Query psy4672
Match_columns 78
No_of_seqs 101 out of 1086
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:51:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4672.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4672hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0084 TatD Mg-dependent DNas 99.9 2.2E-26 4.8E-31 167.3 5.4 73 1-77 154-229 (256)
2 PRK10425 DNase TatD; Provision 99.9 7.8E-23 1.7E-27 147.6 5.5 74 1-77 151-231 (258)
3 PRK11449 putative deoxyribonuc 99.9 5.1E-22 1.1E-26 143.1 6.2 73 1-77 156-231 (258)
4 PRK10812 putative DNAse; Provi 99.8 4.1E-21 8.9E-26 139.0 5.5 73 1-77 154-229 (265)
5 PF01026 TatD_DNase: TatD rela 99.8 4E-20 8.7E-25 131.6 4.8 73 1-77 154-229 (255)
6 KOG3020|consensus 99.6 4.3E-16 9.3E-21 115.8 3.9 70 2-77 180-269 (296)
7 cd00530 PTE Phosphotriesterase 99.4 5.5E-13 1.2E-17 95.3 5.5 73 1-76 183-267 (293)
8 TIGR00010 hydrolase, TatD fami 99.3 3.6E-12 7.8E-17 88.1 5.3 71 2-76 151-224 (252)
9 cd01310 TatD_DNAse TatD like p 99.2 5.7E-11 1.2E-15 81.9 5.5 71 2-76 151-224 (251)
10 TIGR03583 EF_0837 probable ami 97.6 0.0001 2.3E-09 54.5 4.2 59 10-77 225-286 (365)
11 cd01295 AdeC Adenine deaminase 96.1 0.012 2.5E-07 44.8 4.8 47 8-60 165-215 (422)
12 cd01307 Met_dep_hydrolase_B Me 92.1 0.24 5.2E-06 36.3 3.9 53 9-71 208-263 (338)
13 cd01292 metallo-dependent_hydr 91.0 0.85 1.8E-05 30.5 5.4 53 2-59 180-238 (275)
14 PRK09237 dihydroorotase; Provi 79.4 2.3 4.9E-05 31.6 3.1 42 9-56 227-271 (380)
15 COG1099 Predicted metal-depend 73.3 9.7 0.00021 28.3 4.9 53 8-63 166-219 (254)
16 PRK09875 putative hydrolase; P 64.5 16 0.00035 27.1 4.6 53 2-57 186-245 (292)
17 PF13456 RVT_3: Reverse transc 63.7 6.3 0.00014 22.4 1.9 16 39-56 15-30 (87)
18 KOG3484|consensus 49.6 7 0.00015 24.8 0.5 17 37-55 26-42 (91)
19 PF07913 DUF1678: Protein of u 49.0 9.2 0.0002 27.3 1.0 50 4-59 112-164 (201)
20 COG2159 Predicted metal-depend 43.7 62 0.0013 23.8 4.8 54 6-62 204-260 (293)
21 PHA02671 hypothetical protein; 43.2 13 0.00028 26.4 1.1 33 3-36 47-79 (179)
22 COG5495 Uncharacterized conser 42.5 34 0.00075 25.8 3.2 53 1-59 96-151 (289)
23 PRK05659 sulfur carrier protei 42.5 43 0.00094 18.7 3.1 37 20-56 2-38 (66)
24 COG0106 HisA Phosphoribosylfor 41.7 50 0.0011 24.3 4.0 49 6-58 84-133 (241)
25 KOG1017|consensus 38.3 19 0.00042 26.6 1.4 21 34-56 151-171 (267)
26 TIGR03849 arch_ComA phosphosul 37.9 45 0.00097 24.4 3.2 45 11-57 139-195 (237)
27 COG0801 FolK 7,8-dihydro-6-hyd 37.3 23 0.00051 24.5 1.6 55 19-77 4-60 (160)
28 PF04909 Amidohydro_2: Amidohy 37.1 18 0.0004 24.5 1.1 42 18-61 191-238 (273)
29 cd01308 Isoaspartyl-dipeptidas 36.6 85 0.0018 23.2 4.6 44 12-56 234-285 (387)
30 PRK11235 bifunctional antitoxi 34.7 8.6 0.00019 23.7 -0.8 43 9-56 13-56 (80)
31 PHA02983 hypothetical protein; 34.3 17 0.00036 25.9 0.5 33 4-36 48-80 (180)
32 PLN00064 photosystem II protei 33.8 21 0.00046 25.0 0.9 22 4-25 118-139 (166)
33 PRK13587 1-(5-phosphoribosyl)- 31.9 1.1E+02 0.0024 21.7 4.4 46 6-56 85-132 (234)
34 PF02126 PTE: Phosphotriestera 31.2 51 0.0011 24.7 2.7 55 2-58 190-260 (308)
35 cd04723 HisA_HisF Phosphoribos 31.1 1.4E+02 0.003 21.0 4.8 46 6-56 87-134 (233)
36 PRK13586 1-(5-phosphoribosyl)- 30.7 1.3E+02 0.0027 21.5 4.5 47 6-56 82-130 (232)
37 KOG2368|consensus 30.1 51 0.0011 24.9 2.5 43 9-54 172-220 (316)
38 PRK14024 phosphoribosyl isomer 27.7 1.2E+02 0.0026 21.4 4.0 46 6-56 84-131 (241)
39 PF14237 DUF4339: Domain of un 26.4 1.1E+02 0.0024 16.0 3.0 20 33-52 16-35 (45)
40 PF02698 DUF218: DUF218 domain 26.2 70 0.0015 20.4 2.4 25 32-56 55-79 (155)
41 PF07521 RMMBL: RNA-metabolisi 26.1 56 0.0012 17.3 1.6 17 1-17 12-28 (43)
42 PLN00010 cyclin-dependent kina 25.5 30 0.00066 21.8 0.5 17 37-55 24-40 (86)
43 cd00565 ThiS ThiaminS ubiquiti 25.2 1.1E+02 0.0025 17.0 2.9 36 21-56 2-37 (65)
44 PF05989 Chordopox_A35R: Chord 24.6 27 0.0006 24.7 0.2 32 5-36 48-79 (176)
45 PF02492 cobW: CobW/HypB/UreG, 24.3 55 0.0012 21.8 1.7 21 34-56 72-94 (178)
46 PF02679 ComA: (2R)-phospho-3- 23.9 1.9E+02 0.004 21.3 4.5 47 9-57 150-207 (244)
47 KOG3330|consensus 23.7 49 0.0011 23.4 1.3 28 5-32 70-100 (183)
48 PRK05863 sulfur carrier protei 23.4 1.3E+02 0.0029 17.0 3.0 37 21-57 3-39 (65)
49 COG1606 ATP-utilizing enzymes 22.7 1.5E+02 0.0033 22.3 3.8 49 9-62 7-58 (269)
50 PF01111 CKS: Cyclin-dependent 22.2 45 0.00098 20.2 0.8 17 37-55 22-38 (70)
51 TIGR01683 thiS thiamine biosyn 21.7 1.2E+02 0.0026 16.9 2.6 35 22-56 2-36 (64)
52 PRK10657 isoaspartyl dipeptida 21.5 2.4E+02 0.0052 20.7 4.7 46 10-56 234-286 (388)
53 TIGR01975 isoAsp_dipep isoaspa 21.3 3.1E+02 0.0067 21.0 5.4 48 9-57 233-288 (389)
54 TIGR00045 glycerate kinase. Th 20.7 93 0.002 24.2 2.4 27 1-27 106-136 (375)
55 PRK10342 glycerate kinase I; P 20.3 99 0.0021 24.2 2.5 27 1-27 107-137 (381)
No 1
>COG0084 TatD Mg-dependent DNase [DNA replication, recombination, and repair]
Probab=99.93 E-value=2.2e-26 Score=167.26 Aligned_cols=73 Identities=33% Similarity=0.441 Sum_probs=67.8
Q ss_pred CCCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCCC--Ccccchhhhhc
Q psy4672 1 MHRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARAA--KLPIHVRHLVM 77 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~~--neP~~l~~v~~ 77 (78)
|||+|+ +.|+|+++++ ||||||+|.+ ||++++++|++++ .||+||||+||||||++|.|+++ |+|++|.+|++
T Consensus 154 ~HcFsG-s~e~a~~~~d~G~yisisG~i-tfk~a~~~~ev~~--~iPldrLL~ETDsPyl~P~p~rGkrNeP~~v~~v~~ 229 (256)
T COG0084 154 LHCFSG-SAEEARKLLDLGFYISISGIV-TFKNAEKLREVAR--ELPLDRLLLETDAPYLAPVPYRGKRNEPAYVRHVAE 229 (256)
T ss_pred EEccCC-CHHHHHHHHHcCeEEEECcee-ecCCcHHHHHHHH--hCCHhHeEeccCCCCCCCcCCCCCCCCchHHHHHHH
Confidence 699999 5899999999 9999999954 8999999999999 99999999999999999998643 99999999986
No 2
>PRK10425 DNase TatD; Provisional
Probab=99.87 E-value=7.8e-23 Score=147.65 Aligned_cols=74 Identities=26% Similarity=0.523 Sum_probs=66.1
Q ss_pred CCCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCC-----C-CCcccchh
Q psy4672 1 MHRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNAR-----A-AKLPIHVR 73 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~-----~-~neP~~l~ 73 (78)
+|++|+ +.++|+++++ ||||||||.+++++++.++|++++ .+|+||||+||||||++|.++ + +|+|++|+
T Consensus 151 ~H~fsG-~~~~~~~~l~~G~~~si~g~i~~~~~~~~~~~~~~--~ipldrlLlETDaP~l~P~~~~~~~~~~~n~P~~i~ 227 (258)
