 Score=21.37 Aligned_cols=37 Identities=14% Similarity=0.007 Sum_probs=24.6
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEe
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVV 40 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvV 40 (80)
++|++||+.++..+ +.+++..+.+...+.++.+.-++
T Consensus 130 ~~LkpgG~li~~~~--~~~~~~~~~~~~~~~~~~~~~~~ 166 (196)
T PRK07402 130 QYLKPGGRLVATAS--SLEGLYAISEGLAQLQARNIEVV 166 (196)
T ss_pred HhcCCCeEEEEEee--cHHHHHHHHHHHHhcCCCCceEE
Confidence 57899999888875 35566666666666666554443
No 36
>PHA01753 Holliday junction resolvase
Probab=34.11 E-value=39 Score=23.60 Aligned_cols=28 Identities=21% Similarity=0.184 Sum_probs=22.4
Q ss_pred ChHHHHHHHHHHHHccccce---EEeeCCCC
Q psy17720 18 NSAQIELVTSQAMRAGFYGG---LVVDYPHS 45 (80)
Q Consensus 18 n~~Q~emI~~~A~kaGF~GG---lvVD~P~S 45 (80)
+++|++.|..+|-+.||.|| |.|-|+..
T Consensus 65 ~~~Ki~kLi~fa~~fg~~~~~p~i~vkf~~~ 95 (121)
T PHA01753 65 DKFQIEKLFRFCEIFSFCECKPLVMVRYKKY 95 (121)
T ss_pred CHHHHHHHHHHHHHhCccCCeEEEEEEecCc
Confidence 68899999999999999665 56666644
No 37
>PF03456 uDENN: uDENN domain; InterPro: IPR005113 This region is always found associated with IPR001194 from INTERPRO. It is predicted to form an all beta domain [].; PDB: 3TW8_A.
Probab=34.07 E-value=77 Score=18.46 Aligned_cols=49 Identities=14% Similarity=0.190 Sum_probs=23.6
Q ss_pred EEEEEccCChH-HHHHHHHHHHHccccceEEeeCCCCCCcceEEEEEEec
Q psy17720 10 AVFQFYPENSA-QIELVTSQAMRAGFYGGLVVDYPHSTKAKKFFLVLMTG 58 (80)
Q Consensus 10 AV~QfYPen~~-Q~emI~~~A~kaGF~GGlvVD~P~S~kaKK~yLvL~~G 58 (80)
.|+|=||+++. .-.-+-..--.--|=.|+-+.-.......-+..||+..
T Consensus 3 ~il~~yP~~d~~~~~~~~~~i~~FCfP~G~~~~~~~~~~~~~f~FvLT~~ 52 (65)
T PF03456_consen 3 EILDRYPPSDHEPDPPLPPSIPMFCFPDGIEISSQSRPPPQFFSFVLTDE 52 (65)
T ss_dssp EEEEEEST--T---HHHHHHHHHHHS-S-CCCCGGG-GSSCEEEEEEE-T
T ss_pred EEEEECCCCccccCCCChhhCCccCCCCCcEeeccccCCCeEEEEEEECC
Confidence 48999999764 22223333334456666555444344566667777643
No 38
>PF01070 FMN_dh: FMN-dependent dehydrogenase; InterPro: IPR000262 A number of oxidoreductases that act on alpha-hydroxy acids and which are FMN-containing flavoproteins have been shown [, , ] to be structurally related. These enzymes are: Lactate dehydrogenase (1.1.2.3 from EC), which consists of a dehydrogenase domain and a haem-binding domain called cytochrome b2 and which catalyses the conversion of lactate into pyruvate. Glycolate oxidase (1.1.3.15 from EC) ((S)-2-hydroxy-acid oxidase), a peroxisomal enzyme that catalyses the conversion of glycolate and oxygen to glyoxylate and hydrogen peroxide. Long chain alpha-hydroxy acid oxidase from rat (1.1.3.15 from EC), a peroxisomal enzyme. Lactate 2-monooxygenase (1.13.12.4 from EC) (lactate oxidase) from Mycobacterium smegmatis, which catalyses the conversion of lactate and oxygen to acetate, carbon dioxide and water. (S)-mandelate dehydrogenase from Pseudomonas putida (gene mdlB), which catalyses the reduction of (S)-mandelate to benzoylformate. The first step in the reaction mechanism of these enzymes is the abstraction of the proton from the alpha-carbon of the substrate producing a carbanion which can subsequently attach to the N5 atom of FMN. A conserved histidine has been shown [] to be involved in the removal of the proton. The region around this active site residue is highly conserved and contains an arginine residue which is involved in substrate binding.; GO: 0016491 oxidoreductase activity; PDB: 1VCG_C 1VCF_A 1P0N_B 1P0K_A 2A85_A 2A7P_A 3GIY_A 2A7N_A 3DH7_A 2RDU_A ....
Probab=34.06 E-value=66 Score=25.39 Aligned_cols=41 Identities=24% Similarity=0.310 Sum_probs=30.5
Q ss_pred CceEEEEEccC-ChHHHHHHHHHHHHccccc-eEEeeCCCCCC
Q psy17720 7 TARAVFQFYPE-NSAQIELVTSQAMRAGFYG-GLVVDYPHSTK 47 (80)
Q Consensus 7 GaRAV~QfYPe-n~~Q~emI~~~A~kaGF~G-GlvVD~P~S~k 47 (80)
++...||+|+- +.+-++-+.+.|-++||.. .|-||=|...+
T Consensus 109 ~~~~~~Qly~~~d~~~~~~~i~rAe~aG~~Al~vtvD~~~~~~ 151 (356)
T PF01070_consen 109 GGPLWFQLYPPRDRELTRDLIRRAEAAGAKALVVTVDAPQEGN 151 (356)
T ss_dssp TSEEEEEEEGBSSHHHHHHHHHHHHHTTCSEEEEETSHSSHHH
T ss_pred cCCeEEEEEEecCHHHHHHHHHHhhcCCCCEEEEECcCcccCC
Confidence 46789999974 5555666778899999976 77777766543
No 39
>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed
Probab=33.72 E-value=50 Score=23.54 Aligned_cols=30 Identities=10% Similarity=-0.112 Sum_probs=19.9
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGF 34 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF 34 (80)
++|++||+.++..-+. +...+..+++.-|.
