Query 029652
Match_columns 190
No_of_seqs 176 out of 1024
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 16:20:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029652.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029652hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0193 Pth Peptidyl-tRNA hydr 100.0 2.6E-73 5.6E-78 471.1 17.1 168 17-185 1-170 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 2E-72 4.4E-77 467.9 18.3 168 17-184 1-169 (191)
3 cd00462 PTH Peptidyl-tRNA hydr 100.0 2.1E-71 4.6E-76 454.9 18.8 165 20-185 1-166 (171)
4 TIGR00447 pth peptidyl-tRNA hy 100.0 1.1E-70 2.4E-75 456.5 19.3 166 18-184 1-168 (188)
5 PRK05426 peptidyl-tRNA hydrola 100.0 4.8E-69 1E-73 447.0 19.2 166 17-184 1-168 (189)
6 PF01195 Pept_tRNA_hydro: Pept 100.0 1.3E-67 2.7E-72 436.2 15.5 164 20-184 1-166 (184)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 1.3E-54 2.9E-59 360.4 13.6 167 17-183 38-206 (224)
8 COG0680 HyaD Ni,Fe-hydrogenase 89.8 4.7 0.0001 32.8 9.9 108 17-155 2-122 (160)
9 TIGR00130 frhD coenzyme F420-r 88.8 10 0.00022 30.1 12.7 137 17-186 3-151 (153)
10 PRK11544 hycI hydrogenase 3 ma 77.1 36 0.00077 27.2 11.7 130 19-186 3-143 (156)
11 cd06070 H2MP_like-2 Putative [ 69.9 50 0.0011 25.7 11.3 125 20-185 1-139 (140)
12 PF11775 CobT_C: Cobalamin bio 64.3 15 0.00032 31.8 5.0 70 82-153 115-187 (219)
13 TIGR00142 hycI hydrogenase mat 59.8 82 0.0018 24.6 13.0 132 19-186 1-142 (146)
14 cd06062 H2MP_MemB-H2up Endopep 50.6 22 0.00049 27.8 3.7 130 19-185 1-145 (146)
15 TIGR01651 CobT cobaltochelatas 49.5 29 0.00063 34.2 4.8 69 83-154 496-568 (600)
16 PRK10466 hybD hydrogenase 2 ma 47.8 29 0.00062 27.9 3.9 133 18-186 2-149 (164)
17 PRK09256 hypothetical protein; 46.7 10 0.00022 30.3 1.1 26 105-130 3-30 (138)
18 PF14490 HHH_4: Helix-hairpin- 45.9 13 0.00028 27.2 1.5 25 31-55 45-71 (94)
19 cd06064 H2MP_F420-Reduc Endope 43.5 24 0.00051 27.8 2.8 132 20-184 1-148 (150)
20 TIGR00072 hydrog_prot hydrogen 43.3 25 0.00054 27.4 2.9 130 20-185 1-144 (145)
21 PRK10264 hydrogenase 1 maturat 40.6 43 0.00092 28.0 4.0 129 18-183 5-150 (195)
22 PRK02858 germination protease; 38.4 24 0.00052 32.8 2.3 134 16-172 110-265 (369)
23 PRK12362 germination protease; 38.2 41 0.00088 30.7 3.7 118 15-151 97-228 (318)
24 TIGR01441 GPR GPR endopeptidas 38.0 24 0.00052 32.6 2.3 133 16-171 100-254 (358)
25 PF03418 Peptidase_A25: Germin 36.9 31 0.00068 31.8 2.8 93 16-123 95-197 (354)
26 cd06067 H2MP_MemB-H2evol Endop 33.1 43 0.00093 25.9 2.7 90 20-139 1-98 (136)
27 COG4547 CobT Cobalamin biosynt 32.8 53 0.0011 31.9 3.7 72 82-155 516-590 (620)
28 cd00518 H2MP Hydrogenase speci 32.8 47 0.001 25.6 2.9 89 20-139 1-99 (139)
29 cd06068 H2MP_like-1 Putative [ 32.7 40 0.00087 26.3 2.5 128 20-185 1-143 (144)
30 cd06066 H2MP_NAD-link-bidir En 31.0 54 0.0012 25.4 3.0 126 20-185 1-138 (139)
31 cd06063 H2MP_Cyano-H2up This g 30.4 58 0.0013 25.5 3.1 124 20-182 2-143 (146)
32 PF07431 DUF1512: Protein of u 30.1 2.2E+02 0.0047 26.5 7.0 67 37-105 184-253 (355)
33 COG2179 Predicted hydrolase of 29.5 40 0.00086 28.2 2.0 29 85-113 95-123 (175)
34 PF08282 Hydrolase_3: haloacid 28.3 45 0.00097 26.5 2.2 25 86-110 188-212 (254)
35 PF06342 DUF1057: Alpha/beta h 26.3 2.5E+02 0.0055 25.4 6.7 66 105-175 24-91 (297)
36 PRK06437 hypothetical protein; 24.9 94 0.002 21.3 3.0 29 85-113 19-47 (67)
37 PRK05537 bifunctional sulfate 23.7 93 0.002 30.2 3.7 76 19-101 283-370 (568)
38 PF13443 HTH_26: Cro/C1-type H 23.3 20 0.00043 23.5 -0.7 27 83-109 37-63 (63)
39 KOG2882 p-Nitrophenyl phosphat 22.8 71 0.0015 29.0 2.5 38 71-114 218-255 (306)
40 COG2607 Predicted ATPase (AAA+ 22.6 84 0.0018 28.2 2.9 30 91-120 129-158 (287)
41 PRK10513 sugar phosphate phosp 22.4 51 0.0011 27.5 1.5 25 86-110 198-222 (270)
42 PRK10976 putative hydrolase; P 22.3 54 0.0012 27.4 1.6 25 86-110 192-216 (266)
43 PF00472 RF-1: RF-1 domain; I 21.6 64 0.0014 24.5 1.8 22 108-129 5-28 (113)
44 COG2897 SseA Rhodanese-related 21.6 97 0.0021 27.6 3.1 30 80-109 69-98 (285)
45 PF02789 Peptidase_M17_N: Cyto 21.1 84 0.0018 23.0 2.3 32 17-48 53-84 (126)
46 cd06392 PBP1_iGluR_delta_1 N-t 20.9 1E+02 0.0022 28.5 3.2 33 73-110 116-148 (400)
47 COG4046 Uncharacterized protei 20.8 3.7E+02 0.0081 24.9 6.7 68 37-106 197-267 (368)
48 TIGR01485 SPP_plant-cyano sucr 20.1 96 0.0021 25.9 2.7 27 84-110 167-193 (249)
49 COG2344 AT-rich DNA-binding pr 20.1 74 0.0016 27.3 2.0 27 3-29 71-97 (211)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-73 Score=471.08 Aligned_cols=168 Identities=45% Similarity=0.760 Sum_probs=159.4
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCC-CccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHh
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~-~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~ 95 (190)
.|+|||||||||++|+.||||||||++|.||++++.++ +.++|.+.++++.+.+++|+|+||+||||+||++|.++++|
T Consensus 1 ~~kLIVGLGNPG~~Y~~TRHNvGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~l~kP~TyMNlSG~~V~~~~~f 80 (190)
T COG0193 1 MMKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASF 80 (190)
T ss_pred CcEEEEECCCCchhhcccchhHHHHHHHHHHHHhCCCCccccccCceeEEEEeCCcEEEEecCccceeCcHHHHHHHHHH
Confidence 37899999999999999999999999999999999998 56788999999999999999999999999999999999999
Q ss_pred cCCCCCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh
Q 029652 96 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 175 (190)
Q Consensus 96 ~~i~~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~ 175 (190)
|++++++++|||||||||+|++|+|.+||+|||||||||+++| ||++|+|||||||||+.+++|++|||++|+++|++.
T Consensus 81 y~i~~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGlKSi~~~l-Gt~~f~RlRiGIGrP~~~~~v~~~VL~~f~~~E~~~ 159 (190)
T COG0193 81 YKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHL-GTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEEREL 159 (190)
T ss_pred hCCCHHHEEEEeeccCCCCceEEEEcCCCCCCcccHHHHHHHh-CCCccceEEEEcCCCCCCCchhHhhcCCCCHHHHHH
Confidence 9999999999999999999999999999999999999999999 699999999999999988899999999999999999
Q ss_pred -HHHHHHHHHH
Q 029652 176 -DISFDCIIVF 185 (190)
Q Consensus 176 -~~~~~~~~~~ 185 (190)
+++++.+.+.
T Consensus 160 l~~~~~~a~~~ 170 (190)
T COG0193 160 LDKAIDKAADA 170 (190)
T ss_pred HHHHHHHHHHH
Confidence 7777766553
No 2
>cd02406 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH).
Probab=100.00 E-value=2e-72 Score=467.86 Aligned_cols=168 Identities=65% Similarity=1.141 Sum_probs=157.1
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhc
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~ 96 (190)
+|+|||||||||++|++|||||||+++|.||+++++++++.++++.++++.+.+++++|+||+||||+||+||+++++||
T Consensus 1 ~~~LIvGLGNPG~~Y~~TRHNiGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~y 80 (191)
T cd02406 1 TPWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYY 80 (191)
T ss_pred CcEEEEEcCCCchhhCcCchhHHHHHHHHHHHHcCCCccccccceEEEEEEECCeEEEEEeCCCchhcCHHHHHHHHHHh
Confidence 47899999999999999999999999999999999987767788999999999999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh-
Q 029652 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER- 175 (190)
Q Consensus 97 ~i~~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~- 175 (190)
++++++++|||||||||+|++|+|.+||+|||||||||+++|++|++|+|||||||||+.+.++++|||++|+++|++.
T Consensus 81 ki~~~~ilVihDdldl~~G~irlk~gGs~gGHNGlkSI~~~Lggt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~l 160 (191)
T cd02406 81 KVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEHLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQI 160 (191)
T ss_pred CCCHHHEEEEEECCCCCCCeEEEcCCCCCCCcCCHHHHHHHhCCCCCeEEEEEEeCCCCCCCchhhhhcCCCCHHHHHHH
Confidence 9999999999999999999999999999999999999999995578999999999999776789999999999999988
Q ss_pred HHHHHHHHH
Q 029652 176 DISFDCIIV 184 (190)
Q Consensus 176 ~~~~~~~~~ 184 (190)
+++++.+.+
T Consensus 161 ~~~~~~a~~ 169 (191)
T cd02406 161 DTALEQGVD 169 (191)
T ss_pred HHHHHHHHH
Confidence 666555444
No 3
>cd00462 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts.
Probab=100.00 E-value=2.1e-71 Score=454.85 Aligned_cols=165 Identities=52% Similarity=0.912 Sum_probs=155.9
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
|||||||||++|++||||||||++|+||++++.++.+.++.+.++++.+.+++++|+||+||||+||++|++++++|+++
T Consensus 1 LIvGLGNPG~~Y~~TRHNvGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~~i~ 80 (171)
T cd00462 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYKIP 80 (171)
T ss_pred CEEEECCCCcccCcCchHHHHHHHHHHHHHcCCCCCccccCEEEEEEEECCEEEEEEeCCcccccccHHHHHHHHhcCCC
Confidence 69999999999999999999999999999999988777778999999999999999999999999999999999999999
Q ss_pred CCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh-HHH
Q 029652 100 LNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER-DIS 178 (190)
Q Consensus 100 ~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~-~~~ 178 (190)
+++++|||||||+|+|++|+|++||++||||||||+++| +|++|+|||||||||+.+.++++|||++|+++|++. +.+
T Consensus 81 ~~~ilVihDdldl~~G~vrlk~~G~~gGHNGlkSI~~~l-gt~~f~RlriGIGrP~~~~~v~~yVL~~f~~~E~~~l~~~ 159 (171)
T cd00462 81 PEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL-GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEA 159 (171)
T ss_pred hhHEEEEEecCCCCCceEEEeCCCCCCCCCCHHHHHHHh-CCCCeeEEEEEeCCCCCCCChhhhhcCCCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999 689999999999999877799999999999999999 776
Q ss_pred HHHHHHH
Q 029652 179 FDCIIVF 185 (190)
Q Consensus 179 ~~~~~~~ 185 (190)
++.+.+.
