Query 030200
Match_columns 181
No_of_seqs 158 out of 1028
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 10:05:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030200hhsearch_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 1.1E-72 2.3E-77 462.3 16.8 162 18-180 2-164 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 3E-72 6.4E-77 462.0 18.0 164 17-180 1-164 (191)
3 cd00462 PTH Peptidyl-tRNA hydr 100.0 3.4E-71 7.4E-76 448.9 18.1 160 20-180 1-160 (171)
4 TIGR00447 pth peptidyl-tRNA hy 100.0 1.1E-70 2.5E-75 451.7 18.5 162 18-180 1-163 (188)
5 PRK05426 peptidyl-tRNA hydrola 100.0 5.1E-69 1.1E-73 442.2 18.4 161 18-180 2-163 (189)
6 PF01195 Pept_tRNA_hydro: Pept 100.0 1.6E-67 3.5E-72 431.2 14.6 160 20-180 1-161 (184)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 3.8E-55 8.3E-60 359.5 12.9 162 17-178 38-200 (224)
8 cd06070 H2MP_like-2 Putative [ 74.4 29 0.00062 26.7 8.3 119 20-179 1-132 (140)
9 cd06062 H2MP_MemB-H2up Endopep 56.4 16 0.00035 28.3 3.6 124 19-179 1-138 (146)
10 PF11775 CobT_C: Cobalamin bio 56.3 17 0.00036 31.1 3.9 71 82-154 115-188 (219)
11 PF03418 Peptidase_A25: Germin 53.5 17 0.00037 33.1 3.7 28 16-47 95-122 (354)
12 PRK10466 hybD hydrogenase 2 ma 51.9 23 0.00049 28.1 3.9 29 18-50 2-30 (164)
13 PF14490 HHH_4: Helix-hairpin- 49.8 11 0.00024 27.2 1.7 25 31-55 45-71 (94)
14 TIGR00072 hydrog_prot hydrogen 47.9 19 0.00042 27.7 2.9 124 20-179 1-137 (145)
15 cd06064 H2MP_F420-Reduc Endope 47.8 19 0.00041 28.0 2.8 127 20-179 1-142 (150)
16 PRK12362 germination protease; 45.3 73 0.0016 28.7 6.4 103 6-123 88-200 (318)
17 TIGR00130 frhD coenzyme F420-r 44.8 29 0.00062 27.2 3.4 130 17-179 3-143 (153)
18 TIGR01651 CobT cobaltochelatas 41.9 32 0.00069 33.5 3.8 69 83-154 496-568 (600)
19 PRK02858 germination protease; 40.5 21 0.00046 32.7 2.3 28 16-47 110-137 (369)
20 COG0680 HyaD Ni,Fe-hydrogenase 39.4 35 0.00075 27.4 3.2 108 17-155 2-122 (160)
21 TIGR01441 GPR GPR endopeptidas 39.1 23 0.00049 32.4 2.2 28 16-47 100-127 (358)
22 PRK09256 hypothetical protein; 38.6 16 0.00035 28.8 1.1 25 105-129 3-29 (138)
23 cd00518 H2MP Hydrogenase speci 37.7 36 0.00079 25.9 2.9 124 20-180 1-136 (139)
24 cd06067 H2MP_MemB-H2evol Endop 37.5 34 0.00074 26.1 2.8 124 20-180 1-133 (136)
25 cd06068 H2MP_like-1 Putative [ 36.6 34 0.00073 26.4 2.6 26 20-49 1-26 (144)
26 TIGR00142 hycI hydrogenase mat 36.3 38 0.00083 26.2 2.9 125 19-179 1-134 (146)
27 cd06063 H2MP_Cyano-H2up This g 35.3 43 0.00093 25.9 3.1 27 19-49 1-27 (146)
28 cd06066 H2MP_NAD-link-bidir En 35.3 42 0.00092 25.7 3.0 27 20-50 1-27 (139)
29 PRK11544 hycI hydrogenase 3 ma 34.8 48 0.001 26.1 3.3 101 19-151 3-113 (156)
30 PRK10264 hydrogenase 1 maturat 31.3 84 0.0018 25.9 4.3 30 18-51 5-34 (195)
31 COG2179 Predicted hydrolase of 30.7 37 0.0008 28.1 2.0 30 85-114 95-124 (175)
32 COG2897 SseA Rhodanese-related 28.7 62 0.0013 28.5 3.2 30 80-109 69-98 (285)
33 cd06392 PBP1_iGluR_delta_1 N-t 28.0 59 0.0013 29.7 3.1 32 73-109 116-147 (400)
34 PF08282 Hydrolase_3: haloacid 25.6 55 0.0012 25.8 2.2 25 86-110 188-212 (254)
35 PRK05537 bifunctional sulfate 25.1 88 0.0019 30.0 3.8 76 18-100 282-369 (568)
36 PF05017 TMP: TMP repeat; Int 24.3 37 0.00081 15.4 0.6 8 129-136 2-9 (11)
37 PF06342 DUF1057: Alpha/beta h 23.6 2.8E+02 0.0062 24.8 6.4 71 105-180 24-96 (297)
38 COG2607 Predicted ATPase (AAA+ 23.0 83 0.0018 27.8 2.9 30 92-121 130-159 (287)
39 PF02789 Peptidase_M17_N: Cyto 22.8 61 0.0013 23.5 1.8 33 16-48 52-84 (126)
40 PF07431 DUF1512: Protein of u 22.5 4.1E+02 0.0088 24.4 7.3 67 37-105 184-253 (355)
41 PF13443 HTH_26: Cro/C1-type H 21.2 23 0.00051 22.9 -0.6 27 83-109 37-63 (63)
42 PRK06437 hypothetical protein; 21.2 1.2E+02 0.0027 20.4 3.0 29 85-113 19-47 (67)
43 KOG2882 p-Nitrophenyl phosphat 21.1 69 0.0015 28.7 2.1 40 70-115 217-256 (306)
44 PRK10513 sugar phosphate phosp 20.3 59 0.0013 26.9 1.5 25 86-110 198-222 (270)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-72 Score=462.27 Aligned_cols=162 Identities=46% Similarity=0.787 Sum_probs=156.3
Q ss_pred CeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCC-CccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 030200 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (181)
Q Consensus 18 ~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~-~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ 96 (181)
|+|||||||||++|+.||||||||++|.||+++++++ +.++|.+.++++.+.+++++|+||+||||+||++|.++++||
T Consensus 2 ~kLIVGLGNPG~~Y~~TRHNvGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~l~kP~TyMNlSG~~V~~~~~fy 81 (190)
T COG0193 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASFY 81 (190)
T ss_pred cEEEEECCCCchhhcccchhHHHHHHHHHHHHhCCCCccccccCceeEEEEeCCcEEEEecCccceeCcHHHHHHHHHHh
Confidence 7899999999999999999999999999999999998 567888999999999999999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHH
Q 030200 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERE 176 (181)
Q Consensus 97 ki~~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l 176 (181)
++++++++|||||||+|+|++|+|.+||+|||||||||+++| ||++|+|||||||||..+++|++|||++|+++|++.|
T Consensus 82 ~i~~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGlKSi~~~l-Gt~~f~RlRiGIGrP~~~~~v~~~VL~~f~~~E~~~l 160 (190)
T COG0193 82 KIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHL-GTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEERELL 160 (190)
T ss_pred CCCHHHEEEEeeccCCCCceEEEEcCCCCCCcccHHHHHHHh-CCCccceEEEEcCCCCCCCchhHhhcCCCCHHHHHHH
Confidence 999999999999999999999999999999999999999999 5999999999999998888999999999999999999
Q ss_pred Hhhh
Q 030200 177 LNNI 180 (181)
Q Consensus 177 ~~~~ 180 (181)
++++
T Consensus 161 ~~~~ 164 (190)
T COG0193 161 DKAI 164 (190)
T ss_pred HHHH
Confidence 8875
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=3e-72 Score=461.96 Aligned_cols=164 Identities=66% Similarity=1.154 Sum_probs=155.7
Q ss_pred CCeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 030200 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (181)
Q Consensus 17 ~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ 96 (181)
.|+|||||||||++|++|||||||+++|.||+++++++++.++.+.++++.+.+++++|+||+||||+||+||+++++||
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 47899999999999999999999999999999999987666788899999999999999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHH
Q 030200 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERE 176 (181)
Q Consensus 97 ki~~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l 176 (181)
++++++++|||||||+|+|++|+|.+||++||||||||+++|++|++|+|||||||||+.+.++++|||++|+++|++.|
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 99999999999999999999999999999999999999999955789999999999997767899999999999999999
Q ss_pred Hhhh
Q 030200 177 LNNI 180 (181)