T Consensus 133 ~~LkpGG~lv~~~~~~---~~~~l~~~~~~~~~ 162 (187)
T PRK00107 133 PLLKPGGRFLALKGRD---PEEEIAELPKALGG 162 (187)
T ss_pred HhcCCCeEEEEEeCCC---hHHHHHHHHHhcCc
Confidence 6899999999997553 33335555555543
No 40
>PHA03323 nuclear egress membrane protein UL34; Provisional
Probab=33.68 E-value=26 Score=27.82 Aligned_cols=15 Identities=40% Similarity=0.612 Sum_probs=11.4
Q ss_pred cCCceEEEEEccCCh
Q psy17720 5 SRTARAVFQFYPENS 19 (80)
Q Consensus 5 ~rGaRAV~QfYPen~ 19 (80)
+..+||||||-=.+.
T Consensus 40 ~~P~RCvFQF~GqDg 54 (272)
T PHA03323 40 RPPARCVFQFSGQDG 54 (272)
T ss_pred CCCceEEEEecCCCC
Confidence 457899999986543
No 41
>PRK11230 glycolate oxidase subunit GlcD; Provisional
Probab=33.39 E-value=61 Score=26.56 Aligned_cols=20 Identities=15% Similarity=0.273 Sum_probs=18.1
Q ss_pred EccCChHHHHHHHHHHHHcc
Q psy17720 14 FYPENSAQIELVTSQAMRAG 33 (80)
Q Consensus 14 fYPen~~Q~emI~~~A~kaG 33 (80)
++|+|.+|+.-|.+.|.+.|
T Consensus 60 v~P~s~eeV~~iv~~a~~~~ 79 (499)
T PRK11230 60 VLPKQMEQVQALLAVCHRLR 79 (499)
T ss_pred EeeCCHHHHHHHHHHHHHcC
Confidence 67999999999999999865
No 42
>PF06475 Glycolipid_bind: Putative glycolipid-binding; InterPro: IPR009467 This family consists of several hypothetical bacterial proteins. The function of this family is unknown.; PDB: 2H1T_A.
Probab=32.22 E-value=19 Score=26.21 Aligned_cols=10 Identities=60% Similarity=1.069 Sum_probs=7.5
Q ss_pred ceEEeeCCCC
Q psy17720 36 GGLVVDYPHS 45 (80)
Q Consensus 36 GGlvVD~P~S 45 (80)
-|+|+|||.=
T Consensus 166 ~G~V~dYP~l 175 (179)
T PF06475_consen 166 DGFVVDYPGL 175 (179)
T ss_dssp TS-EEEETTT
T ss_pred CceEEeCcch
Confidence 4899999974
No 43
>PRK14532 adenylate kinase; Provisional
Probab=31.74 E-value=1.1e+02 Score=20.68 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=16.7
Q ss_pred CceEEEEEccCChHHHHHHHHHHHHcc
Q psy17720 7 TARAVFQFYPENSAQIELVTSQAMRAG 33 (80)
Q Consensus 7 GaRAV~QfYPen~~Q~emI~~~A~kaG 33 (80)
++-.|+--||.+.+|++.+...+.+.|
T Consensus 78 ~~g~vldg~pr~~~q~~~~~~~l~~~g 104 (188)
T PRK14532 78 AGGAIFDGFPRTVAQAEALDKMLASRG 104 (188)
T ss_pred cCcEEEeCCCCCHHHHHHHHHHHHhcC
Confidence 444666666777777666665555554
No 44
>PF00012 HSP70: Hsp70 protein; InterPro: IPR013126 Heat shock proteins, Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region []. Hsp70 proteins have an average molecular weight of 70 kDa [, , ]. In most species,there are many proteins that belong to the hsp70 family. Some of these are only expressed under stress conditions (strictly inducible), while some are present in cells under normal growth conditions and are not heat-inducible (constitutive or cognate) [, ]. Hsp70 proteins can be found in different cellular compartments(nuclear, cytosolic, mitochondrial, endoplasmic reticulum, for example).; PDB: 2P32_D 3D2F_A 2QXL_A 3D2E_C 3C7N_A 3FE1_C 4ANI_C 2V7Y_A 2KHO_A 3DPQ_B ....
Probab=31.73 E-value=1.7e+02 Score=23.37 Aligned_cols=42 Identities=24% Similarity=0.239 Sum_probs=29.8
Q ss_pred ChHHHHHHHHHHHHccccceEEee--------CCCCCC-cceEEEEEEecC
Q psy17720 18 NSAQIELVTSQAMRAGFYGGLVVD--------YPHSTK-AKKFFLVLMTGG 59 (80)
Q Consensus 18 n~~Q~emI~~~A~kaGF~GGlvVD--------~P~S~k-aKK~yLvL~~G~ 59 (80)
++.|++.+..||..|||.-=-+|+ |-.... ..+.+||+..|+
T Consensus 147 ~~~qr~~~~~Aa~~agl~~~~li~Ep~Aaa~~y~~~~~~~~~~vlv~D~Gg 197 (602)
T PF00012_consen 147 TDEQRQALRDAAELAGLNVLRLINEPTAAALAYGLERSDKGKTVLVVDFGG 197 (602)
T ss_dssp -HHHHHHHHHHHHHTT-EEEEEEEHHHHHHHHTTTTSSSSEEEEEEEEEES
T ss_pred hhhhhhcccccccccccccceeecccccccccccccccccccceecccccc
Confidence 578999999999999997633444 422322 378899999997
No 45
>PRK14968 putative methyltransferase; Provisional
Probab=31.46 E-value=1.5e+02 Score=19.37 Aligned_cols=34 Identities=18% Similarity=0.184 Sum_probs=23.3
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccce
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGG 37 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GG 37 (80)
++|++||+.++.. | +..+.+-+.+...++||.--
T Consensus 136 ~~Lk~gG~~~~~~-~-~~~~~~~l~~~~~~~g~~~~ 169 (188)
T PRK14968 136 RYLKPGGRILLLQ-S-SLTGEDEVLEYLEKLGFEAE 169 (188)
T ss_pred HhcCCCeEEEEEE-c-ccCCHHHHHHHHHHCCCeee
Confidence 6789999887754 3 23345666778888898643
No 46
>PF02676 TYW3: Methyltransferase TYW3; InterPro: IPR003827 The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis []. yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3'-position adjacent the anticodon of phenylalanine tRNA. TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner [].; PDB: 1TLJ_A 2DVK_A 2IT3_B 2IT2_A 2DRV_A 2QG3_B.
