Query 027817
Match_columns 218
No_of_seqs 210 out of 1045
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 15:38:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027817.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027817hhsearch_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 1.2E-78 2.5E-83 513.8 20.2 188 17-205 1-189 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 3.2E-78 6.9E-83 513.8 21.7 190 17-206 1-190 (191)
3 TIGR00447 pth peptidyl-tRNA hy 100.0 4.2E-76 9.1E-81 499.9 22.3 186 18-204 1-188 (188)
4 PRK05426 peptidyl-tRNA hydrola 100.0 1.8E-74 3.9E-79 490.3 22.1 187 17-205 1-188 (189)
5 PF01195 Pept_tRNA_hydro: Pept 100.0 2.3E-73 5E-78 481.1 18.2 183 20-203 1-184 (184)
6 cd00462 PTH Peptidyl-tRNA hydr 100.0 6.5E-73 1.4E-77 474.2 19.7 171 20-191 1-171 (171)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 3.2E-56 6.8E-61 377.7 14.2 183 18-204 39-222 (224)
8 TIGR00130 frhD coenzyme F420-r 91.0 7.5 0.00016 31.6 13.5 133 18-183 4-147 (153)
9 PRK11544 hycI hydrogenase 3 ma 88.8 9.8 0.00021 31.2 11.3 134 19-194 3-146 (156)
10 PRK12362 germination protease; 88.5 14 0.0003 34.4 13.0 126 7-151 89-228 (318)
11 TIGR00072 hydrog_prot hydrogen 88.3 12 0.00025 30.0 13.0 127 20-182 1-140 (145)
12 COG0680 HyaD Ni,Fe-hydrogenase 85.8 19 0.00042 29.9 12.5 140 17-190 2-154 (160)
13 TIGR00142 hycI hydrogenase mat 83.7 21 0.00046 28.7 14.6 128 20-183 2-138 (146)
14 cd06070 H2MP_like-2 Putative [ 82.8 23 0.00049 28.3 11.5 84 20-138 1-96 (140)
15 cd06062 H2MP_MemB-H2up Endopep 78.8 32 0.00069 27.6 12.6 128 20-184 2-143 (146)
16 cd06064 H2MP_F420-Reduc Endope 75.1 42 0.00091 27.0 12.1 131 20-183 1-146 (150)
17 PRK10466 hybD hydrogenase 2 ma 71.9 54 0.0012 26.9 13.9 134 18-187 2-149 (164)
18 PF11775 CobT_C: Cobalamin bio 62.8 18 0.00039 32.0 5.4 70 82-153 115-187 (219)
19 PF03418 Peptidase_A25: Germin 56.3 14 0.0003 34.8 3.8 132 15-170 94-248 (354)
20 PF06154 YagB_YeeU_YfjZ: YagB/ 53.5 24 0.00053 27.6 4.1 33 161-194 33-65 (103)
21 PRK10264 hydrogenase 1 maturat 49.1 1.7E+02 0.0037 25.0 15.0 137 18-191 5-157 (195)
22 PF14490 HHH_4: Helix-hairpin- 46.5 12 0.00025 28.1 1.4 26 31-56 45-72 (94)
23 PRK09256 hypothetical protein; 45.4 10 0.00022 31.0 1.0 25 105-129 3-29 (138)
24 cd06068 H2MP_like-1 Putative [ 42.0 25 0.00054 28.1 2.7 26 20-49 1-26 (144)
25 TIGR01651 CobT cobaltochelatas 41.0 53 0.0011 33.2 5.3 87 83-177 496-586 (600)
26 PRK02858 germination protease; 38.7 23 0.00051 33.6 2.3 28 16-47 110-137 (369)
27 cd06066 H2MP_NAD-link-bidir En 37.8 36 0.00079 27.1 3.1 27 20-50 1-27 (139)
28 TIGR01441 GPR GPR endopeptidas 37.5 25 0.00053 33.3 2.3 28 16-47 100-127 (358)
29 cd06063 H2MP_Cyano-H2up This g 37.2 41 0.00088 27.0 3.3 122 20-180 2-140 (146)
30 PF11458 Mistic: Membrane-inte 33.9 75 0.0016 23.8 3.9 25 167-191 2-26 (84)
31 cd06067 H2MP_MemB-H2evol Endop 31.1 47 0.001 26.3 2.7 124 20-180 1-133 (136)
32 cd00518 H2MP Hydrogenase speci 30.6 52 0.0011 26.0 2.9 124 20-180 1-136 (139)
33 cd00736 bacteriophage_lambda_l 30.6 85 0.0018 26.2 4.2 42 163-204 81-122 (151)
34 PF06466 PCAF_N: PCAF (P300/CB 30.2 58 0.0013 29.4 3.3 45 160-204 150-197 (252)
35 PF12989 DUF3873: Domain of un 29.5 51 0.0011 24.1 2.3 61 128-192 6-66 (69)
36 PF06342 DUF1057: Alpha/beta h 27.4 2.8E+02 0.0062 25.7 7.3 68 105-177 24-93 (297)
37 COG2179 Predicted hydrolase of 27.2 45 0.00098 28.5 2.0 28 85-112 95-122 (175)
38 PRK10870 transcriptional repre 26.4 61 0.0013 26.9 2.7 38 162-199 137-175 (176)
39 cd01614 EutN_CcmL Ethanolamine 26.1 1.5E+02 0.0032 22.3 4.4 44 68-125 19-62 (83)
40 KOG1486 GTP-binding protein DR 25.8 2.7E+02 0.0059 25.9 6.8 72 32-105 148-219 (364)
41 PF08282 Hydrolase_3: haloacid 25.7 51 0.0011 26.9 2.1 25 86-110 188-212 (254)
42 PF07431 DUF1512: Protein of u 24.6 3.1E+02 0.0066 26.1 7.2 68 37-106 184-254 (355)
43 COG2897 SseA Rhodanese-related 24.5 78 0.0017 28.9 3.2 30 80-109 69-98 (285)
44 PF00472 RF-1: RF-1 domain; I 22.4 58 0.0013 25.3 1.7 22 108-129 5-28 (113)
45 PF13443 HTH_26: Cro/C1-type H 22.0 20 0.00043 24.1 -0.9 27 83-109 37-63 (63)
46 PF14681 UPRTase: Uracil phosp 21.9 1.2E+02 0.0026 25.9 3.7 36 69-107 120-158 (207)
47 PRK03604 moaC bifunctional mol 21.7 3E+02 0.0065 25.4 6.5 71 79-150 170-251 (312)
48 PRK08179 prfH peptide chain re 21.1 70 0.0015 27.8 2.1 27 103-129 95-123 (200)
49 cd06392 PBP1_iGluR_delta_1 N-t 21.1 94 0.002 29.4 3.1 33 73-110 116-148 (400)
50 PRK10513 sugar phosphate phosp 20.6 57 0.0012 28.0 1.5 25 86-110 198-222 (270)
51 PF02318 FYVE_2: FYVE-type zin 20.6 1.9E+02 0.0042 22.4 4.4 36 166-202 1-36 (118)
52 PRK10976 putative hydrolase; P 20.5 60 0.0013 27.8 1.6 25 86-110 192-216 (266)
53 cd01896 DRG The developmentall 20.4 3.5E+02 0.0076 23.2 6.4 82 43-146 97-178 (233)
54 PRK06437 hypothetical protein; 20.1 1.5E+02 0.0033 20.8 3.3 29 85-113 19-47 (67)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-78 Score=513.83 Aligned_cols=188 Identities=43% Similarity=0.765 Sum_probs=181.9
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCC-CccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHH
Q 027817 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (218)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~-~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~ 95 (218)
.|+|||||||||++|+.||||||||++|.||++++.++ +.++|.+.++++.+.+++++|+||+||||+||++|.++++|
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 55789999999999999999999999999999999999999
Q ss_pred cCCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHH
Q 027817 96 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 175 (218)
Q Consensus 96 ~ki~~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~ 175 (218)
|++++++++|||||||||+|++|+|.+||+|||||||||+++| ||++|+|||||||||..+++|++|||++|+++|++.
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 699999999999999888899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHhhhch
Q 027817 176 IDTALQEGVEVLKLLLSKGLTESARHFNTI 205 (218)
Q Consensus 176 l~~~i~~a~~~~~~~i~~~~~~amn~~n~~ 205 (218)
+++++++|++|++.++++++++|||+||+.