Q Consensus 177 ~~~~ 180 (181)
++++
T Consensus 161 ~~~~ 164 (191)
T cd02406 161 DTAL 164 (191)
T ss_pred HHHH
Confidence 8764
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=3.4e-71 Score=448.92 Aligned_cols=160 Identities=54% Similarity=0.948 Sum_probs=153.4
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki~ 99 (181)
|||||||||++|++|||||||+++|+||++++.++.+.++.+.++++.+.+++++|+||+||||+||++|++++++|+++
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 69999999999999999999999999999999988776778899999999999999999999999999999999999999
Q ss_pred CCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHHHhh
Q 030200 100 LNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERELNN 179 (181)
Q Consensus 100 ~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l~~~ 179 (181)
+++++|||||||+|+|++|+|++||++||||||||+++| ||++|+|||||||||+.+.++++|||++|+++|++.++++
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 6899999999999998777899999999999999999876
Q ss_pred h
Q 030200 180 I 180 (181)
Q Consensus 180 ~ 180 (181)
+
T Consensus 160 ~ 160 (171)
T cd00462 160 I 160 (171)
T ss_pred H
Confidence 5
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=451.71 Aligned_cols=162 Identities=44% Similarity=0.762 Sum_probs=153.5
Q ss_pred CeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCC-ccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 030200 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (181)
Q Consensus 18 ~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~-~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ 96 (181)
|+|||||||||++|+.|||||||+++|+||++++.++. +.++.+.+++..+.+++++|+||+||||+||++|++++++|
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 68999999999999999999999999999999998876 34577888888898999999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHH
Q 030200 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERE 176 (181)
Q Consensus 97 ki~~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l 176 (181)
++++++++|||||||+|+|++|+|++||++||||||||+++| ||++|+|||||||||+++.++++|||++|+++|++.+
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 6899999999999998767899999999999999999
Q ss_pred Hhhh
Q 030200 177 LNNI 180 (181)
Q Consensus 177 ~~~~ 180 (181)
++++
T Consensus 160 ~~~i 163 (188)
T TIGR00447 160 EKAL 163 (188)
T ss_pred HHHH
Confidence 8865
No 5
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=5.1e-69 Score=442.21 Aligned_cols=161 Identities=46% Similarity=0.808 Sum_probs=151.9
Q ss_pred CeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCC-ccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 030200 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (181)
Q Consensus 18 ~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~-~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ 96 (181)
|+|||||||||++|++|||||||+++|.||++++..+. ..++.+.+++..+.+++++|+||+||||+||++|++++++|
T Consensus 2 ~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~ 81 (189)
T PRK05426 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANFY 81 (189)
T ss_pred cEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCCCCcccccccEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHHh
Confidence 78999999999999999999999999999999887664 45677899999998899999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHH
Q 030200 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERE 176 (181)
Q Consensus 97 ki~~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l 176 (181)
++++++++|||||+|+|+|++|+|.+||++||||||||+++| ||++|+|||||||||+ ..++++|||++|+++|++.+
T Consensus 82 ~i~~~~ilVihDdldl~~G~~r~k~gGs~~GHNGlkSI~~~l-gt~~f~RlriGIGrP~-~~~v~~yVL~~f~~~E~~~l 159 (189)
T PRK05426 82 KIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHL-GTQDFWRLRIGIGRPD-KKKVVDYVLGKFSKEEQELL 159 (189)
T ss_pred CCCHHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHh-CCCCeeEEEEEeCCCC-CCCcchhhcCCCCHHHHHHH
Confidence 999999999999999999999999999999999999999999 5889999999999997 56799999999999999999
Q ss_pred Hhhh
Q 030200 177 LNNI 180 (181)
Q Consensus 177 ~~~~ 180 (181)
++++
T Consensus 160 ~~~~ 163 (189)
T PRK05426 160 DKAI 163 (189)
T ss_pred HHHH
Confidence 8765
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=1.6e-67 Score=431.18 Aligned_cols=160 Identities=48% Similarity=0.860 Sum_probs=138.9
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccc-cceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~-~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki 98 (181)
|||||||||++|++|||||||+++|+||++++.++.+.+ +.+.++++.+.+++++|+||+||||+||++|++++++|++
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 799999999999999999999999999999999886544 7788888889999999999999999999999999999999
Q ss_pred CCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHHHh
Q 030200 99 PLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERELN 178 (181)
Q Consensus 99 ~~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l~~ 178 (181)
++++++|||||+|+|+|++|+|++||++||||||||+++| +|++|+|||||||||++..++++|||++|+++|++.|++
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 589999999999999877789999999999999999988
Q ss_pred hh
Q 030200 179 NI 180 (181)
Q Consensus 179 ~~ 180 (181)
++
T Consensus 160 ~~ 161 (184)
T PF01195_consen 160 VI 161 (184)
T ss_dssp HH
T ss_pred HH
Confidence 64
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-55 Score=359.49 Aligned_cols=162 Identities=57% Similarity=1.027 Sum_probs=151.0
Q ss_pred CCeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 030200 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (181)
Q Consensus 17 ~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ 96 (181)
.+|+|+||||||++|..||||+||.++|.||+++++...+...++..+-+.+.+.++++++|++|||.||++|.+++..|
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 46999999999999999999999999999999999986655555666777888999999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHH-H
Q 030200 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE-R 175 (181)
Q Consensus 97 ki~~~~ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~-~ 175 (181)
+++.++++||||||++|+|++|+|++||++||||+||+++++.+...|+||+||||||++++|+.+|||++|++.|++ .
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 999999999999999999999999999999999999999999777799999999999999999999999999999999 4
Q ss_pred HHh
Q 030200 176 ELN 178 (181)
Q Consensus 176 l~~ 178 (181)
|+.
T Consensus 198 Let 200 (224)
T KOG2255|consen 198 LET 200 (224)
T ss_pred HHH
Confidence 443
No 8
>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=74.43 E-value=29 Score=26.71 Aligned_cols=119 Identities=16% Similarity=0.224 Sum_probs=63.3
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki~ 99 (181)
||+|+|||=. .-==+|+.++++|++ .+ +-++.-.| .| -.++.++ .