Probab=30.27 E-value=2.2e+02 Score=20.91 Aligned_cols=42 Identities=14% Similarity=0.213 Sum_probs=29.9
Q ss_pred EEEccCChHHHHHHHHHHHHcccc-ceEEeeCCCCCCcceEEEEEEec
Q psy17720 12 FQFYPENSAQIELVTSQAMRAGFY-GGLVVDYPHSTKAKKFFLVLMTG 58 (80)
Q Consensus 12 ~QfYPen~~Q~emI~~~A~kaGF~-GGlvVD~P~S~kaKK~yLvL~~G 58 (80)
|-++=.+.+-...|.++|+.|||- -|+..--+ +++.+.+.++
T Consensus 113 lHV~c~~l~~A~~Ll~~A~~aGFr~SGi~s~~~-----~~~iVaIrs~ 155 (205)
T PF02676_consen 113 LHVQCRDLESAQKLLKIARSAGFRESGITSLSS-----KRVIVAIRSS 155 (205)
T ss_dssp EEEEESSHHHHHHHHHHHHHCT-TTEEEEEECT-----SCEEEEEE-S
T ss_pred EEEEeCCHHHHHHHHHHHHHhCccccCceeccC-----CceEEEEecc
Confidence 445557899999999999999995 47775443 6777666655
No 47
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=29.26 E-value=2e+02 Score=22.82 Aligned_cols=26 Identities=15% Similarity=0.166 Sum_probs=18.2
Q ss_pred CcccCCceEEEEE---c-cCChHHHHHHHH
Q psy17720 2 RYCSRTARAVFQF---Y-PENSAQIELVTS 27 (80)
Q Consensus 2 ~~~~rGaRAV~Qf---Y-Pen~~Q~emI~~ 27 (80)
++|++||+-|+-- + .||.++++-...
T Consensus 360 ~~LkpGG~lvystcs~~~~Ene~~v~~~l~ 389 (427)
T PRK10901 360 PLLKPGGTLLYATCSILPEENEQQIKAFLA 389 (427)
T ss_pred HhcCCCCEEEEEeCCCChhhCHHHHHHHHH
Confidence 5799999999654 4 477776665543
No 48
>cd03707 EFTU_III Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix
Probab=29.10 E-value=49 Score=20.18 Aligned_cols=17 Identities=0% Similarity=-0.185 Sum_probs=15.4
Q ss_pred cccCCceEEEEEccCCh
Q psy17720 3 YCSRTARAVFQFYPENS 19 (80)
Q Consensus 3 ~~~rGaRAV~QfYPen~ 19 (80)
+|++|..|..|+.++.+
T Consensus 51 ~i~~g~~~~v~l~l~~p 67 (90)
T cd03707 51 MVMPGDNVKMTVELIHP 67 (90)
T ss_pred ccCCCCEEEEEEEECCc
Confidence 58899999999999877
No 49
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=28.87 E-value=48 Score=21.47 Aligned_cols=14 Identities=21% Similarity=0.475 Sum_probs=8.9
Q ss_pred cccceEEeeCCCCC
Q psy17720 33 GFYGGLVVDYPHST 46 (80)
Q Consensus 33 GF~GGlvVD~P~S~ 46 (80)
.+.+|+++++||.+
T Consensus 83 ~~~~~F~f~NPna~ 96 (107)
T PRK09502 83 GLNEGFKFTNPNVK 96 (107)
T ss_pred CCCceEEEECCCCC
Confidence 34566777777764
No 50
>PF05078 DUF679: Protein of unknown function (DUF679); InterPro: IPR007770 This family contains uncharacterised plant proteins of unknown function.
Probab=28.87 E-value=71 Score=23.60 Aligned_cols=35 Identities=17% Similarity=0.405 Sum_probs=27.5
Q ss_pred EEccCCh-HHHHHHHHHHHHcccc-ceEEeeCCCCCC
Q psy17720 13 QFYPENS-AQIELVTSQAMRAGFY-GGLVVDYPHSTK 47 (80)
Q Consensus 13 QfYPen~-~Q~emI~~~A~kaGF~-GGlvVD~P~S~k 47 (80)
=|||.-. ++.|++..--+-.||. +.+.+-||...+
T Consensus 130 Cf~P~~~~~~~~~l~~lP~~vG~~~S~vF~~FPt~R~ 166 (170)
T PF05078_consen 130 CFFPSPSSETKEVLMNLPLGVGVLCSMVFMIFPTTRH 166 (170)
T ss_pred ecCCCCchhHHHHHHHhHHHHHHhHeeEEEECCCCCC
Confidence 4789755 5678888888999995 678899998743
No 51
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=28.67 E-value=47 Score=22.77 Aligned_cols=25 Identities=36% Similarity=0.595 Sum_probs=19.6
Q ss_pred EEEccCChH-----------HHHHHHHHHHHccccc
Q psy17720 12 FQFYPENSA-----------QIELVTSQAMRAGFYG 36 (80)
Q Consensus 12 ~QfYPen~~-----------Q~emI~~~A~kaGF~G 36 (80)
-|-||||++ .-.+++.+-.|.||+-
T Consensus 21 WqEy~eNde~~~PlTEDElkEF~~kseQlrrNGf~k 56 (97)
T PF15337_consen 21 WQEYPENDENCLPLTEDELKEFQVKSEQLRRNGFGK 56 (97)
T ss_pred ccccCcCCcccCcCcHHHHHHHHHHHHHHHHccccc
Confidence 488999987 3457788889999963
No 52
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=28.25 E-value=90 Score=21.91 Aligned_cols=31 Identities=13% Similarity=0.003 Sum_probs=24.0
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGF 34 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF 34 (80)
++|++||+-++.. .+.++.+-+.....+.|+
T Consensus 144 ~~LkpgG~l~i~~--~~~~~~~~~~~~~~~~g~ 174 (202)
T PRK00121 144 RKLKPGGEIHFAT--DWEGYAEYMLEVLSAEGG 174 (202)
T ss_pred HHcCCCCEEEEEc--CCHHHHHHHHHHHHhCcc
Confidence 4789999888765 467777777788888886
No 53
>cd04747 OYE_like_5_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=27.62 E-value=1.4e+02 Score=23.64 Aligned_cols=25 Identities=24% Similarity=0.280 Sum_probs=16.4
Q ss_pred HHHHccccc-eEEeeC---------CCCCCcceEE
Q psy17720 28 QAMRAGFYG-GLVVDY---------PHSTKAKKFF 52 (80)
Q Consensus 28 ~A~kaGF~G-GlvVD~---------P~S~kaKK~y 52 (80)
-|.+|||-| .|---. |.+.+...-|
T Consensus 152 ~a~~aGfDgVeih~ahGyLl~qFLSp~~N~RtDeY 186 (361)
T cd04747 152 DARRLGFDGIELHGAHGYLIDQFFWAGTNRRADGY 186 (361)
T ss_pred HHHHcCCCEEEEecccchHHHHhcCCCCCCCCCCC