T Consensus 160 ~~~~~~~ 166 (171)
T cd00462 160 IEKAADA 166 (171)
T ss_pred HHHHHHH
Confidence 6665553
No 4
>TIGR00447 pth peptidyl-tRNA hydrolase. The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function.
Probab=100.00 E-value=1.1e-70 Score=456.46 Aligned_cols=166 Identities=43% Similarity=0.761 Sum_probs=154.7
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCC-ccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhc
Q 029652 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (190)
Q Consensus 18 ~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~-~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~ 96 (190)
|+|||||||||++|++|||||||+++|+||++++.++. +.++.+.+++..+.+++++|+||+||||+||++|++++++|
T Consensus 1 ~~LIvGLGNPG~~Y~~TRHNiGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~ 80 (188)
T TIGR00447 1 IKLIVGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKPLTYMNLSGEAVRALASFY 80 (188)
T ss_pred CEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCcCCcccccceEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHHh
Confidence 68999999999999999999999999999999999876 34677888888898899999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh-
Q 029652 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER- 175 (190)
Q Consensus 97 ~i~~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~- 175 (190)
++++++++|||||||+|+|++|+|++||++||||||||+++| +|++|+|||||||||+.+.++++|||++|+++|++.
T Consensus 81 ~i~~~~ilVihDdldl~~G~irlk~~G~~gGHNGlkSI~~~l-gt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~e~~~l 159 (188)
T TIGR00447 81 RIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL-GTNNFNRLRIGIGSPGGSNKVVEFVLSKFTKSELPLL 159 (188)
T ss_pred CCChHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHh-CCCCcceEEEEeCCCCCCCchhhhccCCCCHHHHHHH
Confidence 999999999999999999999999999999999999999999 689999999999999877789999999999999998
Q ss_pred HHHHHHHHH
Q 029652 176 DISFDCIIV 184 (190)
Q Consensus 176 ~~~~~~~~~ 184 (190)
+++++.+.+
T Consensus 160 ~~~i~~~~~ 168 (188)
T TIGR00447 160 EKALDKAVE 168 (188)
T ss_pred HHHHHHHHH
Confidence 766555444
No 5
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=4.8e-69 Score=446.97 Aligned_cols=166 Identities=45% Similarity=0.789 Sum_probs=153.8
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCC-ccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHh
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~-~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~ 95 (190)
.|+|||||||||++|++|||||||+++|.||++++..+. ..++.+.++++.+.+++++|+||+||||+||++|++++++
T Consensus 1 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~ 80 (189)
T PRK05426 1 MMKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANF 80 (189)
T ss_pred CcEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCCCCcccccccEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHH
Confidence 378999999999999999999999999999999887664 4567889999999889999999999999999999999999
Q ss_pred cCCCCCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh
Q 029652 96 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 175 (190)
Q Consensus 96 ~~i~~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~ 175 (190)
|++++++++|||||+|+|+|++|+|.+||++||||||||+++| +|++|+|||||||||+ ..++++|||++|+++|++.
T Consensus 81 ~~i~~~~ilVihDdldl~~G~~r~k~gGs~~GHNGlkSI~~~l-gt~~f~RlriGIGrP~-~~~v~~yVL~~f~~~E~~~ 158 (189)
T PRK05426 81 YKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHL-GTQDFWRLRIGIGRPD-KKKVVDYVLGKFSKEEQEL 158 (189)
T ss_pred hCCCHHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHh-CCCCeeEEEEEeCCCC-CCCcchhhcCCCCHHHHHH
Confidence 9999999999999999999999999999999999999999999 5889999999999997 5689999999999999998
Q ss_pred -HHHHHHHHH
Q 029652 176 -DISFDCIIV 184 (190)
Q Consensus 176 -~~~~~~~~~ 184 (190)
+++++.+.+
T Consensus 159 l~~~~~~a~~ 168 (189)
T PRK05426 159 LDKAIDKAAD 168 (189)
T ss_pred HHHHHHHHHH
Confidence 766655544
No 6
>PF01195 Pept_tRNA_hydro: Peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis [, ]. Bacterial PTH has been found to be evolutionary related to a yeast protein [].; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 3KJZ_A 3KK0_A 3P2J_A 3V2I_A 3TCN_A 3TD6_A 2Z2K_A 3TD2_A 2Z2J_B 2JRC_A ....
Probab=100.00 E-value=1.3e-67 Score=436.17 Aligned_cols=164 Identities=46% Similarity=0.840 Sum_probs=140.6
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccc-cceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~-~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i 98 (190)
|||||||||++|++|||||||+++|+||++++.++...+ +.+.++++.+.+++++|+||+||||+||++|++++++|++
T Consensus 1 LivGLGNPG~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~KP~TyMN~SG~~V~~~~~~~~i 80 (184)
T PF01195_consen 1 LIVGLGNPGPKYENTRHNVGFMVLDRLASRLGLSWKQKKKFKSLISEGSIKGEKVILLKPQTYMNLSGKAVKKILSFYKI 80 (184)
T ss_dssp EEEE---SSTTTTTSGGGHHHHHHHHHHHHTT---EEEGGGTEEEEEEEETTEEEEEEEESSTGGGHHHHHHHHHHHTT-
T ss_pred CEEEcCCCChhhcCCCcCchHHHHHHHHHHhCCCccccccceeEEEEEEEeeeeEEEEcCCCeEeCccHhHHHHHHHhCC
Confidence 799999999999999999999999999999999886554 7888889889999999999999999999999999999999
Q ss_pred CCCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh-HH
Q 029652 99 PLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER-DI 177 (190)
Q Consensus 99 ~~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~-~~ 177 (190)
++++++|||||+|+|+|++|+|.+||++||||||||+++| +|++|+|||||||||+++.++++|||++|+++|++. ++
T Consensus 81 ~~~~ilVihDdldl~~G~irlk~~Gs~~GHNGlkSI~~~L-gt~~f~RlrIGIGrp~~~~~v~~yVL~~f~~~E~~~l~~ 159 (184)
T PF01195_consen 81 PPENILVIHDDLDLPLGKIRLKKGGSSGGHNGLKSIIQHL-GTEDFPRLRIGIGRPPSKEDVADYVLSKFSPEERELLDK 159 (184)
T ss_dssp -GGGEEEEEEETTSSTTEEEEEESS--TT-HHHHHHHHHC-TSSGSEEEEEEE--TSTTSGHHHHHTSB-HHHHHHHHHH
T ss_pred CcceEEEEEeccCCCCCeEEEccCCCCCCCCCHHHHHHHh-ccccceeEEEecCCCCCcchHHHHHhcCCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999 689999999999999877799999999999999998 66
Q ss_pred HHHHHHH
Q 029652 178 SFDCIIV 184 (190)
Q Consensus 178 ~~~~~~~ 184 (190)
+++.+..
T Consensus 160 ~~~~a~~ 166 (184)
T PF01195_consen 160 VIPQAAE 166 (184)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 6665544
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-54 Score=360.45 Aligned_cols=167 Identities=56% Similarity=1.020 Sum_probs=153.3
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhc
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~ 96 (190)
.+|+|+||||||++|..|||||||.++|.||++.+++..+.+.++..+-+.+++..+++++|++|||.||++|.+++..|
T Consensus 38 k~wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y 117 (224)
T KOG2255|consen 38 KPWLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALY 117 (224)
T ss_pred CceEEEecCCCcccccccchhhHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhh
Confidence 36899999999999999999999999999999999986665556666777888899999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh-
Q 029652 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER- 175 (190)
Q Consensus 97 ~i~~~~ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~- 175 (190)
+++.++++||||||++|+|++|+|.+||++||||+||+++++.+...|+||+||||||++++|+.+|||++|++.|++.
T Consensus 118 ~i~~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgHNGvrs~~~~l~g~~~fpRL~iGIGrppg~~d~~a~vLskfsp~e~ke~ 197 (224)
T KOG2255|consen 118 KIPLRHIVVIHDELELPLGKLRLRPGGSHRGHNGVRSVFNCLNGRRSFPRLSIGIGRPPGNEDVKAFVLSKFSPAEQKEL 197 (224)
T ss_pred cchheeEEEEeccccCcCceEEeccCCCccccccHHHHHhhccCCcccceeeeecCCCCCchhhhHHHHHhcChhhhHHH
Confidence 9999999999999999999999999999999999999999997777999999999999999999999999999999983
Q ss_pred -HHHHHHHH
Q 029652 176 -DISFDCII 183 (190)
Q Consensus 176 -~~~~~~~~ 183 (190)
+..++.++
T Consensus 198 Let~l~~~~ 206 (224)
T KOG2255|consen 198 LETLLEHVK 206 (224)
T ss_pred HHHHHhhhH
Confidence 55444443
No 8
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=89.81 E-value=4.7 Score=32.85 Aligned_cols=108 Identities=18% Similarity=0.186 Sum_probs=64.7
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCc-hhccCchhHHHHHHh
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQT-YMNLSGESTGPLAAY 95 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~T-yMNlSG~aV~~~~~~ 95 (190)
.+.+|+|+|||=- .-==+|-.+++.|++++...- ++-++.-.| -+|+.+
T Consensus 2 ~~ilIlG~GN~L~----~DDG~Gv~vae~L~~~~~~~~-----------------~v~vid~Gt~~~~l~~--------- 51 (160)
T COG0680 2 MRILILGVGNILM----GDDGFGVRVAEKLKKRYKPPE-----------------NVEVIDGGTAGPNLLG--------- 51 (160)
T ss_pred CeEEEEeeCCccc----ccCcccHHHHHHHHHhcCCCC-----------------CeEEEEcCCCcHHHHH---------
Confidence 4679999999942 344689999999988753210 122222211 133322
Q ss_pred cCCCCCcEEEEeccCCC--CCceEEEec------CCCCC---CCC-chhhHHHhhcCCCCcceEEEcccCCC
Q 029652 96 YKLPLNRVLVFHDDMGL--PCGVLRLRH------NGGHG---GHN-GLKSVMNNFRGNREFARLRIGIGRPP 155 (190)
Q Consensus 96 ~~i~~~~ilVihDdldl--~~G~vrlk~------gGs~~---GHN-GLkSI~~~l~gt~df~RlrIGIGrP~ 155 (190)
.+...+-++|-|=++. .+|++++-. ...+. .|+ ++..+++.+....++...-+|+.-|.
T Consensus 52 -~l~~~d~vIIVDav~~g~epG~v~~i~~e~i~~~~~~~~~s~H~~~~~~~L~~~~~~~~~~~~~~~~~v~~ 122 (160)
T COG0680 52 -LLAGYDPVIIVDAVLFGLEPGEVRIIDPEEIPAYSSASKDSAHELPLSELLALLKELGGLPVLILGVQVPI 122 (160)
T ss_pred -HhcCCCcEEEEEeeecCCCCceEEEechhhcccccccCCCccccCCHHHHHHHHHHhcCCceEEEEEeece
Confidence 2233444888886555 599998643 22343 565 67777777743345577888888654
No 9
>TIGR00130 frhD coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit). FrhD is not part of the active FRH heterotrimer, but is probably a protease required for maturation. Alternative name: 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) subunit delta.
Probab=88.85 E-value=10 Score=30.06 Aligned_cols=137 Identities=15% Similarity=0.130 Sum_probs=75.0
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHH-cCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHh
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~-~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~ 95 (190)
.+.+|+|+|||-. .-==+|..++++|+++ +..+ ..+.++. ........+...