T Consensus 160 l~~~~~~a~~~~~~~~~~~~~~~mn~~~~~ 189 (190)
T COG0193 160 LDKAIDKAADALELLLEGDFEKAMNKLNAL 189 (190)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHhcc
Confidence 999999999999999999999999999974
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=3.2e-78 Score=513.83 Aligned_cols=190 Identities=65% Similarity=1.131 Sum_probs=181.6
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 027817 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (218)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ 96 (218)
.|+|||||||||++|++|||||||+++|.||+++++++++.++.+.+++..+.+++++|+||+||||+||+||+++++||
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 47899999999999999999999999999999999988767888999999999999999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHH
Q 027817 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERI 176 (218)
Q Consensus 97 ki~~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~l 176 (218)
++++++++|||||||||+|++|+|.+||+|||||||||+++|+||++|+|||||||||+.+.++++|||++|+++|++.+
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 99999999999999999999999999999999999999999965789999999999997667899999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHhhhchh
Q 027817 177 DTALQEGVEVLKLLLSKGLTESARHFNTIQ 206 (218)
Q Consensus 177 ~~~i~~a~~~~~~~i~~~~~~amn~~n~~~ 206 (218)
+++++.|+++++.|+.+++++|||+||+.+
T Consensus 161 ~~~~~~a~~~~~~~~~~~~~~~~n~~n~~~ 190 (191)
T cd02406 161 DTALEQGVDAVRTLVLKGFNGSAERFNLVQ 190 (191)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHhCCC
Confidence 999999999999999999999999999654
No 3
>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=4.2e-76 Score=499.90 Aligned_cols=186 Identities=44% Similarity=0.771 Sum_probs=178.0
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCc-cccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 027817 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNT-VHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (218)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~-~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ 96 (218)
|+|||||||||++|++|||||||+++|+||++++.++.+ .++.+.+++..+.+++++|+||+||||+||++|+++++||
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 689999999999999999999999999999999998763 5677888888899999999999999999999999999999
Q ss_pred CCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHH
Q 027817 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERI 176 (218)
Q Consensus 97 ki~~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~l 176 (218)
++++++++|||||||||+|++|+|++||+|||||||||+++| ||++|+|||||||||+.+.++++|||++|+++|++.+
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 6899999999999997767899999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcC-HHHHHHhhhc
Q 027817 177 DTALQEGVEVLKLLLSKG-LTESARHFNT 204 (218)
Q Consensus 177 ~~~i~~a~~~~~~~i~~~-~~~amn~~n~ 204 (218)
+++++.++++++.|++++ +++|||+||+
T Consensus 160 ~~~i~~~~~~~~~~~~~~~~~~~~n~~n~ 188 (188)
T TIGR00447 160 EKALDKAVEALEMSFSEGAFLKAMNRFNS 188 (188)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHhhC
Confidence 999999999999999999 9999999985
No 4
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=1.8e-74 Score=490.27 Aligned_cols=187 Identities=43% Similarity=0.794 Sum_probs=177.7
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCC-ccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHH
Q 027817 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (218)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~-~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~ 95 (218)
.|||||||||||++|++|||||||+++|.||++++..+. ..++.+.+++..+.+++++|+||+||||+||++|++++++
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 378999999999999999999999999999999887665 4567789999999889999999999999999999999999
Q ss_pred cCCCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHH
Q 027817 96 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 175 (218)
Q Consensus 96 ~ki~~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~ 175 (218)
|++++++++|||||+|+|+|++|+|.+||+|||||||||+++| ||++|+|||||||||+ ..++++|||++|+++|++.
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 6889999999999997 5679999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHhhhch
Q 027817 176 IDTALQEGVEVLKLLLSKGLTESARHFNTI 205 (218)
Q Consensus 176 l~~~i~~a~~~~~~~i~~~~~~amn~~n~~ 205 (218)
++++++.|+++++.|++++++++||++|+.
T Consensus 159 l~~~~~~a~~~v~~~~~~~~~~~~~~~n~~ 188 (189)
T PRK05426 159 LDKAIDKAADAIELLLEGGFEKAMNKFNSK 188 (189)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHhCC
Confidence 999999999999999999999999999964
No 5
>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=2.3e-73 Score=481.10 Aligned_cols=183 Identities=44% Similarity=0.844 Sum_probs=163.1
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccc-cceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k-~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 98 (218)
|||||||||++|++|||||||+++|+||++++.++.+.+ +.+.++...+.+.+++|+||+||||+||++|++++++|++
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 799999999999999999999999999999999886654 7788888889999999999999999999999999999999
Q ss_pred CCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHHH
Q 027817 99 PLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDT 178 (218)
Q Consensus 99 ~~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~l~~ 178 (218)
++++++|||||+|+|+|++|+|.+||+|||||||||+++| +|++|+|||||||||++..++++|||++|+++|++.+++
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 689999999999999877789999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHhhh
Q 027817 179 ALQEGVEVLKLLLSKGLTESARHFN 203 (218)
Q Consensus 179 ~i~~a~~~~~~~i~~~~~~amn~~n 203 (218)
+++.|+++++.|+++++++|||+||
T Consensus 160 ~~~~a~~~l~~~i~~~~~~~mn~~n 184 (184)
T PF01195_consen 160 VIPQAAEALEQIIEGGFEKAMNKFN 184 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHhC
Confidence 9999999999999999999999998
No 6
>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=6.5e-73 Score=474.15 Aligned_cols=171 Identities=51% Similarity=0.938 Sum_probs=164.3
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
|||||||||++|++|||||||+++|+||++++.++.+.++.+.+++..+.+++++|+||+||||+||++|+++++||+++
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 69999999999999999999999999999999988777778899999999999999999999999999999999999999
Q ss_pred CCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHHHH
Q 027817 100 LNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTA 179 (218)
Q Consensus 100 ~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~l~~~ 179 (218)
+++++|||||||||+|++|+|++||+|||||||||+++| ||++|+|||||||||+.+.++++|||++|+++|++.++++
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 6899999999999998777999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 027817 180 LQEGVEVLKLLL 191 (218)
Q Consensus 180 i~~a~~~~~~~i 191 (218)
++.|+++++.|+
T Consensus 160 ~~~~~~~~~~~~ 171 (171)
T cd00462 160 IEKAADALEDIL 171 (171)
T ss_pred HHHHHHHHHHhC
Confidence 999999998763
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-56 Score=377.74 Aligned_cols=183 Identities=56% Similarity=0.998 Sum_probs=163.6
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcC
Q 027817 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 97 (218)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~k 97 (218)
+|+|+||||||++|..|||||||.++|.||++++++..+.+.++..+-+.+++..+++++|++|||.||++|.+++..|+
T Consensus 39 ~wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y~ 118 (224)
T KOG2255|consen 39 PWLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALYK 118 (224)
T ss_pred ceEEEecCCCcccccccchhhHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhhc
Confidence 58999999999999999999999999999999999876655566667778889999999999999999999999999999
Q ss_pred CCCCcEEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHH-HH
Q 027817 98 LPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE-RI 176 (218)
Q Consensus 98 i~~~~ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~-~l 176 (218)
++.++++||||||++|+|++|+|++||++||||+||+++++.|...|+||+||||||++++|+.+|||++|++.|++ .|
T Consensus 119 i~~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgHNGvrs~~~~l~g~~~fpRL~iGIGrppg~~d~~a~vLskfsp~e~ke~L 198 (224)
T KOG2255|consen 119 IPLRHIVVIHDELELPLGKLRLRPGGSHRGHNGVRSVFNCLNGRRSFPRLSIGIGRPPGNEDVKAFVLSKFSPAEQKELL 198 (224)
T ss_pred chheeEEEEeccccCcCceEEeccCCCccccccHHHHHhhccCCcccceeeeecCCCCCchhhhHHHHHhcChhhhHHHH
Confidence 99999999999999999999999999999999999999999877799999999999999999999999999999988 45
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHhhhc
Q 027817 177 DTALQEGVEVLKLLLSKGLTESARHFNT 204 (218)
Q Consensus 177 ~~~i~~a~~~~~~~i~~~~~~amn~~n~ 204 (218)
+..++. ++.++.+++..-.++||-
T Consensus 199 et~l~~----~~~lil~~l~~~is~~~l 222 (224)
T KOG2255|consen 199 ETLLEH----VKTLILQGLQQSISRFNL 222 (224)
T ss_pred HHHHhh----hHHHHHHHHHHhcccCcC
Confidence 554444 444555566666666663
No 8
>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=90.96 E-value=7.5 Score=31.61 Aligned_cols=133 Identities=17% Similarity=0.147 Sum_probs=69.9
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHH-cCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHc
Q 027817 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (218)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~-~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ 96 (218)
+.+|+|+|||-. .===+|..++++|+++ +..+ ..+.+ ++........+..+.
T Consensus 4 ~ilVlGiGN~l~----gDDGvG~~v~~~L~~~~~~~~-----------------~~v~v------id~gt~~~~~l~~~~ 56 (153)
T TIGR00130 4 EILVVGCGNILF----GDDGFGPAVIEYLKENGVEKP-----------------DNVCL------IDAGTGAPHFVFTLI 56 (153)
T ss_pred eEEEEEeCcccc----ccCcHhHHHHHHHHHhCCCCC-----------------CCeEE------EECCCcHHHHHHHHh
Confidence 468999999953 2235999999999863 2111 01111 221111111111221
Q ss_pred CCCCCcEEEEeec--CCCCCceEEEec------CCC-CCCCCchhhHHHhhcCCCCccEEEE-eecCCCCCCCccccccC
Q 027817 97 KLPLNRVLVFHDD--MGLPCGVLRLRH------NGG-HGGHNGLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQ 166 (218)
Q Consensus 97 ki~~~~ilVihDD--ldlp~G~vrlk~------gGs-~gGHNGLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yVLs 166 (218)
.+...+.+||-|= .+.++|+++.-. ..+ +..+-|+..+++.+. .. .++.| ||- |.. -+..+|= -
T Consensus 57 ~~~~~d~vIivDA~~~~~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~-~~--~~~~iiGi~-p~~-~~~~~~~-~ 130 (153)
T TIGR00130 57 PQSKWKKIIVVDIADFGAEPGTLRVLNVDELPNGRYMDAHGWSLAYPLHDLE-ER--IDIRVVGCQ-PKY-VSQPDVD-I 130 (153)
T ss_pred hhcCCCEEEEEEccCCCcCCCEEEEEchHHcCCCCCCCCccCCHHHHHHHhc-CC--CCEEEEEEE-EeE-ecCCCCC-C
Confidence 2334566777785 578999998742 212 344459999998773 22 45555 553 321 1111222 2
Q ss_pred cCCHHHHHHHHHHHHHH
Q 027817 167 KFNAIARERIDTALQEG 183 (218)
Q Consensus 167 ~f~~~E~~~l~~~i~~a 183 (218)
.+|++=++.++++++.+
T Consensus 131 ~LS~~v~~a~~~~~~~i 147 (153)
T TIGR00130 131 GLTEEVNKAIPRAVEII 147 (153)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 56665555555444433
No 9
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=88.85 E-value=9.8 Score=31.18 Aligned_cols=134 Identities=16% Similarity=0.188 Sum_probs=71.3
Q ss_pred eEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCC
Q 027817 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (218)
Q Consensus 19 ~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 98 (218)
.+|+|+|||-.. ===+|..++++|++.. . . .+.++.-.| .|.-+-.+++.+
T Consensus 3 ~lVlGiGN~L~g----DDGvG~~v~~~L~~~~-~--~----------------~v~vid~gt----~~~~~~~~i~~~-- 53 (156)
T PRK11544 3 DVVLTVGNSMMG----DDGAGPLLAEKLAAAP-K--G----------------GWVVIDGGS----APENDIVAIREL-- 53 (156)
T ss_pred EEEEEeCccccc----cCcHHHHHHHHHhccC-C--C----------------CeEEEECCC----CHHHHHHHHHhc--
Confidence 589999999643 3359999999997642 1 0 011121112 122221222211
Q ss_pred CCCcEEEEeec--CCCCCceEEEecCC------CCCCCC-chhhHHHhhcCCCCccEEEE-eecCCCCCCCccccccCcC
Q 027817 99 PLNRVLVFHDD--MGLPCGVLRLRHNG------GHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKF 168 (218)
Q Consensus 99 ~~~~ilVihDD--ldlp~G~vrlk~gG------s~gGHN-GLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yVLs~f 168 (218)
.+ +.+||.|= .+.++|+++.-... +...|. ||..++..+.+ ..+++.+ ||= |. ++ +| =...