Confidence 356689976 555555 7776666655
No 54
>KOG3201|consensus
Probab=26.93 E-value=61 Score=24.76 Aligned_cols=41 Identities=20% Similarity=0.324 Sum_probs=35.3
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEeeCC
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVDYP 43 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvVD~P 43 (80)
+.|++-|||.| |=|.--+-.+-+.+.+-.+||.-.+--||-
T Consensus 128 ~lL~p~g~Al~-fsPRRg~sL~kF~de~~~~gf~v~l~enyd 168 (201)
T KOG3201|consen 128 SLLRPSGRALL-FSPRRGQSLQKFLDEVGTVGFTVCLEENYD 168 (201)
T ss_pred HHhCcccceeE-ecCcccchHHHHHHHHHhceeEEEecccHh
Confidence 35888899776 999999999999999999999888877774
No 55
>cd07361 MEMO_like Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility. This subfamily is composed of Memo (mediator of ErbB2-driven cell motility) and similar proteins. Memo is a protein that is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility. It is required for the ErbB2-driven cell mobility and is found in protein complexes with cofilin, ErbB2 and PLCgamma1. However, Memo is not homologous to any known signaling proteins, and its function in ErbB2 signaling is not known. Structural studies show that Memo binds directly to a specific ErbB2-derived phosphopeptide. Memo is homologous to class III nonheme iron-dependent extradiol dioxygenases, however, no metal binding or enzymatic activity can be detected for Memo. This subfamily also contains a few members containing a C-terminal AMMECR1-like domain. The AMMECR1 protein was proposed to be a regulatory factor that is potentia
Probab=26.84 E-value=52 Score=24.28 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=16.3
Q ss_pred EEEccCChHHHHHHHHHHHHc
Q psy17720 12 FQFYPENSAQIELVTSQAMRA 32 (80)
Q Consensus 12 ~QfYPen~~Q~emI~~~A~ka 32 (80)
=+|||.++++++...+.-...
T Consensus 6 G~fYp~~~~~l~~~l~~~~~~ 26 (266)
T cd07361 6 GSFYPADPEELRRQLEAFLAA 26 (266)
T ss_pred CCCCCCCHHHHHHHHHHHHHh
Confidence 379999999987777766554
No 56
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=26.81 E-value=70 Score=24.86 Aligned_cols=35 Identities=11% Similarity=0.152 Sum_probs=23.3
Q ss_pred CcccCCceEEEEEcc-----------CCh-H---------HHHHHHHHHHHccccc
Q psy17720 2 RYCSRTARAVFQFYP-----------ENS-A---------QIELVTSQAMRAGFYG 36 (80)
Q Consensus 2 ~~~~rGaRAV~QfYP-----------en~-~---------Q~emI~~~A~kaGF~G 36 (80)
++|++||+-|+.... ... . -.+.+.....++||.=
T Consensus 213 r~LkpGG~Lvletl~i~g~~~~~l~p~~ry~k~~nv~flpS~~~L~~~L~~aGF~~ 268 (314)
T TIGR00452 213 HQLVIKGELVLETLVIDGDLNTVLVPKDRYAKMKNVYFIPSVSALKNWLEKVGFEN 268 (314)
T ss_pred HhcCCCCEEEEEEEEecCccccccCchHHHHhccccccCCCHHHHHHHHHHCCCeE
Confidence 689999999987432 110 0 1345567788999974
No 57
>PRK04235 hypothetical protein; Provisional
Probab=26.76 E-value=1.7e+02 Score=21.64 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=30.2
Q ss_pred ccCChHHHHHHHHHHHHcccc-ceEEeeCCCCCCcceEEEEEEecCCCCCCC
Q psy17720 15 YPENSAQIELVTSQAMRAGFY-GGLVVDYPHSTKAKKFFLVLMTGGDLPLPP 65 (80)
Q Consensus 15 YPen~~Q~emI~~~A~kaGF~-GGlvVD~P~S~kaKK~yLvL~~G~~~~lp~ 65 (80)
+-.+-+-...+.++|+.|||- -|+..- +.||+.+.+.++-....|-
T Consensus 106 ~c~~le~A~~Ll~~A~~~Gfr~SGI~s~-----~~~r~iV~Irs~~~ld~Pl 152 (196)
T PRK04235 106 AARDLETAKKLLELAREAGFKHSGIKSI-----SDKRVLVEIRTTERMDAPL 152 (196)
T ss_pred eeCCHHHHHHHHHHHHHcCchhhcceec-----CCCcEEEEEecCCcEEEEE
Confidence 346778888999999999994 466542 2256666666543344443
No 58
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=25.85 E-value=67 Score=22.91 Aligned_cols=31 Identities=26% Similarity=0.453 Sum_probs=22.1
Q ss_pred EEcc-CChHHHHHHHHHHHHccccceEEeeCCCCCCcc
Q psy17720 13 QFYP-ENSAQIELVTSQAMRAGFYGGLVVDYPHSTKAK 49 (80)
Q Consensus 13 QfYP-en~~Q~emI~~~A~kaGF~GGlvVD~P~S~kaK 49 (80)
.+++ =++.|++.| ..|.+.||. |||.....+
T Consensus 151 ~~~~~LTdrQ~~vL-~~A~~~GYF-----d~PR~~~l~ 182 (215)
T COG3413 151 IGKNDLTDRQLEVL-RLAYKMGYF-----DYPRRVSLK 182 (215)
T ss_pred cccccCCHHHHHHH-HHHHHcCCC-----CCCccCCHH
Confidence 3444 467777766 899999985 888876543
No 59
>PRK14967 putative methyltransferase; Provisional
Probab=25.76 E-value=65 Score=22.74 Aligned_cols=38 Identities=13% Similarity=0.146 Sum_probs=23.1
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEee
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVD 41 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvVD 41 (80)
++|++||+.++- +++ ..+.+.+.+...+.||.=.....