T Consensus 1 lVlGiGN~l~----~DDg~G~~v~~~L~~-~~---------------------v~vi~~g~----~~---~~ll~~i--~ 45 (140)
T cd06070 1 LIIGVGNRLY----GDDGFGSCLAEALEQ-CG---------------------APVFDGGL----DG---FGLLSHL--E 45 (140)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHhh-CC---------------------CEEEECCC----cH---HHHHHHH--c
Confidence 6899999942 233599999999976 11 11111111 12 2334333 2
Q ss_pred CCcEEEEeecCC--CCCceEEEecC---------CCCCCCC-chhhHHHhhcCCCCccEEE-EcccCCCCCCCcccccCC
Q 030200 100 LNRVLVFHDDMG--LPCGVLRLRHN---------GGHGGHN-GLKSVMNNFRGNREFARLR-IGIGRPPGQMDPKAFLLQ 166 (181)
Q Consensus 100 ~~~ilVvhDdld--l~~G~vrlk~~---------Gs~~GHN-GlkSI~~~l~gt~~f~Rlr-IGIGrP~~~~~~~~yVL~ 166 (181)
..+.+|+-|=++ .++|.++++.. .+...|+ |+.++.+.+.-...-.++. +||= |. ++ +|- .
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 355566667654 68998887542 2224666 9999876652100112322 2332 21 22 322 4
Q ss_pred CCCHHHHHHHHhh
Q 030200 167 KFNAIARERELNN 179 (181)
Q Consensus 167 ~f~~~E~~~l~~~ 179 (181)
.+|++=++.++++
T Consensus 120 ~LS~~v~~av~~~ 132 (140)
T cd06070 120 GLSEAVIARAEKA 132 (140)
T ss_pred CCCHHHHHHHHHH
Confidence 6677666666554
No 9
>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=56.42 E-value=16 Score=28.31 Aligned_cols=124 Identities=18% Similarity=0.206 Sum_probs=64.8
Q ss_pred eeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 030200 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (181)
Q Consensus 19 ~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki 98 (181)
.+|+|+|||-. .-==+|+.+++.|++.++... .+.++.- |...-.++..+.
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 37999999942 223599999999988643221 0111111 111112333222
Q ss_pred CCCcEEEEeecC--CCCCceEEEecC---------CCCCCCCchhhHHHhhc--CCCCccEEEE-cccCCCCCCCccccc
Q 030200 99 PLNRVLVFHDDM--GLPCGVLRLRHN---------GGHGGHNGLKSVMNNFR--GNREFARLRI-GIGRPPGQMDPKAFL 164 (181)
Q Consensus 99 ~~~~ilVvhDdl--dl~~G~vrlk~~---------Gs~~GHNGlkSI~~~l~--gt~~f~RlrI-GIGrP~~~~~~~~yV 164 (181)
..+.+|+-|=+ +.++|+++.-.. ..+..+-++..+.+.+. +. .-.++.| ||= |. ++ +|-
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 24667777764 779999876421 12345556777776542 11 1123333 432 21 11 222
Q ss_pred CCCCCHHHHHHHHhh
Q 030200 165 LQKFNAIARERELNN 179 (181)
Q Consensus 165 L~~f~~~E~~~l~~~ 179 (181)
..+|++=++.++++
T Consensus 125 -~~LS~~v~~av~~~ 138 (146)
T cd06062 125 -LELSPEVAAALPTA 138 (146)
T ss_pred -CCCCHHHHHHHHHH
Confidence 36677666666654
No 10
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=56.26 E-value=17 Score=31.09 Aligned_cols=71 Identities=23% Similarity=0.297 Sum_probs=40.8
Q ss_pred ccccchhHHHHHHHcCCCCC--c-EEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCC
Q 030200 82 MNLSGESTGPLAAYYKLPLN--R-VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRP 154 (181)
Q Consensus 82 MN~SG~aV~~~~~~~ki~~~--~-ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP 154 (181)
=|..|+|+..+.+...-.++ + ++||.|= -|...--+..+.+.-=.+=||.+++......+.-=+.||||..
T Consensus 115 eniDGeAl~~a~~rL~~r~e~rkiLiViSDG--~P~d~st~~~n~~~~L~~HLr~vi~~ie~~~~Vel~aiGIg~D 188 (219)
T PF11775_consen 115 ENIDGEALRWAAERLLARPEQRKILIVISDG--APADDSTLSANDGDYLDAHLRQVIAEIETRSDVELIAIGIGHD 188 (219)
T ss_pred cCCcHHHHHHHHHHHHcCCccceEEEEEeCC--CcCcccccccCChHHHHHHHHHHHHHHhccCCcEEEEEEcCCC
Confidence 58999999876655433333 3 5677773 2333222222222222344788888873223565689999863
No 11
>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=53.47 E-value=17 Score=33.10 Aligned_cols=28 Identities=29% Similarity=0.396 Sum_probs=18.4
Q ss_pred CCCeeEEEecCCCCCCCcCcchHHHHHHHHHH
Q 030200 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (181)
Q Consensus 16 ~~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la 47 (181)
....|||||||.. -|--..|-.++|.+.
T Consensus 95 ~~~iLVVGLGN~~----vTPDALGP~vv~~l~ 122 (354)
T PF03418_consen 95 EASILVVGLGNWN----VTPDALGPRVVENLL 122 (354)
T ss_dssp T--EEEEE-S-SS----SGGG-HHHHHHHT--
T ss_pred CCeEEEEeCCCcC----CCccccchhhhhhhh
Confidence 4568999999974 699999999999663
No 12
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=51.85 E-value=23 Score=28.15 Aligned_cols=29 Identities=24% Similarity=0.410 Sum_probs=22.6
Q ss_pred CeeEEEecCCCCCCCcCcchHHHHHHHHHHHHc
Q 030200 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (181)
Q Consensus 18 ~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~ 50 (181)
+.+|+|+|||- .+-==+|..++++|++.+
T Consensus 2 ~ilVlGiGN~l----~gDDGvG~~va~~L~~~~ 30 (164)
T PRK10466 2 RILVLGVGNIL----LTDEAIGVRIVEALEQRY 30 (164)
T ss_pred ceEEEEECchh----hccCcHHHHHHHHHHHhc
Confidence 46899999994 233459999999998765
No 13
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=49.83 E-value=11 Score=27.20 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=19.7
Q ss_pred CCcCc--chHHHHHHHHHHHHcCCCCC
Q 030200 31 YKGTR--HNVGFEMIDAFAESQGISMN 55 (181)
Q Consensus 31 Y~~TR--HNvG~~~ld~la~~~~~~~~ 55 (181)
|.-.. --+||..+|.+|.++|+...
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 14
>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=47.90 E-value=19 Score=27.74 Aligned_cols=124 Identities=19% Similarity=0.192 Sum_probs=64.9
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki~ 99 (181)
||+|+|||-. .-==+|..++++|++++... . .+-++.-.| .|. .++.+..