T Consensus 54 ~~-d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~~--~~p~v~iigI~-~~---~~-~~-g~~L 124 (156)
T PRK11544 54 RP-ERLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKE--DVPEVIFLGIQ-PD---IV-GF-YYPM 124 (156)
T ss_pred CC-CEEEEEECCccCcCCCEEEEEchhhcccccCCCCCcCCHHHHHHHHhc--CCCcEEEEEEE-ee---ec-cC-CCCC
Confidence 23 55566674 56799999873211 123444 88888888743 3345544 552 32 22 22 2355
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcC
Q 027817 169 NAIARERIDTALQEGVEVLKLLLSKG 194 (218)
Q Consensus 169 ~~~E~~~l~~~i~~a~~~~~~~i~~~ 194 (218)
|++=++ .++++++.++.|..++
T Consensus 125 S~~v~~----av~~~~~~l~~~~~~~ 146 (156)
T PRK11544 125 TQPVKD----AVETVYQRLEGWEGNG 146 (156)
T ss_pred CHHHHH----HHHHHHHHHHHhhccC
Confidence 654444 4556666777776543
No 10
>PRK12362 germination protease; Provisional
Probab=88.48 E-value=14 Score=34.41 Aligned_cols=126 Identities=19% Similarity=0.256 Sum_probs=72.1
Q ss_pred HHHHhccCCCCCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECC-eeEEEEeC----CCc
Q 027817 7 LRRGFCTAVARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKP----QTY 81 (218)
Q Consensus 7 ~~~~~~~~~~~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~-~~v~L~KP----~Ty 81 (218)
+++.+........|||||||.- -|--..|..|++.|.-.... ..++++..-.+ ..|.-+-| +|=
T Consensus 89 L~~ll~~~~~~~iLVvGLGN~~----vTpDaLGP~Vv~~l~vTrhl-------~~~~~~~~~~~~~pV~AiaPGVmg~TG 157 (318)
T PRK12362 89 LKKLINLDKEMTVLVVGLGNWN----VTPDALGPKVVSKLMVTRHL-------KEYAPEEIDEGIRPVCAIAPGVLGITG 157 (318)
T ss_pred HHHHhCCCCCCcEEEEEcCCCC----cCccccchhhhhhhhhhhhh-------hhhcCchhcCCCCcceEecCCcccccc
Confidence 3444422345678999999964 59999999999988643111 01111111111 23444434 566
Q ss_pred ccccchhHHHHHHHcCCCCCcEEEEeecCC----CCCc-eEEEecCC---CCCCCCchhhHH-HhhcCCCCccEEEEee
Q 027817 82 MNLSGESTGPLAAYYKLPLNRVLVFHDDMG----LPCG-VLRLRHNG---GHGGHNGLKSVM-NNFRGNREFARLRIGI 151 (218)
Q Consensus 82 MN~SG~aV~~~~~~~ki~~~~ilVihDDld----lp~G-~vrlk~gG---s~gGHNGLkSIi-~~L~gt~~f~RlrIGI 151 (218)
||. ++-++.+.+.++ .+++|.-|-+- --+| +|.+...| |+|=.|==+.|. +.| | .+=+.|||
T Consensus 158 iet-~Eii~gIv~k~k---pd~IIAIDALaar~~~Rl~~tIQisdtGI~PGSGVGN~R~~l~~etL-G---VPVIAIGV 228 (318)
T PRK12362 158 IET-AEIIKGVVEKIK---PDLVIAIDALAARSVERVNTTIQISDTGISPGSGVGNKRMGINEETL-G---VPVIAIGV 228 (318)
T ss_pred hhH-HHHHHHHHHhcC---CCEEEEEeccccCCHHHccCeEEECCCCCCCCccCCCcccccCHHHc-C---CCEEEEcC
Confidence 766 455667766654 46777778775 2467 88888766 343334333333 344 3 56666666
No 11
>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=88.28 E-value=12 Score=30.04 Aligned_cols=127 Identities=17% Similarity=0.193 Sum_probs=66.7
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
||+|+|||-.. ===+|..++++|++++.... .+-+ ++. |.....++.+..
T Consensus 1 lViGiGN~l~~----DDg~G~~v~~~L~~~~~~~~-----------------~v~~------id~-g~~~~~l~~~l~-- 50 (145)
T TIGR00072 1 LVLGIGNILRG----DDGFGPRVAERLEERYEFPP-----------------GVEV------LDG-GTLGLELLDAIE-- 50 (145)
T ss_pred CEEEECchhcc----cCcHHHHHHHHHHHhcCCCC-----------------CeEE------EEC-CCCHHHHHHHHh--
Confidence 58999999532 23599999999988653210 0111 111 111123333332
Q ss_pred CCcEEEEeecC--CCCCceEEEec--------CCC-CCCCCchhhHHHhhcCCCCcc-EEEE-eecCCCCCCCccccccC
Q 027817 100 LNRVLVFHDDM--GLPCGVLRLRH--------NGG-HGGHNGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAFLLQ 166 (218)
Q Consensus 100 ~~~ilVihDDl--dlp~G~vrlk~--------gGs-~gGHNGLkSIi~~L~gt~~f~-RlrI-GIGrP~~~~~v~~yVLs 166 (218)
..+.+||.|=. +.++|+++.-. .++ +..+-|+..+++.+.-....+ ++.+ ||= |. ++ +|- .
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 24566677765 55999988632 123 333448888887663112343 4444 552 21 22 222 3
Q ss_pred cCCHHHHHHHHHHHHH
Q 027817 167 KFNAIARERIDTALQE 182 (218)
Q Consensus 167 ~f~~~E~~~l~~~i~~ 182 (218)
.+|++=++.++++++.
T Consensus 125 ~LS~~v~~~~~~~~~~ 140 (145)
T TIGR00072 125 GLSPEVAAAVPAAVEL 140 (145)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 6666655555544443
No 12
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=85.78 E-value=19 Score=29.94 Aligned_cols=140 Identities=17% Similarity=0.168 Sum_probs=81.1
Q ss_pred CCeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCC-cccccchhHHHHHHH
Q 027817 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQT-YMNLSGESTGPLAAY 95 (218)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~T-yMN~SG~aV~~~~~~ 95 (218)
.+.+|+|+|||=. .-==+|-.++++|.+++...- ++-++.--| -+|+.+
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 3578999999953 334689999999988753211 111222111 133322
Q ss_pred cCCCCCcEEEEeecCCC--CCceEEEec------CCCCC---CCC-chhhHHHhhcCCCCccEEEEeecCCCCCCCcccc
Q 027817 96 YKLPLNRVLVFHDDMGL--PCGVLRLRH------NGGHG---GHN-GLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAF 163 (218)
Q Consensus 96 ~ki~~~~ilVihDDldl--p~G~vrlk~------gGs~g---GHN-GLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~y 163 (218)
.+...+-++|.|=++. .+|++++-. ...+. .|+ ++..+++.+.-..++...-+|+.-|.. ...+
T Consensus 52 -~l~~~d~vIIVDav~~g~epG~v~~i~~e~i~~~~~~~~~s~H~~~~~~~L~~~~~~~~~~~~~~~~~v~~~--~~~~- 127 (160)
T COG0680 52 -LLAGYDPVIIVDAVLFGLEPGEVRIIDPEEIPAYSSASKDSAHELPLSELLALLKELGGLPVLILGVQVPIV--SLPE- 127 (160)
T ss_pred -HhcCCCcEEEEEeeecCCCCceEEEechhhcccccccCCCccccCCHHHHHHHHHHhcCCceEEEEEeecee--cccc-
Confidence 1233344778886555 599998643 23343 565 677777777433456778888886542 2112
Q ss_pred ccCcCCHHHHHHHHHHHHHHHHHHHHH
Q 027817 164 LLQKFNAIARERIDTALQEGVEVLKLL 190 (218)
Q Consensus 164 VLs~f~~~E~~~l~~~i~~a~~~~~~~ 190 (218)
+...+|++=++.++.+++.+.+.+..+
T Consensus 128 ~~~~lS~ev~~a~~~av~~i~~~l~~~ 154 (160)
T COG0680 128 FGGGLSPEVEEAVDKAVERILEELREW 154 (160)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHhh
Confidence 225566666666666666666655543
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=83.68 E-value=21 Score=28.67 Aligned_cols=128 Identities=16% Similarity=0.168 Sum_probs=68.1
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
+|+|+|||-.. ===+|..++++|.+.+... .+.++.-.| .|.-.-.+.+.+ .