T PRK10425 151 LHCFTG-TREEMQACLARGLYIGITGWVCDERRGLELRELLP--LIPAERLLLETDAPYLLPRDLTPKPASRRNEPAFLP 227 (258)
T ss_pred EEecCC-CHHHHHHHHHCCCEEEECceeecccccHHHHHHHH--hCChHHEEEeccCCCCCCCCcCCCCCCCCCCcHHHH
Confidence 599998 5899999999 999999998766676778999999 999999999999999999764 2 39999999
Q ss_pred hhhc
Q psy4672 74 HLVM 77 (78)
Q Consensus 74 ~v~~ 77 (78)
++++
T Consensus 228 ~v~~ 231 (258)
T PRK10425 228 HILQ 231 (258)
T ss_pred HHHH
Confidence 9875
No 3
>PRK11449 putative deoxyribonuclease YjjV; Provisional
Probab=99.86 E-value=5.1e-22 Score=143.13 Aligned_cols=73 Identities=19% Similarity=0.228 Sum_probs=66.0
Q ss_pred CCCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCC-C-Ccccchhhhhc
Q psy4672 1 MHRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARA-A-KLPIHVRHLVM 77 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~-~-neP~~l~~v~~ 77 (78)
+|++|+ +.++|+++++ ||||||+|.+ ++++++++|++++ .+|+||||+|||+||++|.+++ + |+|.++..+++
T Consensus 156 ~H~fsG-~~~~a~~~l~~G~~iS~~g~i-t~~~~~~~~~~~~--~ipldriL~ETD~P~l~p~~~~~~~n~p~~~~~~~~ 231 (258)
T PRK11449 156 VHGFSG-SLQQAERFVQLGYKIGVGGTI-TYPRASKTRDVIA--KLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFD 231 (258)
T ss_pred EEcCCC-CHHHHHHHHHCCCEEEeCccc-cccCcHHHHHHHH--hCChhhEEEecCCCCCCCCCCCCCCCCChHHHHHHH
Confidence 699997 5899999999 9999999965 8888899999999 9999999999999999988754 3 99999999874
No 4
>PRK10812 putative DNAse; Provisional
Probab=99.83 E-value=4.1e-21 Score=139.00 Aligned_cols=73 Identities=27% Similarity=0.408 Sum_probs=65.7
Q ss_pred CCCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCC-C-Ccccchhhhhc
Q psy4672 1 MHRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARA-A-KLPIHVRHLVM 77 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~-~-neP~~l~~v~~ 77 (78)
+|++|. +.++++++++ |+||||+|.+ ++++++.++++++ .+|+||||+|||+||++|.+++ + |+|.+|..+++
T Consensus 154 ~H~fsG-~~~~a~~~~~~G~~is~~g~~-t~~~~~~~~~~~~--~ipldrlLlETD~P~~~p~~~~g~~n~P~~i~~v~~ 229 (265)
T PRK10812 154 LHCFTE-DRETAGKLLDLGFYISFSGIV-TFRNAEQLRDAAR--YVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAE 229 (265)
T ss_pred EEeecC-CHHHHHHHHHCCCEEEECeee-ecCccHHHHHHHH--hCChhhEEEecCCCCCCCcCCCCCCCCcHHHHHHHH
Confidence 599975 6999999999 9999999965 8888889999999 9999999999999999998864 3 99999999774
No 5
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=99.80 E-value=4e-20 Score=131.64 Aligned_cols=73 Identities=27% Similarity=0.410 Sum_probs=58.8
Q ss_pred CCCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCC-C-Ccccchhhhhc
Q psy4672 1 MHRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARA-A-KLPIHVRHLVM 77 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~-~-neP~~l~~v~~ 77 (78)
+|++++ +.++++++++ |+||||+|.+ +++++++.+++++ .+|+||||+|||+||+.|.+++ + |+|.+|+.+++
T Consensus 154 ~H~f~g-~~~~~~~~~~~g~~~S~~~~~-~~~~~~~~~~~~~--~ip~drillETD~P~~~~~~~~~~~~~p~~i~~~~~ 229 (255)
T PF01026_consen 154 FHCFSG-SPEEAKKFLDLGCYFSFSGAI-TFKNSKKVRELIK--AIPLDRILLETDAPYLAPDPYRGKPNEPSNIPKVAQ 229 (255)
T ss_dssp ETT--S--HHHHHHHHHTTEEEEEEGGG-GSTTSHHHHHHHH--HS-GGGEEEE-BTTSSECTTSTTSE--GGGHHHHHH
T ss_pred EecCCC-CHHHHHHHHhcCceEEecccc-cccccHHHHHHHh--cCChhhEEEcCCCCcCCccccCCCCCChHHHHHHHH
Confidence 599888 4899999999 9999999975 6766788999999 9999999999999999997765 3 99999998875
No 6
>KOG3020|consensus
Probab=99.61 E-value=4.3e-16 Score=115.77 Aligned_cols=70 Identities=24% Similarity=0.372 Sum_probs=58.9
Q ss_pred CCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCC----------------
Q psy4672 2 HRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNAR---------------- 64 (78)
Q Consensus 2 ~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~---------------- 64 (78)
|++-+ +.+.++++++ |+||||+|.+ .+.. .-.++++ .||+||||+||||||+.|...
T Consensus 180 HsFtG-s~e~~~~~lk~~~yig~~g~~--~k~~-e~~~vlr--~iP~erlllETDsP~~~pk~~~~~~~~~~~~~~~~~~ 253 (296)
T KOG3020|consen 180 HSFTG-SAEEAQKLLKLGLYIGFTGCS--LKTE-ENLEVLR--SIPLERLLLETDSPYCGPKPSSHAGPKYVKTLFSESY 253 (296)
T ss_pred EeccC-CHHHHHHHHHccEEeccccee--eech-hhHHHHh--hCCHhHeeeccCCccccCCccccccchhhhhhhhhhc
Confidence 66655 8999999999 9999999954 3333 4568899 999999999999999999872
Q ss_pred ---CCCcccchhhhhc
Q psy4672 65 ---AAKLPIHVRHLVM 77 (78)
Q Consensus 65 ---~~neP~~l~~v~~ 77 (78)
++|+|+++.++++
T Consensus 254 ~~~~~neP~~~~~~~e 269 (296)
T KOG3020|consen 254 PLKGRNEPCNVLQVAE 269 (296)
T ss_pred cccccCCchHHHHHHH
Confidence 3599999999876
No 7
>cd00530 PTE Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal center, at the C-terminal end of a TIM alpha- beta barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active.
Probab=99.39 E-value=5.5e-13 Score=95.25 Aligned_cols=73 Identities=16% Similarity=0.003 Sum_probs=59.5
Q ss_pred CCCCCCCCHHHHHHHhc-CceeEecCcccccC---------CchHHHhhhhcCCCCCCceEeecCCCCCCCCCC--CCCc
Q psy4672 1 MHRSSIPMLEPLNKALL-ILILCWSGYICKDS---------SEAGLQGMLESGELPMDRILVESDAPFLYPNAR--AAKL 68 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~---------~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~--~~ne 68 (78)
.|++..++.+.++++++ |+||||++.. +++ +.+.++++++ .+|+||||+|||+||+.|.+. .+|.
T Consensus 183 ~H~~~~~~~~~~~~~~~~G~~i~~~~~~-~~~~~~~~~~~~~~~~l~~~~~--~~~~d~ill~TD~p~~~~~~~~~~~~~ 259 (293)
T cd00530 183 GHLDRNDDPDYLLKIAALGAYLEFDGIG-KDKIFGYPSDETRADAVKALID--EGYGDRLLLSHDVFRKSYLEKRYGGHG 259 (293)
T ss_pred eCCCCCCCHHHHHHHHhCCCEEEeCCCC-cccccCCCCHHHHHHHHHHHHH--CCCcCCEEEeCCcCchhhhhhccCCCC
Confidence 38874457899999999 9999999954 454 5667999999 999999999999999987643 3499
Q ss_pred ccchhhhh
Q psy4672 69 PIHVRHLV 76 (78)
Q Consensus 69 P~~l~~v~ 76 (78)
|.++..++
T Consensus 260 ~~~~~~~~ 267 (293)
T cd00530 260 YDYILTRF 267 (293)
T ss_pred hHHHHHHH
Confidence 99986544
No 8
>TIGR00010 hydrolase, TatD family. Several genomes have multiple paralogs related to this family. However, a set of 17 proteins can be found, one each from 17 of the first 20 genomes, such that each member forms a bidirectional best hit across genomes with all other members of the set. This core set (and one other near-perfect member), but not the other paralogs, form the seed for this model. Additionally, members of the seed alignment and all trusted hits, but not all paralogs, have a conserved motif DxHxH near the amino end. The member from E. coli was recently shown to have DNase activity.