T Consensus 3 ~~ilVlGiGN~l~----gDDGvG~~v~~~L~~~~~~~~-----------------~~v~vid------~gt~~~~~l~~~ 55 (153)
T TIGR00130 3 HEILVVGCGNILF----GDDGFGPAVIEYLKENGVEKP-----------------DNVCLID------AGTGAPHFVFTL 55 (153)
T ss_pred ceEEEEEeCcccc----ccCcHhHHHHHHHHHhCCCCC-----------------CCeEEEE------CCCcHHHHHHHH
Confidence 3578999999942 2335999999999863 2111 0121221 111111111111
Q ss_pred cCCCCCcEEEEecc--CCCCCceEEEec------CCC-CCCCCchhhHHHhhcCCCCcceEEE-cccCCCCCCCcccccc
Q 029652 96 YKLPLNRVLVFHDD--MGLPCGVLRLRH------NGG-HGGHNGLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLL 165 (190)
Q Consensus 96 ~~i~~~~ilVihDd--ldl~~G~vrlk~------gGs-~~GHNGLkSI~~~l~gt~df~RlrI-GIGrP~~~~~v~~yVL 165 (190)
..+...+.+||-|= .+.++|+++.-. ..+ +..+-|+..+++.+. .. .++.| ||= |.. -+..+|=
T Consensus 56 ~~~~~~d~vIivDA~~~~~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~-~~--~~~~iiGi~-p~~-~~~~~~~- 129 (153)
T TIGR00130 56 IPQSKWKKIIVVDIADFGAEPGTLRVLNVDELPNGRYMDAHGWSLAYPLHDLE-ER--IDIRVVGCQ-PKY-VSQPDVD- 129 (153)
T ss_pred hhhcCCCEEEEEEccCCCcCCCEEEEEchHHcCCCCCCCCccCCHHHHHHHhc-CC--CCEEEEEEE-EeE-ecCCCCC-
Confidence 12334567777785 578999998742 112 344459999998774 22 45554 553 321 1111222
Q ss_pred CCCCHHHHhh-HHHHHHHHHHh
Q 029652 166 QKFNAIARER-DISFDCIIVFY 186 (190)
Q Consensus 166 ~~f~~~E~~~-~~~~~~~~~~~ 186 (190)
-.+|++=++. +++.+.+....
T Consensus 130 ~~LS~~v~~a~~~~~~~i~~~l 151 (153)
T TIGR00130 130 IGLTEEVNKAIPRAVEIILKEL 151 (153)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 2667766666 77777776654
No 10
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=77.10 E-value=36 Score=27.18 Aligned_cols=130 Identities=15% Similarity=0.193 Sum_probs=71.8
Q ss_pred eEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCC
Q 029652 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (190)
Q Consensus 19 ~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i 98 (190)
.+|+|+|||-. .-==+|..++++|++.. . . .+.++.-.| .|.-+-..++.+
T Consensus 3 ~lVlGiGN~L~----gDDGvG~~v~~~L~~~~-~--~----------------~v~vid~gt----~~~~~~~~i~~~-- 53 (156)
T PRK11544 3 DVVLTVGNSMM----GDDGAGPLLAEKLAAAP-K--G----------------GWVVIDGGS----APENDIVAIREL-- 53 (156)
T ss_pred EEEEEeCcccc----ccCcHHHHHHHHHhccC-C--C----------------CeEEEECCC----CHHHHHHHHHhc--
Confidence 58999999953 23359999999997642 1 0 111222222 122221222211
Q ss_pred CCCcEEEEecc--CCCCCceEEEecCC------CCCCCC-chhhHHHhhcCCCCcceEEE-cccCCCCCCCccccccCCC
Q 029652 99 PLNRVLVFHDD--MGLPCGVLRLRHNG------GHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKF 168 (190)
Q Consensus 99 ~~~~ilVihDd--ldl~~G~vrlk~gG------s~~GHN-GLkSI~~~l~gt~df~RlrI-GIGrP~~~~~v~~yVL~~f 168 (190)
. .+.+||-|= .+.++|+++.-... +...|. ||..+++.+.+ +.+++.+ || .|. ++ +| =...
T Consensus 54 ~-~d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~~--~~p~v~iigI-~~~---~~-~~-g~~L 124 (156)
T PRK11544 54 R-PERLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKE--DVPEVIFLGI-QPD---IV-GF-YYPM 124 (156)
T ss_pred C-CCEEEEEECCccCcCCCEEEEEchhhcccccCCCCCcCCHHHHHHHHhc--CCCcEEEEEE-Eee---ec-cC-CCCC
Confidence 2 256666674 56799999873211 123444 88888888743 2345444 44 232 22 33 2466
Q ss_pred CHHHHhh-HHHHHHHHHHh
Q 029652 169 NAIARER-DISFDCIIVFY 186 (190)
Q Consensus 169 ~~~E~~~-~~~~~~~~~~~ 186 (190)
|++=++. +++.+.+..|-
T Consensus 125 S~~v~~av~~~~~~l~~~~ 143 (156)
T PRK11544 125 TQPVKDAVETVYQRLEGWE 143 (156)
T ss_pred CHHHHHHHHHHHHHHHHhh
Confidence 7766666 77777777664
No 11
>cd06070 H2MP_like-2 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=69.91 E-value=50 Score=25.65 Aligned_cols=125 Identities=15% Similarity=0.227 Sum_probs=69.4
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
||+|+|||-. .-==+|+.++++|++ .+ +-++.- |...-.++.++ .
T Consensus 1 lVlGiGN~l~----~DDg~G~~v~~~L~~-~~---------------------v~vi~~-------g~~~~~ll~~i--~ 45 (140)
T cd06070 1 LIIGVGNRLY----GDDGFGSCLAEALEQ-CG---------------------APVFDG-------GLDGFGLLSHL--E 45 (140)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHhh-CC---------------------CEEEEC-------CCcHHHHHHHH--c
Confidence 6899999942 233599999999976 11 111111 11222334333 2
Q ss_pred CCcEEEEeccCC--CCCceEEEecC---------CCCCCCC-chhhHHHhhcCCCCcceEE-EcccCCCCCCCccccccC
Q 029652 100 LNRVLVFHDDMG--LPCGVLRLRHN---------GGHGGHN-GLKSVMNNFRGNREFARLR-IGIGRPPGQMDPKAFLLQ 166 (190)
Q Consensus 100 ~~~ilVihDdld--l~~G~vrlk~g---------Gs~~GHN-GLkSI~~~l~gt~df~Rlr-IGIGrP~~~~~v~~yVL~ 166 (190)
..+.+||-|=++ .++|.++++.. .+...|+ |+..+.+.+.....-.++. +||= |. ++ +|- .
T Consensus 46 ~~d~viiVDA~~~~~~pG~~~~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~~~~~~~~ivgi~-~~---~~-~~g-~ 119 (140)
T cd06070 46 NYDIVIFIDVAVIDEDVGVFKITPEPASVAEQISFETDAHRLGPAHLLLLLKSSGRRPKAYIVGVK-PE---SI-EFA-R 119 (140)
T ss_pred CCCEEEEEEeecCCCCCeEEEEecCchhccccccCCCCCCcCCHHHHHHHHHHcCCCCeEEEEEEe-ee---ec-ccC-C
Confidence 456677777654 68998887543 2224666 9999876652100112332 2332 21 22 332 4
Q ss_pred CCCHHHHhh-HHHHHHHHHH
Q 029652 167 KFNAIARER-DISFDCIIVF 185 (190)
Q Consensus 167 ~f~~~E~~~-~~~~~~~~~~ 185 (190)
.+|++=++. +++++.+..|
T Consensus 120 ~LS~~v~~av~~~~~~i~~~ 139 (140)
T cd06070 120 GLSEAVIARAEKALEELKKL 139 (140)
T ss_pred CCCHHHHHHHHHHHHHHHHh
Confidence 677766666 7777777655
No 12
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=64.30 E-value=15 Score=31.80 Aligned_cols=70 Identities=23% Similarity=0.304 Sum_probs=42.4
Q ss_pred hccCchhHHHHHHhcCCCCC--c-EEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccC
Q 029652 82 MNLSGESTGPLAAYYKLPLN--R-VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGR 153 (190)
Q Consensus 82 MNlSG~aV~~~~~~~~i~~~--~-ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGr 153 (190)
=|..|+|+..+.+...-.++ + ++||.|= -|...--+..+.+.-=.+=||.+++.+....+.-=+.||||.
T Consensus 115 eniDGeAl~~a~~rL~~r~e~rkiLiViSDG--~P~d~st~~~n~~~~L~~HLr~vi~~ie~~~~Vel~aiGIg~ 187 (219)
T PF11775_consen 115 ENIDGEALRWAAERLLARPEQRKILIVISDG--APADDSTLSANDGDYLDAHLRQVIAEIETRSDVELIAIGIGH 187 (219)
T ss_pred cCCcHHHHHHHHHHHHcCCccceEEEEEeCC--CcCcccccccCChHHHHHHHHHHHHHHhccCCcEEEEEEcCC
Confidence 58999999877665543333 3 5677774 344332233333333234578888888323466679999986
No 13
>TIGR00142 hycI hydrogenase maturation protease HycI. Hydrogenase maturation protease is a protease that is involved in the C-terminal processing of HycE,the large subunit of hydrogenase 3 from E.Coli. This protein seems to be found in E.Coli and in Archaea.
Probab=59.85 E-value=82 Score=24.60 Aligned_cols=132 Identities=14% Similarity=0.177 Sum_probs=74.2
Q ss_pred eEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCC
Q 029652 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (190)
Q Consensus 19 ~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i 98 (190)
.+|+|+|||-.. -==+|..++++|++.+... .+.++.-.| .|.-.-.+++.++
T Consensus 1 ~lVlGiGN~l~~----DDG~G~~v~~~L~~~~~~~------------------~v~v~d~gt----~~~~~~~~~~~~~- 53 (146)
T TIGR00142 1 LVLLCVGNELMG----DDGAGPYLAEKCAAAPKEE------------------NWVVINAGT----VPENFTVAIRELR- 53 (146)
T ss_pred CEEEEeCccccc----cCcHHHHHHHHHHhccCCC------------------CEEEEECCC----ChHHHHHHHHhcC-
Confidence 379999999532 3359999999998653210 122222222 1221112222221
Q ss_pred CCCcEEEEeccC--CCCCceEEEecC-----CCCCCCC-chhhHHHhhcCCCCcceEEE-cccCCCCCCCccccccCCCC
Q 029652 99 PLNRVLVFHDDM--GLPCGVLRLRHN-----GGHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKFN 169 (190)
Q Consensus 99 ~~~~ilVihDdl--dl~~G~vrlk~g-----Gs~~GHN-GLkSI~~~l~gt~df~RlrI-GIGrP~~~~~v~~yVL~~f~ 169 (190)
.+.++|-|-+ +.++|+++.-.. .+..-|+ |+..+.+.+.+ .--.++.| ||- |. ++ +|- ...|
T Consensus 54 --~d~viivDA~~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~ll~~~~~-~~~~~~~ligi~-~~---~~-~~g-~~LS 124 (146)
T TIGR00142 54 --PTHILIVDATDMGLNPGEVRIIDDDIIEMYSMSTHNMPLSYLVDYLKE-DINGEIIFLGIQ-PD---IV-GFY-YPMS 124 (146)
T ss_pred --CCEEEEEECcccCCCCCeEEEEChhhccccccCcCcCCHHHHHHHHHh-cCCCeEEEEEEe-ee---ee-ecC-CCCC
Confidence 3566666765 569999887432 1223454 99999877732 21234554 552 32 33 444 4777
Q ss_pred HHHHhh-HHHHHHHHHHh
Q 029652 170 AIARER-DISFDCIIVFY 186 (190)
Q Consensus 170 ~~E~~~-~~~~~~~~~~~ 186 (190)
++=++. +++++.+..+.
T Consensus 125 ~~v~~a~~~~~~~i~~~i 142 (146)
T TIGR00142 125 QPVKDAVETLYQRLIGWE 142 (146)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 777666 88777777664
No 14
>cd06062 H2MP_MemB-H2up Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.