T Consensus 2 lVlGiGN~l~~----DDG~G~~v~~~L~~~~~~~------------------~v~v~d~gt----~~~~~~~~~~~~--~ 53 (146)
T TIGR00142 2 VLLCVGNELMG----DDGAGPYLAEKCAAAPKEE------------------NWVVINAGT----VPENFTVAIREL--R 53 (146)
T ss_pred EEEEeCccccc----cCcHHHHHHHHHHhccCCC------------------CEEEEECCC----ChHHHHHHHHhc--C
Confidence 79999999643 2349999999998653210 122222222 122111222222 2
Q ss_pred CCcEEEEeecC--CCCCceEEEecC-----CCCCCCC-chhhHHHhhcCCCCccEEEE-eecCCCCCCCccccccCcCCH
Q 027817 100 LNRVLVFHDDM--GLPCGVLRLRHN-----GGHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKFNA 170 (218)
Q Consensus 100 ~~~ilVihDDl--dlp~G~vrlk~g-----Gs~gGHN-GLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yVLs~f~~ 170 (218)
.+.++|.|-. +.++|+++.-.. .+..-|. |+..+++.+.+ .--.++.+ ||- |. ++ +|- ...|+
T Consensus 54 -~d~viivDA~~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~ll~~~~~-~~~~~~~ligi~-~~---~~-~~g-~~LS~ 125 (146)
T TIGR00142 54 -PTHILIVDATDMGLNPGEVRIIDDDIIEMYSMSTHNMPLSYLVDYLKE-DINGEIIFLGIQ-PD---IV-GFY-YPMSQ 125 (146)
T ss_pred -CCEEEEEECcccCCCCCeEEEEChhhccccccCcCcCCHHHHHHHHHh-cCCCeEEEEEEe-ee---ee-ecC-CCCCH
Confidence 3556666764 569999887432 1223454 99998877732 21234554 553 32 23 333 46676
Q ss_pred HHHHHHHHHHHHH
Q 027817 171 IARERIDTALQEG 183 (218)
Q Consensus 171 ~E~~~l~~~i~~a 183 (218)
+=++.++++++.+
T Consensus 126 ~v~~a~~~~~~~i 138 (146)
T TIGR00142 126 PVKDAVETLYQRL 138 (146)
T ss_pred HHHHHHHHHHHHH
Confidence 6555555444433
No 14
>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=82.76 E-value=23 Score=28.30 Aligned_cols=84 Identities=18% Similarity=0.209 Sum_probs=50.7
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
||+|+|||-.. ===+|+.++++|++ .+ +-++.- |.....++.++ .
T Consensus 1 lVlGiGN~l~~----DDg~G~~v~~~L~~-~~---------------------v~vi~~-------g~~~~~ll~~i--~ 45 (140)
T cd06070 1 LIIGVGNRLYG----DDGFGSCLAEALEQ-CG---------------------APVFDG-------GLDGFGLLSHL--E 45 (140)
T ss_pred CEEEECchhcc----cCcHHHHHHHHHhh-CC---------------------CEEEEC-------CCcHHHHHHHH--c
Confidence 68999999532 23599999999976 11 111111 22222344433 2
Q ss_pred CCcEEEEeecCC--CCCceEEEecC---------CCCCCCC-chhhHHHhh
Q 027817 100 LNRVLVFHDDMG--LPCGVLRLRHN---------GGHGGHN-GLKSVMNNF 138 (218)
Q Consensus 100 ~~~ilVihDDld--lp~G~vrlk~g---------Gs~gGHN-GLkSIi~~L 138 (218)
..+.+||.|=++ .++|.++++.. .+...|+ |+.++.+.+
T Consensus 46 ~~d~viiVDA~~~~~~pG~~~~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~ 96 (140)
T cd06070 46 NYDIVIFIDVAVIDEDVGVFKITPEPASVAEQISFETDAHRLGPAHLLLLL 96 (140)
T ss_pred CCCEEEEEEeecCCCCCeEEEEecCchhccccccCCCCCCcCCHHHHHHHH
Confidence 455666777654 68998888553 2224566 999987655
No 15
>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=78.84 E-value=32 Score=27.58 Aligned_cols=128 Identities=20% Similarity=0.258 Sum_probs=69.0
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
+|+|+|||-.. ===+|+.+++.|++.+..+.. +.+ ++. |.....++..+.
T Consensus 2 lV~GiGN~l~g----DDG~G~~va~~L~~~~~~~~~-----------------v~v------i~~-~~~~~~l~~~l~-- 51 (146)
T cd06062 2 LVLGIGNILLA----DEGIGVHAVERLEENYSFPEN-----------------VEL------IDG-GTLGLELLPYIE-- 51 (146)
T ss_pred EEEEECccccc----cCcHHHHHHHHHHHhcCCCCC-----------------eEE------EEC-CCCHHHHHHHHh--
Confidence 79999999532 235999999999887533210 111 111 222223333322
Q ss_pred CCcEEEEeecC--CCCCceEEEecC---------CCCCCCCchhhHHHhhc--CCCCccEEEE-eecCCCCCCCcccccc
Q 027817 100 LNRVLVFHDDM--GLPCGVLRLRHN---------GGHGGHNGLKSVMNNFR--GNREFARLRI-GIGRPPGQMDPKAFLL 165 (218)
Q Consensus 100 ~~~ilVihDDl--dlp~G~vrlk~g---------Gs~gGHNGLkSIi~~L~--gt~~f~RlrI-GIGrP~~~~~v~~yVL 165 (218)
..+.+|+.|=+ +.++|+++.-.. ..+..+-|+..+++.+. +. .-.++.| ||= |. ++ +|-
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 34677777864 779999876421 22445566888776542 11 1124443 442 21 22 222
Q ss_pred CcCCHHHHHHHHHHHHHHH
Q 027817 166 QKFNAIARERIDTALQEGV 184 (218)
Q Consensus 166 s~f~~~E~~~l~~~i~~a~ 184 (218)
..+|++=++.++++++.+.
T Consensus 125 ~~LS~~v~~av~~~~~~i~ 143 (146)
T cd06062 125 LELSPEVAAALPTAIEAVL 143 (146)
T ss_pred CCCCHHHHHHHHHHHHHHH
Confidence 4677766666665555443
No 16
>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=75.08 E-value=42 Score=27.01 Aligned_cols=131 Identities=15% Similarity=0.193 Sum_probs=69.1
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHH-HHHcC-
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPL-AAYYK- 97 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~-~~~~k- 97 (218)
||+|+|||-. .===+|+.++++|++++..+ . .+.++. .|...-.+ ..+..
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 5899999963 23359999999998764211 0 122222 23312111 12211
Q ss_pred CCCCcEEEEeecC--CCCCceEEEecC------C---CCCCCCchhhHHHhhcCCCCcc-EEEE-eecCCCCCCCccccc
Q 027817 98 LPLNRVLVFHDDM--GLPCGVLRLRHN------G---GHGGHNGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAFL 164 (218)
Q Consensus 98 i~~~~ilVihDDl--dlp~G~vrlk~g------G---s~gGHNGLkSIi~~L~gt~~f~-RlrI-GIGrP~~~~~v~~yV 164 (218)
....+.+||.|=+ +.++|+++.... . .+-.+-|+..+++.+.+ ..+ ++.+ ||- |.. .+..+|=
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 1235677777874 779999887432 1 24566799999987732 222 4443 543 321 1100121
Q ss_pred cCcCCHHHHHHHHHHHHHH
Q 027817 165 LQKFNAIARERIDTALQEG 183 (218)
Q Consensus 165 Ls~f~~~E~~~l~~~i~~a 183 (218)
..+|++=++.++++++.+
T Consensus 129 -~~LS~~v~~a~~~~~~~i 146 (150)
T cd06064 129 -PGLSEEVEKAVPKAVEII 146 (150)
T ss_pred -CCCCHHHHHHHHHHHHHH
Confidence 356666555555544443
No 17
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=71.91 E-value=54 Score=26.89 Aligned_cols=134 Identities=20% Similarity=0.260 Sum_probs=67.9
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcC
Q 027817 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 97 (218)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~k 97 (218)
+.+|+|+|||-. +===+|..++++|.+.+..+. .+. +++. |.....++.++
T Consensus 2 ~ilVlGiGN~l~----gDDGvG~~va~~L~~~~~~~~-----------------~v~------vid~-gt~~~~ll~~l- 52 (164)
T PRK10466 2 RILVLGVGNILL----TDEAIGVRIVEALEQRYILPD-----------------YVE------ILDG-GTAGMELLGDM- 52 (164)
T ss_pred ceEEEEECchhh----ccCcHHHHHHHHHHHhcCCCC-----------------CeE------EEec-cccHHHHHHHH-
Confidence 358999999953 233599999999987653311 011 1211 22222344433
Q ss_pred CCCCcEEEEeecC--CCC-CceEEEecC--------CCCCCC-CchhhHHHhhcCCCCcc-EEEE-eecCCCCCCCcccc
Q 027817 98 LPLNRVLVFHDDM--GLP-CGVLRLRHN--------GGHGGH-NGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAF 163 (218)
Q Consensus 98 i~~~~ilVihDDl--dlp-~G~vrlk~g--------Gs~gGH-NGLkSIi~~L~gt~~f~-RlrI-GIGrP~~~~~v~~y 163 (218)
...+.+||.|=. +.+ +|+++.-.. .+...| -|+..+...+.-..+.+ ++.+ ||- |. ++ +|
T Consensus 53 -~~~d~vIiVDA~~~g~~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~L~~~~~~g~~p~~v~lvgie-p~---~~-~~ 126 (164)
T PRK10466 53 -ANRDHLIIADAIVSKKNAPGTIMVLRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVI-PE---SL-EP 126 (164)
T ss_pred -hCCCEEEEEEecCCCCCCCCEEEEEchhhccccccCCCCcccCCHHHHHHHHHHcCCCCCeEEEEEEE-Ee---ec-cC
Confidence 234567777865 434 999876321 111234 45666665432112333 4444 774 32 11 23
Q ss_pred ccCcCCHHHHHHHHHHHHHHHHHH
Q 027817 164 LLQKFNAIARERIDTALQEGVEVL 187 (218)
Q Consensus 164 VLs~f~~~E~~~l~~~i~~a~~~~ 187 (218)
= ..+|++=++.++++++.+.+.+
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 3666655555554444443333
No 18
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=62.78 E-value=18 Score=31.95 Aligned_cols=70 Identities=23% Similarity=0.304 Sum_probs=42.5
Q ss_pred ccccchhHHHHHHHcCCCCC--c-EEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecC
Q 027817 82 MNLSGESTGPLAAYYKLPLN--R-VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGR 153 (218)
Q Consensus 82 MN~SG~aV~~~~~~~ki~~~--~-ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGr 153 (218)
=|..|+|+..+.+...-.++ + ++||.|= -|...--+..+++.-=++=||.+++......+.-=+.||||.