T Consensus 1 lViGiGN~l~----~DDg~G~~v~~~L~~~~~~~--~---------------~v~~id~g~----~~~---~l~~~l~-- 50 (145)
T TIGR00072 1 LVLGIGNILR----GDDGFGPRVAERLEERYEFP--P---------------GVEVLDGGT----LGL---ELLDAIE-- 50 (145)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHHHhcCCC--C---------------CeEEEECCC----CHH---HHHHHHh--
Confidence 6899999942 23359999999998865321 0 011111100 122 2333332
Q ss_pred CCcEEEEeecC--CCCCceEEEec--------CCCCCCC-CchhhHHHhhcCCCCcc-EEEE-cccCCCCCCCcccccCC
Q 030200 100 LNRVLVFHDDM--GLPCGVLRLRH--------NGGHGGH-NGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAFLLQ 166 (181)
Q Consensus 100 ~~~ilVvhDdl--dl~~G~vrlk~--------~Gs~~GH-NGlkSI~~~l~gt~~f~-RlrI-GIGrP~~~~~~~~yVL~ 166 (181)
..+.+|+-|=. +.++|+++.-. ..+...| -|+..+++.+.-..+.+ ++.+ ||= |. ++ +|- .
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 24556666765 55999988632 1132344 48888887663112233 4433 443 21 11 222 3
Q ss_pred CCCHHHHHHHHhh
Q 030200 167 KFNAIARERELNN 179 (181)
Q Consensus 167 ~f~~~E~~~l~~~ 179 (181)
.+|++=++.++++
T Consensus 125 ~LS~~v~~~~~~~ 137 (145)
T TIGR00072 125 GLSPEVAAAVPAA 137 (145)
T ss_pred CCCHHHHHHHHHH
Confidence 6666666666554
No 15
>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=47.79 E-value=19 Score=28.02 Aligned_cols=127 Identities=14% Similarity=0.182 Sum_probs=67.1
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHH-HHHcC-
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPL-AAYYK- 97 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~-~~~~k- 97 (181)
||+|+|||-. .-==+|+.++++|++.+... . .+.++. .|...-.+ ..+..
T Consensus 1 lViGiGN~l~----gDDgvG~~va~~l~~~~~~~--~---------------~v~vid-------~g~~~~~~~~~~~~~ 52 (150)
T cd06064 1 LVVGCGNILF----GDDGFGPAVIEELEKLELLP--D---------------NVQVID-------AGTGAPHLLFTLLDE 52 (150)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhccCCC--C---------------CEEEEE-------CCCcHHHHHHHHHhc
Confidence 6899999952 33459999999998754210 0 122222 22211111 11111
Q ss_pred CCCCcEEEEeecC--CCCCceEEEecC------C---CCCCCCchhhHHHhhcCCCCc-cEEEE-cccCCCCCCCccccc
Q 030200 98 LPLNRVLVFHDDM--GLPCGVLRLRHN------G---GHGGHNGLKSVMNNFRGNREF-ARLRI-GIGRPPGQMDPKAFL 164 (181)
Q Consensus 98 i~~~~ilVvhDdl--dl~~G~vrlk~~------G---s~~GHNGlkSI~~~l~gt~~f-~RlrI-GIGrP~~~~~~~~yV 164 (181)
....+.+|+-|=+ +.++|+++.... . .+-.+-|+..+++.+.+ .. .++.+ ||- |.. -+..+|=
T Consensus 53 ~~~~d~viivDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~--~~~~~~~iigi~-p~~-~~~~~~~ 128 (150)
T cd06064 53 ESKPKKIIIVDAIDFGLEPGTLKKISVDELPPGKYYDFDAHSWPLADPLHELKD--KYGIEIVVIGCQ-PKR-VPEPDVE 128 (150)
T ss_pred cCCCCEEEEEEecCCCCCCCeEEEEehhhcccccCCCcCCCcCCHHHHHHHHHh--cCCCeEEEEEEE-Eee-ecCCCCC
Confidence 1225667777874 779999887432 1 24566799999987742 22 23333 443 221 1100122
Q ss_pred CCCCCHHHHHHHHhh
Q 030200 165 LQKFNAIARERELNN 179 (181)
Q Consensus 165 L~~f~~~E~~~l~~~ 179 (181)
..+|++=++.++++
T Consensus 129 -~~LS~~v~~a~~~~ 142 (150)
T cd06064 129 -PGLSEEVEKAVPKA 142 (150)
T ss_pred -CCCCHHHHHHHHHH
Confidence 35666666666554
No 16
>PRK12362 germination protease; Provisional
Probab=45.29 E-value=73 Score=28.71 Aligned_cols=103 Identities=17% Similarity=0.195 Sum_probs=59.3
Q ss_pred HHHHhhhcCCCCCeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECC-eeEEEEeC----CC
Q 030200 6 FLRRGFCTAVARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKP----QT 80 (181)
Q Consensus 6 ~~~~~~~~~~~~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~-~~v~L~kP----~T 80 (181)
.+.+++........|||||||.. -|--..|-.+++.|.-.... ..++++..-.+ .+|.-+-| +|
T Consensus 88 ~L~~ll~~~~~~~iLVvGLGN~~----vTpDaLGP~Vv~~l~vTrhl-------~~~~~~~~~~~~~pV~AiaPGVmg~T 156 (318)
T PRK12362 88 ELKKLINLDKEMTVLVVGLGNWN----VTPDALGPKVVSKLMVTRHL-------KEYAPEEIDEGIRPVCAIAPGVLGIT 156 (318)
T ss_pred HHHHHhCCCCCCcEEEEEcCCCC----cCccccchhhhhhhhhhhhh-------hhhcCchhcCCCCcceEecCCccccc
Confidence 33444422234668999999974 69999999999988643111 11112111112 23444444 45
Q ss_pred cccccchhHHHHHHHcCCCCCcEEEEeecCC----CCCc-eEEEecCC
Q 030200 81 YMNLSGESTGPLAAYYKLPLNRVLVFHDDMG----LPCG-VLRLRHNG 123 (181)
Q Consensus 81 yMN~SG~aV~~~~~~~ki~~~~ilVvhDdld----l~~G-~vrlk~~G 123 (181)
=||.+ +.++.+...++ .+++|.-|-+- --+| +|++.-.|
T Consensus 157 Giet~-Eii~gIv~k~k---pd~IIAIDALaar~~~Rl~~tIQisdtG 200 (318)
T PRK12362 157 GIETA-EIIKGVVEKIK---PDLVIAIDALAARSVERVNTTIQISDTG 200 (318)
T ss_pred chhHH-HHHHHHHHhcC---CCEEEEEeccccCCHHHccCeEEECCCC
Confidence 56543 44555665544 46777778776 2467 78887655
No 17
>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=44.81 E-value=29 Score=27.17 Aligned_cols=130 Identities=16% Similarity=0.134 Sum_probs=68.0
Q ss_pred CCeeEEEecCCCCCCCcCcchHHHHHHHHHHHH-cCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHH
Q 030200 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (181)
Q Consensus 17 ~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~-~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~ 95 (181)
.+.+|+|+|||-. .-==+|..++++|++. +..+ ..+.++. -.......+..+
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 0111111 111111111111
Q ss_pred cCCCCCcEEEEeec--CCCCCceEEEecC-----C-C-CCCCCchhhHHHhhcCCCCccEEEE-cccCCCCCCCcccccC
Q 030200 96 YKLPLNRVLVFHDD--MGLPCGVLRLRHN-----G-G-HGGHNGLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLL 165 (181)
Q Consensus 96 ~ki~~~~ilVvhDd--ldl~~G~vrlk~~-----G-s-~~GHNGlkSI~~~l~gt~~f~RlrI-GIGrP~~~~~~~~yVL 165 (181)
..+...+.+|+-|= .+.++|+++.-.. + + +..+-|+..+.+.+. .. .++.| ||- |.. -+..+|=
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 12334566667775 5789999987421 2 2 344459999998774 22 45554 553 321 1111122
Q ss_pred CCCCHHHHHHHHhh
Q 030200 166 QKFNAIARERELNN 179 (181)
Q Consensus 166 ~~f~~~E~~~l~~~ 179 (181)
-.+|++=++.++++
T Consensus 130 ~~LS~~v~~a~~~~ 143 (153)
T TIGR00130 130 IGLTEEVNKAIPRA 143 (153)
T ss_pred CCCCHHHHHHHHHH
Confidence 25666666665554
No 18
>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=41.94 E-value=32 Score=33.51 Aligned_cols=69 Identities=23% Similarity=0.283 Sum_probs=42.5
Q ss_pred cccchhHHHHHHHcCCCCC--c-EEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCC-CccEEEEcccCC
Q 030200 83 NLSGESTGPLAAYYKLPLN--R-VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNR-EFARLRIGIGRP 154 (181)
Q Consensus 83 N~SG~aV~~~~~~~ki~~~--~-ilVvhDdldl~~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~-~f~RlrIGIGrP 154 (181)
|..|+||..+.....-.++ + ++||.|=-=.+-.++ ..+.+.-=++=||.+|+... +. ..-=+.||||..