Probab=50.61 E-value=22 Score=27.78 Aligned_cols=130 Identities=17% Similarity=0.225 Sum_probs=70.6
Q ss_pred eEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCC
Q 029652 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (190)
Q Consensus 19 ~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i 98 (190)
.+|+|+|||-. .-==+|..+++.|++++..+. .+.++.- |...-.++..+.
T Consensus 1 ilV~GiGN~l~----gDDG~G~~va~~L~~~~~~~~-----------------~v~vi~~-------~~~~~~l~~~l~- 51 (146)
T cd06062 1 ILVLGIGNILL----ADEGIGVHAVERLEENYSFPE-----------------NVELIDG-------GTLGLELLPYIE- 51 (146)
T ss_pred CEEEEECcccc----ccCcHHHHHHHHHHHhcCCCC-----------------CeEEEEC-------CCCHHHHHHHHh-
Confidence 37999999952 233599999999988753321 0111111 111122333222
Q ss_pred CCCcEEEEeccC--CCCCceEEEecC---------CCCCCCCchhhHHHhhc--CCCCcceEEE-cccCCCCCCCccccc
Q 029652 99 PLNRVLVFHDDM--GLPCGVLRLRHN---------GGHGGHNGLKSVMNNFR--GNREFARLRI-GIGRPPGQMDPKAFL 164 (190)
Q Consensus 99 ~~~~ilVihDdl--dl~~G~vrlk~g---------Gs~~GHNGLkSI~~~l~--gt~df~RlrI-GIGrP~~~~~v~~yV 164 (190)
..+.+|+-|=+ +.++|+++.-.. ..+..+-++..+++.+. +. .-.++.| ||= |. ++ +|-
T Consensus 52 -~~d~viiVDA~~~g~~pG~i~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~~~-~~~~v~ivgie-~~---~~-~~g 124 (146)
T cd06062 52 -EADRLIIVDAVDAGGPPGTVYRFEGEDVPAFLSAKLSAHQVGLLEVLALAELLGD-LPPEIVLIGVQ-PE---SI-EWG 124 (146)
T ss_pred -cCCEEEEEEcccCCCCCCeEEEEechhccccccCCcCcccCCHHHHHHHHHHcCC-CCCeEEEEEEE-Ee---ec-cCC
Confidence 34777777864 679999876421 12445556777776542 11 1123433 442 21 22 222
Q ss_pred cCCCCHHHHhh-HHHHHHHHHH
Q 029652 165 LQKFNAIARER-DISFDCIIVF 185 (190)
Q Consensus 165 L~~f~~~E~~~-~~~~~~~~~~ 185 (190)
..+|++=++. +++++.+...
T Consensus 125 -~~LS~~v~~av~~~~~~i~~~ 145 (146)
T cd06062 125 -LELSPEVAAALPTAIEAVLAE 145 (146)
T ss_pred -CCCCHHHHHHHHHHHHHHHhh
Confidence 3677766666 7777776653
No 15
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=49.54 E-value=29 Score=34.18 Aligned_cols=69 Identities=22% Similarity=0.262 Sum_probs=43.7
Q ss_pred ccCchhHHHHHHhcCCCCCc---EEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCC-CcceEEEcccCC
Q 029652 83 NLSGESTGPLAAYYKLPLNR---VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNR-EFARLRIGIGRP 154 (190)
Q Consensus 83 NlSG~aV~~~~~~~~i~~~~---ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~-df~RlrIGIGrP 154 (190)
|..|+|+..+.....-.++. ++||.|=-=.+-.++ ....+.-=++=||.+|+.. .+. ..-=+.||||..
T Consensus 496 N~DGeAl~wa~~rL~~R~e~rKiL~ViSDG~P~D~~Tl--svN~~~~l~~hLr~vi~~~-e~~~~vel~aigIg~D 568 (600)
T TIGR01651 496 NIDGEALMWAHQRLIARPEQRRILMMISDGAPVDDSTL--SVNPGNYLERHLRAVIEEI-ETRSPVELLAIGIGHD 568 (600)
T ss_pred CCchHHHHHHHHHHhcCcccceEEEEEeCCCcCCcccc--ccCchhHHHHHHHHHHHHH-hccCCceEEEeecccc
Confidence 88899998877655444433 678888543332332 2222223345599999998 453 566699999974
No 16
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=47.82 E-value=29 Score=27.86 Aligned_cols=133 Identities=17% Similarity=0.226 Sum_probs=69.6
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcC
Q 029652 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 97 (190)
Q Consensus 18 ~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~ 97 (190)
+.+|+|+|||-. +-==+|..++++|++.+..+. .+.++.- |...-.++.++.
T Consensus 2 ~ilVlGiGN~l~----gDDGvG~~va~~L~~~~~~~~-----------------~v~vid~-------gt~~~~ll~~l~ 53 (164)
T PRK10466 2 RILVLGVGNILL----TDEAIGVRIVEALEQRYILPD-----------------YVEILDG-------GTAGMELLGDMA 53 (164)
T ss_pred ceEEEEECchhh----ccCcHHHHHHHHHHHhcCCCC-----------------CeEEEec-------cccHHHHHHHHh
Confidence 468999999942 334599999999987653211 1111111 111223333332
Q ss_pred CCCCcEEEEeccCC--CC-CceEEEecC--------CCCCCC-CchhhHHHhhcCCCCcc-eEEE-cccCCCCCCCcccc
Q 029652 98 LPLNRVLVFHDDMG--LP-CGVLRLRHN--------GGHGGH-NGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAF 163 (190)
Q Consensus 98 i~~~~ilVihDdld--l~-~G~vrlk~g--------Gs~~GH-NGLkSI~~~l~gt~df~-RlrI-GIGrP~~~~~v~~y 163 (190)
..+.+||-|=++ .+ +|+++.-.. .+...| -|+..+.+.+.-..+.+ ++.+ ||- |. ++ +|
T Consensus 54 --~~d~vIiVDA~~~g~~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~L~~~~~~g~~p~~v~lvgie-p~---~~-~~ 126 (164)
T PRK10466 54 --NRDHLIIADAIVSKKNAPGTIMVLRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVI-PE---SL-EP 126 (164)
T ss_pred --CCCEEEEEEecCCCCCCCCEEEEEchhhccccccCCCCcccCCHHHHHHHHHHcCCCCCeEEEEEEE-Ee---ec-cC
Confidence 346677778664 34 999876321 112234 45666665432111233 4444 764 32 11 33
Q ss_pred ccCCCCHHHHhh-HHHHHHHHHHh
Q 029652 164 LLQKFNAIARER-DISFDCIIVFY 186 (190)
Q Consensus 164 VL~~f~~~E~~~-~~~~~~~~~~~ 186 (190)
= ..+|++=++. +.+++.+..+.
T Consensus 127 g-~~LS~~V~~av~~~~~~i~~~l 149 (164)
T PRK10466 127 H-IGLTPTVEAMIEPALEQVLAAL 149 (164)
T ss_pred C-CCCCHHHHHHHHHHHHHHHHHH
Confidence 2 3666666666 77666665543
No 17
>PRK09256 hypothetical protein; Provisional
Probab=46.70 E-value=10 Score=30.28 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=20.9
Q ss_pred EEeccCCCCCceEEEe--cCCCCCCCCc
Q 029652 105 VFHDDMGLPCGVLRLR--HNGGHGGHNG 130 (190)
Q Consensus 105 VihDdldl~~G~vrlk--~gGs~~GHNG 130 (190)
-|.+++++|...++++ +++|.||+|=
T Consensus 3 ~~~~~~~i~~~~l~~~~~RSSGPGGQ~V 30 (138)
T PRK09256 3 RITRRLVIPENELEWRFIRASGPGGQNV 30 (138)
T ss_pred ccCccCccCHHHeEEEEEEcCCCCcccc
Confidence 3678899998888776 6889999873
No 18
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=45.94 E-value=13 Score=27.19 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=19.5
Q ss_pred cCcCc--chHHHHHHHHHHHHcCCCCC
Q 029652 31 YKGTR--HNVGFEMIDAFAESQGISMN 55 (190)
Q Consensus 31 Y~~TR--HNvGf~~ld~la~~~~~~~~ 55 (190)
|.-.. --+||..+|.+|.++|++..
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 66666 68999999999999998754
No 19
>cd06064 H2MP_F420-Reduc Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to the gene cluster of 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum delta H. FrhD subunit is putatively involved in the processing of the coenzyme F420 hydrogenase-processing. It is similar to those frhD genes found in Methanomicrobia and Methanobacteria. It is different from the FrhD conserved domain found in methyl viologen-reducing hydrogenase and F420-non-reducing hydrogenase iron-sulfur subunit D.
Probab=43.48 E-value=24 Score=27.80 Aligned_cols=132 Identities=14% Similarity=0.200 Sum_probs=70.2
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhH-HHHHHhcC-
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGEST-GPLAAYYK- 97 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV-~~~~~~~~- 97 (190)
||+|+|||-. .-==+|+.++++|+++...+ ..+.++. .|... ..+..+..
T Consensus 1 lViGiGN~l~----gDDgvG~~va~~l~~~~~~~-----------------~~v~vid-------~g~~~~~~~~~~~~~ 52 (150)
T cd06064 1 LVVGCGNILF----GDDGFGPAVIEELEKLELLP-----------------DNVQVID-------AGTGAPHLLFTLLDE 52 (150)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhccCCC-----------------CCEEEEE-------CCCcHHHHHHHHHhc
Confidence 6899999952 33459999999998754211 0122222 22211 11111111
Q ss_pred CCCCcEEEEeccC--CCCCceEEEecC------C---CCCCCCchhhHHHhhcCCCCc-ceEEE-cccCCCCCCCccccc
Q 029652 98 LPLNRVLVFHDDM--GLPCGVLRLRHN------G---GHGGHNGLKSVMNNFRGNREF-ARLRI-GIGRPPGQMDPKAFL 164 (190)
Q Consensus 98 i~~~~ilVihDdl--dl~~G~vrlk~g------G---s~~GHNGLkSI~~~l~gt~df-~RlrI-GIGrP~~~~~v~~yV 164 (190)
....+.+||-|=+ +.++|+++.... . .+-.+-|+..+++.+.+ .. .++.+ ||- |. .-+..+|=
T Consensus 53 ~~~~d~viivDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~--~~~~~~~iigi~-p~-~~~~~~~~ 128 (150)
T cd06064 53 ESKPKKIIIVDAIDFGLEPGTLKKISVDELPPGKYYDFDAHSWPLADPLHELKD--KYGIEIVVIGCQ-PK-RVPEPDVE 128 (150)
T ss_pred cCCCCEEEEEEecCCCCCCCeEEEEehhhcccccCCCcCCCcCCHHHHHHHHHh--cCCCeEEEEEEE-Ee-eecCCCCC
Confidence 1225677777875 779999887432 1 24466799999987742 22 23333 442 32 11100222
Q ss_pred cCCCCHHHHhh-HHHHHHHHH
Q 029652 165 LQKFNAIARER-DISFDCIIV 184 (190)
Q Consensus 165 L~~f~~~E~~~-~~~~~~~~~ 184 (190)
..+|++=++. +.+.+.+..
T Consensus 129 -~~LS~~v~~a~~~~~~~i~~ 148 (150)
T cd06064 129 -PGLSEEVEKAVPKAVEIILE 148 (150)
T ss_pred -CCCCHHHHHHHHHHHHHHHH
Confidence 3566665555 666655543
No 20
>TIGR00072 hydrog_prot hydrogenase maturation protease. HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase.
Probab=43.29 E-value=25 Score=27.43 Aligned_cols=130 Identities=18% Similarity=0.199 Sum_probs=70.7
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
||+|+|||-. .-==+|..++++|++++..+. .+-++.-.| .|. .++.+..