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 58999999877665432232 3 4577763 444433333333333345588888888422456668999986
No 19
>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=56.30 E-value=14 Score=34.82 Aligned_cols=132 Identities=22% Similarity=0.350 Sum_probs=47.3
Q ss_pred CCCCeEEEEecCCCCCcCcCcchHHHHHHHHHHH-HcCCCCCccccceEEEEEEECC-eeEEEEeCCCcccccc----hh
Q 027817 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAE-SQGISMNTVHCKATFGQGFVGD-APVLLAKPQTYMNLSG----ES 88 (218)
Q Consensus 15 ~~~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~-~~~~~~~~~k~~~~~~~~~~~~-~~v~L~KP~TyMN~SG----~a 88 (218)
.....|||||||.. -|--..|-.++|.+.- ++=..+..... ..+ ..|.-+-| --|=..| +.
T Consensus 94 ~~~~iLVVGLGN~~----vTPDALGP~vv~~l~VTRHL~~~~pe~~--------~~g~r~VsaiaP-GVmg~TGiET~eI 160 (354)
T PF03418_consen 94 KEASILVVGLGNWN----VTPDALGPRVVENLLVTRHLFELQPEEV--------DEGYRPVSAIAP-GVMGQTGIETAEI 160 (354)
T ss_dssp TT--EEEEE-S-SS----SGGG-HHHHHHHT----HHHHHHS--SS---------SS---EEEE-S-GGG---SS-HHHH
T ss_pred CCCeEEEEeCCCcC----CCccccchhhhhhhhhhhhhhhhCchhh--------ccCcceeeEEcC-CccccccccHHHH
Confidence 34567999999964 5999999999996632 11000000000 011 23444455 3344444 45
Q ss_pred HHHHHHHcCCCCCcEEEEeecCCC-----CCceEEEecCC-----CCCCC-CchhhHHHhhcCCCCccEEEEeecCCCC-
Q 027817 89 TGPLAAYYKLPLNRVLVFHDDMGL-----PCGVLRLRHNG-----GHGGH-NGLKSVMNNFRGNREFARLRIGIGRPPG- 156 (218)
Q Consensus 89 V~~~~~~~ki~~~~ilVihDDldl-----p~G~vrlk~gG-----s~gGH-NGLkSIi~~L~gt~~f~RlrIGIGrP~~- 156 (218)
|+.+++..| -+++|.-|-|-- =--+|.+.--| |-|-| ++|-. +.| | .+=+.||| |.-
T Consensus 161 i~gvv~~~k---Pd~VIaIDALAaRs~~Rl~~TIQisDTGI~PGSGVGN~R~~l~~--etL-G---vPVIAIGV--PTVV 229 (354)
T PF03418_consen 161 IKGVVEKIK---PDLVIAIDALAARSLERLNTTIQISDTGIHPGSGVGNHRKELNE--ETL-G---VPVIAIGV--PTVV 229 (354)
T ss_dssp HHHHHHHH-----SEEEEEEEE--SSGGGSSSEEEEETT-B-S-SSSS----BSSS-----------------------E
T ss_pred HHHHHHhhC---CCEEEEehhhhcCchhhccCeEEecCCCcCCCCCcCcccccCCH--HHc-C---CCEEEEcC--Ceee
Confidence 566666544 356666676532 23456665444 33444 33321 334 2 44555555 531
Q ss_pred -----CCCccccccCcCCH
Q 027817 157 -----QMDPKAFLLQKFNA 170 (218)
Q Consensus 157 -----~~~v~~yVLs~f~~ 170 (218)
-.|..++++..|..
T Consensus 230 dA~tI~~Dtid~~~~~~~~ 248 (354)
T PF03418_consen 230 DAATIVNDTIDYLLKHFGR 248 (354)
T ss_dssp EEEEEE--EES---HHHHT
T ss_pred chHHHHHHHHHHHHHHHHH
Confidence 02445677766644
No 20
>PF06154 YagB_YeeU_YfjZ: YagB/YeeU/YfjZ family; InterPro: IPR009320 This family of proteins includes three proteins from Escherichia coli proteins YagB, YeeU and YfjZ. The function of these proteins is unknown. They are about 120 amino acids in length.; PDB: 2H28_A 2INW_B 2JN7_A 2EA9_A.
Probab=53.48 E-value=24 Score=27.62 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=24.8
Q ss_pred cccccCcCCHHHHHHHHHHHHHHHHHHHHHHhcC
Q 027817 161 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 194 (218)
Q Consensus 161 ~~yVLs~f~~~E~~~l~~~i~~a~~~~~~~i~~~ 194 (218)
++++ +.||++|...|+++++...+-++..+..|
T Consensus 33 A~i~-G~Fs~~~~~~Ld~aFP~~ikqlE~ml~sG 65 (103)
T PF06154_consen 33 AGIT-GTFSEEEAQHLDQAFPLFIKQLELMLTSG 65 (103)
T ss_dssp EEEE-S---HHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred CCeE-EEcCHHHHHHHHhHhHHHHHHHHHHHhcC
Confidence 4444 89999999999999999999888887643
No 21
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=49.09 E-value=1.7e+02 Score=25.02 Aligned_cols=137 Identities=20% Similarity=0.237 Sum_probs=78.1
Q ss_pred CeEEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcC
Q 027817 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 97 (218)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~k 97 (218)
..+|+|+|||=. .===+|..++++|.+++..+. .+.++.- |.....++.+..
T Consensus 5 rilVlGiGN~L~----gDDGvG~~va~~L~~~~~~~~-----------------~V~vid~-------Gt~g~~ll~~i~ 56 (195)
T PRK10264 5 RVVVMGLGNLLW----ADEGFGVRVAERLYAHYHWPE-----------------YVEIVDG-------GTQGLNLLGYVE 56 (195)
T ss_pred CEEEEEeCcccc----ccCcHHHHHHHHHHhhcCCCC-----------------CeEEEEC-------CCCHHHHHHHHc
Confidence 468999999942 223599999999987653221 0111111 111113333332
Q ss_pred CCCCcEEEEeecC--CCCCceEEEecCC---------C-CCCCCchhhHHHh--hcCCCCcc-EEE-EeecCCCCCCCcc
Q 027817 98 LPLNRVLVFHDDM--GLPCGVLRLRHNG---------G-HGGHNGLKSVMNN--FRGNREFA-RLR-IGIGRPPGQMDPK 161 (218)
Q Consensus 98 i~~~~ilVihDDl--dlp~G~vrlk~gG---------s-~gGHNGLkSIi~~--L~gt~~f~-Rlr-IGIGrP~~~~~v~ 161 (218)
..+.+||-|=+ +.++|+++.-... + +-.+-|+..++.. +.| +.+ ++. |||= |. ++.
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 34566677854 5689998874321 1 2233688888753 322 343 566 4774 32 111
Q ss_pred ccccCcCCHHHHHHHHHHHHHHHHHHHHHH
Q 027817 162 AFLLQKFNAIARERIDTALQEGVEVLKLLL 191 (218)
Q Consensus 162 ~yVLs~f~~~E~~~l~~~i~~a~~~~~~~i 191 (218)
..=-.+|++=++.++++++.+.+.++.|.
T Consensus 129 -~~g~~LSp~V~~av~~~v~~i~~~l~~~~ 157 (195)
T PRK10264 129 -DYGGSLSELAREQLPAAEQAALAQLAAWG 157 (195)
T ss_pred -CCCCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 12247788777888888777777776665
No 22
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=46.47 E-value=12 Score=28.10 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=19.8
Q ss_pred cCcCc--chHHHHHHHHHHHHcCCCCCc
Q 027817 31 YKGTR--HNVGFEMIDAFAESQGISMNT 56 (218)
Q Consensus 31 Y~~TR--HNvGf~vld~La~~~~~~~~~ 56 (218)
|.-.. --+||..+|.+|.++|+....
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~d 72 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPDD 72 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT-
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCCC
Confidence 77676 689999999999999987543
No 23
>PRK09256 hypothetical protein; Provisional
Probab=45.39 E-value=10 Score=30.98 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=20.7
Q ss_pred EEeecCCCCCceEEEe--cCCCCCCCC
Q 027817 105 VFHDDMGLPCGVLRLR--HNGGHGGHN 129 (218)
Q Consensus 105 VihDDldlp~G~vrlk--~gGs~gGHN 129 (218)
-|.+|+++|...++++ .++|+||+|
T Consensus 3 ~~~~~~~i~~~~l~~~~~RSSGPGGQ~ 29 (138)
T PRK09256 3 RITRRLVIPENELEWRFIRASGPGGQN 29 (138)
T ss_pred ccCccCccCHHHeEEEEEEcCCCCccc
Confidence 3678899998888776 688999987
No 24
>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=42.04 E-value=25 Score=28.14 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=20.5
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHH
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~ 49 (218)
||+|+|||-.. ===+|..++++|+++
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~ 26 (144)
T cd06068 1 LVAGVGNIFLG----DDGFGVEVARRLRPR 26 (144)
T ss_pred CEEEECccccc----cCcHHHHHHHHHhcc
Confidence 68999999643 224999999999865
No 25
>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=41.04 E-value=53 Score=33.17 Aligned_cols=87 Identities=21% Similarity=0.286 Sum_probs=51.4
Q ss_pred cccchhHHHHHHHcCCCCC--c-EEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCC-CccEEEEeecCCCCCC
Q 027817 83 NLSGESTGPLAAYYKLPLN--R-VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNR-EFARLRIGIGRPPGQM 158 (218)
Q Consensus 83 N~SG~aV~~~~~~~ki~~~--~-ilVihDDldlp~G~vrlk~gGs~gGHNGLkSIi~~L~gt~-~f~RlrIGIGrP~~~~ 158 (218)
|..|+|+..+....--.++ . ++||.|=- |...--+....+.-=++=||.+|+... +. ..-=+.||||..