T Consensus 147 ~~Lk~gG~l~~~-~~~-~~~~~~~~~~l~~~g~~~~~~~~ 184 (223)
T PRK14967 147 ALLAPGGSLLLV-QSE-LSGVERTLTRLSEAGLDAEVVAS 184 (223)
T ss_pred HhcCCCcEEEEE-Eec-ccCHHHHHHHHHHCCCCeEEEEe
Confidence 578999998753 222 23445555666777886444433
No 60
>PRK08317 hypothetical protein; Provisional
Probab=25.52 E-value=1.2e+02 Score=20.41 Aligned_cols=13 Identities=23% Similarity=0.069 Sum_probs=10.6
Q ss_pred CcccCCceEEEEE
Q psy17720 2 RYCSRTARAVFQF 14 (80)
Q Consensus 2 ~~~~rGaRAV~Qf 14 (80)
++|++||+-++..
T Consensus 112 ~~L~~gG~l~~~~ 124 (241)
T PRK08317 112 RVLRPGGRVVVLD 124 (241)
T ss_pred HHhcCCcEEEEEe
Confidence 5799999998754
No 61
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=25.14 E-value=34 Score=25.86 Aligned_cols=15 Identities=27% Similarity=0.237 Sum_probs=12.5
Q ss_pred CcccCCceEEEEEcc
Q psy17720 2 RYCSRTARAVFQFYP 16 (80)
Q Consensus 2 ~~~~rGaRAV~QfYP 16 (80)
++|++||++++|..-
T Consensus 154 ~~LkpgG~~~lq~i~ 168 (273)
T PF02353_consen 154 RLLKPGGRLVLQTIT 168 (273)
T ss_dssp HHSETTEEEEEEEEE
T ss_pred HhcCCCcEEEEEecc
Confidence 579999999999643
No 62
>PRK09372 ribonuclease activity regulator protein RraA; Provisional
Probab=24.73 E-value=65 Score=22.94 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=15.0
Q ss_pred HHHHHHHHHccccceEEee
Q psy17720 23 ELVTSQAMRAGFYGGLVVD 41 (80)
Q Consensus 23 emI~~~A~kaGF~GGlvVD 41 (80)
|+++.+|+..|..| +|||
T Consensus 76 ~~~~~~a~~~G~~G-~Vid 93 (159)
T PRK09372 76 DNLAELAVDNGWEG-IVVY 93 (159)
T ss_pred HHHHHHHHHcCCeE-EEec
Confidence 78899999999876 6666
No 63
>TIGR01935 NOT-MenG RraA famliy. This model was initially classified as a "hypothetical equivalog" expressing the tentative hypothesis that all members might have the same function as the E. coli enzyme. Considering the second clade of enterobacterial sequences within this family, that appears to be less tenable. The function of these sequences outside of the narrow RraA equivalog model (TIGR02998) remains obscure. All of these were initially annotated as MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error in the case of the E. coli protein.
Probab=24.54 E-value=70 Score=22.60 Aligned_cols=18 Identities=22% Similarity=0.457 Sum_probs=15.0
Q ss_pred HHHHHHHHHccccceEEee
Q psy17720 23 ELVTSQAMRAGFYGGLVVD 41 (80)
Q Consensus 23 emI~~~A~kaGF~GGlvVD 41 (80)
|+++.+|+..|..| +|||
T Consensus 72 ~~~~~~a~~~G~~G-~Vid 89 (150)
T TIGR01935 72 DNLAVLAEENGWEG-VIVN 89 (150)
T ss_pred HHHHHHHHHCCCEE-EEEe
Confidence 78999999999877 6665
No 64
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=24.47 E-value=36 Score=25.78 Aligned_cols=15 Identities=20% Similarity=0.317 Sum_probs=10.2
Q ss_pred CcccCCceEE-EEEcc
Q psy17720 2 RYCSRTARAV-FQFYP 16 (80)
Q Consensus 2 ~~~~rGaRAV-~QfYP 16 (80)
||||+|||.+ +=|.+
T Consensus 144 RVlKpgG~~~vle~~~ 159 (238)
T COG2226 144 RVLKPGGRLLVLEFSK 159 (238)
T ss_pred HhhcCCeEEEEEEcCC
Confidence 7888888864 44443
No 65
>PRK08245 hypothetical protein; Validated
Probab=24.47 E-value=67 Score=23.92 Aligned_cols=37 Identities=22% Similarity=0.339 Sum_probs=23.8
Q ss_pred ccCCceEEEEEccCChHH--HHHHHHHHHHccccceEEee
Q psy17720 4 CSRTARAVFQFYPENSAQ--IELVTSQAMRAGFYGGLVVD 41 (80)
Q Consensus 4 ~~rGaRAV~QfYPen~~Q--~emI~~~A~kaGF~GGlvVD 41 (80)
+.+|.--|++-.-....- =|+++.+|++.|..| +|||
T Consensus 85 ~~~GdVlVid~~g~~~~a~~G~~~~~~a~~~G~~G-~Vid 123 (240)
T PRK08245 85 CPPGCVLVVDARGDARAGSFGDILCTRLKKRGVAG-LVTD 123 (240)
T ss_pred cCCCeEEEEECCCCCCccccHHHHHHHHHHCCCeE-EEEe
Confidence 455555666543222211 288999999999987 7776
No 66
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=24.35 E-value=65 Score=20.74 Aligned_cols=12 Identities=17% Similarity=0.315 Sum_probs=7.2
Q ss_pred cceEEeeCCCCC
Q psy17720 35 YGGLVVDYPHST 46 (80)
Q Consensus 35 ~GGlvVD~P~S~ 46 (80)
.+|+++++||.+
T Consensus 83 ~~~F~~~nPna~ 94 (105)
T TIGR02011 83 NEGFKFTNPNVK 94 (105)
T ss_pred cceEEEECCCCC
Confidence 355666666654
No 67
>TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species.