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--SVNPGNYLERHLRAVIEEIE-TRSPVELLAIGIGHD 568 (600)
T ss_pred CCchHHHHHHHHHHhcCcccceEEEEEeCCCcCCcccc--ccCchhHHHHHHHHHHHHHh-ccCCceEEEeecccc
Confidence 8889999877665443333 3 578888433332222 22222233445899998883 43 466699999974
No 19
>PRK02858 germination protease; Provisional
Probab=40.52 E-value=21 Score=32.70 Aligned_cols=28 Identities=29% Similarity=0.361 Sum_probs=23.0
Q ss_pred CCCeeEEEecCCCCCCCcCcchHHHHHHHHHH
Q 030200 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (181)
Q Consensus 16 ~~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la 47 (181)
....|||||||- .-|--..|-.+++.|.
T Consensus 110 ~~~vLVVGLGN~----~VTPDALGP~vv~~l~ 137 (369)
T PRK02858 110 EASCLIVGLGNW----NVTPDALGPLVVENVL 137 (369)
T ss_pred CCcEEEEeCCCc----CCCccccChheeccee
Confidence 356899999996 3689999999998664
No 20
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=39.45 E-value=35 Score=27.41 Aligned_cols=108 Identities=18% Similarity=0.174 Sum_probs=63.9
Q ss_pred CCeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCC-cccccchhHHHHHHH
Q 030200 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQT-YMNLSGESTGPLAAY 95 (181)
Q Consensus 17 ~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~T-yMN~SG~aV~~~~~~ 95 (181)
.+++|+|+|||= ..-==+|-.+++.|++.+.... ++-++.-.| -+|+.+
T Consensus 2 ~~ilIlG~GN~L----~~DDG~Gv~vae~L~~~~~~~~-----------------~v~vid~Gt~~~~l~~--------- 51 (160)
T COG0680 2 MRILILGVGNIL----MGDDGFGVRVAEKLKKRYKPPE-----------------NVEVIDGGTAGPNLLG--------- 51 (160)
T ss_pred CeEEEEeeCCcc----cccCcccHHHHHHHHHhcCCCC-----------------CeEEEEcCCCcHHHHH---------
Confidence 468999999994 2445689999999988652210 122222211 123322
Q ss_pred cCCCCCcEEEEeecCCC--CCceEEEec-----CC-CCC---CCC-chhhHHHhhcCCCCccEEEEcccCCC
Q 030200 96 YKLPLNRVLVFHDDMGL--PCGVLRLRH-----NG-GHG---GHN-GLKSVMNNFRGNREFARLRIGIGRPP 155 (181)
Q Consensus 96 ~ki~~~~ilVvhDdldl--~~G~vrlk~-----~G-s~~---GHN-GlkSI~~~l~gt~~f~RlrIGIGrP~ 155 (181)
.+...+-++|-|=++. .+|++++-. .+ .+. .|+ ++..+++.+.-..++...-+|+.-|+
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 1223344777786555 599998743 22 343 565 67777777742334577788888654
No 21
>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=39.13 E-value=23 Score=32.39 Aligned_cols=28 Identities=29% Similarity=0.400 Sum_probs=23.1
Q ss_pred CCCeeEEEecCCCCCCCcCcchHHHHHHHHHH
Q 030200 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (181)
Q Consensus 16 ~~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la 47 (181)
....|||||||- .-|--..|-.+++.|.
T Consensus 100 ~~~iLVVGLGN~----~VTPDALGP~vv~~l~ 127 (358)
T TIGR01441 100 DMTCLVVGLGNW----NVTPDALGPKVVENLL 127 (358)
T ss_pred CCcEEEEeCCCc----CCCccccChheeccee
Confidence 356899999996 3689999999998774
No 22
>PRK09256 hypothetical protein; Provisional
Probab=38.64 E-value=16 Score=28.83 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=20.5
Q ss_pred EEeecCCCCCceEEEe--cCCCCCCCC
Q 030200 105 VFHDDMGLPCGVLRLR--HNGGHGGHN 129 (181)
Q Consensus 105 VvhDdldl~~G~vrlk--~~Gs~~GHN 129 (181)
-|.+++++|...++++ +++|+||+|
T Consensus 3 ~~~~~~~i~~~~l~~~~~RSSGPGGQ~ 29 (138)
T PRK09256 3 RITRRLVIPENELEWRFIRASGPGGQN 29 (138)
T ss_pred ccCccCccCHHHeEEEEEEcCCCCccc
Confidence 3678899998888876 688899987
No 23
>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=37.73 E-value=36 Score=25.92 Aligned_cols=124 Identities=17% Similarity=0.152 Sum_probs=66.4
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki~ 99 (181)
+|+|+|||=. .-==+|..++++|+++... ..+-++.-.| .|. .++....
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~~~------------------~~v~~id~gt----~~~---~l~~~l~-- 49 (139)
T cd00518 1 LVLGIGNPLR----GDDGFGPAVAERLEERYLP------------------PGVEVIDGGT----LGL---ELLDLLE-- 49 (139)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcCCC------------------CCeEEEECCC----CHH---HHHHHHh--
Confidence 5899999942 2345999999999886420 0121221111 111 2233222
Q ss_pred CCcEEEEeecCC--CCCceEEEec-----CCCC--CCCC-chhhHHHhhcCCC-CccEEEE-cccCCCCCCCcccccCCC
Q 030200 100 LNRVLVFHDDMG--LPCGVLRLRH-----NGGH--GGHN-GLKSVMNNFRGNR-EFARLRI-GIGRPPGQMDPKAFLLQK 167 (181)
Q Consensus 100 ~~~ilVvhDdld--l~~G~vrlk~-----~Gs~--~GHN-GlkSI~~~l~gt~-~f~RlrI-GIGrP~~~~~~~~yVL~~ 167 (181)
..+.+|+-|=.+ .++|+++.-. .... ..|. |+..+++.+.... .-.++.+ ||= |. ++ +|= ..