Probab=99.30 E-value=3.6e-12 Score=88.14 Aligned_cols=71 Identities=28% Similarity=0.409 Sum_probs=57.7
Q ss_pred CCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCC-C-Ccccchhhhh
Q psy4672 2 HRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARA-A-KLPIHVRHLV 76 (78)
Q Consensus 2 ~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~-~-neP~~l~~v~ 76 (78)
|..+ ++.+.++++++ |+|+|+++.. ++++.+.++++++ .+|.||||+|||+||+.|...+ + |.|.++..++
T Consensus 151 H~~~-~~~~~~~~~~~~g~~~~~~~~~-~~~~~~~~~~~i~--~~~~dril~~TD~p~~~~~~~~~~~~~p~~i~~~~ 224 (252)
T TIGR00010 151 HCFT-GDAELAKKLLDLGFYISISGIV-TFKNAKSLREVVR--KIPLERLLVETDSPYLAPVPYRGKRNEPAFVRYTV 224 (252)
T ss_pred EccC-CCHHHHHHHHHCCCeEeeceeE-ecCCcHHHHHHHH--hCCHHHeEecccCCCCCCCCCCCCCCCChhHHHHH
Confidence 6654 46899999999 9999999854 4555567999999 9999999999999998865432 3 8999988753
No 9
>cd01310 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.
Probab=99.16 E-value=5.7e-11 Score=81.91 Aligned_cols=71 Identities=27% Similarity=0.438 Sum_probs=56.7
Q ss_pred CCCCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCC-CC-Ccccchhhhh
Q psy4672 2 HRSSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNAR-AA-KLPIHVRHLV 76 (78)
Q Consensus 2 ~~~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~-~~-neP~~l~~v~ 76 (78)
|..+ ++.++++++++ |+|||+++.. .+.+...++++++ .+|.||||+|||+||..+... ++ +.|.++..++
T Consensus 151 H~~~-~~~~~~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~--~~~~dril~~TD~p~~~~~~~~~~~~~~~~~~~~~ 224 (251)
T cd01310 151 HCFS-GSAEEAKELLDLGFYISISGIV-TFKNANELREVVK--EIPLERLLLETDSPYLAPVPFRGKRNEPAYVKHVA 224 (251)
T ss_pred EccC-CCHHHHHHHHHcCCEEEeeeee-ccCCCHHHHHHHH--hCChHHEEEcccCCCCCCCCCCCCCCCChhHHHHH
Confidence 6555 45789999999 9999999965 3444456899999 999999999999999987652 33 8888877664
No 10
>TIGR03583 EF_0837 probable amidohydrolase EF_0837/AHA_3915. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. These proteins resemble aminohydrolases (see pfam01979), including dihydroorotases. The function is unknown.
Probab=97.56 E-value=0.0001 Score=54.45 Aligned_cols=59 Identities=14% Similarity=0.077 Sum_probs=40.3
Q ss_pred HHHHHHhc-CceeEec-CcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCCCCcccc-hhhhhc
Q psy4672 10 EPLNKALL-ILILCWS-GYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARAAKLPIH-VRHLVM 77 (78)
Q Consensus 10 e~a~~~l~-G~yisi~-g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~~neP~~-l~~v~~ 77 (78)
+.+++.++ |+|++++ |. .++. -+....++ . +++++|||+|++... ...|.|.+ +..+++
T Consensus 225 ~~~~~~l~~G~i~d~~hg~-~~~~--~~~~~~~~--~---~~~~~~td~~d~~~~-~~~~gp~~~l~~~~~ 286 (365)
T TIGR03583 225 PSVLEAYNRGVILDVGHGT-ASFS--FHVAEKAK--R---AGIFPDTISTDIYIR-NRINGPVYSLATVMS 286 (365)
T ss_pred HHHHHHHhCeEEEEeCCCC-CCch--HHHHHHHH--h---CCCCCcccccccccC-CCccCccccHHHHHH
Confidence 88888899 9999999 64 4553 12222233 2 578899999998422 23488988 777654
No 11
>cd01295 AdeC Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source in bacteria and archea.
Probab=96.09 E-value=0.012 Score=44.83 Aligned_cols=47 Identities=13% Similarity=0.056 Sum_probs=35.7
Q ss_pred CHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCC---CCceEeecCCCCCC
Q psy4672 8 MLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELP---MDRILVESDAPFLY 60 (78)
Q Consensus 8 ~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iP---ldrlllETDsP~~~ 60 (78)
+.+++.+.++ |+|+++.+... +..++++++ .++ .++++++||+|...
T Consensus 165 ~~eea~e~l~~G~~i~i~~g~~----~~~~~~~~~--~l~~~~~~~i~l~TD~~~~~ 215 (422)
T cd01295 165 TGEEALEKLRLGMYVMLREGSI----AKNLEALLP--AITEKNFRRFMFCTDDVHPD 215 (422)
T ss_pred cHHHHHHHHHCCCEEEEECccc----HhhHHHHHH--hhhhccCCeEEEEcCCCCch
Confidence 4688888889 99999985332 245677778 887 69999999998543
No 12
>cd01307 Met_dep_hydrolase_B Metallo-dependent hydrolases, subgroup B is 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. The vast majority of the members 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. The function of this subgroup is unknown.
Probab=92.09 E-value=0.24 Score=36.32 Aligned_cols=53 Identities=19% Similarity=0.119 Sum_probs=29.2
Q ss_pred HHHHHHHhc-CceeEec-Cc-ccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCCCCCCcccc
Q psy4672 9 LEPLNKALL-ILILCWS-GY-ICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNARAAKLPIH 71 (78)
Q Consensus 9 ~e~a~~~l~-G~yisi~-g~-~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~~~~neP~~ 71 (78)
.+.++++++ |+||+++ |. ..+++ ..+++++.|-+|. .+.||.|+ .. ..|.|.+
T Consensus 208 ~~~~~~~~~~G~~~d~~~G~~~~~~~---~~~~l~~~G~~~~---~lstD~~~---~~-~~~~p~~ 263 (338)
T cd01307 208 LPLVRRARERGVIFDVGHGTASFSFR---VARAAIAAGLLPD---TISSDIHG---RN-RTNGPVY 263 (338)
T ss_pred HHHHHHHHhCCEEEEeCCCCCchhHH---HHHHHHHCCCCCe---eecCCccc---cC-CCCCccc
Confidence 378899999 9999988 42 22332 3445555333332 24555542 21 1367766
No 13
>cd01292 metallo-dependent_hydrolases Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members 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. The family includes urease alpha, adenosine deaminase, phosphotriesterase dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others.
Probab=90.98 E-value=0.85 Score=30.50 Aligned_cols=53 Identities=23% Similarity=0.109 Sum_probs=37.2
Q ss_pred CCCCCCCHHHHHHHhc-CceeEecCccccc-----CCchHHHhhhhcCCCCCCceEeecCCCCC
Q psy4672 2 HRSSIPMLEPLNKALL-ILILCWSGYICKD-----SSEAGLQGMLESGELPMDRILVESDAPFL 59 (78)
Q Consensus 2 ~~~~~~~~e~a~~~l~-G~yisi~g~~~~~-----~~~~~~r~~~~~~~iPldrlllETDsP~~ 59 (78)
|++.. +.+.++.+.+ |.++++++....+ .....++++++.| .++++.||+|..
T Consensus 180 H~~~~-~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g----~~~~lgTD~~~~ 238 (275)
T cd01292 180 HVSHL-DPELLELLKEAGVSLEVCPLSNYLLGRDGEGAEALRRLLELG----IRVTLGTDGPPH 238 (275)
T ss_pred CCccC-CHHHHHHHHHcCCeEEECCcccccccCCcCCcccHHHHHHCC----CcEEEecCCCCC
Confidence 66655 4678888888 9999999853221 1123467777744 799999999875
No 14
>PRK09237 dihydroorotase; Provisional
Probab=79.41 E-value=2.3 Score=31.61 Aligned_cols=42 Identities=17% Similarity=0.045 Sum_probs=26.4
Q ss_pred HHHHHHHhc-CceeEec--CcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 9 LEPLNKALL-ILILCWS--GYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 9 ~e~a~~~l~-G~yisi~--g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
.+.++++++ |+|++|+ +....++ ..+++++.|.+|. .++||.
T Consensus 227 ~~~a~~~l~~G~~~~ig~g~~~~~~~---~~~~l~~~g~~~~---~l~tD~ 271 (380)
T PRK09237 227 RPSVLEALERGVRLDVGHGTASFSFK---VAEAAIAAGILPD---TISTDI 271 (380)
T ss_pred hHHHHHHHHCCEEEEecCCCCcccHH---HHHHHHHCCCCce---EEECCC
Confidence 478999999 9999997 3122333 3555666332333 578874
No 15
>COG1099 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]
Probab=73.31 E-value=9.7 Score=28.33 Aligned_cols=53 Identities=17% Similarity=0.099 Sum_probs=38.6
Q ss_pred CHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCCC
Q psy4672 8 MLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPNA 63 (78)
Q Consensus 8 ~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~~ 63 (78)
..|.....|+ +||+|++=..-.. .....-++++ +---+||++-||+-|....+
T Consensus 166 N~etv~~vld~e~~vGlTvqPgKl-t~~eAveIV~--ey~~~r~ilnSD~~s~~sd~ 219 (254)
T COG1099 166 NEETVDEVLDEEFYVGLTVQPGKL-TVEEAVEIVR--EYGAERIILNSDAGSAASDP 219 (254)
T ss_pred cHHHHHHHHhccceEEEEecCCcC-CHHHHHHHHH--HhCcceEEEecccccccccc
Confidence 4577788999 9999997432111 2345667888 88899999999999876544
No 16
>PRK09875 putative hydrolase; Provisional
Probab=64.54 E-value=16 Score=27.12 Aligned_cols=53 Identities=17% Similarity=0.177 Sum_probs=34.4
Q ss_pred CCCCCCCHHHHHHHhc-CceeEecCcc--cccCCchHHHhhhhcCCC---C-CCceEeecCCC
Q psy4672 2 HRSSIPMLEPLNKALL-ILILCWSGYI--CKDSSEAGLQGMLESGEL---P-MDRILVESDAP 57 (78)
Q Consensus 2 ~~~~~~~~e~a~~~l~-G~yisi~g~~--~~~~~~~~~r~~~~~~~i---P-ldrlllETDsP 57 (78)
|....++.+..+++++ |+|++|...- ..+...+.. ++++ .+ - .||||+=+|..