T Consensus 496 N~DGeAl~wa~~rL~~R~e~rKiL~ViSDG~--P~D~~TlsvN~~~~l~~hLr~vi~~~e-~~~~vel~aigIg~D---- 568 (600)
T TIGR01651 496 NIDGEALMWAHQRLIARPEQRRILMMISDGA--PVDDSTLSVNPGNYLERHLRAVIEEIE-TRSPVELLAIGIGHD---- 568 (600)
T ss_pred CCchHHHHHHHHHHhcCcccceEEEEEeCCC--cCCccccccCchhHHHHHHHHHHHHHh-ccCCceEEEeecccc----
Confidence 8889999887765443333 3 56788743 433222333333334555999999983 43 566699999963
Q ss_pred CccccccCcCCHHHHHHHH
Q 027817 159 DPKAFLLQKFNAIARERID 177 (218)
Q Consensus 159 ~v~~yVLs~f~~~E~~~l~ 177 (218)
|..|-=..++-.+.+.|.
T Consensus 569 -v~r~Y~~~v~i~~~~eL~ 586 (600)
T TIGR01651 569 -VTRYYRRAVTIVDAEELA 586 (600)
T ss_pred -HHHHccccceecCHHHHH
Confidence 444443334444444443
No 26
>PRK02858 germination protease; Provisional
Probab=38.66 E-value=23 Score=33.55 Aligned_cols=28 Identities=29% Similarity=0.361 Sum_probs=22.8
Q ss_pred CCCeEEEEecCCCCCcCcCcchHHHHHHHHHH
Q 027817 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (218)
Q Consensus 16 ~~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La 47 (218)
....|||||||- .-|--..|-.|++.|.
T Consensus 110 ~~~vLVVGLGN~----~VTPDALGP~vv~~l~ 137 (369)
T PRK02858 110 EASCLIVGLGNW----NVTPDALGPLVVENVL 137 (369)
T ss_pred CCcEEEEeCCCc----CCCccccChheeccee
Confidence 456899999995 4688899999999664
No 27
>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=37.77 E-value=36 Score=27.05 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=21.3
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHc
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~ 50 (218)
||+|+|||=. .===+|+.++++|++++
T Consensus 1 lVlGvGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPLR----GDDGLGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCccc----cccchhHHHHHHHHhhC
Confidence 5899999953 23359999999998774
No 28
>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=37.53 E-value=25 Score=33.28 Aligned_cols=28 Identities=29% Similarity=0.400 Sum_probs=22.9
Q ss_pred CCCeEEEEecCCCCCcCcCcchHHHHHHHHHH
Q 027817 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (218)
Q Consensus 16 ~~~~LIvGLGNPG~~Y~~TRHNvGf~vld~La 47 (218)
....|||||||- .-|--..|-.+++.|.
T Consensus 100 ~~~iLVVGLGN~----~VTPDALGP~vv~~l~ 127 (358)
T TIGR01441 100 DMTCLVVGLGNW----NVTPDALGPKVVENLL 127 (358)
T ss_pred CCcEEEEeCCCc----CCCccccChheeccee
Confidence 356799999996 4588899999999764
No 29
>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=37.23 E-value=41 Score=27.00 Aligned_cols=122 Identities=14% Similarity=0.114 Sum_probs=63.6
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
+|+|+|||-.. ===+|..++++|++.. .+ . .+.++-- |.....++... .
T Consensus 2 lVlGiGN~L~~----DDG~G~~v~~~L~~~~-~~--~---------------~v~~id~-------gt~~~~l~~~l--~ 50 (146)
T cd06063 2 TIIGCGNLNRG----DDGVGPILIRRLQAYL-LP--P---------------HVRLVDC-------GTAGMEVMFRA--R 50 (146)
T ss_pred EEEEECCcccc----cCcHHHHHHHHHhhcC-CC--C---------------CeEEEEC-------CCCHHHHHHHh--c
Confidence 79999999532 2359999999998642 11 0 0111111 11122333322 2
Q ss_pred CCcEEEEeecC--CCCCceEEEe------c---CCCCCCCCchhhHHHh----hcCCCCcc-EEE-EeecCCCCCCCccc
Q 027817 100 LNRVLVFHDDM--GLPCGVLRLR------H---NGGHGGHNGLKSVMNN----FRGNREFA-RLR-IGIGRPPGQMDPKA 162 (218)
Q Consensus 100 ~~~ilVihDDl--dlp~G~vrlk------~---gGs~gGHNGLkSIi~~----L~gt~~f~-Rlr-IGIGrP~~~~~v~~ 162 (218)
..+.+||.|=. +.++|+++.- . ...+..+=|+.++++. ++ ...+ ++. +|| .|. ++ +
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 1233 554 477 332 22 2
Q ss_pred cccCcCCHHHHHHHHHHH
Q 027817 163 FLLQKFNAIARERIDTAL 180 (218)
Q Consensus 163 yVLs~f~~~E~~~l~~~i 180 (218)
|= ..+|++=++.+++++
T Consensus 124 ~g-~~LS~~v~~a~~~~~ 140 (146)
T cd06063 124 FG-LELSPPVKQAAERVA 140 (146)
T ss_pred CC-CCCCHHHHHHHHHHH
Confidence 22 356655555444443
No 30
>PF11458 Mistic: Membrane-integrating protein Mistic; InterPro: IPR021078 Mistic is an integral membrane protein that folds autonomously into the membrane []. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
Probab=33.95 E-value=75 Score=23.84 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=19.7
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHH
Q 027817 167 KFNAIARERIDTALQEGVEVLKLLL 191 (218)
Q Consensus 167 ~f~~~E~~~l~~~i~~a~~~~~~~i 191 (218)
+.+.+|++.|..++++..+.++.|+
T Consensus 2 KVt~~EkeQLS~AID~mnEGLD~fI 26 (84)
T PF11458_consen 2 KVTDQEKEQLSTAIDRMNEGLDTFI 26 (84)
T ss_pred CCchHHHHHHHHHHHHHHhhHHHHH
Confidence 4577899999998888777776665
No 31
>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=31.11 E-value=47 Score=26.29 Aligned_cols=124 Identities=16% Similarity=0.195 Sum_probs=64.1
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
+|+|+|||-.. ===+|..++++|.++. . . .+-++.-.| .|.-+ +......
T Consensus 1 ~VlGiGN~L~~----DDgvG~~v~~~L~~~~-~--~----------------~v~vid~gt----~~~~~---~~~l~~~ 50 (136)
T cd06067 1 VLLGVGNELRG----DDGAGPLLAEKLEDLP-N--P----------------NWLVIDGGT----VPENF---TGKIREE 50 (136)
T ss_pred CEEEeCccccc----cCcHHHHHHHHHHhcC-C--C----------------CEEEEECCC----CHHHH---HHHHHhc
Confidence 58999999532 3359999999998753 1 0 011111111 22221 2221111
Q ss_pred CCcEEEEeecC--CCCCceEEEecCC------CCCCCCchhhHHHhhcCCCCccEEEE-eecCCCCCCCccccccCcCCH
Q 027817 100 LNRVLVFHDDM--GLPCGVLRLRHNG------GHGGHNGLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKFNA 170 (218)
Q Consensus 100 ~~~ilVihDDl--dlp~G~vrlk~gG------s~gGHNGLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yVLs~f~~ 170 (218)
..+.+||.|=. +.++|+++.-... .+..+-|+..+.+.+. ...-.++.+ ||- |. ++ +|- ..+|+
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 34566677875 4599999874321 2334448888887763 211233333 442 22 22 332 36666
Q ss_pred HHHHHHHHHH
Q 027817 171 IARERIDTAL 180 (218)
Q Consensus 171 ~E~~~l~~~i 180 (218)
+=++.+++++
T Consensus 124 ~v~~a~~~~~ 133 (136)
T cd06067 124 EVKDAAEELA 133 (136)
T ss_pred HHHHHHHHHH
Confidence 5555554443
No 32
>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=30.62 E-value=52 Score=25.95 Aligned_cols=124 Identities=17% Similarity=0.170 Sum_probs=66.0
Q ss_pred EEEEecCCCCCcCcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCC
Q 027817 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (218)
Q Consensus 20 LIvGLGNPG~~Y~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~ 99 (218)
+|+|+|||=. .===+|..++++|+++... ..+-+ ++. |...-.++....
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~~~------------------~~v~~------id~-gt~~~~l~~~l~-- 49 (139)
T cd00518 1 LVLGIGNPLR----GDDGFGPAVAERLEERYLP------------------PGVEV------IDG-GTLGLELLDLLE-- 49 (139)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcCCC------------------CCeEE------EEC-CCCHHHHHHHHh--
Confidence 5899999953 2235999999999876420 01111 111 111123333322
Q ss_pred CCcEEEEeecCC--CCCceEEEec------CCC-CCCCC-chhhHHHhhcCCC-CccEEEE-eecCCCCCCCccccccCc
Q 027817 100 LNRVLVFHDDMG--LPCGVLRLRH------NGG-HGGHN-GLKSVMNNFRGNR-EFARLRI-GIGRPPGQMDPKAFLLQK 167 (218)
Q Consensus 100 ~~~ilVihDDld--lp~G~vrlk~------gGs-~gGHN-GLkSIi~~L~gt~-~f~RlrI-GIGrP~~~~~v~~yVLs~ 167 (218)
..+.+||.|=.+ .++|+++.-. ..+ ...|. |+..+++.+.... .-.++.| ||= |. ++ +|= ..
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 256677778764 6999988732 122 12455 9999988773111 1233443 442 22 11 121 56
Q ss_pred CCHHHHHHHHHHH
Q 027817 168 FNAIARERIDTAL 180 (218)
Q Consensus 168 f~~~E~~~l~~~i 180 (218)
+|++=++.+++++
T Consensus 124 LS~~v~~a~~~~~ 136 (139)
T cd00518 124 LSPEVAAAVPKAV 136 (139)
T ss_pred CCHHHHHHHHHHH
Confidence 7766655555443
No 33
>cd00736 bacteriophage_lambda_lysozyme The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli. However, they differ structurally.