T Consensus 50 ~~d~viiVDA~~~~~~pG~i~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~~~~~~~~~lvgi~-~~---~~-~~g-~~ 123 (139)
T cd00518 50 GADRVIIVDAVDSGGEPGTVRRLEPEELPAYLSALSTHQLGLAELLALLRLLGGLPPEVVLIGIQ-PE---SL-ELG-EG 123 (139)
T ss_pred cCCeEEEEECccCCCCCCeEEEEchhhcccccCCCCCccCCHHHHHHHHHHhCCCCCeEEEEEEE-ee---ec-CCC-CC
Confidence 256677777764 6999988732 1111 3455 9999988773110 1123333 442 21 11 221 57
Q ss_pred CCHHHHHHHHhhh
Q 030200 168 FNAIARERELNNI 180 (181)
Q Consensus 168 f~~~E~~~l~~~~ 180 (181)
+|++=++.+++++
T Consensus 124 LS~~v~~a~~~~~ 136 (139)
T cd00518 124 LSPEVAAAVPKAV 136 (139)
T ss_pred CCHHHHHHHHHHH
Confidence 7777777776653
No 24
>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=37.53 E-value=34 Score=26.15 Aligned_cols=124 Identities=16% Similarity=0.181 Sum_probs=65.7
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki~ 99 (181)
+|+|+|||-. .-==+|..++++|++.. . . .+-++.-.| .|..+ +......
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 5899999942 23459999999998753 1 0 111111111 22221 1111111
Q ss_pred CCcEEEEeecC--CCCCceEEEecC----C--CCCCCCchhhHHHhhcCCCCccEEEE-cccCCCCCCCcccccCCCCCH
Q 030200 100 LNRVLVFHDDM--GLPCGVLRLRHN----G--GHGGHNGLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKFNA 170 (181)
Q Consensus 100 ~~~ilVvhDdl--dl~~G~vrlk~~----G--s~~GHNGlkSI~~~l~gt~~f~RlrI-GIGrP~~~~~~~~yVL~~f~~ 170 (181)
..+.+|+-|=. +.++|+++.-.. . .+..+-|+..+.+.++ ...-.++.+ ||- |. ++ +|- ..+|+
T Consensus 51 ~~d~vIiVDAv~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~~L~~~~-~~~~~~~~~vgi~-~~---~~-~~g-~~LS~ 123 (136)
T cd06067 51 KPDLIVIVDAADMGLEPGEIRIIDPEEIAEYFFSTHTLPLSILIDYLR-ESTGAEVIFLGIQ-PE---NL-EFG-EPLSP 123 (136)
T ss_pred CCCEEEEEECCccCcCCCEEEEEchhhcccccCCCCcCCHHHHHHHHH-hcCCCcEEEEEee-ee---ee-ecC-CCCCH
Confidence 24556666765 459999987432 1 2334448888887763 211123333 332 22 12 332 47777
Q ss_pred HHHHHHHhhh
Q 030200 171 IARERELNNI 180 (181)
Q Consensus 171 ~E~~~l~~~~ 180 (181)
+=++.+++++
T Consensus 124 ~v~~a~~~~~ 133 (136)
T cd06067 124 EVKDAAEELA 133 (136)
T ss_pred HHHHHHHHHH
Confidence 7777776654
No 25
>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=36.57 E-value=34 Score=26.42 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=20.3
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHH
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~ 49 (181)
||+|+|||-.. -==+|..++++|+++
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~ 26 (144)
T cd06068 1 LVAGVGNIFLG----DDGFGVEVARRLRPR 26 (144)
T ss_pred CEEEECccccc----cCcHHHHHHHHHhcc
Confidence 68999999522 234999999999865
No 26
>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=36.32 E-value=38 Score=26.19 Aligned_cols=125 Identities=14% Similarity=0.132 Sum_probs=67.2
Q ss_pred eeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 030200 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (181)
Q Consensus 19 ~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki 98 (181)
.+|+|+|||-.. -==+|..++++|++.+.. . .+.++.-.| .|.-.-.+...+
T Consensus 1 ~lVlGiGN~l~~----DDG~G~~v~~~L~~~~~~---~---------------~v~v~d~gt----~~~~~~~~~~~~-- 52 (146)
T TIGR00142 1 LVLLCVGNELMG----DDGAGPYLAEKCAAAPKE---E---------------NWVVINAGT----VPENFTVAIREL-- 52 (146)
T ss_pred CEEEEeCccccc----cCcHHHHHHHHHHhccCC---C---------------CEEEEECCC----ChHHHHHHHHhc--
Confidence 379999999522 235999999999865311 0 122222222 122111222222
Q ss_pred CCCcEEEEeecC--CCCCceEEEecC-----CCCCCCC-chhhHHHhhcCCCCccEEEE-cccCCCCCCCcccccCCCCC
Q 030200 99 PLNRVLVFHDDM--GLPCGVLRLRHN-----GGHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKFN 169 (181)
Q Consensus 99 ~~~~ilVvhDdl--dl~~G~vrlk~~-----Gs~~GHN-GlkSI~~~l~gt~~f~RlrI-GIGrP~~~~~~~~yVL~~f~ 169 (181)
..+.+++-|-+ +.++|+++.-.. .+..-|+ |+..+.+.+.+ .--.++.+ ||- |. ++ +|- ..+|
T Consensus 53 -~~d~viivDA~~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~ll~~~~~-~~~~~~~ligi~-~~---~~-~~g-~~LS 124 (146)
T TIGR00142 53 -RPTHILIVDATDMGLNPGEVRIIDDDIIEMYSMSTHNMPLSYLVDYLKE-DINGEIIFLGIQ-PD---IV-GFY-YPMS 124 (146)
T ss_pred -CCCEEEEEECcccCCCCCeEEEEChhhccccccCcCcCCHHHHHHHHHh-cCCCeEEEEEEe-ee---ee-ecC-CCCC
Confidence 13556666764 569999887432 1223444 99999877732 21234444 543 32 22 333 4677
Q ss_pred HHHHHHHHhh
Q 030200 170 AIARERELNN 179 (181)
Q Consensus 170 ~~E~~~l~~~ 179 (181)
++=++.++++
T Consensus 125 ~~v~~a~~~~ 134 (146)
T TIGR00142 125 QPVKDAVETL 134 (146)
T ss_pred HHHHHHHHHH
Confidence 7766666654
No 27
>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=35.32 E-value=43 Score=25.91 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=20.8
Q ss_pred eeEEEecCCCCCCCcCcchHHHHHHHHHHHH
Q 030200 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (181)
Q Consensus 19 ~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~ 49 (181)
.+|+|+|||-. .-==+|..++++|++.