T Consensus 1 lViGiGN~l~----~DDg~G~~v~~~L~~~~~~~~-----------------~v~~id~g~----~~~---~l~~~l~-- 50 (145)
T TIGR00072 1 LVLGIGNILR----GDDGFGPRVAERLEERYEFPP-----------------GVEVLDGGT----LGL---ELLDAIE-- 50 (145)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHHHhcCCCC-----------------CeEEEECCC----CHH---HHHHHHh--
Confidence 5899999942 233599999999998653210 111111111 122 2333332
Q ss_pred CCcEEEEeccC--CCCCceEEEec--------CCCCCCC-CchhhHHHhhcCCCCcc-eEEE-cccCCCCCCCccccccC
Q 029652 100 LNRVLVFHDDM--GLPCGVLRLRH--------NGGHGGH-NGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAFLLQ 166 (190)
Q Consensus 100 ~~~ilVihDdl--dl~~G~vrlk~--------gGs~~GH-NGLkSI~~~l~gt~df~-RlrI-GIGrP~~~~~v~~yVL~ 166 (190)
..+.+||-|=. +.++|+++.-. ..+...| -|+..+++.+.-..+.+ ++.+ ||= |. ++ +|- .
T Consensus 51 ~~d~viiVDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~g~~p~~~~lvgi~-~~---~~-~~g-~ 124 (145)
T TIGR00072 51 GADRVIVVDAVDSGAEPGTVRRLPGEDLPAFLGGKLSTHQLGLSEVLALLELLGALPPEVVLLGIQ-PE---SL-EFG-L 124 (145)
T ss_pred CCCEEEEEEccCCCcCCceEEEEchhhccccccCCCCcCcCCHHHHHHHHHHcCCCCCeEEEEEEE-ee---ec-ccC-C
Confidence 24567777865 55999988632 1232344 48888887663112333 4443 552 21 22 322 4
Q ss_pred CCCHHHHhh-HHHHHHHHHH
Q 029652 167 KFNAIARER-DISFDCIIVF 185 (190)
Q Consensus 167 ~f~~~E~~~-~~~~~~~~~~ 185 (190)
.+|++=++. +++.+.+..+
T Consensus 125 ~LS~~v~~~~~~~~~~i~~~ 144 (145)
T TIGR00072 125 GLSPEVAAAVPAAVELILAE 144 (145)
T ss_pred CCCHHHHHHHHHHHHHHHhh
Confidence 667766666 7777776654
No 21
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=40.63 E-value=43 Score=28.03 Aligned_cols=129 Identities=20% Similarity=0.276 Sum_probs=67.3
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcC
Q 029652 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 97 (190)
Q Consensus 18 ~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~ 97 (190)
+.+|+|+|||=- .-==+|..++++|++++..+. .+.++.-.| .|. .++.+..
T Consensus 5 rilVlGiGN~L~----gDDGvG~~va~~L~~~~~~~~-----------------~V~vid~Gt----~g~---~ll~~i~ 56 (195)
T PRK10264 5 RVVVMGLGNLLW----ADEGFGVRVAERLYAHYHWPE-----------------YVEIVDGGT----QGL---NLLGYVE 56 (195)
T ss_pred CEEEEEeCcccc----ccCcHHHHHHHHHHhhcCCCC-----------------CeEEEECCC----CHH---HHHHHHc
Confidence 478999999931 233599999999987653221 121221111 111 3333332
Q ss_pred CCCCcEEEEeccC--CCCCceEEEecCC---------C-CCCCCchhhHHHh--hcCCCCcc-eEE-EcccCCCCCCCcc
Q 029652 98 LPLNRVLVFHDDM--GLPCGVLRLRHNG---------G-HGGHNGLKSVMNN--FRGNREFA-RLR-IGIGRPPGQMDPK 161 (190)
Q Consensus 98 i~~~~ilVihDdl--dl~~G~vrlk~gG---------s-~~GHNGLkSI~~~--l~gt~df~-Rlr-IGIGrP~~~~~v~ 161 (190)
..+.+||-|=+ +.++|+++.-... + +-.+-|+..+.+. +.+ +.+ ++. |||= |. ++.
T Consensus 57 --~~d~vIiVDAv~~g~~PGtv~~~~~~~~~~~~~~~~~S~H~~~l~~~L~l~~l~g--~~P~~v~iiGie-p~---~~~ 128 (195)
T PRK10264 57 --SASHLLILDAIDYGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSEVLALADIRG--HLPAHIALVGLQ-PA---MLD 128 (195)
T ss_pred --CCCEEEEEECCccCCCCCeEEEEehhhcccccccCCcCcccCCHHHHHHHHHHcC--CCCCeEEEEEEE-Ee---Eec
Confidence 34667777854 5589998874321 1 2234688888753 322 233 555 4763 32 111
Q ss_pred ccccCCCCHHHHhh-HHHHHHHH
Q 029652 162 AFLLQKFNAIARER-DISFDCII 183 (190)
Q Consensus 162 ~yVL~~f~~~E~~~-~~~~~~~~ 183 (190)
+| =-.+|++=++. +++++.+.
T Consensus 129 ~~-g~~LSp~V~~av~~~v~~i~ 150 (195)
T PRK10264 129 DY-GGSLSELAREQLPAAEQAAL 150 (195)
T ss_pred CC-CCCCCHHHHHHHHHHHHHHH
Confidence 11 13555555554 55544443
No 22
>PRK02858 germination protease; Provisional
Probab=38.42 E-value=24 Score=32.75 Aligned_cols=134 Identities=19% Similarity=0.308 Sum_probs=68.0
Q ss_pred CCCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECC-eeEEEEeCCchhccC----chhHH
Q 029652 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKPQTYMNLS----GESTG 90 (190)
Q Consensus 16 ~~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~-~~v~L~kP~TyMNlS----G~aV~ 90 (190)
....|||||||- .-|--..|-.+++.|.-...+ ..++.+..-.+ ..|.-+-| --|=.. ++.|+
T Consensus 110 ~~~vLVVGLGN~----~VTPDALGP~vv~~l~VTRHL-------~~~~p~~~~~g~r~VsAiaP-GVmg~TGiET~EIIk 177 (369)
T PRK02858 110 EASCLIVGLGNW----NVTPDALGPLVVENVLVTRHL-------FQLQPESVEEGFRPVSAIAP-GVMGITGIETSDIIY 177 (369)
T ss_pred CCcEEEEeCCCc----CCCccccChheecceeeehhh-------hhhcchhhccCCceeeEEcC-CcccccchhHHHHHH
Confidence 356899999996 469999999999866421111 00000000011 23444445 334444 44556
Q ss_pred HHHHhcCCCCCcEEEEeccCCCC-----CceEEEecCC-----CCCCCCchhhHH-HhhcCCCCcceEEEcccCCCC-C-
Q 029652 91 PLAAYYKLPLNRVLVFHDDMGLP-----CGVLRLRHNG-----GHGGHNGLKSVM-NNFRGNREFARLRIGIGRPPG-Q- 157 (190)
Q Consensus 91 ~~~~~~~i~~~~ilVihDdldl~-----~G~vrlk~gG-----s~~GHNGLkSI~-~~l~gt~df~RlrIGIGrP~~-~- 157 (190)
.+.+..| .+++|.-|-|--- -=+|+|---| |-|-|. +.|. +.| | .+=+.||| |-- .
T Consensus 178 gIVek~K---PD~VIaIDALAaRs~~Rln~TIQIsDTGI~PGSGVGN~R--~~l~~etL-G---VPVIAIGV--PTVVdA 246 (369)
T PRK02858 178 GIIEKTK---PDFVIAIDALAARSIERVNTTIQISDTGIHPGSGVGNKR--KELSKETL-G---IPVIAIGV--PTVVDA 246 (369)
T ss_pred HHHHhhC---CCEEEEechhhcCchhhccCeEEecCCCcCCCCCcCccc--cccCHHHc-C---CCEEEEcC--Ceeech
Confidence 6665443 3667777865321 2245555444 233332 2333 334 2 45566666 521 0
Q ss_pred ----CCccccccCCCCHHH
Q 029652 158 ----MDPKAFLLQKFNAIA 172 (190)
Q Consensus 158 ----~~v~~yVL~~f~~~E 172 (190)
.|..+|+|..|..++
T Consensus 247 ~tI~~Dtid~~l~~~~~~~ 265 (369)
T PRK02858 247 VTITSDTIDFILKHFGREM 265 (369)
T ss_pred HHHHHHHHHHHHHHHhhhh
Confidence 244577777665443
No 23
>PRK12362 germination protease; Provisional
Probab=38.18 E-value=41 Score=30.66 Aligned_cols=118 Identities=19% Similarity=0.267 Sum_probs=67.9
Q ss_pred CCCCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECC-eeEEEEeC----CchhccCchhH
Q 029652 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKP----QTYMNLSGEST 89 (190)
Q Consensus 15 ~~~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~-~~v~L~kP----~TyMNlSG~aV 89 (190)
.....|||||||.. -|--..|-.+++.|.-.... ...+++..-.+ ..|.-+-| +|=||.+ +.+
T Consensus 97 ~~~~iLVvGLGN~~----vTpDaLGP~Vv~~l~vTrhl-------~~~~~~~~~~~~~pV~AiaPGVmg~TGiet~-Eii 164 (318)
T PRK12362 97 KEMTVLVVGLGNWN----VTPDALGPKVVSKLMVTRHL-------KEYAPEEIDEGIRPVCAIAPGVLGITGIETA-EII 164 (318)
T ss_pred CCCcEEEEEcCCCC----cCccccchhhhhhhhhhhhh-------hhhcCchhcCCCCcceEecCCcccccchhHH-HHH
Confidence 44678999999974 69999999999988653211 01111111111 23444444 4556643 445
Q ss_pred HHHHHhcCCCCCcEEEEeccCC----CCCc-eEEEecCC---CCCCCCchhhHH-HhhcCCCCcceEEEcc
Q 029652 90 GPLAAYYKLPLNRVLVFHDDMG----LPCG-VLRLRHNG---GHGGHNGLKSVM-NNFRGNREFARLRIGI 151 (190)
Q Consensus 90 ~~~~~~~~i~~~~ilVihDdld----l~~G-~vrlk~gG---s~~GHNGLkSI~-~~l~gt~df~RlrIGI 151 (190)
+.+.+.++ .+++|.-|-+- --+| +|++...| |+|=.|==+.|. +.| | .+=+.|||
T Consensus 165 ~gIv~k~k---pd~IIAIDALaar~~~Rl~~tIQisdtGI~PGSGVGN~R~~l~~etL-G---VPVIAIGV 228 (318)
T PRK12362 165 KGVVEKIK---PDLVIAIDALAARSVERVNTTIQISDTGISPGSGVGNKRMGINEETL-G---VPVIAIGV 228 (318)
T ss_pred HHHHHhcC---CCEEEEEeccccCCHHHccCeEEECCCCCCCCccCCCcccccCHHHc-C---CCEEEEcC
Confidence 56666554 46777778775 2467 88888766 333333333343 334 2 45566666
No 24
>TIGR01441 GPR GPR endopeptidase. This model describes a tetrameric protease that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs.