Probab=24.14 E-value=1.2e+02 Score=21.08 Aligned_cols=13 Identities=15% Similarity=0.056 Sum_probs=10.9
Q ss_pred CcccCCceEEEEE
Q psy17720 2 RYCSRTARAVFQF 14 (80)
Q Consensus 2 ~~~~rGaRAV~Qf 14 (80)
++|++||+.++.-
T Consensus 139 ~~Lk~gG~l~~~~ 151 (231)
T TIGR02752 139 RVVKPGGKVVCLE 151 (231)
T ss_pred HHcCcCeEEEEEE
Confidence 6899999998864
No 68
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=23.80 E-value=2.4e+02 Score=22.23 Aligned_cols=26 Identities=27% Similarity=0.345 Sum_probs=20.0
Q ss_pred CcccCCceEEEE---Ecc-CChHHHHHHHH
Q psy17720 2 RYCSRTARAVFQ---FYP-ENSAQIELVTS 27 (80)
Q Consensus 2 ~~~~rGaRAV~Q---fYP-en~~Q~emI~~ 27 (80)
++|++||+-|.. +.| ||.+|++-+.+
T Consensus 356 ~~LkpgG~lvystcs~~~~Ene~~v~~~l~ 385 (426)
T TIGR00563 356 PLLKTGGTLVYATCSVLPEENSEQIKAFLQ 385 (426)
T ss_pred HhcCCCcEEEEEeCCCChhhCHHHHHHHHH
Confidence 579999999965 555 78888876665
No 69
>PLN02244 tocopherol O-methyltransferase
Probab=23.71 E-value=91 Score=23.90 Aligned_cols=44 Identities=11% Similarity=0.073 Sum_probs=29.2
Q ss_pred CcccCCceEEEEEcc------CC----hH------------------HHHHHHHHHHHccccceEEeeCCCC
Q psy17720 2 RYCSRTARAVFQFYP------EN----SA------------------QIELVTSQAMRAGFYGGLVVDYPHS 45 (80)
Q Consensus 2 ~~~~rGaRAV~QfYP------en----~~------------------Q~emI~~~A~kaGF~GGlvVD~P~S 45 (80)
|+|++||+-++.-+. .. +. ..+-+.+.+..+||..=-+.|+...
T Consensus 211 rvLkpGG~lvi~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~p~~~s~~~~~~~l~~aGf~~v~~~d~s~~ 282 (340)
T PLN02244 211 RVAAPGGRIIIVTWCHRDLEPGETSLKPDEQKLLDKICAAYYLPAWCSTSDYVKLAESLGLQDIKTEDWSEH 282 (340)
T ss_pred HHcCCCcEEEEEEecccccccccccCCHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHCCCCeeEeeeCcHH
Confidence 689999999986532 11 01 1334556788999987677777654
No 70
>PF09969 DUF2203: Uncharacterized conserved protein (DUF2203); InterPro: IPR018699 This family has no known function.
Probab=23.38 E-value=2.1e+02 Score=19.50 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHcccc--ce--EEeeCCCCCCcceEEEEEEec
Q psy17720 20 AQIELVTSQAMRAGFY--GG--LVVDYPHSTKAKKFFLVLMTG 58 (80)
Q Consensus 20 ~Q~emI~~~A~kaGF~--GG--lvVD~P~S~kaKK~yLvL~~G 58 (80)
.|++.+++.-..-|.. |= .+||||---..+-.|||=--|
T Consensus 57 ~~~~~~i~~i~~~Gv~vKd~~~gLvDFPa~~dg~~v~LCWk~G 99 (120)
T PF09969_consen 57 ARLRELIDEIEELGVEVKDLDPGLVDFPAKLDGREVYLCWKEG 99 (120)
T ss_pred HHHHHHHHHHHHcCcEEeCCcceeEeCCcccCCCEEEEEeCCC
Confidence 4555666666677773 32 479999999999999997655
No 71
>cd01305 archeal_chlorohydrolases Predicted chlorohydrolases. These metallo-dependent hydrolases from archea are part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. They have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. Some members of this subgroup are predicted to be chlorohyrolases.
Probab=22.29 E-value=2e+02 Score=20.52 Aligned_cols=44 Identities=14% Similarity=0.073 Sum_probs=34.4
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHccccceEEeeCCCC
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVDYPHS 45 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaGF~GGlvVD~P~S 45 (80)
.+|+.|--+++-|++...+..+.+.+++...|.-+-.+.|.|..