T Consensus 1 ~lVlGiGN~L~----~DDG~G~~v~~~L~~~ 27 (146)
T cd06063 1 LTIIGCGNLNR----GDDGVGPILIRRLQAY 27 (146)
T ss_pred CEEEEECCccc----ccCcHHHHHHHHHhhc
Confidence 37999999942 2235999999999864
No 28
>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=35.26 E-value=42 Score=25.73 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=21.2
Q ss_pred eEEEecCCCCCCCcCcchHHHHHHHHHHHHc
Q 030200 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (181)
Q Consensus 20 LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~ 50 (181)
+|+|+|||=- .-==+|..++++|++++
T Consensus 1 lVlGvGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPLR----GDDGLGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCccc----cccchhHHHHHHHHhhC
Confidence 5899999942 33459999999998764
No 29
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=34.77 E-value=48 Score=26.12 Aligned_cols=101 Identities=17% Similarity=0.197 Sum_probs=54.3
Q ss_pred eeEEEecCCCCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 030200 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (181)
Q Consensus 19 ~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~~ki 98 (181)
.+|+|+|||-. .-==+|..++++|++.. +. .+.++.-.| .|.-+-.++..+
T Consensus 3 ~lVlGiGN~L~----gDDGvG~~v~~~L~~~~---~~----------------~v~vid~gt----~~~~~~~~i~~~-- 53 (156)
T PRK11544 3 DVVLTVGNSMM----GDDGAGPLLAEKLAAAP---KG----------------GWVVIDGGS----APENDIVAIREL-- 53 (156)
T ss_pred EEEEEeCcccc----ccCcHHHHHHHHHhccC---CC----------------CeEEEECCC----CHHHHHHHHHhc--
Confidence 58999999952 23359999999997642 10 111222222 122221222211
Q ss_pred CCCcEEEEeec--CCCCCceEEEecCC------CCCCCC-chhhHHHhhcCCCCccEEEE-cc
Q 030200 99 PLNRVLVFHDD--MGLPCGVLRLRHNG------GHGGHN-GLKSVMNNFRGNREFARLRI-GI 151 (181)
Q Consensus 99 ~~~~ilVvhDd--ldl~~G~vrlk~~G------s~~GHN-GlkSI~~~l~gt~~f~RlrI-GI 151 (181)
.+ +.+|+-|= .+.++|+++.-... +...|. |+..+...+.+ +.+++.+ ||
T Consensus 54 ~~-d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~~--~~p~v~iigI 113 (156)
T PRK11544 54 RP-ERLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKE--DVPEVIFLGI 113 (156)
T ss_pred CC-CEEEEEECCccCcCCCEEEEEchhhcccccCCCCCcCCHHHHHHHHhc--CCCcEEEEEE
Confidence 22 55555564 56799999874211 123444 88888888742 2345444 44
No 30
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=31.29 E-value=84 Score=25.95 Aligned_cols=30 Identities=17% Similarity=0.202 Sum_probs=22.9
Q ss_pred CeeEEEecCCCCCCCcCcchHHHHHHHHHHHHcC
Q 030200 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQG 51 (181)
Q Consensus 18 ~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~~~~ 51 (181)
+.+|+|+|||= ..-==+|..++++|++++.
T Consensus 5 rilVlGiGN~L----~gDDGvG~~va~~L~~~~~ 34 (195)
T PRK10264 5 RVVVMGLGNLL----WADEGFGVRVAERLYAHYH 34 (195)
T ss_pred CEEEEEeCccc----cccCcHHHHHHHHHHhhcC
Confidence 47999999993 1233599999999987653
No 31
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=30.69 E-value=37 Score=28.06 Aligned_cols=30 Identities=17% Similarity=0.153 Sum_probs=25.9
Q ss_pred cchhHHHHHHHcCCCCCcEEEEeecCCCCC
Q 030200 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLPC 114 (181)
Q Consensus 85 SG~aV~~~~~~~ki~~~~ilVvhDdldl~~ 114 (181)
++.++.++++.++++++++++|-|.|=.+.
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL~TDV 124 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQLFTDV 124 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchhhhhh
Confidence 678888899999999999999999885543
No 32
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=28.72 E-value=62 Score=28.54 Aligned_cols=30 Identities=23% Similarity=0.133 Sum_probs=27.1
Q ss_pred CcccccchhHHHHHHHcCCCCCcEEEEeec
Q 030200 80 TYMNLSGESTGPLAAYYKLPLNRVLVFHDD 109 (181)
Q Consensus 80 TyMN~SG~aV~~~~~~~ki~~~~ilVvhDd 109 (181)
.=|=.+.+...++++..+|..++.||+|||
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd 98 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDD 98 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECC
Confidence 467778889999999999999999999999
No 33
>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=28.01 E-value=59 Score=29.67 Aligned_cols=32 Identities=25% Similarity=0.417 Sum_probs=25.3
Q ss_pred EEEEeCCCcccccchhHHHHHHHcCCCCCcEEEEeec
Q 030200 73 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDD 109 (181)
Q Consensus 73 v~L~kP~TyMN~SG~aV~~~~~~~ki~~~~ilVvhDd 109 (181)
.++++|..+.| .|+..++.+|++ .++++||||
T Consensus 116 ~~~lrp~~~~~---~Ai~dlV~~~~W--~~v~~iYD~ 147 (400)
T cd06392 116 TLAARPPVRLN---DVMLKLVTELRW--QKFIVFYDS 147 (400)
T ss_pred eEEecCchHHH---HHHHHHHHhCCC--cEEEEEEEC
Confidence 57888853333 399999999988 799999975
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=25.62 E-value=55 Score=25.77 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=22.4
Q ss_pred chhHHHHHHHcCCCCCcEEEEeecC
Q 030200 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (181)
Q Consensus 86 G~aV~~~~~~~ki~~~~ilVvhDdl 110 (181)
|.+++.+++.+++++++++++=|+.
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 6778899999999999999999875
No 35
>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
Probab=25.05 E-value=88 Score=30.03 Aligned_cols=76 Identities=17% Similarity=0.122 Sum_probs=45.3
Q ss_pred CeeEEE-----ecCC---CCCCCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEe----CCCccccc
Q 030200 18 PWLFVG-----LGNP---GDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK----PQTYMNLS 85 (181)
Q Consensus 18 ~~LivG-----LGNP---g~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~k----P~TyMN~S 85 (181)
..+||| +|-| |+-|. +|.++.++|.++..+++..-...-..++.+ ...+...+ ...+.+.|
T Consensus 282 th~ivGrdhAg~~~~~~~g~~Y~---~~~a~~i~~~~~~~l~i~~~~~~~~~Y~~~----~~~~~~~~~cph~~~~~~~s 354 (568)
T PRK05537 282 THFIVGRDHAGPGKDSRGKPFYG---PYDAQELFAKYADEIGITMVPFKEMVYVQD----KAQYVPVDEVPQGATVLTIS 354 (568)
T ss_pred CeEEECCCCCCCCCCCcCcccCC---chHHHHHHHhCccccCceEEecceeEEEcC----CCeEEecCcCCCCcceeccC
Confidence 357887 5444 44444 788999999998778776432111111100 01222222 35699999
Q ss_pred chhHHHHHHHcCCCC
Q 030200 86 GESTGPLAAYYKLPL 100 (181)
Q Consensus 86 G~aV~~~~~~~ki~~ 100 (181)
|..++.+++.=..+|
T Consensus 355 gt~ir~~l~~G~~pP 369 (568)
T PRK05537 355 GTELRRRLREGLEIP 369 (568)
T ss_pred HHHHHHHHHCCCCCC
Confidence 999998887644444
No 36
>PF05017 TMP: TMP repeat; InterPro: IPR007713 This short repeat consists of the motif WXXh where X can be any residue and h is a hydrophobic residue. The repeat is named TMP after its occurrence in the tape measure protein (TMP). Tape measure protein is a component of phage tail and probably forms a beta-helix. Truncated forms of TMP lead to shortened tail fibres []. This repeat is also found in non-phage proteins where it may play a structural role.