Probab=38.01 E-value=24 Score=32.60 Aligned_cols=133 Identities=19% Similarity=0.339 Sum_probs=68.1
Q ss_pred CCCeEEEEecCCCCCcCcCcchHHHHHHHHHHH-HcCCCCCccccceEEEEEEECCeeEEEEeCCchhccC----chhHH
Q 029652 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAE-SQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLS----GESTG 90 (190)
Q Consensus 16 ~~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~-~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlS----G~aV~ 90 (190)
....|||||||- .-|--..|-.+++.|.- ++=......+. .+ +-..|.-+-| --|=.. ++.|+
T Consensus 100 ~~~iLVVGLGN~----~VTPDALGP~vv~~l~VTRHL~~~~p~~~----~~---g~r~VsaiaP-GVmg~TGiET~EIIk 167 (358)
T TIGR01441 100 DMTCLVVGLGNW----NVTPDALGPKVVENLLVTRHLFKLIPESV----DE---GIRPVSAVAP-GVMGITGIETSDIIR 167 (358)
T ss_pred CCcEEEEeCCCc----CCCccccChheecceeeehhhhhhcchhh----cc---CCceeeEEcC-CccccccccHHHHHH
Confidence 356899999996 36999999999987642 11111100000 00 1123444555 334444 45566
Q ss_pred HHHHhcCCCCCcEEEEeccCCCC-----CceEEEecCC-----CCCCCCchhhHH-HhhcCCCCcceEEEcccCCCC-C-
Q 029652 91 PLAAYYKLPLNRVLVFHDDMGLP-----CGVLRLRHNG-----GHGGHNGLKSVM-NNFRGNREFARLRIGIGRPPG-Q- 157 (190)
Q Consensus 91 ~~~~~~~i~~~~ilVihDdldl~-----~G~vrlk~gG-----s~~GHNGLkSI~-~~l~gt~df~RlrIGIGrP~~-~- 157 (190)
.+.+..| .+++|.-|-|--- -=+|+|---| |-|-|. +.|. +.| | .+=+.||| |-- .
T Consensus 168 giVek~k---PD~VIaIDALAaRs~~Rln~TIQIsDTGI~PGSGVGN~R--~~l~~etL-G---VPVIAIGV--PTVVdA 236 (358)
T TIGR01441 168 GIIEQIK---PDFVIAIDALAARKMERVNSTIQISDTGIHPGSGVGNKR--KELSKKTL-G---VPVIAVGV--PTVVDA 236 (358)
T ss_pred HHHHhhC---CCEEEEechhhcCchhhccCeEEecCCCcCCCCCcCccc--cccCHHHc-C---CCEEEEcC--Ceeech
Confidence 6665443 3667777765321 2345555444 223332 2333 334 2 45566666 531 0
Q ss_pred ----CCccccccCCCCHH
Q 029652 158 ----MDPKAFLLQKFNAI 171 (190)
Q Consensus 158 ----~~v~~yVL~~f~~~ 171 (190)
.|..+|+|..|..+
T Consensus 237 ~tI~~Dtid~~l~~~~~~ 254 (358)
T TIGR01441 237 VTIASDTIDYVLKHFGRE 254 (358)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 24457777766444
No 25
>PF03418 Peptidase_A25: Germination protease This family belongs to family A25 of the peptidase classification.; InterPro: IPR005080 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date []. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family A25 (gpr protease family, clan AE). These are tetrameric proteases that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species during spore germination. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0009847 spore germination; PDB: 1C8B_A.
Probab=36.91 E-value=31 Score=31.83 Aligned_cols=93 Identities=18% Similarity=0.232 Sum_probs=40.6
Q ss_pred CCCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECC-eeEEEEeCCchhccCc----hhHH
Q 029652 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKPQTYMNLSG----ESTG 90 (190)
Q Consensus 16 ~~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~-~~v~L~kP~TyMNlSG----~aV~ 90 (190)
....|||||||.. -|--..|-.++|.+.-...+ ..+..+....+ ..|.-+-| --|=..| +.|+
T Consensus 95 ~~~iLVVGLGN~~----vTPDALGP~vv~~l~VTRHL-------~~~~pe~~~~g~r~VsaiaP-GVmg~TGiET~eIi~ 162 (354)
T PF03418_consen 95 EASILVVGLGNWN----VTPDALGPRVVENLLVTRHL-------FELQPEEVDEGYRPVSAIAP-GVMGQTGIETAEIIK 162 (354)
T ss_dssp T--EEEEE-S-SS----SGGG-HHHHHHHT----HHH-------HHHS--SS-SS---EEEE-S-GGG---SS-HHHHHH
T ss_pred CCeEEEEeCCCcC----CCccccchhhhhhhhhhhhh-------hhhCchhhccCcceeeEEcC-CccccccccHHHHHH
Confidence 4568999999974 69999999999966421111 00000000111 24555555 3454444 4455
Q ss_pred HHHHhcCCCCCcEEEEeccCCC-----CCceEEEecCC
Q 029652 91 PLAAYYKLPLNRVLVFHDDMGL-----PCGVLRLRHNG 123 (190)
Q Consensus 91 ~~~~~~~i~~~~ilVihDdldl-----~~G~vrlk~gG 123 (190)
.+.+..+ .+++|.-|-|-- =--+|++---|
T Consensus 163 gvv~~~k---Pd~VIaIDALAaRs~~Rl~~TIQisDTG 197 (354)
T PF03418_consen 163 GVVEKIK---PDLVIAIDALAARSLERLNTTIQISDTG 197 (354)
T ss_dssp HHHHHH-----SEEEEEEEE--SSGGGSSSEEEEETT-
T ss_pred HHHHhhC---CCEEEEehhhhcCchhhccCeEEecCCC
Confidence 5665544 366777776532 23456666544
No 26
>cd06067 H2MP_MemB-H2evol Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases. Such hydrogenases as those from Methanosarcina barkeri (EchCE) and Rhodospirillum rubrum (CooLH) also belong to this group of membrane-bound hydrogen evolving hydrogenase. Sequence comparison of the large subunits from related hydrogenase indicates that in contrast to EchE (358 amino acids) and CooH (361 amino acids), the large subunit HycE (569 amino acids) contains an extra carboxy-terminal stretch of 32 amino acids that is cleaved during the maturation process. In
Probab=33.11 E-value=43 Score=25.88 Aligned_cols=90 Identities=17% Similarity=0.180 Sum_probs=50.5
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
+|+|+|||-. .-==+|..++++|+++. . . .+-++.-.| .|.-+ +......
T Consensus 1 ~VlGiGN~L~----~DDgvG~~v~~~L~~~~-~--~----------------~v~vid~gt----~~~~~---~~~l~~~ 50 (136)
T cd06067 1 VLLGVGNELR----GDDGAGPLLAEKLEDLP-N--P----------------NWLVIDGGT----VPENF---TGKIREE 50 (136)
T ss_pred CEEEeCcccc----ccCcHHHHHHHHHHhcC-C--C----------------CEEEEECCC----CHHHH---HHHHHhc
Confidence 5899999952 23459999999998753 1 0 111122111 22221 1111111
Q ss_pred CCcEEEEeccC--CCCCceEEEecCC------CCCCCCchhhHHHhhc
Q 029652 100 LNRVLVFHDDM--GLPCGVLRLRHNG------GHGGHNGLKSVMNNFR 139 (190)
Q Consensus 100 ~~~ilVihDdl--dl~~G~vrlk~gG------s~~GHNGLkSI~~~l~ 139 (190)
..+.+||-|=+ +.++|+++.-... .+..+-|+..+.+.++
T Consensus 51 ~~d~vIiVDAv~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~~L~~~~ 98 (136)
T cd06067 51 KPDLIVIVDAADMGLEPGEIRIIDPEEIAEYFFSTHTLPLSILIDYLR 98 (136)
T ss_pred CCCEEEEEECCccCcCCCEEEEEchhhcccccCCCCcCCHHHHHHHHH
Confidence 34567777876 4599999874321 2334448888887763
No 27
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=32.85 E-value=53 Score=31.88 Aligned_cols=72 Identities=18% Similarity=0.199 Sum_probs=47.7
Q ss_pred hccCchhHHHHHHhcCCCCCc---EEEEeccCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCC
Q 029652 82 MNLSGESTGPLAAYYKLPLNR---VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPP 155 (190)
Q Consensus 82 MNlSG~aV~~~~~~~~i~~~~---ilVihDdldl~~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~ 155 (190)
=|..|+++-++...+--.|++ ++||.|-.-..--++.+.. |+.=|.=||-+|+.+-+..+.--+.||||+..
T Consensus 516 eNiDGEal~wah~rl~gRpEqrkIlmmiSDGAPvddstlsvnp--GnylerHLRaVieeIEtrSpveLlAIGighDv 590 (620)
T COG4547 516 ENIDGEALMWAHQRLIGRPEQRKILMMISDGAPVDDSTLSVNP--GNYLERHLRAVIEEIETRSPVELLAIGIGHDV 590 (620)
T ss_pred ccCChHHHHHHHHHHhcChhhceEEEEecCCCcccccccccCC--chHHHHHHHHHHHHHhcCCchhheeeeccccc
Confidence 389999997766544333443 6788886544444444443 44456668999998843356667999999843
No 28
>cd00518 H2MP Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.
Probab=32.79 E-value=47 Score=25.57 Aligned_cols=89 Identities=19% Similarity=0.182 Sum_probs=52.0
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
+|+|+|||=. .-==+|..++++|+++... ..+-++.-.| ..-.++....
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~~~------------------~~v~~id~gt-------~~~~l~~~l~-- 49 (139)
T cd00518 1 LVLGIGNPLR----GDDGFGPAVAERLEERYLP------------------PGVEVIDGGT-------LGLELLDLLE-- 49 (139)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcCCC------------------CCeEEEECCC-------CHHHHHHHHh--
Confidence 5899999942 2345999999999886420 0122222111 1112333222
Q ss_pred CCcEEEEeccCC--CCCceEEEec------CCC-CCCCC-chhhHHHhhc
Q 029652 100 LNRVLVFHDDMG--LPCGVLRLRH------NGG-HGGHN-GLKSVMNNFR 139 (190)
Q Consensus 100 ~~~ilVihDdld--l~~G~vrlk~------gGs-~~GHN-GLkSI~~~l~ 139 (190)
..+.+||.|=++ .++|+++.-. ... ...|. |+..+++.+.
T Consensus 50 ~~d~viiVDA~~~~~~pG~i~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~ 99 (139)
T cd00518 50 GADRVIIVDAVDSGGEPGTVRRLEPEELPAYLSALSTHQLGLAELLALLR 99 (139)
T ss_pred cCCeEEEEECccCCCCCCeEEEEchhhcccccCCCCCccCCHHHHHHHHH
Confidence 256777778765 6999988732 111 13455 9999988773
No 29
>cd06068 H2MP_like-1 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=32.67 E-value=40 Score=26.26 Aligned_cols=128 Identities=20% Similarity=0.141 Sum_probs=68.1
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHH-HhcCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLA-AYYKL 98 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~-~~~~i 98 (190)
||+|+|||-.. -==+|..++++|+++.. + ..+.++-..|- | -.++ ....
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~~~-~-----------------~~v~~~d~g~~----~---~~l~~~~~~- 50 (144)
T cd06068 1 LVAGVGNIFLG----DDGFGVEVARRLRPRQL-P-----------------PGVRVADFGIR----G---IHLAYELLD- 50 (144)
T ss_pred CEEEECccccc----cCcHHHHHHHHHhccCC-C-----------------CCeEEEECCCC----H---HHHHHHHHh-
Confidence 68999999532 23499999999986521 0 01222222111 1 1222 1222
Q ss_pred CCCcEEEEeccC--CCCCceEEEecC------C-CCCCCC-chhhHHHhhc--CCCCcceEEE-cccCCCCCCCcccccc
Q 029652 99 PLNRVLVFHDDM--GLPCGVLRLRHN------G-GHGGHN-GLKSVMNNFR--GNREFARLRI-GIGRPPGQMDPKAFLL 165 (190)
Q Consensus 99 ~~~~ilVihDdl--dl~~G~vrlk~g------G-s~~GHN-GLkSI~~~l~--gt~df~RlrI-GIGrP~~~~~v~~yVL 165 (190)
..+.+||-|=. +.++|+++.... . +..-|. |+..+.+.+. +. .-.++.| ||= |. ++ +| =
T Consensus 51 -~~d~viiVDA~~~g~~PG~v~~~~~~~~~~~~~~~s~H~~~~~~~l~~~~~l~~-~~~~~~lvgi~-~~---~~-~~-g 122 (144)
T cd06068 51 -GYDTLILVDAVPRGGEPGTLYVIELEDVDAAPELLDAHGMNPDAVLALLRALGG-TPPRVVVVGCE-PA---DV-DE-G 122 (144)
T ss_pred -cCCEEEEEEeccCCcCCCEEEEEechhcccccCCCCCCCCCHHHHHHHHHHhCC-CCCeEEEEEEE-ec---cc-CC-C
Confidence 24556666754 569999887321 1 223444 7877754431 11 1234444 553 32 22 34 2
Q ss_pred CCCCHHHHhh-HHHHHHHHHH
Q 029652 166 QKFNAIARER-DISFDCIIVF 185 (190)
Q Consensus 166 ~~f~~~E~~~-~~~~~~~~~~ 185 (190)
...|++=++. +++.+.+..|
T Consensus 123 ~~LS~~v~~a~~~~~~~i~~~ 143 (144)
T cd06068 123 IGLSEPVAAAVPEAVRLVRDV 143 (144)
T ss_pred CCcCHHHHHHHHHHHHHHHHh
Confidence 4667766666 7777777766
No 30
>cd06066 H2MP_NAD-link-bidir Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the NiFe-hydrogenase.