T Consensus 186 H~d~~~d~~~~~~l~~~G~~l~fD~~g~~~~~pd~~r~-~~i~--~L~~~Gy~drilLS~D~~ 245 (292)
T PRK09875 186 HCDLKDNLDNILKMIDLGAYVQFDTIGKNSYYPDEKRI-AMLH--ALRDRGLLNRVMLSMDIT 245 (292)
T ss_pred CCCCCCCHHHHHHHHHcCCEEEeccCCCcccCCHHHHH-HHHH--HHHhcCCCCeEEEeCCCC
Confidence 5556678999999999 9999995411 012222222 3333 33 5 89999999963
No 17
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=63.73 E-value=6.3 Score=22.39 Aligned_cols=16 Identities=44% Similarity=0.626 Sum_probs=11.9
Q ss_pred hhhcCCCCCCceEeecCC
Q psy4672 39 MLESGELPMDRILVESDA 56 (78)
Q Consensus 39 ~~~~~~iPldrlllETDs 56 (78)
.+. +..+.+|.+|||+
T Consensus 15 ~a~--~~g~~~i~v~sDs 30 (87)
T PF13456_consen 15 LAW--ELGIRKIIVESDS 30 (87)
T ss_dssp HHH--CCT-SCEEEEES-
T ss_pred HHH--HCCCCEEEEEecC
Confidence 455 7889999999997
No 18
>KOG3484|consensus
Probab=49.63 E-value=7 Score=24.76 Aligned_cols=17 Identities=24% Similarity=0.550 Sum_probs=15.1
Q ss_pred HhhhhcCCCCCCceEeecC
Q psy4672 37 QGMLESGELPMDRILVESD 55 (78)
Q Consensus 37 r~~~~~~~iPldrlllETD 55 (78)
+++++ .||-+|||.||.
T Consensus 26 k~~~K--~vPk~rllsE~E 42 (91)
T KOG3484|consen 26 KEVAK--LVPKNRLLSETE 42 (91)
T ss_pred HHHHh--hCCccccccHHH
Confidence 56788 999999999987
No 19
>PF07913 DUF1678: Protein of unknown function (DUF1678); InterPro: IPR012465 This family is composed of uncharacterised proteins expressed by Methanopyrus kandleri, a hyperthermophilic archaeon.
Probab=49.02 E-value=9.2 Score=27.30 Aligned_cols=50 Identities=26% Similarity=0.399 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCC--CceEeecCCCCC
Q psy4672 4 SSIPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPM--DRILVESDAPFL 59 (78)
Q Consensus 4 ~~~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPl--drlllETDsP~~ 59 (78)
++.| .+.|.+.+. |+-+.|++-- ..+.++++++. ++|. +.++++|=+||-
T Consensus 112 s~lp-yk~ar~VL~rglal~FdarP---~~sp~IrdlLe--~lPdrlesflvrtLg~WP 164 (201)
T PF07913_consen 112 SDLP-YKKARRVLARGLALAFDARP---SESPRIRDLLE--ELPDRLESFLVRTLGGWP 164 (201)
T ss_pred hcCh-HHHHHHHHHhcccccccCCC---CCCchHHHHHH--hCccHHHHHHHHHhcCCc
Confidence 4555 577888899 9989998733 34566999999 9995 789999999984
No 20
>COG2159 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]
Probab=43.67 E-value=62 Score=23.84 Aligned_cols=54 Identities=30% Similarity=0.215 Sum_probs=36.2
Q ss_pred CCCHHHHHHHhc---CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCC
Q psy4672 6 IPMLEPLNKALL---ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPN 62 (78)
Q Consensus 6 ~~~~e~a~~~l~---G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~ 62 (78)
.|...++..... ..|+-.++..-++- ...+-+.+. +++.||||.=||.|+..|.
T Consensus 204 ~p~~~~a~~~a~~~~nvy~d~s~~~~~~~-~~~~~~~~~--~~~~dkilFGSD~P~~~~~ 260 (293)
T COG2159 204 YPWELEAIELAYAHPNVYLDTSGVRPKYF-APPLLEFLK--ELGPDKILFGSDYPAIHPE 260 (293)
T ss_pred CchhHHHHHHHHhCCCceeeeeccccccC-ChHHHHHHH--hcccCeEEecCCCCCcCHH
Confidence 444444433322 69998888532222 224666777 7999999999999998875
No 21
>PHA02671 hypothetical protein; Provisional
Probab=43.15 E-value=13 Score=26.35 Aligned_cols=33 Identities=18% Similarity=0.213 Sum_probs=21.6
Q ss_pred CCCCCCHHHHHHHhcCceeEecCcccccCCchHH
Q psy4672 3 RSSIPMLEPLNKALLILILCWSGYICKDSSEAGL 36 (78)
Q Consensus 3 ~~~~~~~e~a~~~l~G~yisi~g~~~~~~~~~~~ 36 (78)
..++| ++++.+.+..|||+.+|.++.-.+..++
T Consensus 47 ~~~v~-~~~i~~~l~dCYia~nG~il~CS~~~rL 79 (179)
T PHA02671 47 FTSLP-LTQVNMLMSDCYFAVNGNLLPCTEDFRL 79 (179)
T ss_pred eeecc-HHHHhhhhhceEEEECCEEEecCccccc
Confidence 35666 4666666668999999987544443333
No 22
>COG5495 Uncharacterized conserved protein [Function unknown]
Probab=42.54 E-value=34 Score=25.79 Aligned_cols=53 Identities=17% Similarity=-0.126 Sum_probs=38.6
Q ss_pred CCCCCCCCHHHHHHHhc-Cc-eeEecCcccccCCchHHHhhhhcCCCCCCceEe-ecCCCCC
Q psy4672 1 MHRSSIPMLEPLNKALL-IL-ILCWSGYICKDSSEAGLQGMLESGELPMDRILV-ESDAPFL 59 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G~-yisi~g~~~~~~~~~~~r~~~~~~~iPldrlll-ETDsP~~ 59 (78)
.|||.....+...+.-+ || =.||-+.+ +|.. +.+-+. .++..-+.+ |+|.|-.
T Consensus 96 ~HcSga~~~~il~~~gr~g~~~asiHP~f-~Fsg---l~edl~--rl~d~~~~i~eaD~~g~ 151 (289)
T COG5495 96 AHCSGANGSGILAPLGRQGCIPASIHPAF-SFSG---LDEDLS--RLKDTIFGITEADDVGY 151 (289)
T ss_pred EEccCCCchhhhhhhhhcCCcceeecccc-cccC---CHHHHH--hCcccEEEeeccccccc
Confidence 49999999999998877 84 47888865 5643 334455 677777776 9998854
No 23
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=42.46 E-value=43 Score=18.71 Aligned_cols=37 Identities=16% Similarity=0.160 Sum_probs=28.0
Q ss_pred eeEecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 20 ILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 20 yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
.|.+||....+..+..++++++.-.++.+++.+|=|.
T Consensus 2 ~i~vNG~~~~~~~~~tl~~lL~~l~~~~~~vav~vNg 38 (66)
T PRK05659 2 NIQLNGEPRELPDGESVAALLAREGLAGRRVAVEVNG 38 (66)
T ss_pred EEEECCeEEEcCCCCCHHHHHHhcCCCCCeEEEEECC
Confidence 4678887666666667888888666788899888775
No 24
>COG0106 HisA Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]
Probab=41.74 E-value=50 Score=24.34 Aligned_cols=49 Identities=27% Similarity=0.168 Sum_probs=36.9
Q ss_pred CCCHHHHHHHhc-CceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCC
Q psy4672 6 IPMLEPLNKALL-ILILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPF 58 (78)
Q Consensus 6 ~~~~e~a~~~l~-G~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~ 58 (78)
+-+.+.++++++ |+-.-+-|.. ..++-+.++++++ +.| +||++-=|+=-
T Consensus 84 IRs~~~v~~ll~~G~~rViiGt~-av~~p~~v~~~~~--~~g-~rivv~lD~r~ 133 (241)
T COG0106 84 IRSLEDVEALLDAGVARVIIGTA-AVKNPDLVKELCE--EYG-DRIVVALDARD 133 (241)
T ss_pred cCCHHHHHHHHHCCCCEEEEecc-eecCHHHHHHHHH--HcC-CcEEEEEEccC
Confidence 346789999999 9544444434 3556678999999 999 99999888643
No 25
>KOG1017|consensus
Probab=38.35 E-value=19 Score=26.57 Aligned_cols=21 Identities=29% Similarity=0.547 Sum_probs=19.9
Q ss_pred hHHHhhhhcCCCCCCceEeecCC
Q psy4672 34 AGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 34 ~~~r~~~~~~~iPldrlllETDs 56 (78)
+.+|+.++ .|-+.+||+++|.