Probab=30.57 E-value=85 Score=26.18 Aligned_cols=42 Identities=12% Similarity=0.201 Sum_probs=30.9
Q ss_pred cccCcCCHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHhhhc
Q 027817 163 FLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 204 (218)
Q Consensus 163 yVLs~f~~~E~~~l~~~i~~a~~~~~~~i~~~~~~amn~~n~ 204 (218)
+=|..|+|+.++.+.-.+-+...++..+....+++||+++..
T Consensus 81 ~gl~~F~P~~QD~~A~~Li~~~gal~~i~~G~~~~a~~~La~ 122 (151)
T cd00736 81 YGLYDFSPESQDLVAYQLIRERGALPDILAGRIEQAIAKLSN 122 (151)
T ss_pred cCCCCCCHHHHHHHHHHHHHHcCcHHHHHcCCHHHHHHHHHh
Confidence 335899999998875433333447888888889999998774
No 34
>PF06466 PCAF_N: PCAF (P300/CBP-associated factor) N-terminal domain; InterPro: IPR009464 This region is spliced out of Q92830 from SWISSPROT isoform 2. It is predicted to be of a mixed alpha/beta fold - though predominantly helical.; GO: 0004402 histone acetyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=30.20 E-value=58 Score=29.42 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=30.1
Q ss_pred ccccccCcCC---HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHhhhc
Q 027817 160 PKAFLLQKFN---AIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 204 (218)
Q Consensus 160 v~~yVLs~f~---~~E~~~l~~~i~~a~~~~~~~i~~~~~~amn~~n~ 204 (218)
|.+||+.+|+ +.|.+.+-++.....-.+..|--+..+.-.+..+.
T Consensus 150 V~nfv~~kf~~l~~~E~q~m~elakmFL~~lN~W~le~ps~~~~~~~~ 197 (252)
T PF06466_consen 150 VTNFVLYKFSHLPQKEWQTMYELAKMFLHCLNHWKLEAPSQRRQRSNA 197 (252)
T ss_pred HHHHHHHHccCCCcHHHHHHHHHHHHHHHHHhhccCCChHHHHhhcCc
Confidence 3489999885 56777776665555666666665666666666654
No 35
>PF12989 DUF3873: Domain of unknown function, B. Theta Gene description (DUF3873); InterPro: IPR024356 This entry represents a family of uncharacterised proteins found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].
Probab=29.53 E-value=51 Score=24.15 Aligned_cols=61 Identities=20% Similarity=0.318 Sum_probs=39.0
Q ss_pred CCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 027817 128 HNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLS 192 (218)
Q Consensus 128 HNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~l~~~i~~a~~~~~~~i~ 192 (218)
+||+ ||-+.- |.+.|-+.+.|+|+... ....|=--..+.+=..-+...++.+-.+-+.|+.
T Consensus 6 ~nG~-S~c~~~-G~E~Y~~f~~~~~~k~~--~~~qYdYr~~~GeLFscV~~tLeEcRr~rd~WL~ 66 (69)
T PF12989_consen 6 KNGV-SICQTP-GEEKYEKFQLGIGRKGV--TKYQYDYRHTDGELFSCVAPTLEECRRLRDEWLS 66 (69)
T ss_pred cCCe-eecCCC-Cceeeeeeeeccccccc--eEEEEeeecCCccchhhhhccHHHHHHHHHHHHh
Confidence 5675 555555 68899999999987532 2223322333444445556677777777888875
No 36
>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=27.36 E-value=2.8e+02 Score=25.67 Aligned_cols=68 Identities=22% Similarity=0.338 Sum_probs=46.4
Q ss_pred EEeecCCCC--CceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHH
Q 027817 105 VFHDDMGLP--CGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERID 177 (218)
Q Consensus 105 VihDDldlp--~G~vrlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVLs~f~~~E~~~l~ 177 (218)
|..|++.-. +|+| +-.-||.|.||-.|=|...|. . .=.|+ |||--|..+ -+..|--..++.+|+...-
T Consensus 24 ~y~D~~~~gs~~gTV-v~~hGsPGSH~DFkYi~~~l~-~-~~iR~-I~iN~PGf~-~t~~~~~~~~~n~er~~~~ 93 (297)
T PF06342_consen 24 VYEDSLPSGSPLGTV-VAFHGSPGSHNDFKYIRPPLD-E-AGIRF-IGINYPGFG-FTPGYPDQQYTNEERQNFV 93 (297)
T ss_pred EEEecCCCCCCceeE-EEecCCCCCccchhhhhhHHH-H-cCeEE-EEeCCCCCC-CCCCCcccccChHHHHHHH
Confidence 344665443 6654 678899999999999999983 2 22343 788878653 4445666778888887553
No 37
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=27.22 E-value=45 Score=28.55 Aligned_cols=28 Identities=18% Similarity=0.172 Sum_probs=24.9
Q ss_pred cchhHHHHHHHcCCCCCcEEEEeecCCC
Q 027817 85 SGESTGPLAAYYKLPLNRVLVFHDDMGL 112 (218)
Q Consensus 85 SG~aV~~~~~~~ki~~~~ilVihDDldl 112 (218)
++.+..++++.++++++++++|-|.|=.
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL~T 122 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQLFT 122 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchhhh
Confidence 4788999999999999999999998843
No 38
>PRK10870 transcriptional repressor MprA; Provisional
Probab=26.40 E-value=61 Score=26.92 Aligned_cols=38 Identities=11% Similarity=0.229 Sum_probs=27.7
Q ss_pred ccccCcCCHHHHHHHHHHHHHHHHHHHHHHhcC-HHHHH
Q 027817 162 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKG-LTESA 199 (218)
Q Consensus 162 ~yVLs~f~~~E~~~l~~~i~~a~~~~~~~i~~~-~~~am 199 (218)
+-+++.++++|++.+...+.+..+.++..-++| +-+||
T Consensus 137 ~~~~~~ls~~e~~~l~~~L~kl~~~l~~~~~~~~~~~~~ 175 (176)
T PRK10870 137 HQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAM 175 (176)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHhhCCCchhhhhc
Confidence 456788888888888888888877777665544 55554
No 39
>cd01614 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation,
Probab=26.10 E-value=1.5e+02 Score=22.27 Aligned_cols=44 Identities=25% Similarity=0.375 Sum_probs=35.7
Q ss_pred ECCeeEEEEeCCCcccccchhHHHHHHHcCCCCCcEEEEeecCCCCCceEEEecCCCC
Q 027817 68 VGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGH 125 (218)
Q Consensus 68 ~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDldlp~G~vrlk~gGs~ 125 (218)
+.+.++++++|. +..|+ +..+.+|..|.+.--.|..-+-..||+
T Consensus 19 L~G~kLliVq~~---~~~~~-----------~~g~~~VA~D~vGAG~Ge~Vlv~~Gs~ 62 (83)
T cd01614 19 LAGKKLLVVQPL---DGEGK-----------PKGEPLVAVDPVGAGVGEWVLVATGSA 62 (83)
T ss_pred CCCcEEEEEEEC---ccCCC-----------cCCCEEEEEECCCCCCCCEEEEeCChH
Confidence 457899999995 44443 567889999999999999999887764
No 40
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=25.79 E-value=2.7e+02 Score=25.90 Aligned_cols=72 Identities=19% Similarity=0.181 Sum_probs=58.0
Q ss_pred CcCcchHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCCCCcEEE
Q 027817 32 KGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLV 105 (218)
Q Consensus 32 ~~TRHNvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilV 105 (218)
.-|+|+.--..++.=.+..|+.+.+.+..-++.....+|-++-.--|.|-||. +.+..++..|+|.-.++++
T Consensus 148 Datk~e~qr~~le~ELe~vGiRLNk~~Pniy~k~kk~gGi~f~~T~~lT~~~e--k~i~~ILheykI~Naevl~ 219 (364)
T KOG1486|consen 148 DATKSEDQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPLTHCDE--KLIYTILHEYKIHNAEVLF 219 (364)
T ss_pred cCCcchhHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeeccccccH--HHHHHHHHHHeeccceEEE
Confidence 35888888888888888899998887777677666777888888889887775 7788999999998777664
No 41
>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=25.68 E-value=51 Score=26.89 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=23.0
Q ss_pred chhHHHHHHHcCCCCCcEEEEeecC
Q 027817 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (218)
Q Consensus 86 G~aV~~~~~~~ki~~~~ilVihDDl 110 (218)
|.+++.+++.+++++++++++=|+.