Probab=31.04 E-value=54 Score=25.44 Aligned_cols=126 Identities=13% Similarity=0.138 Sum_probs=66.2
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
||+|+|||=. .-==+|..++++|++++ .+ .+.++.-.| .|. .++... .
T Consensus 1 lVlGvGN~l~----~DDGvG~~v~~~L~~~~-~~------------------~v~~id~g~----~g~---~l~~~l--~ 48 (139)
T cd06066 1 LVIGYGNPLR----GDDGLGPAVAERIEEWL-LP------------------GVEVLAVHQ----LTP---ELAEDL--A 48 (139)
T ss_pred CEEEeCCccc----cccchhHHHHHHHHhhC-CC------------------CeEEEEcCC----CCH---HHHHHh--c
Confidence 5899999942 33359999999998874 10 122222222 121 122222 2
Q ss_pred CCcEEEEeccCCCC-CceEEEec--CC---CCCCCC-chhhHHH---hhcCCCCcce-EEEcccCCCCCCCccccccCCC
Q 029652 100 LNRVLVFHDDMGLP-CGVLRLRH--NG---GHGGHN-GLKSVMN---NFRGNREFAR-LRIGIGRPPGQMDPKAFLLQKF 168 (190)
Q Consensus 100 ~~~ilVihDdldl~-~G~vrlk~--gG---s~~GHN-GLkSI~~---~l~gt~df~R-lrIGIGrP~~~~~v~~yVL~~f 168 (190)
..+.+||-|=++.. +|.+++.. .. +...|+ |+.++.. .+++. -.+ +=+||- |. .. +| -..+
T Consensus 49 ~~d~vIivDA~~~~~~g~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~l~~~--~~~~~i~gi~-~~-~~---~~-g~~L 120 (139)
T cd06066 49 GADRVIFIDASLGGSPAPFRIVRLEPRRDSSFTSHALSPAALLALAQALYGH--APPAWLLTIP-GY-NF---EL-GEPL 120 (139)
T ss_pred CCCEEEEEEccCCCCCCceEEEEecCCCCCCcCCCCCCHHHHHHHHHHhcCC--CCCEEEEEee-cc-cC---cc-CCCC
Confidence 34667777765554 88777751 11 112355 7666654 34321 122 344552 32 11 22 2566
Q ss_pred CHHHHhh-HHHHHHHHHH
Q 029652 169 NAIARER-DISFDCIIVF 185 (190)
Q Consensus 169 ~~~E~~~-~~~~~~~~~~ 185 (190)
|++=++. +.+++.+..|
T Consensus 121 S~~v~~av~~~~~~i~~~ 138 (139)
T cd06066 121 SPAAEAALAAALELLRKL 138 (139)
T ss_pred CHHHHHHHHHHHHHHHHh
Confidence 7666666 7777777665
No 31
>cd06063 H2MP_Cyano-H2up This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial hydrogenase and are involved in the C-terminal cleavage of the hydrogenase large subunit precursor protein. Cyanobacterial nickel-iron (NiFe)-hydrogenases are found exclusively in the N2-fixing strains and are encoded by hup (hydrogen uptake) genes. These uptake hydrogenases are heterodimers with a large (hupL) and small subunit (hupS) and catalyze the consumption of the H2 produced during N2 fixation. Sequence similarity shows that the putative metal-binding resides are well conserved in this group of hydrogen maturation proteases. This group also includes such proteins as the hydrogenase III from Aquifex aeolicus.
Probab=30.44 E-value=58 Score=25.47 Aligned_cols=124 Identities=15% Similarity=0.118 Sum_probs=64.5
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCchhccCchhHHHHHHhcCCC
Q 029652 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (190)
Q Consensus 20 LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMNlSG~aV~~~~~~~~i~ 99 (190)
+|+|+|||-. .-==+|..++++|++.. .+ . .+.++.- |.....++... .
T Consensus 2 lVlGiGN~L~----~DDG~G~~v~~~L~~~~-~~--~---------------~v~~id~-------gt~~~~l~~~l--~ 50 (146)
T cd06063 2 TIIGCGNLNR----GDDGVGPILIRRLQAYL-LP--P---------------HVRLVDC-------GTAGMEVMFRA--R 50 (146)
T ss_pred EEEEECCccc----ccCcHHHHHHHHHhhcC-CC--C---------------CeEEEEC-------CCCHHHHHHHh--c
Confidence 7999999952 22359999999998642 11 0 0111111 11112233222 2
Q ss_pred CCcEEEEeccC--CCCCceEEEe------c---CCCCCCCCchhhHHHh----hcCCCCcc-eEE-EcccCCCCCCCccc
Q 029652 100 LNRVLVFHDDM--GLPCGVLRLR------H---NGGHGGHNGLKSVMNN----FRGNREFA-RLR-IGIGRPPGQMDPKA 162 (190)
Q Consensus 100 ~~~ilVihDdl--dl~~G~vrlk------~---gGs~~GHNGLkSI~~~----l~gt~df~-Rlr-IGIGrP~~~~~v~~ 162 (190)
..+.+||.|=. +.++|+++.- . ...+..+=++.++++. ++ .... ++. +|| .|. ++ +
T Consensus 51 ~~d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~~~--~~~p~~v~~vgI-~~~---~~-~ 123 (146)
T cd06063 51 GAKQLIIIDASSTGSEPGAVFEVPGEELEALPEPSYNLHDFRWDHALAAGRKIFG--DDFPKDVTVYLI-EAK---SL-D 123 (146)
T ss_pred CCCEEEEEEeCCCCCCCCeEEEEcchhccccccCCcCcccCCHHHHHHHHHHHhc--CCCCCeEEEEEE-eec---cC-c
Confidence 34667777875 5599998752 1 1223445578887653 32 1232 554 377 332 22 3
Q ss_pred cccCCCCHHHHhh-HHHHHHH
Q 029652 163 FLLQKFNAIARER-DISFDCI 182 (190)
Q Consensus 163 yVL~~f~~~E~~~-~~~~~~~ 182 (190)
|= ..+|++=++. +.+.+.+
T Consensus 124 ~g-~~LS~~v~~a~~~~~~~i 143 (146)
T cd06063 124 FG-LELSPPVKQAAERVAEMI 143 (146)
T ss_pred CC-CCCCHHHHHHHHHHHHHH
Confidence 22 3556555555 5555544
No 32
>PF07431 DUF1512: Protein of unknown function (DUF1512); InterPro: IPR009995 This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown.
Probab=30.13 E-value=2.2e+02 Score=26.47 Aligned_cols=67 Identities=10% Similarity=0.094 Sum_probs=47.4
Q ss_pred hHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEe---CCchhccCchhHHHHHHhcCCCCCcEEE
Q 029652 37 NVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK---PQTYMNLSGESTGPLAAYYKLPLNRVLV 105 (190)
Q Consensus 37 NvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~k---P~TyMNlSG~aV~~~~~~~~i~~~~ilV 105 (190)
.+|=+++-.|...... ...-++-.+++..+.+.+++++| |..=.=.=|++|.++.+.++-.++.++-
T Consensus 184 gaGPLVA~~l~~~~~~--~~~~~dtv~~e~~~egRrv~viKA~GPGstVGrpgeave~i~~~~~~k~~~IIT 253 (355)
T PF07431_consen 184 GAGPLVAGRLMENCSK--WEIAKDTVIAECEFEGRRVYVIKAEGPGSTVGRPGEAVEYIVEKLGGKVDLIIT 253 (355)
T ss_pred CcchHHHHHHHhcCcc--cccccccEEEEEEECCcEEEEEeccCCCccCCChHHHHHHHHHHhcCCccEEEE
Confidence 4667777777765543 22234567788999999999999 4555566688899999888666665554
No 33
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=29.46 E-value=40 Score=28.24 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=25.2
Q ss_pred CchhHHHHHHhcCCCCCcEEEEeccCCCC
Q 029652 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (190)
Q Consensus 85 SG~aV~~~~~~~~i~~~~ilVihDdldl~ 113 (190)
++.+..++++.++++++++++|-|.|=..
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL~TD 123 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQLFTD 123 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchhhhh
Confidence 57788889999999999999999988544
No 34
>PF08282 Hydrolase_3: haloacid dehalogenase-like hydrolase; InterPro: IPR013200 The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification []. This HAD domain is found in several distinct enzymes including: Phospholipid-transporting ATPase 1 (3.6.3.1 from EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [] 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (3.1.3.45 from EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [] Mannosyl-3-phosphoglycerate phosphatase (3.1.3.70 from EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [] Phosphoglycolate phopshatase (3.1.3.18 from EC), which catalyses the dephosphorylation of 2-phosphoglycolate [] ; PDB: 2B30_B 3R4C_A 1XVI_B 3IJ5_B 3MMZ_C 3L7Y_A 1XPJ_C 1RLT_B 1RLM_B 2HF2_A ....
Probab=28.26 E-value=45 Score=26.52 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=22.6
Q ss_pred chhHHHHHHhcCCCCCcEEEEeccC
Q 029652 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (190)
Q Consensus 86 G~aV~~~~~~~~i~~~~ilVihDdl 110 (190)
|.+++.+++.+++++++++++=|+.
T Consensus 188 ~~ai~~l~~~~~i~~~~~~~~GD~~ 212 (254)
T PF08282_consen 188 GSAIKYLLEYLGISPEDIIAFGDSE 212 (254)
T ss_dssp HHHHHHHHHHHTTSGGGEEEEESSG
T ss_pred HHHHHHHhhhcccccceeEEeeccc
Confidence 6778999999999999999999875
No 35
>PF06342 DUF1057: Alpha/beta hydrolase of unknown function (DUF1057); InterPro: IPR010463 This entry consists of proteins of unknown function which have an alpha/beta hydrolase fold.
Probab=26.26 E-value=2.5e+02 Score=25.39 Aligned_cols=66 Identities=23% Similarity=0.345 Sum_probs=45.6
Q ss_pred EEeccCCCC--CceEEEecCCCCCCCCchhhHHHhhcCCCCcceEEEcccCCCCCCCccccccCCCCHHHHhh
Q 029652 105 VFHDDMGLP--CGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 175 (190)
Q Consensus 105 VihDdldl~--~G~vrlk~gGs~~GHNGLkSI~~~l~gt~df~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~ 175 (190)
|..|++.-. +|+| +-.-||.|.||-.|=|...|. . .=.|+ |||--|.. ..+..|---.++.+|+..