T Consensus 151 qgLRdCCR--sIRIGKILi~sd~ 171 (267)
T KOG1017|consen 151 QGLRDCCR--SIRIGKILIGSDQ 171 (267)
T ss_pred HHHHHHHH--HheeeeEEecccc
Confidence 67999999 9999999999997
No 26
>TIGR03849 arch_ComA phosphosulfolactate synthase. This model finds the ComA (Coenzyme M biosynthesis A) protein, phosphosulfolactate synthase, in methanogenic archaea. The ComABC pathway is one of at least two pathways to the intermediate sulfopyruvate. Coenzyme M occurs rarely and sporadically outside of the archaea, as for expoxide metabolism in Xanthobacter autotrophicus Py2, but candidate phosphosulfolactate synthases from that and other species occur fall below the cutoff and outside the scope of this model. This model deliberately is narrower in scope than pfam02679.
Probab=37.91 E-value=45 Score=24.45 Aligned_cols=45 Identities=18% Similarity=0.247 Sum_probs=27.4
Q ss_pred HHHHHhc-C-ceeEecC-------ccccc---CCchHHHhhhhcCCCCCCceEeecCCC
Q psy4672 11 PLNKALL-I-LILCWSG-------YICKD---SSEAGLQGMLESGELPMDRILVESDAP 57 (78)
Q Consensus 11 ~a~~~l~-G-~yisi~g-------~~~~~---~~~~~~r~~~~~~~iPldrlllETDsP 57 (78)
.+++.|+ | .++=+-+ -++.. -+..-+.++++ ++|+++++.|-..|
T Consensus 139 ~~~~~LeAGA~~ViiEarEsg~~~Gi~~~~g~~r~d~v~~i~~--~l~~eklifEAp~k 195 (237)
T TIGR03849 139 LINKDLEAGADYVIIEGRESGKNIGLFDEKGNVKEDELDVLAE--NVDINKVIFEAPQK 195 (237)
T ss_pred HHHHHHHCCCcEEEEeehhcCCCcceeCCCCCCchHHHHHHHh--hCChhcEEEECCCH
Confidence 4555588 8 5555443 12211 12233556688 99999999996554
No 27
>COG0801 FolK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase [Coenzyme metabolism]
Probab=37.35 E-value=23 Score=24.47 Aligned_cols=55 Identities=16% Similarity=0.181 Sum_probs=30.2
Q ss_pred ceeEecCcccccCCchHHHhhhhc-CCCCCCceEeecCCCCCCCCCCCC-Ccccchhhhhc
Q psy4672 19 LILCWSGYICKDSSEAGLQGMLES-GELPMDRILVESDAPFLYPNARAA-KLPIHVRHLVM 77 (78)
Q Consensus 19 ~yisi~g~~~~~~~~~~~r~~~~~-~~iPldrlllETDsP~~~p~~~~~-neP~~l~~v~~ 77 (78)
.|||+|+.+ -.+ .+.++++++. ++.+.-+++.+ ||...-.|.+. +.|.++..+++
T Consensus 4 vyl~LGSNl-gd~-~~~l~~A~~~L~~~~~~~v~~~--S~~y~t~p~G~~~Q~~FlN~v~~ 60 (160)
T COG0801 4 VYLGLGSNL-GDR-LKQLRAALAALDALADIRVVAV--SPIYETPPVGYEDQPDFLNAVVE 60 (160)
T ss_pred EEEEecCCC-CCH-HHHHHHHHHHHHhCCCceEEEe--ccceecCCCCCCCCcchheEEEE
Confidence 699999976 332 2334444441 15665555555 44433333343 77877776654
No 28
>PF04909 Amidohydro_2: Amidohydrolase; InterPro: IPR006992 These proteins are related to the metal-dependent hydrolase superfamily []. The family includes 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase which converts alpha-amino-beta-carboxymuconate-epsilon- semialdehyde (ACMS) to alpha-aminomuconate semialdehyde (AMS). ACMS can be converted non-enzymatically to quinolate, a potent endogenous excitoxin of neuronal cells which is implicated in the pathogenesis of various neurodegenerative disorders. In the presence of AMCSD, ACMS is converted to AMS, a benign catabolite. 2-amino-3-(3-oxoprop-2-enyl)-but-2-enedioate = 2-aminomuconate semialdehyde + CO2. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2QPX_A 4D8L_A 3K4W_I 3IRS_B 4DZI_B 3S4T_G 2GWG_B 3IJ6_A 2DVX_C 2DVT_C ....
Probab=37.13 E-value=18 Score=24.49 Aligned_cols=42 Identities=26% Similarity=0.191 Sum_probs=27.5
Q ss_pred CceeEecCcc------cccCCchHHHhhhhcCCCCCCceEeecCCCCCCC
Q psy4672 18 ILILCWSGYI------CKDSSEAGLQGMLESGELPMDRILVESDAPFLYP 61 (78)
Q Consensus 18 G~yisi~g~~------~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p 61 (78)
+.|+-+++.. ........++.++. ...-||||.-||.|+...
T Consensus 191 nvy~d~s~~~~~~~~~~~~~~~~~l~~~~~--~~g~drilfGSD~P~~~~ 238 (273)
T PF04909_consen 191 NVYVDLSGIPPFWYFWPPSFDRPFLRRAVD--EFGPDRILFGSDYPHPDG 238 (273)
T ss_dssp TEEEECHSHHSSEEEETTHHCHHHHHHHHH--HHTGGGEEEE--TTSSTH
T ss_pred cccccccccccccccCcccccHHHHHHHHH--HhCCceEEecCCCCCCCc
Confidence 6898877721 00112345778888 888899999999998653
No 29
>cd01308 Isoaspartyl-dipeptidase Isoaspartyl dipeptidase hydrolyzes the beta-L-isoaspartyl linkages in dipeptides, as part of the degradative pathway to eliminate proteins with beta-L-isoaspartyl peptide bonds, bonds whereby the beta-group of an aspartate forms the peptide link with the amino group of the following amino acid. Formation of this bond is a spontaneous nonenzymatic reaction in nature and can profoundly effect the function of the protein. Isoaspartyl dipeptidase is an octameric enzyme that contains a binuclear zinc center in the active site of each subunit and shows a strong preference of hydrolyzing Asp-Leu dipeptides.
Probab=36.60 E-value=85 Score=23.16 Aligned_cols=44 Identities=20% Similarity=0.189 Sum_probs=28.6
Q ss_pred HHHHhc-CceeEecCccccc-------CCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 12 LNKALL-ILILCWSGYICKD-------SSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 12 a~~~l~-G~yisi~g~~~~~-------~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
+.+.++ |.|+.|....+.+ ++.+.++.+++. .++.|+|++=||+
T Consensus 234 ~~~~~~~G~~v~i~~~~~~~~~~~~~~~~~~~l~~~~~~-g~~~d~i~l~TD~ 285 (387)
T cd01308 234 GVEFAKMGGTIDLTSSIDPQFRKEGEVRPSEALKRLLEQ-GVPLERITFSSDG 285 (387)
T ss_pred HHHHHHcCCcEEEECCCCccccccCccChHHHHHHHHHh-CCCCCcEEEEECC
Confidence 455666 8888887533221 133456667762 2577999999997
No 30
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=34.75 E-value=8.6 Score=23.71 Aligned_cols=43 Identities=28% Similarity=0.198 Sum_probs=28.0
Q ss_pred HHHHHHHhcCceeEecCcccccCCchHHHhhhhcCCCCCC-ceEeecCC
Q psy4672 9 LEPLNKALLILILCWSGYICKDSSEAGLQGMLESGELPMD-RILVESDA 56 (78)
Q Consensus 9 ~e~a~~~l~G~yisi~g~~~~~~~~~~~r~~~~~~~iPld-rlllETDs 56 (78)
.+.|++.++.+-++.+.++- --++++++.|.||.+ .++.|.|.