Probab=24.25 E-value=37 Score=15.44 Aligned_cols=8 Identities=50% Similarity=0.883 Sum_probs=5.9
Q ss_pred CchhhHHH
Q 030200 129 NGLKSVMN 136 (181)
Q Consensus 129 NGlkSI~~ 136 (181)
||+|++.+
T Consensus 2 n~Ik~~~s 9 (11)
T PF05017_consen 2 NGIKSFFS 9 (11)
T ss_pred chHHHHhh
Confidence 78888764
No 37
>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=23.62 E-value=2.8e+02 Score=24.78 Aligned_cols=71 Identities=23% Similarity=0.352 Sum_probs=46.6
Q ss_pred EEeecCCCC--CceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEcccCCCCCCCcccccCCCCCHHHHHHHHhhh
Q 030200 105 VFHDDMGLP--CGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERELNNI 180 (181)
Q Consensus 105 VvhDdldl~--~G~vrlk~~Gs~~GHNGlkSI~~~l~gt~~f~RlrIGIGrP~~~~~~~~yVL~~f~~~E~~~l~~~~ 180 (181)
|..|++.-. +|+| +-.-||.|-||-.|=|...|. . .=.|+ |||--|..+ .+..|---.++.+|+...-+.+
T Consensus 24 ~y~D~~~~gs~~gTV-v~~hGsPGSH~DFkYi~~~l~-~-~~iR~-I~iN~PGf~-~t~~~~~~~~~n~er~~~~~~l 96 (297)
T PF06342_consen 24 VYEDSLPSGSPLGTV-VAFHGSPGSHNDFKYIRPPLD-E-AGIRF-IGINYPGFG-FTPGYPDQQYTNEERQNFVNAL 96 (297)
T ss_pred EEEecCCCCCCceeE-EEecCCCCCccchhhhhhHHH-H-cCeEE-EEeCCCCCC-CCCCCcccccChHHHHHHHHHH
Confidence 445766544 6655 668899999999999999983 2 22333 677777543 3345555677777876654443
No 38
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=22.99 E-value=83 Score=27.84 Aligned_cols=30 Identities=17% Similarity=0.318 Sum_probs=23.2
Q ss_pred HHHHcCCCCCcEEEEeecCCCCCceEEEec
Q 030200 92 LAAYYKLPLNRVLVFHDDMGLPCGVLRLRH 121 (181)
Q Consensus 92 ~~~~~ki~~~~ilVvhDdldl~~G~vrlk~ 121 (181)
++...+..++.+||.+||+..+-|.-..|.
T Consensus 130 l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~ 159 (287)
T COG2607 130 LVELLRARPEKFILFCDDLSFEEGDDAYKA 159 (287)
T ss_pred HHHHHhcCCceEEEEecCCCCCCCchHHHH
Confidence 444455667899999999999999776653
No 39
>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=22.75 E-value=61 Score=23.54 Aligned_cols=33 Identities=24% Similarity=0.319 Sum_probs=19.3
Q ss_pred CCCeeEEEecCCCCCCCcCcchHHHHHHHHHHH
Q 030200 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAE 48 (181)
Q Consensus 16 ~~~~LivGLGNPg~~Y~~TRHNvG~~~ld~la~ 48 (181)
...+++||||+....-..+--.++-.++..+.+
T Consensus 52 ~~~v~lvGlG~~~~~~~~~~r~a~~~~~~~l~~ 84 (126)
T PF02789_consen 52 AKRVLLVGLGKKEKLTAESLRKAGAAAARALKK 84 (126)
T ss_dssp CSEEEEEEEESCTGBCHHHHHHHHHHHHHHHHH
T ss_pred ccEEEEEECCCcCcCCHHHHHHHHHHHHHHHhh
Confidence 346899999999753222333444455555544
No 40
>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=22.52 E-value=4.1e+02 Score=24.41 Aligned_cols=67 Identities=9% Similarity=0.084 Sum_probs=45.4
Q ss_pred hHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCC---CcccccchhHHHHHHHcCCCCCcEEE
Q 030200 37 NVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQ---TYMNLSGESTGPLAAYYKLPLNRVLV 105 (181)
Q Consensus 37 NvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~---TyMN~SG~aV~~~~~~~ki~~~~ilV 105 (181)
.+|=+++-.|...... + ..-+.-.+++..+.+.+++++|+. .=.=.=|++|..+...++-.++.+|-
T Consensus 184 gaGPLVA~~l~~~~~~-~-~~~~dtv~~e~~~egRrv~viKA~GPGstVGrpgeave~i~~~~~~k~~~IIT 253 (355)
T PF07431_consen 184 GAGPLVAGRLMENCSK-W-EIAKDTVIAECEFEGRRVYVIKAEGPGSTVGRPGEAVEYIVEKLGGKVDLIIT 253 (355)
T ss_pred CcchHHHHHHHhcCcc-c-ccccccEEEEEEECCcEEEEEeccCCCccCCChHHHHHHHHHHhcCCccEEEE
Confidence 4677777777765433 2 222345678889999999999954 44455577888888887656665554
No 41
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.24 E-value=23 Score=22.87 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=17.6
Q ss_pred cccchhHHHHHHHcCCCCCcEEEEeec
Q 030200 83 NLSGESTGPLAAYYKLPLNRVLVFHDD 109 (181)
Q Consensus 83 N~SG~aV~~~~~~~ki~~~~ilVvhDd 109 (181)
+.|-..+.++++++++++++++...+|
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 455677888999999999998877665
No 42
>PRK06437 hypothetical protein; Provisional
Probab=21.23 E-value=1.2e+02 Score=20.44 Aligned_cols=29 Identities=7% Similarity=-0.011 Sum_probs=23.8
Q ss_pred cchhHHHHHHHcCCCCCcEEEEeecCCCC
Q 030200 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (181)
Q Consensus 85 SG~aV~~~~~~~ki~~~~ilVvhDdldl~ 113 (181)
.+.+|+++++.++++++.+.|.++.--+|
T Consensus 19 ~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 19 HELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 44678999999999999998888876665
No 43
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=21.10 E-value=69 Score=28.71 Aligned_cols=40 Identities=23% Similarity=0.360 Sum_probs=32.2
Q ss_pred CeeEEEEeCCCcccccchhHHHHHHHcCCCCCcEEEEeecCCCCCc
Q 030200 70 DAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCG 115 (181)
Q Consensus 70 ~~~v~L~kP~TyMN~SG~aV~~~~~~~ki~~~~ilVvhDdldl~~G 115 (181)
.+.+++=||.++|= ..+.+.|++.+++.+.|-|-||.+..
T Consensus 217 R~P~v~GKP~~~m~------~~l~~~~~i~psRt~mvGDRL~TDIl 256 (306)
T KOG2882|consen 217 RQPIVLGKPSTFMF------EYLLEKFNIDPSRTCMVGDRLDTDIL 256 (306)
T ss_pred CCCeecCCCCHHHH------HHHHHHcCCCcceEEEEcccchhhhh
Confidence 35688999999983 24678899999999999998877643
No 44
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=20.35 E-value=59 Score=26.87 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=22.4
Q ss_pred chhHHHHHHHcCCCCCcEEEEeecC
Q 030200 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (181)
Q Consensus 86 G~aV~~~~~~~ki~~~~ilVvhDdl 110 (181)
|.+++.+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 6888999999999999999998864
Done!