T Consensus 24 ~y~D~~~~gs~~gTV-v~~hGsPGSH~DFkYi~~~l~-~-~~iR~-I~iN~PGf-~~t~~~~~~~~~n~er~~ 91 (297)
T PF06342_consen 24 VYEDSLPSGSPLGTV-VAFHGSPGSHNDFKYIRPPLD-E-AGIRF-IGINYPGF-GFTPGYPDQQYTNEERQN 91 (297)
T ss_pred EEEecCCCCCCceeE-EEecCCCCCccchhhhhhHHH-H-cCeEE-EEeCCCCC-CCCCCCcccccChHHHHH
Confidence 445776544 7765 678999999999999999993 2 22343 68877754 344556666778888766
No 36
>PRK06437 hypothetical protein; Provisional
Probab=24.88 E-value=94 Score=21.32 Aligned_cols=29 Identities=7% Similarity=-0.011 Sum_probs=24.3
Q ss_pred CchhHHHHHHhcCCCCCcEEEEeccCCCC
Q 029652 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (190)
Q Consensus 85 SG~aV~~~~~~~~i~~~~ilVihDdldl~ 113 (190)
.+..|+.+++.++++++.+.|.++.--+|
T Consensus 19 ~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 19 HELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 44678999999999999999988877666
No 37
>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
Probab=23.69 E-value=93 Score=30.20 Aligned_cols=76 Identities=18% Similarity=0.103 Sum_probs=45.4
Q ss_pred eEEEE-----ecCC---CCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEe----CCchhccCc
Q 029652 19 WLFVG-----LGNP---GDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK----PQTYMNLSG 86 (190)
Q Consensus 19 ~LivG-----LGNP---G~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~k----P~TyMNlSG 86 (190)
.+||| +|-| |+=|. +|-++-++|.+++.+++.... +...+.... . ..+...+ ...+.+.||
T Consensus 283 h~ivGrdhAg~~~~~~~g~~Y~---~~~a~~i~~~~~~~l~i~~~~--~~~~~Y~~~-~-~~~~~~~~cph~~~~~~~sg 355 (568)
T PRK05537 283 HFIVGRDHAGPGKDSRGKPFYG---PYDAQELFAKYADEIGITMVP--FKEMVYVQD-K-AQYVPVDEVPQGATVLTISG 355 (568)
T ss_pred eEEECCCCCCCCCCCcCcccCC---chHHHHHHHhCccccCceEEe--cceeEEEcC-C-CeEEecCcCCCCcceeccCH
Confidence 47887 5444 43443 788999999998777776432 211111000 0 1222222 356999999
Q ss_pred hhHHHHHHhcCCCCC
Q 029652 87 ESTGPLAAYYKLPLN 101 (190)
Q Consensus 87 ~aV~~~~~~~~i~~~ 101 (190)
..++.+++.=..+|+
T Consensus 356 t~ir~~l~~G~~pP~ 370 (568)
T PRK05537 356 TELRRRLREGLEIPE 370 (568)
T ss_pred HHHHHHHHCCCCCCh
Confidence 999998876555553
No 38
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.29 E-value=20 Score=23.49 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=17.9
Q ss_pred ccCchhHHHHHHhcCCCCCcEEEEecc
Q 029652 83 NLSGESTGPLAAYYKLPLNRVLVFHDD 109 (190)
Q Consensus 83 NlSG~aV~~~~~~~~i~~~~ilVihDd 109 (190)
+.|-..+.++++++++++++++...+|
T Consensus 37 ~~~~~~l~~ia~~l~~~~~el~~~~~d 63 (63)
T PF13443_consen 37 NPSLDTLEKIAKALNCSPEELFEYEPD 63 (63)
T ss_dssp ---HHHHHHHHHHHT--HHHCTECCE-
T ss_pred cccHHHHHHHHHHcCCCHHHHhhcCCC
Confidence 455677889999999999999887665
No 39
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=22.79 E-value=71 Score=29.00 Aligned_cols=38 Identities=24% Similarity=0.419 Sum_probs=31.6
Q ss_pred eeEEEEeCCchhccCchhHHHHHHhcCCCCCcEEEEeccCCCCC
Q 029652 71 APVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPC 114 (190)
Q Consensus 71 ~~v~L~kP~TyMNlSG~aV~~~~~~~~i~~~~ilVihDdldl~~ 114 (190)
+.+++=||.++|= ..+.+.+++.|++.+.|-|-||...
T Consensus 218 ~P~v~GKP~~~m~------~~l~~~~~i~psRt~mvGDRL~TDI 255 (306)
T KOG2882|consen 218 QPIVLGKPSTFMF------EYLLEKFNIDPSRTCMVGDRLDTDI 255 (306)
T ss_pred CCeecCCCCHHHH------HHHHHHcCCCcceEEEEcccchhhh
Confidence 4688999999983 3567889999999999999887654
No 40
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=22.58 E-value=84 Score=28.15 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=23.6
Q ss_pred HHHHhcCCCCCcEEEEeccCCCCCceEEEe
Q 029652 91 PLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120 (190)
Q Consensus 91 ~~~~~~~i~~~~ilVihDdldl~~G~vrlk 120 (190)
.++...+..++.+||++||+...-|.-..|
T Consensus 129 ~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK 158 (287)
T COG2607 129 DLVELLRARPEKFILFCDDLSFEEGDDAYK 158 (287)
T ss_pred HHHHHHhcCCceEEEEecCCCCCCCchHHH
Confidence 445556667899999999999998876554
No 41
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=22.41 E-value=51 Score=27.54 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=22.6
Q ss_pred chhHHHHHHhcCCCCCcEEEEeccC
Q 029652 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (190)
Q Consensus 86 G~aV~~~~~~~~i~~~~ilVihDdl 110 (190)
|.+++.+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 6888999999999999999999865
No 42
>PRK10976 putative hydrolase; Provisional
Probab=22.31 E-value=54 Score=27.38 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=22.6
Q ss_pred chhHHHHHHhcCCCCCcEEEEeccC
Q 029652 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (190)
Q Consensus 86 G~aV~~~~~~~~i~~~~ilVihDdl 110 (190)
|.+++.+++++++++++++++=|..
T Consensus 192 g~al~~l~~~lgi~~~~viafGD~~ 216 (266)
T PRK10976 192 GHALEAVAKKLGYSLKDCIAFGDGM 216 (266)
T ss_pred HHHHHHHHHHcCCCHHHeEEEcCCc
Confidence 7888999999999999999998864
No 43
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=21.65 E-value=64 Score=24.50 Aligned_cols=22 Identities=27% Similarity=0.634 Sum_probs=16.5
Q ss_pred ccCCCCCceEEEe--cCCCCCCCC
Q 029652 108 DDMGLPCGVLRLR--HNGGHGGHN 129 (190)
Q Consensus 108 Ddldl~~G~vrlk--~gGs~~GHN 129 (190)
.++++|...+.+. +++|+||+|
T Consensus 5 ~~~~i~~~dl~~~~~RssGpGGQ~ 28 (113)
T PF00472_consen 5 KEIDIPEKDLEISFSRSSGPGGQN 28 (113)
T ss_dssp SSSCC-GGGEEEEEEESSSSSSCH
T ss_pred cccccCHHHeEEEEEecCCCCCCc
Confidence 4677888877776 688999986
No 44
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=21.56 E-value=97 Score=27.62 Aligned_cols=30 Identities=23% Similarity=0.133 Sum_probs=27.0
Q ss_pred chhccCchhHHHHHHhcCCCCCcEEEEecc
Q 029652 80 TYMNLSGESTGPLAAYYKLPLNRVLVFHDD 109 (190)
Q Consensus 80 TyMNlSG~aV~~~~~~~~i~~~~ilVihDd 109 (190)
.=|=.+.+...+++...+|..++.||+|||
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd 98 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDD 98 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECC
Confidence 467778888999999999999999999999
No 45
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=21.06 E-value=84 Score=23.05 Aligned_cols=32 Identities=22% Similarity=0.304 Sum_probs=19.0
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHH
Q 029652 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAE 48 (190)
Q Consensus 17 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~ 48 (190)
...++||||+...-=..+--.++-.++..+.+
T Consensus 53 ~~v~lvGlG~~~~~~~~~~r~a~~~~~~~l~~ 84 (126)
T PF02789_consen 53 KRVLLVGLGKKEKLTAESLRKAGAAAARALKK 84 (126)
T ss_dssp SEEEEEEEESCTGBCHHHHHHHHHHHHHHHHH
T ss_pred cEEEEEECCCcCcCCHHHHHHHHHHHHHHHhh
Confidence 45789999999753222333444455555544
No 46
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=20.93 E-value=1e+02 Score=28.51 Aligned_cols=33 Identities=24% Similarity=0.317 Sum_probs=25.7
Q ss_pred EEEEeCCchhccCchhHHHHHHhcCCCCCcEEEEeccC
Q 029652 73 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDM 110 (190)
Q Consensus 73 v~L~kP~TyMNlSG~aV~~~~~~~~i~~~~ilVihDdl 110 (190)
.+.++|..+.|. |+..+..+|++ .++++||||=
T Consensus 116 ~~~lrp~~~~~~---Ai~dlV~~~~W--~~v~~iYD~d 148 (400)
T cd06392 116 TLAARPPVRLND---VMLKLVTELRW--QKFIVFYDSE 148 (400)
T ss_pred eEEecCchHHHH---HHHHHHHhCCC--cEEEEEEECc
Confidence 568888644444 99999999998 5999999753
No 47
>COG4046 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.79 E-value=3.7e+02 Score=24.88 Aligned_cols=68 Identities=6% Similarity=0.066 Sum_probs=46.8
Q ss_pred hHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCch---hccCchhHHHHHHhcCCCCCcEEEE
Q 029652 37 NVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTY---MNLSGESTGPLAAYYKLPLNRVLVF 106 (190)
Q Consensus 37 NvGf~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~Ty---MNlSG~aV~~~~~~~~i~~~~ilVi 106 (190)
++|=++.-.|..+- ..|. ......+++..+.+.+++++||.-= .-.=|+||.++.+.|+-.+..++-|
T Consensus 197 saGPlvA~~L~~~~-~~~e-~~~etV~~e~e~eGRkl~IvKa~GpgstvGr~g~AvE~vv~~~g~~~k~IItI 267 (368)
T COG4046 197 SAGPLVAARLIGNR-DVRE-HEKETVYAEKELEGRKLYIVKAEGPGSTVGRLGEAVEEVVERLGAVPKEIITI 267 (368)
T ss_pred CcchHHHHHHHhcc-cccc-ccccceEEEEeecCcEEEEEecCCCCcccCChHHHHHHHHHHhccCcceEEEe
Confidence 57778888887664 2232 2334567788899999999997544 4556788888888886555545443
No 48
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=20.14 E-value=96 Score=25.87 Aligned_cols=27 Identities=19% Similarity=0.114 Sum_probs=23.4
Q ss_pred cCchhHHHHHHhcCCCCCcEEEEeccC
Q 029652 84 LSGESTGPLAAYYKLPLNRVLVFHDDM 110 (190)
Q Consensus 84 lSG~aV~~~~~~~~i~~~~ilVihDdl 110 (190)
..|.+++.+++.+++++++++++=|..
T Consensus 167 ~K~~al~~l~~~~~i~~~~~i~~GD~~ 193 (249)
T TIGR01485 167 GKGQALQYLLQKLAMEPSQTLVCGDSG 193 (249)
T ss_pred ChHHHHHHHHHHcCCCccCEEEEECCh
Confidence 347788899999999999999999874
No 49
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=20.07 E-value=74 Score=27.35 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=20.1
Q ss_pred HhHHHHHhhccCCCCCeEEEEecCCCC
Q 029652 3 INRFLRRGFCTAVARPWLFVGLGNPGD 29 (190)
Q Consensus 3 ~~~~~~~~~~~~~~~~~LivGLGNPG~ 29 (190)
+.+|+...+...+..-.+|||.||-|.
T Consensus 71 L~~ff~~~Lg~~~~tnviiVG~GnlG~ 97 (211)
T COG2344 71 LRDFFDDLLGQDKTTNVIIVGVGNLGR 97 (211)
T ss_pred HHHHHHHHhCCCcceeEEEEccChHHH
Confidence 456677777766666778999999764
Done!