T Consensus 13 K~~A~~vl~~lGls~S~Ai~-----~fl~qi~~~~~iPF~~~~~s~ed~ 56 (80)
T PRK11235 13 KARAYAVLEKLGVTPSEALR-----LLLQYVAENGRLPFKTVLLSDEDA 56 (80)
T ss_pred HHHHHHHHHHhCCCHHHHHH-----HHHHHHHHhCCCCCCCCCCCHHHH
Confidence 35677777755556655442 236778888999999 55555543
No 31
>PHA02983 hypothetical protein; Provisional
Probab=34.34 E-value=17 Score=25.86 Aligned_cols=33 Identities=21% Similarity=0.281 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHhcCceeEecCcccccCCchHH
Q psy4672 4 SSIPMLEPLNKALLILILCWSGYICKDSSEAGL 36 (78)
Q Consensus 4 ~~~~~~e~a~~~l~G~yisi~g~~~~~~~~~~~ 36 (78)
..+|.-+..++.+..|||+.+|.++.-.+..++
T Consensus 48 ~pi~~~~i~~~~l~dCYia~nG~i~~CS~~~rL 80 (180)
T PHA02983 48 VPIPVNDIKQSDLQKCYISYNGKIVHCSKDNRL 80 (180)
T ss_pred EECCHHHhchhhhcCeEEEECCEEEecCccccc
Confidence 345544555567778999999987544443333
No 32
>PLN00064 photosystem II protein Psb27; Provisional
Probab=33.85 E-value=21 Score=25.04 Aligned_cols=22 Identities=9% Similarity=-0.041 Sum_probs=18.1
Q ss_pred CCCCCHHHHHHHhcCceeEecC
Q psy4672 4 SSIPMLEPLNKALLILILCWSG 25 (78)
Q Consensus 4 ~~~~~~e~a~~~l~G~yisi~g 25 (78)
.|+-+++.|...+.|.|.||++
T Consensus 118 ~SFttMyTALNaLAGHY~Sfgp 139 (166)
T PLN00064 118 PSFRDMYSALNAVSGHYISFGP 139 (166)
T ss_pred ccHHHHHHHHHHHHHHhhccCC
Confidence 4667778888888899999985
No 33
>PRK13587 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=31.89 E-value=1.1e+02 Score=21.69 Aligned_cols=46 Identities=17% Similarity=0.074 Sum_probs=35.4
Q ss_pred CCCHHHHHHHhc-C-ceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 6 IPMLEPLNKALL-I-LILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 6 ~~~~e~a~~~l~-G-~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
+-+.|.++++++ | -.+-+|.. ++++-+-++++.+ ..| ++|++-=|.
T Consensus 85 Irs~e~v~~~l~~Ga~kvvigt~--a~~~~~~l~~~~~--~fg-~~ivvslD~ 132 (234)
T PRK13587 85 IRTKSQIMDYFAAGINYCIVGTK--GIQDTDWLKEMAH--TFP-GRIYLSVDA 132 (234)
T ss_pred cCCHHHHHHHHHCCCCEEEECch--HhcCHHHHHHHHH--HcC-CCEEEEEEe
Confidence 447899999999 8 67777763 4555567888888 887 888888775
No 34
>PF02126 PTE: Phosphotriesterase family; InterPro: IPR001559 Synonym(s): Paraoxonase, A-esterase, Aryltriphosphatase, Phosphotriesterase, Paraoxon hydrolase Bacteria such as Brevundimonas diminuta (Pseudomonas diminuta) harbour a plasmid that carries the gene for Aryldialkylphosphatase (3.1.8.1 from EC) (PTE) (also known as parathion hydrolase). This enzyme has attracted interest because of its potential use in the detoxification of chemical waste and warfare agents and its ability to degrade agricultural pesticides such as parathion. It acts specifically on synthetic organophosphate triesters and phosphorofluoridates. It does not seem to have a natural occuring substrate and may thus have optimally evolved for utilizing paraoxon. Aryldialkylphosphatase belongs to a family [, ] of enzymes that possess a binuclear zinc metal centre at their active site. The two zinc ions are coordinated by six different residues, six of which being histidines. This family so far includes, in addition to the parathion hydrolase, the following proteins: Escherichia coli protein Php, the substrate of which is not yet known. Mycobacterium tuberculosis phosphotriesterase homology protein Rv0230C. Mammalian phosphotriesterase related protein (PTER) (RPR-1). ; GO: 0008270 zinc ion binding, 0016788 hydrolase activity, acting on ester bonds, 0009056 catabolic process; PDB: 3MSR_A 3OVG_D 3K2G_C 1BF6_B 3OQE_A 3C86_A 3SO7_A 2D2G_A 2R1P_A 2D2H_A ....
Probab=31.23 E-value=51 Score=24.65 Aligned_cols=55 Identities=20% Similarity=0.059 Sum_probs=34.6
Q ss_pred CCCCCCCHHHHHHHhc-CceeEecCc-----cc------ccC----CchHHHhhhhcCCCCCCceEeecCCCC
Q psy4672 2 HRSSIPMLEPLNKALL-ILILCWSGY-----IC------KDS----SEAGLQGMLESGELPMDRILVESDAPF 58 (78)
Q Consensus 2 ~~~~~~~~e~a~~~l~-G~yisi~g~-----~~------~~~----~~~~~r~~~~~~~iPldrlllETDsP~ 58 (78)
|.-..++.+..+++++ |+|++|-.. -. .+. +.+.+.++++ +==.||||+=+|.=.
T Consensus 190 H~D~~~D~~y~~~la~~G~~l~~D~~g~~~~g~~~~~~~~~~~d~~ri~~l~~L~~--~Gy~~qIlLS~D~~~ 260 (308)
T PF02126_consen 190 HMDRNPDLDYHRELADRGVYLEFDTIGREFSGKDKNPRVGYPPDEERIELLKELIE--EGYADQILLSHDIGR 260 (308)
T ss_dssp SGGGST-HHHHHHHHHTT-EEEETTTT-B-TTTTTCHSCTTS-HHHHHHHHHHHHH--TTTGGGEEE-HHHES
T ss_pred CCCCCCCHHHHHHHHhcCCEEEecCCcccccCcccCccCCCCCHHHHHHHHHHHHH--cCCcCcEEEeccccc
Confidence 5566788889999999 999999773 00 011 1124555666 445689999999654
No 35
>cd04723 HisA_HisF Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and pl
Probab=31.13 E-value=1.4e+02 Score=21.03 Aligned_cols=46 Identities=20% Similarity=0.036 Sum_probs=36.9
Q ss_pred CCCHHHHHHHhc-C-ceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 6 IPMLEPLNKALL-I-LILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 6 ~~~~e~a~~~l~-G-~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
+-+.|.+++++. | ..+.+|.. ++++ +-++++++ ..+-+|+++-=|.
T Consensus 87 ir~~edv~~~l~~Ga~~viigt~--~~~~-~~~~~~~~--~~~~~~iivslD~ 134 (233)
T cd04723 87 IRSLENAQEWLKRGASRVIVGTE--TLPS-DDDEDRLA--ALGEQRLVLSLDF 134 (233)
T ss_pred cCCHHHHHHHHHcCCCeEEEcce--eccc-hHHHHHHH--hcCCCCeEEEEec
Confidence 346799999999 8 78888873 4666 67889999 8987799988775
No 36
>PRK13586 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=30.72 E-value=1.3e+02 Score=21.49 Aligned_cols=47 Identities=21% Similarity=0.191 Sum_probs=37.3
Q ss_pred CCCHHHHHHHhc-C-ceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 6 IPMLEPLNKALL-I-LILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 6 ~~~~e~a~~~l~-G-~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
+-+.|.++++++ | -.+.+|.. ++++-+-++++++ ..+-+++++-=|.
T Consensus 82 Irs~e~~~~~l~~Ga~kvvigt~--a~~~p~~~~~~~~--~~g~~~ivvslD~ 130 (232)
T PRK13586 82 IRDIEKAKRLLSLDVNALVFSTI--VFTNFNLFHDIVR--EIGSNRVLVSIDY 130 (232)
T ss_pred cCCHHHHHHHHHCCCCEEEECch--hhCCHHHHHHHHH--HhCCCCEEEEEEc
Confidence 447899999999 8 78888774 4556677889999 8888899977776
No 37
>KOG2368|consensus
Probab=30.11 E-value=51 Score=24.93 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=26.0
Q ss_pred HHHHHHHhc-Cce-eEecCcccccCCc----hHHHhhhhcCCCCCCceEeec
Q psy4672 9 LEPLNKALL-ILI-LCWSGYICKDSSE----AGLQGMLESGELPMDRILVES 54 (78)
Q Consensus 9 ~e~a~~~l~-G~y-isi~g~~~~~~~~----~~~r~~~~~~~iPldrlllET 54 (78)
.+.++++.+ ||| ||++-.+ --..- +-+..+.+ .+|.+.|-+--
T Consensus 172 a~V~k~ly~mGCyEiSLGDTI-GvGTpgtm~~ML~~Vmk--~vPa~~LAVH~ 220 (316)
T KOG2368|consen 172 AEVVKKLYEMGCYEISLGDTI-GVGTPGTMKRMLDAVMK--VVPAEKLAVHC 220 (316)
T ss_pred HHHHHHHHhCCcEEEeccccc-ccCCchhHHHHHHHHHH--hCCHHHhhhhh
Confidence 467889999 977 6665422 11111 23556667 99998776543
No 38
>PRK14024 phosphoribosyl isomerase A; Provisional
Probab=27.71 E-value=1.2e+02 Score=21.43 Aligned_cols=46 Identities=22% Similarity=0.052 Sum_probs=33.2
Q ss_pred CCCHHHHHHHhc-Cc-eeEecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 6 IPMLEPLNKALL-IL-ILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 6 ~~~~e~a~~~l~-G~-yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
+-+.|.++++++ |+ .+.+|... .++-+.++++++ .++ +++.+--|.