T Consensus 60 e~l~~GtTt~~d~~~~~~~~~~a~~~a~~~~g~r~~~~~~~~~~ 103 (263)
T cd01305 60 DMRETGIGAFADFREGGVEGIELLRRALGKLPVPFEVILGRPTE 103 (263)
T ss_pred HHHhcCCeEEEEccCcchhHHHHHHHHHHhcCCCceEEeccCCc
Confidence 35788888999998776777888888999988876555677754
No 72
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=22.17 E-value=56 Score=23.21 Aligned_cols=13 Identities=8% Similarity=-0.018 Sum_probs=11.8
Q ss_pred CcccCCceEEEEE
Q psy17720 2 RYCSRTARAVFQF 14 (80)
Q Consensus 2 ~~~~rGaRAV~Qf 14 (80)
++|++||+.++++
T Consensus 118 ~~LkpgG~~~~~~ 130 (258)
T PRK01683 118 SLLAPGGVLAVQM 130 (258)
T ss_pred HhcCCCcEEEEEC
Confidence 5799999999997
No 73
>COG2819 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]
Probab=21.88 E-value=57 Score=25.47 Aligned_cols=25 Identities=24% Similarity=0.190 Sum_probs=19.6
Q ss_pred CCceEEEEEccCChHHHHHHHHHHHH
Q psy17720 6 RTARAVFQFYPENSAQIELVTSQAMR 31 (80)
Q Consensus 6 rGaRAV~QfYPen~~Q~emI~~~A~k 31 (80)
-|.++|||+|| +..|...|-....+
T Consensus 229 ~g~~~~f~~~~-~~~H~~~~~~~~~~ 253 (264)
T COG2819 229 TGARLVFQEEP-LEHHGSVIHASLPS 253 (264)
T ss_pred cCCceEecccc-cccccchHHHHHHH
Confidence 58999999999 87887777655443
No 74
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=21.84 E-value=1e+02 Score=22.16 Aligned_cols=18 Identities=17% Similarity=0.220 Sum_probs=15.4
Q ss_pred CcccCCceEEEEEccCCh
Q psy17720 2 RYCSRTARAVFQFYPENS 19 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~ 19 (80)
++|++||+-++.||..+.
T Consensus 137 ~~LkpgG~l~i~~~n~~~ 154 (255)
T PRK11036 137 SVLRPGGALSLMFYNANG 154 (255)
T ss_pred HHcCCCeEEEEEEECccH
Confidence 689999999999988654
No 75
>TIGR00091 tRNA (guanine-N(7)-)-methyltransferase. In E. coli, this protein flanks the DNA repair protein MutY, also called micA.
Probab=21.69 E-value=1.5e+02 Score=20.47 Aligned_cols=30 Identities=10% Similarity=0.046 Sum_probs=19.9
Q ss_pred CcccCCceEEEEEccCChHHHHHHHHHHHHcc
Q psy17720 2 RYCSRTARAVFQFYPENSAQIELVTSQAMRAG 33 (80)
Q Consensus 2 ~~~~rGaRAV~QfYPen~~Q~emI~~~A~kaG 33 (80)
++|++||+-.|+. .+....+-+.....+.+
T Consensus 120 r~LkpgG~l~~~t--d~~~~~~~~~~~~~~~~ 149 (194)
T TIGR00091 120 NVLKKGGVIHFKT--DNEPLFEDMLKVLSEND 149 (194)
T ss_pred HHhCCCCEEEEEe--CCHHHHHHHHHHHHhCC
Confidence 5789999987766 44555665555555554
No 76
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=21.64 E-value=78 Score=20.43 Aligned_cols=14 Identities=21% Similarity=0.437 Sum_probs=7.9
Q ss_pred cccceEEeeCCCCC
Q psy17720 33 GFYGGLVVDYPHST 46 (80)
Q Consensus 33 GF~GGlvVD~P~S~ 46 (80)
++.+|+++++||.+
T Consensus 83 ~~~~~F~~~NPn~~ 96 (107)
T TIGR01997 83 TLRQGFKFNNPNAT 96 (107)
T ss_pred CCcceEEEECCCCC
Confidence 34456666666653
No 77
>PF03737 Methyltransf_6: Demethylmenaquinone methyltransferase; InterPro: IPR005493 This entry represents a structural motif found in demethylmenaquinone methyltransferases and in the regulator of ribonuclease E activity A (RraA). These proteins contain a swivelling 3-layer beta/beta/alpha domain that appears to be mobile in most multi-domain proteins known to contain it. These proteins are structurally similar, and may have distant homology, to the phosphohistidine domain of pyruvate phosphate dikinase. The RraA fold is an ancient platform that has been adapted for a wide range of functions. RraA had been identified as a putative demethylmenaquinone methyltransferase and was annotated as MenG, but further analysis showed that RraA lacked the structural motifs usually required for methylases. The Escherichia coli protein regulator RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing []. RNase E forms the core of a large RNA-catalysis machine termed the degradosomes. RraA (and RraB) causes remodelling of degradosome composition, which is associated with alterations in RNA decay and global transcript abundance and as such is a bacterial mechanism for the regulation of RNA cleavage. Demethylmenaquinone methyltransferases convert dimethylmenaquinone (DMK) to menaquinone (MK) in the final step of menaquinone biosynthesis. This region is also found at the C terminus of the DlpA protein Q48806 from SWISSPROT.; PDB: 3C8O_A 2PCN_A 3K4I_B 2YJV_A 1Q5X_B 2C5Q_D 2YJT_B 1NXJ_B 3NOJ_A 1J3L_A ....
Probab=21.41 E-value=1.1e+02 Score=21.07 Aligned_cols=18 Identities=39% Similarity=0.648 Sum_probs=13.8
Q ss_pred HHHHHHHHHccccceEEee
Q psy17720 23 ELVTSQAMRAGFYGGLVVD 41 (80)
Q Consensus 23 emI~~~A~kaGF~GGlvVD 41 (80)
|++...|++.|.. |+|||
T Consensus 77 ~~~a~~a~~~G~~-G~Vid 94 (154)
T PF03737_consen 77 ELMATAAKARGVA-GVVID 94 (154)
T ss_dssp HHHHHHHHHTTBS-EEEEE
T ss_pred HHHHHHHHHCCCe-EEECC
Confidence 6788888888876 66663
No 78
>PRK00782 hypothetical protein; Provisional
Probab=21.40 E-value=78 Score=23.69 Aligned_cols=21 Identities=29% Similarity=0.419 Sum_probs=15.7
Q ss_pred EEEEccCChHHHHHHHHHHHH
Q psy17720 11 VFQFYPENSAQIELVTSQAMR 31 (80)
Q Consensus 11 V~QfYPen~~Q~emI~~~A~k 31 (80)
.=+|||.++++++-..+..+.