T Consensus 84 irs~edv~~~l~~Ga~kvviGs~~--l~~p~l~~~i~~--~~~-~~i~vsld~ 131 (241)
T PRK14024 84 IRDDESLEAALATGCARVNIGTAA--LENPEWCARVIA--EHG-DRVAVGLDV 131 (241)
T ss_pred CCCHHHHHHHHHCCCCEEEECchH--hCCHHHHHHHHH--Hhh-hhEEEEEEE
Confidence 457899999999 95 77887754 445567888888 775 666665554
No 39
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=26.43 E-value=1.1e+02 Score=16.04 Aligned_cols=20 Identities=25% Similarity=0.423 Sum_probs=14.8
Q ss_pred chHHHhhhhcCCCCCCceEe
Q psy4672 33 EAGLQGMLESGELPMDRILV 52 (78)
Q Consensus 33 ~~~~r~~~~~~~iPldrlll 52 (78)
.+.+++++++|.|..+-++=
T Consensus 16 ~~el~~l~~~g~i~~~tlvw 35 (45)
T PF14237_consen 16 LEELRQLISSGEIDPDTLVW 35 (45)
T ss_pred HHHHHHHHHcCCCCCCCeEe
Confidence 36688888888888776653
No 40
>PF02698 DUF218: DUF218 domain; InterPro: IPR003848 This domain of unknown function is found in several uncharacterised proteins.; PDB: 3CA8_A.
Probab=26.18 E-value=70 Score=20.40 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=13.5
Q ss_pred CchHHHhhhhcCCCCCCceEeecCC
Q psy4672 32 SEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 32 ~~~~~r~~~~~~~iPldrlllETDs 56 (78)
.++.+++.+....||-++|++|+.+
T Consensus 55 ea~~~~~~l~~~gvp~~~I~~e~~s 79 (155)
T PF02698_consen 55 EAEAMRDYLIELGVPEERIILEPKS 79 (155)
T ss_dssp HHHHHHHHHHHT---GGGEEEE---
T ss_pred HHHHHHHHHHhcccchheeEccCCC
Confidence 3455667665557999999998764
No 41
>PF07521 RMMBL: RNA-metabolising metallo-beta-lactamase; InterPro: IPR011108 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism [].; PDB: 3ZQ4_D 2I7T_A 2I7V_A 2YCB_B 3BK1_A 3T3N_A 3BK2_A 3T3O_A 3AF5_A 3AF6_A ....
Probab=26.12 E-value=56 Score=17.25 Aligned_cols=17 Identities=18% Similarity=-0.033 Sum_probs=10.5
Q ss_pred CCCCCCCCHHHHHHHhc
Q psy4672 1 MHRSSIPMLEPLNKALL 17 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~ 17 (78)
+|+|++.+.+.+.++++
T Consensus 12 ~~fSgHad~~~L~~~i~ 28 (43)
T PF07521_consen 12 IDFSGHADREELLEFIE 28 (43)
T ss_dssp SGCSSS-BHHHHHHHHH
T ss_pred EeecCCCCHHHHHHHHH
Confidence 45677777777766654
No 42
>PLN00010 cyclin-dependent kinases regulatory subunit; Provisional
Probab=25.52 E-value=30 Score=21.83 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=14.7
Q ss_pred HhhhhcCCCCCCceEeecC
Q psy4672 37 QGMLESGELPMDRILVESD 55 (78)
Q Consensus 37 r~~~~~~~iPldrlllETD 55 (78)
+++++ .||-++||.|+.
T Consensus 24 k~~~k--~ipk~~LL~E~E 40 (86)
T PLN00010 24 PEVAK--LLPKNRLLSENE 40 (86)
T ss_pred HHHHH--hCCcCcccCHHH
Confidence 46788 999999999976
No 43
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=25.17 E-value=1.1e+02 Score=17.05 Aligned_cols=36 Identities=19% Similarity=0.121 Sum_probs=21.5
Q ss_pred eEecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 21 LCWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 21 isi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
|.+||....++.+.+++++++.-.++.+++.++=|.
T Consensus 2 i~iNg~~~~~~~~~tv~~ll~~l~~~~~~i~V~vNg 37 (65)
T cd00565 2 ITVNGEPREVEEGATLAELLEELGLDPRGVAVALNG 37 (65)
T ss_pred EEECCeEEEcCCCCCHHHHHHHcCCCCCcEEEEECC
Confidence 456666555554556777776444566666666554
No 44
>PF05989 Chordopox_A35R: Chordopoxvirus A35R protein; InterPro: IPR009247 This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein. The function of this family is unknown.
Probab=24.62 E-value=27 Score=24.67 Aligned_cols=32 Identities=19% Similarity=0.181 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHhcCceeEecCcccccCCchHH
Q psy4672 5 SIPMLEPLNKALLILILCWSGYICKDSSEAGL 36 (78)
Q Consensus 5 ~~~~~e~a~~~l~G~yisi~g~~~~~~~~~~~ 36 (78)
.++.-+..+.-+..|||+.+|.++.-.+..++
T Consensus 48 ~i~~~~i~~~~i~dCYia~nG~i~~Cs~~~~L 79 (176)
T PF05989_consen 48 PISMNLINQRDIQDCYIAYNGNILHCSEDNRL 79 (176)
T ss_pred EcCHHHhhhhccccEEEEECCEEEeccchhhc
Confidence 34433334444668999999987655444333
No 45
>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.
Probab=24.28 E-value=55 Score=21.76 Aligned_cols=21 Identities=33% Similarity=0.602 Sum_probs=16.2
Q ss_pred hHHHhhhhcCCC--CCCceEeecCC
Q psy4672 34 AGLQGMLESGEL--PMDRILVESDA 56 (78)
Q Consensus 34 ~~~r~~~~~~~i--PldrlllETDs 56 (78)
..++++.+ .- ..|+|++||.+
T Consensus 72 ~~l~~l~~--~~~~~~d~IiIE~sG 94 (178)
T PF02492_consen 72 EALRRLLR--EYEERPDRIIIETSG 94 (178)
T ss_dssp HHHHHHCC--CCHGC-SEEEEEEEC
T ss_pred HHHHHHHH--hcCCCcCEEEECCcc
Confidence 45777777 77 89999999987
No 46
>PF02679 ComA: (2R)-phospho-3-sulfolactate synthase (ComA); InterPro: IPR003830 Methanogenic archaea produce methane via the anaerobic reduction of acetate or single carbon compounds []. Coenzyme M (CoM; 2-mercaptoethanesulphonic acid) serves as the terminal methyl carrier for this process. Previously thought to be unique to methanogenic archaea, CoM has also been found in methylotrophic bacteria. Biosynthesis of CoM begins with the Michael addition of sulphite to phosphoenolpyruvate, forming 2-phospho-3-sulpholactate (PSL). This reaction is catalyzed by members of this family, PSL synthase (ComA) []. Subsequently, PSL is dephosphorylated by phosphosulpholactate phosphatase (ComB) to form 3-sulpholactate [], which is then converted to 3-sulphopyruvate by L-sulpholactate dehydrogenase (ComC; 1.1.1.272 from EC) []. Sulphopyruvate decarboxylase (ComDE; 4.1.1.79 from EC) converts 3-sulphopyruvate to sulphoacetaldehyde []. Reductive thiolation of sulphoacetaldehyde is the final step.; GO: 0019295 coenzyme M biosynthetic process; PDB: 1U83_A 1QWG_A.
Probab=23.91 E-value=1.9e+02 Score=21.28 Aligned_cols=47 Identities=13% Similarity=0.211 Sum_probs=26.6
Q ss_pred HHHHHHHhc-C-ceeEecCc------ccccC---CchHHHhhhhcCCCCCCceEeecCCC
Q psy4672 9 LEPLNKALL-I-LILCWSGY------ICKDS---SEAGLQGMLESGELPMDRILVESDAP 57 (78)
Q Consensus 9 ~e~a~~~l~-G-~yisi~g~------~~~~~---~~~~~r~~~~~~~iPldrlllETDsP 57 (78)
.+++++.++ | .++=+-+- ++... +..-+.+++. .+|+++|+.|-..|
T Consensus 150 i~~~~~dLeAGA~~ViiEarEsG~~Gi~~~~g~~r~d~v~~i~~--~~~~~~lifEAp~k 207 (244)
T PF02679_consen 150 IEQAKRDLEAGADKVIIEARESGKGGIYDNDGEVRTDLVEKIIE--RLGLEKLIFEAPQK 207 (244)
T ss_dssp HHHHHHHHHHTECEEEE--TTT--STTB-TTS-B-HHHHHHHHT--TS-GGGEEEE--SH
T ss_pred HHHHHHHHHCCCCEEEEeeeccCCCCccCCCCCccHHHHHHHHH--hCCHhHEEEeCCCH
Confidence 456778888 8 55544332 22111 2245778888 99999999995433
No 47
>KOG3330|consensus
Probab=23.73 E-value=49 Score=23.42 Aligned_cols=28 Identities=18% Similarity=0.019 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhc-C--ceeEecCcccccCC
Q psy4672 5 SIPMLEPLNKALL-I--LILCWSGYICKDSS 32 (78)
Q Consensus 5 ~~~~~e~a~~~l~-G--~yisi~g~~~~~~~ 32 (78)
|+...|.|+.+-+ | +|++|++.+..|..