T Consensus 8 AG~fYp~~~~~L~~~i~~~~~ 28 (267)
T PRK00782 8 AGQFYPLSPEELLKMLSEFFR 28 (267)
T ss_pred cCCCCCCCHHHHHHHHHHHHh
Confidence 348999999998766665554
No 79
>PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional
Probab=21.34 E-value=3.1e+02 Score=19.49 Aligned_cols=49 Identities=18% Similarity=0.327 Sum_probs=29.3
Q ss_pred CcccCCceEEEEEc-cCChHHHHHHHHHHHHccccceEEeeCCCCCCcc--eEEEEE
Q psy17720 2 RYCSRTARAVFQFY-PENSAQIELVTSQAMRAGFYGGLVVDYPHSTKAK--KFFLVL 55 (80)
Q Consensus 2 ~~~~rGaRAV~QfY-Pen~~Q~emI~~~A~kaGF~GGlvVD~P~S~kaK--K~yLvL 55 (80)
++|++||+.|+=.+ ++.-.+. + ..++..|.. +-|--|.|.|.. ..|+|.
T Consensus 153 ~~LkpGG~~vi~~~~~~~~~~~--l--~~l~~~f~~-v~~~Kp~ssr~~s~e~~~~~ 204 (209)
T PRK11188 153 DVLAPGGSFVVKVFQGEGFDEY--L--REIRSLFTK-VKVRKPDSSRARSREVYIVA 204 (209)
T ss_pred HHcCCCCEEEEEEecCcCHHHH--H--HHHHhCceE-EEEECCccccccCceeEEEe
Confidence 58999999999444 4443432 2 456667753 455667666543 345443
No 80
>TIGR02350 prok_dnaK chaperone protein DnaK. Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.
Probab=21.28 E-value=2.5e+02 Score=23.10 Aligned_cols=42 Identities=26% Similarity=0.296 Sum_probs=31.3
Q ss_pred ChHHHHHHHHHHHHccccceEEeeCCC--------CC-CcceEEEEEEecC
Q psy17720 18 NSAQIELVTSQAMRAGFYGGLVVDYPH--------ST-KAKKFFLVLMTGG 59 (80)
Q Consensus 18 n~~Q~emI~~~A~kaGF~GGlvVD~P~--------S~-kaKK~yLvL~~G~ 59 (80)
++.|++.+..||..|||.-=-+|+=|- .. ...+.+||+..|+
T Consensus 142 ~~~qR~a~~~Aa~~AGl~v~~li~EptAAAl~y~~~~~~~~~~vlV~D~Gg 192 (595)
T TIGR02350 142 NDAQRQATKDAGKIAGLEVLRIINEPTAAALAYGLDKSKKDEKILVFDLGG 192 (595)
T ss_pred CHHHHHHHHHHHHHcCCceEEEecchHHHHHHHhhcccCCCcEEEEEECCC
Confidence 578999999999999998655565552 11 3457789988886
No 81
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=21.21 E-value=96 Score=18.87 Aligned_cols=17 Identities=24% Similarity=0.298 Sum_probs=15.4
Q ss_pred ChHHHHHHHHHHHHccc
Q psy17720 18 NSAQIELVTSQAMRAGF 34 (80)
Q Consensus 18 n~~Q~emI~~~A~kaGF 34 (80)
+++|.+.+.+.+.+.|+
T Consensus 9 t~~Q~~~Le~~fe~~~y 25 (58)
T TIGR01565 9 TAEQKEKMRDFAEKLGW 25 (58)
T ss_pred CHHHHHHHHHHHHHcCC
Confidence 78999999999999886
No 82
>PHA02324 hypothetical protein
Probab=21.02 E-value=29 Score=20.95 Aligned_cols=14 Identities=21% Similarity=0.430 Sum_probs=11.5
Q ss_pred HHHccccceEEeeC
Q psy17720 29 AMRAGFYGGLVVDY 42 (80)
Q Consensus 29 A~kaGF~GGlvVD~ 42 (80)
+.+.||+||.+|.-
T Consensus 2 ~~~~~lsggk~IES 15 (47)
T PHA02324 2 AKKPSLSGGKQIES 15 (47)
T ss_pred ccccccCCcceeec
Confidence 56789999999874
No 83
>cd02930 DCR_FMN 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provi
Probab=20.55 E-value=1.6e+02 Score=22.66 Aligned_cols=10 Identities=10% Similarity=0.288 Sum_probs=7.7
Q ss_pred cCCceEEEEE
Q psy17720 5 SRTARAVFQF 14 (80)
Q Consensus 5 ~rGaRAV~Qf 14 (80)
+.|+++++|+
T Consensus 88 ~~g~~~~~QL 97 (353)
T cd02930 88 AEGGKIALQI 97 (353)
T ss_pred HcCCEEEeec
Confidence 4578888887
No 84
>TIGR01991 HscA Fe-S protein assembly chaperone HscA. The Heat Shock Cognate proteins HscA and HscB act together as chaperones. HscA resembles DnaK but belongs in a separate clade. The apparent function is to aid assembly of iron-sulfur cluster proteins. Homologs from Buchnera and Wolbachia are clearly in the same clade but are highly derived and score lower than some examples of DnaK.
Probab=20.19 E-value=1.5e+02 Score=24.66 Aligned_cols=42 Identities=21% Similarity=0.272 Sum_probs=31.8
Q ss_pred ChHHHHHHHHHHHHccccceEEeeCCCC--------CCcceEEEEEEecC
Q psy17720 18 NSAQIELVTSQAMRAGFYGGLVVDYPHS--------TKAKKFFLVLMTGG 59 (80)
Q Consensus 18 n~~Q~emI~~~A~kaGF~GGlvVD~P~S--------~kaKK~yLvL~~G~ 59 (80)
|+.|++.+..||..|||.-=-+|+=|-. ....+.+||+..|+
T Consensus 141 ~~~qR~a~~~Aa~~AGl~v~~li~EPtAAAlay~~~~~~~~~vlV~DlGg 190 (599)
T TIGR01991 141 DDAQRQATKDAARLAGLNVLRLLNEPTAAAVAYGLDKASEGIYAVYDLGG 190 (599)
T ss_pred CHHHHHHHHHHHHHcCCCceEEecCHHHHHHHHhhccCCCCEEEEEEcCC
Confidence 5789999999999999986555665532 12456789999887
Done!