T Consensus 70 C~dfretaevlak~afkmyLgitpsitswss 100 (183)
T KOG3330|consen 70 CVDFRETAEVLAKVAFKMYLGITPSITSWSS 100 (183)
T ss_pred hhhHHHHHHHHHHhhhheeeecccceeeecC
Confidence 3445677777666 5 99999998866654
No 48
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=23.42 E-value=1.3e+02 Score=16.97 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=24.8
Q ss_pred eEecCcccccCCchHHHhhhhcCCCCCCceEeecCCC
Q psy4672 21 LCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAP 57 (78)
Q Consensus 21 isi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP 57 (78)
|-+||....+..+..+.++++.-.+|.+.+-+|=+.=
T Consensus 3 i~vNG~~~~~~~~~tl~~ll~~l~~~~~~vav~~N~~ 39 (65)
T PRK05863 3 VVVNEEQVEVDEQTTVAALLDSLGFPEKGIAVAVDWS 39 (65)
T ss_pred EEECCEEEEcCCCCcHHHHHHHcCCCCCcEEEEECCc
Confidence 5566765555545567777776667777888887654
No 49
>COG1606 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]
Probab=22.66 E-value=1.5e+02 Score=22.33 Aligned_cols=49 Identities=27% Similarity=0.424 Sum_probs=29.4
Q ss_pred HHHHHHHhc-C--ceeEecCcccccCCchHHHhhhhcCCCCCCceEeecCCCCCCCC
Q psy4672 9 LEPLNKALL-I--LILCWSGYICKDSSEAGLQGMLESGELPMDRILVESDAPFLYPN 62 (78)
Q Consensus 9 ~e~a~~~l~-G--~yisi~g~~~~~~~~~~~r~~~~~~~iPldrlllETDsP~~~p~ 62 (78)
++....+++ + .++.|+|-+ . +.-+-.+++ ..+-.+-+.+=-|+||++++
T Consensus 7 l~~l~~~ik~~~kv~vAfSGGv--D--SslLa~la~-~~lG~~v~AvTv~sP~~p~~ 58 (269)
T COG1606 7 LERLKKAIKEKKKVVVAFSGGV--D--SSLLAKLAK-EALGDNVVAVTVDSPYIPRR 58 (269)
T ss_pred HHHHHHHHhhcCeEEEEecCCc--c--HHHHHHHHH-HHhccceEEEEEecCCCChh
Confidence 466677777 3 799999964 2 234544443 14443334444589998764
No 50
>PF01111 CKS: Cyclin-dependent kinase regulatory subunit; InterPro: IPR000789 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division []. The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded beta-barrel structure []. Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs []. Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation [, ].; GO: 0016538 cyclin-dependent protein kinase regulator activity, 0007049 cell cycle; PDB: 1CKS_C 3QY2_B 1QB3_C 1SCE_B 1PUC_A 1DKS_B 2AST_C 1BUH_B 1DKT_B 2ASS_C.
Probab=22.22 E-value=45 Score=20.20 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=10.9
Q ss_pred HhhhhcCCCCCCceEeecC
Q psy4672 37 QGMLESGELPMDRILVESD 55 (78)
Q Consensus 37 r~~~~~~~iPldrlllETD 55 (78)
+++++ .+|-+++|.|+.
T Consensus 22 k~~~k--~vp~~~llsE~E 38 (70)
T PF01111_consen 22 KEIAK--LVPKDRLLSEEE 38 (70)
T ss_dssp HHHHG--TS-CCS---HHH
T ss_pred HHHHh--hCccCcccCHHH
Confidence 46788 999999999987
No 51
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=21.66 E-value=1.2e+02 Score=16.91 Aligned_cols=35 Identities=23% Similarity=0.183 Sum_probs=20.4
Q ss_pred EecCcccccCCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 22 CWSGYICKDSSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 22 si~g~~~~~~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
.+||....++.+.+++++++.-.++.+.+.+|=|.
T Consensus 2 ~iNg~~~~~~~~~tv~~ll~~l~~~~~~v~v~vN~ 36 (64)
T TIGR01683 2 TVNGEPVEVEDGLTLAALLESLGLDPRRVAVAVNG 36 (64)
T ss_pred EECCeEEEcCCCCcHHHHHHHcCCCCCeEEEEECC
Confidence 45555544444445667766444566677777665
No 52
>PRK10657 isoaspartyl dipeptidase; Provisional
Probab=21.50 E-value=2.4e+02 Score=20.70 Aligned_cols=46 Identities=20% Similarity=0.174 Sum_probs=28.6
Q ss_pred HHHHHHhc-CceeEecC-ccc-cc----CCchHHHhhhhcCCCCCCceEeecCC
Q psy4672 10 EPLNKALL-ILILCWSG-YIC-KD----SSEAGLQGMLESGELPMDRILVESDA 56 (78)
Q Consensus 10 e~a~~~l~-G~yisi~g-~~~-~~----~~~~~~r~~~~~~~iPldrlllETDs 56 (78)
+...++++ |.++.+.- ... .. ++.+.+.++++.|. +.||+.+-||.
T Consensus 234 ~~~~~~~~~G~~~~v~~~~~~~~~~~~~~~~~~l~~~~~~G~-~~d~v~l~tD~ 286 (388)
T PRK10657 234 EQALEFAKKGGVIDLTTSDPDFLGEGEVAPAEALKRALEAGV-PLSRVTLSSDG 286 (388)
T ss_pred HHHHHHHHcCCeEEEecCCCcccccCccCHHHHHHHHHHcCC-ChhheEEECCC
Confidence 55667777 88886652 100 01 12244667777443 79999999996
No 53
>TIGR01975 isoAsp_dipep isoaspartyl dipeptidase IadA. The L-isoaspartyl derivative of Asp arises non-enzymatically over time as a form of protein damage. In this isomerization, the connectivity of the polypeptide changes to pass through the beta-carboxyl of the side chain. Much but not all of this damage can be repaired by protein-L-isoaspartate (D-aspartate) O-methyltransferase. This model describes the isoaspartyl dipeptidase IadA, apparently one of two such enzymes in E. coli, an enzyme that degrades isoaspartyl dipeptides and may unblock degradation of proteins that cannot be repaired. This model also describes closely related proteins from other species (e.g. Clostridium perfringens, Thermoanaerobacter tengcongensis) that we assume to be equivalent in function. This family shows homology to dihydroorotases.
Probab=21.27 E-value=3.1e+02 Score=21.01 Aligned_cols=48 Identities=17% Similarity=0.179 Sum_probs=31.1
Q ss_pred HHHHHHHhc-CceeEecCcccc-------cCCchHHHhhhhcCCCCCCceEeecCCC
Q psy4672 9 LEPLNKALL-ILILCWSGYICK-------DSSEAGLQGMLESGELPMDRILVESDAP 57 (78)
Q Consensus 9 ~e~a~~~l~-G~yisi~g~~~~-------~~~~~~~r~~~~~~~iPldrlllETDsP 57 (78)
.+++.++++ |-++-++..... ++..+.++.+.++ .+|++|+.+=||+.
T Consensus 233 ~~~~i~~~~~gg~iDv~~~~~~~~l~~~~~~~~~~~~~~~~~-Gv~~~~i~isSD~~ 288 (389)
T TIGR01975 233 FEAGLEFAKKGGTIDLTSSIDPQFRKEGEVAPAEGIKKALEA-GVPLEKVTFSSDGN 288 (389)
T ss_pred HHHHHHHHHhCCcEEEeCCCCccchhccccChHHHHHHHHHc-CCCcceEEEEeCCC
Confidence 466777778 877777653211 1222345555553 48899999999985
No 54
>TIGR00045 glycerate kinase. The only characterized member of this family so far is the glycerate kinase GlxK (EC 2.7.1.31) of E. coli. This enzyme acts after glyoxylate carboligase and 2-hydroxy-3-oxopropionate reductase (tartronate semialdehyde reductase) in the conversion of glyoxylate to 3-phosphoglycerate (the D-glycerate pathway) as a part of allantoin degradation.
Probab=20.67 E-value=93 Score=24.20 Aligned_cols=27 Identities=30% Similarity=0.188 Sum_probs=23.2
Q ss_pred CCCCCCCCHHHHHHHhc-C---ceeEecCcc
Q psy4672 1 MHRSSIPMLEPLNKALL-I---LILCWSGYI 27 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G---~yisi~g~~ 27 (78)
|+.||.++=|....+++ | ++|+++|.-
T Consensus 106 ~~atTyG~GelI~~Al~~G~~~iiiGlGGSA 136 (375)
T TIGR00045 106 LQTSSYGTGELIRHALDHGAKKIILGIGGSA 136 (375)
T ss_pred cccccccHHHHHHHHHHCCCCEEEEeccCcc
Confidence 45688888899999999 8 999999975
No 55
>PRK10342 glycerate kinase I; Provisional
Probab=20.26 E-value=99 Score=24.16 Aligned_cols=27 Identities=22% Similarity=0.090 Sum_probs=23.4
Q ss_pred CCCCCCCCHHHHHHHhc-C---ceeEecCcc
Q psy4672 1 MHRSSIPMLEPLNKALL-I---LILCWSGYI 27 (78)
Q Consensus 1 ~~~~~~~~~e~a~~~l~-G---~yisi~g~~ 27 (78)
++.||.++=|..+.+++ | ++|+++|.-
T Consensus 107 ~~atT~G~GelI~~Al~~G~~~iiiGlGGSA 137 (381)
T PRK10342 107 LVTTSRGTGELILQALESGATNIIIGIGGSA 137 (381)
T ss_pred cccccccHHHHHHHHHHCCCCEEEEeecccc
Confidence 45788888899999999 8 999999975
Done!