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 7888999999999999999999975
No 42
>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=24.63 E-value=3.1e+02 Score=26.09 Aligned_cols=68 Identities=9% Similarity=0.057 Sum_probs=47.9
Q ss_pred hHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeC---CCcccccchhHHHHHHHcCCCCCcEEEE
Q 027817 37 NVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKP---QTYMNLSGESTGPLAAYYKLPLNRVLVF 106 (218)
Q Consensus 37 NvGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP---~TyMN~SG~aV~~~~~~~ki~~~~ilVi 106 (218)
.+|=+|+-.|...... ...-+...+++..+.+++++++|+ -.=.=.=|+||..+.+.++-.++.|+-|
T Consensus 184 gaGPLVA~~l~~~~~~--~~~~~dtv~~e~~~egRrv~viKA~GPGstVGrpgeave~i~~~~~~k~~~IITV 254 (355)
T PF07431_consen 184 GAGPLVAGRLMENCSK--WEIAKDTVIAECEFEGRRVYVIKAEGPGSTVGRPGEAVEYIVEKLGGKVDLIITV 254 (355)
T ss_pred CcchHHHHHHHhcCcc--cccccccEEEEEEECCcEEEEEeccCCCccCCChHHHHHHHHHHhcCCccEEEEe
Confidence 4677788777765443 222345667888999999999995 4445556888999999887667766543
No 43
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=24.52 E-value=78 Score=28.91 Aligned_cols=30 Identities=23% Similarity=0.133 Sum_probs=27.1
Q ss_pred CcccccchhHHHHHHHcCCCCCcEEEEeec
Q 027817 80 TYMNLSGESTGPLAAYYKLPLNRVLVFHDD 109 (218)
Q Consensus 80 TyMN~SG~aV~~~~~~~ki~~~~ilVihDD 109 (218)
.=|=.|.+...+++...+|..++.||+|||
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd 98 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDD 98 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECC
Confidence 457778888999999999999999999999
No 44
>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=22.36 E-value=58 Score=25.35 Aligned_cols=22 Identities=27% Similarity=0.634 Sum_probs=16.8
Q ss_pred ecCCCCCceEEEe--cCCCCCCCC
Q 027817 108 DDMGLPCGVLRLR--HNGGHGGHN 129 (218)
Q Consensus 108 DDldlp~G~vrlk--~gGs~gGHN 129 (218)
.++++|...+.+. .++|+||+|
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 4678888888776 688999986
No 45
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=22.04 E-value=20 Score=24.08 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=18.0
Q ss_pred cccchhHHHHHHHcCCCCCcEEEEeec
Q 027817 83 NLSGESTGPLAAYYKLPLNRVLVFHDD 109 (218)
Q Consensus 83 N~SG~aV~~~~~~~ki~~~~ilVihDD 109 (218)
+.|-..+..+++++++++++++...+|
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 455677889999999999999877665
No 46
>PF14681 UPRTase: Uracil phosphoribosyltransferase; PDB: 1V9S_B 1UPF_A 1UPU_D 1JLR_B 1BD4_A 1BD3_C 1JLS_D 1XTV_C 1XTU_H 3G6W_C ....
Probab=21.89 E-value=1.2e+02 Score=25.89 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=26.8
Q ss_pred CCeeEEEEeCCCcccccchhHHHHHH---HcCCCCCcEEEEe
Q 027817 69 GDAPVLLAKPQTYMNLSGESTGPLAA---YYKLPLNRVLVFH 107 (218)
Q Consensus 69 ~~~~v~L~KP~TyMN~SG~aV~~~~~---~~ki~~~~ilVih 107 (218)
.+.+|+|+-| |-.+|.++..+++ .+++++++|++++
T Consensus 120 ~~~~VillDp---mlaTG~s~~~ai~~L~~~G~~~~~I~~v~ 158 (207)
T PF14681_consen 120 ENRKVILLDP---MLATGGSAIAAIEILKEHGVPEENIIIVS 158 (207)
T ss_dssp TTSEEEEEES---EESSSHHHHHHHHHHHHTTG-GGEEEEEE
T ss_pred cCCEEEEEec---cccchhhHHHHHHHHHHcCCCcceEEEEE
Confidence 4578999999 8899999866544 4567888887764
No 47
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional
Probab=21.74 E-value=3e+02 Score=25.40 Aligned_cols=71 Identities=13% Similarity=0.087 Sum_probs=54.2
Q ss_pred CCcccccchhHHHHHHHcCCCCCcEEEEeecCC--------C--CCceEEEecCC-CCCCCCchhhHHHhhcCCCCccEE
Q 027817 79 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMG--------L--PCGVLRLRHNG-GHGGHNGLKSVMNNFRGNREFARL 147 (218)
Q Consensus 79 ~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDld--------l--p~G~vrlk~gG-s~gGHNGLkSIi~~L~gt~~f~Rl 147 (218)
...=|.+|..+..+++.++......-++-||.+ + .--.+=+--|| |.+-..=....+..+ +..+|+.+
T Consensus 170 G~i~Dsn~~~L~~~L~~~G~~v~~~~iVpDD~~~I~~al~~a~~~~~DlIITTGGtg~g~~D~tpeAl~~l-g~~~~~Gv 248 (312)
T PRK03604 170 GTKEDRSGKLIVEGLEEAGFEVSHYTIIPDEPAEIAAAVAAWIAEGYALIITTGGTGLGPRDVTPEALAPL-LERRLPGI 248 (312)
T ss_pred CcEEEhHHHHHHHHHHHCCCEEEEEEEcCCCHHHHHHHHHHhhhCCCCEEEECCCCCCCCCccHHHHHHHh-cCccccch
Confidence 445699999999999999988888888999987 2 22356666777 566677778888888 46788887
Q ss_pred EEe
Q 027817 148 RIG 150 (218)
Q Consensus 148 rIG 150 (218)
+..
T Consensus 249 ae~ 251 (312)
T PRK03604 249 AEA 251 (312)
T ss_pred HHH
Confidence 754
No 48
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=21.11 E-value=70 Score=27.79 Aligned_cols=27 Identities=22% Similarity=0.412 Sum_probs=21.8
Q ss_pred EEEEeecCCCCCceEEEe--cCCCCCCCC
Q 027817 103 VLVFHDDMGLPCGVLRLR--HNGGHGGHN 129 (218)
Q Consensus 103 ilVihDDldlp~G~vrlk--~gGs~gGHN 129 (218)
+.|+-.+++++...+++. +.+|+||+|
T Consensus 95 V~v~~~~~~i~~~dl~~~~~RssGpGGQ~ 123 (200)
T PRK08179 95 IGRFSADEEEQSDEIRFETLRSSGPGGQH 123 (200)
T ss_pred EEEeCCcCccCHHHeEEEEEEccCCcccc
Confidence 456667889999999976 688999995
No 49
>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=21.09 E-value=94 Score=29.40 Aligned_cols=33 Identities=24% Similarity=0.384 Sum_probs=25.3
Q ss_pred EEEEeCCCcccccchhHHHHHHHcCCCCCcEEEEeecC
Q 027817 73 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDM 110 (218)
Q Consensus 73 v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDl 110 (218)
.++++|..+.| .|+..++.+|++ .++++||||=
T Consensus 116 ~~~lrp~~~~~---~Ai~dlV~~~~W--~~v~~iYD~d 148 (400)
T cd06392 116 TLAARPPVRLN---DVMLKLVTELRW--QKFIVFYDSE 148 (400)
T ss_pred eEEecCchHHH---HHHHHHHHhCCC--cEEEEEEECc
Confidence 46888853333 399999999987 7899999753
No 50
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=20.63 E-value=57 Score=27.96 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=22.8
Q ss_pred chhHHHHHHHcCCCCCcEEEEeecC
Q 027817 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (218)
Q Consensus 86 G~aV~~~~~~~ki~~~~ilVihDDl 110 (218)
|.+++.+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 7889999999999999999999865
No 51
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=20.61 E-value=1.9e+02 Score=22.42 Aligned_cols=36 Identities=19% Similarity=0.195 Sum_probs=23.5
Q ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHhh
Q 027817 166 QKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHF 202 (218)
Q Consensus 166 s~f~~~E~~~l~~~i~~a~~~~~~~i~~~~~~amn~~ 202 (218)
|..|++|++.|.+++.++.+ ++..-++-+.+..+++
T Consensus 1 s~Lt~eE~~~I~~Vl~R~~~-l~~~E~~Ri~kLk~~L 36 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQRDEE-LRKKEEERIRKLKQEL 36 (118)
T ss_dssp TTS-CHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHHHH
Confidence 56789999999999998776 3333334455555544
No 52
>PRK10976 putative hydrolase; Provisional
Probab=20.52 E-value=60 Score=27.79 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=22.8
Q ss_pred chhHHHHHHHcCCCCCcEEEEeecC
Q 027817 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (218)
Q Consensus 86 G~aV~~~~~~~ki~~~~ilVihDDl 110 (218)
|.+++.+++.+++++++++++=|..
T Consensus 192 g~al~~l~~~lgi~~~~viafGD~~ 216 (266)
T PRK10976 192 GHALEAVAKKLGYSLKDCIAFGDGM 216 (266)
T ss_pred HHHHHHHHHHcCCCHHHeEEEcCCc
Confidence 8889999999999999999998864
No 53
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=20.41 E-value=3.5e+02 Score=23.18 Aligned_cols=82 Identities=20% Similarity=0.303 Sum_probs=46.4
Q ss_pred HHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHHcCCCCCcEEEEeecCCCCCceEEEecC
Q 027817 43 IDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHN 122 (218)
Q Consensus 43 ld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDldlp~G~vrlk~g 122 (218)
+....+..|+.+.+....-.+.....++-.+.-.-+++- .+-+.|+++++.|+|...++ .+.+|+.
T Consensus 97 ~~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~~~~~~--~~~~~v~~~l~~~~i~~~~v-~~~~~~~----------- 162 (233)
T cd01896 97 LERELEGVGIRLNKRPPNITIKKKKKGGINITSTVPLTK--LDEKTIKAILREYKIHNADV-LIREDIT----------- 162 (233)
T ss_pred HHHHHHHcCceecCCCCeEEEEEEecCCEEEeccCCCCC--CCHHHHHHHHHHhCeeeEEE-EEccCCC-----------
Confidence 334445566654433222223333334444443334444 46688999999999976665 5666664
Q ss_pred CCCCCCCchhhHHHhhcCCCCccE
Q 027817 123 GGHGGHNGLKSVMNNFRGNREFAR 146 (218)
Q Consensus 123 Gs~gGHNGLkSIi~~L~gt~~f~R 146 (218)
+.++++.+.|+..|..
T Consensus 163 --------~~~~~~~~~~~~~y~p 178 (233)
T cd01896 163 --------VDDLIDVIEGNRVYIP 178 (233)
T ss_pred --------HHHHHHHHhCCceEee
Confidence 4688888865544544
No 54
>PRK06437 hypothetical protein; Provisional
Probab=20.12 E-value=1.5e+02 Score=20.79 Aligned_cols=29 Identities=7% Similarity=-0.011 Sum_probs=24.5
Q ss_pred cchhHHHHHHHcCCCCCcEEEEeecCCCC
Q 027817 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (218)
Q Consensus 85 SG~aV~~~~~~~ki~~~~ilVihDDldlp 113 (218)
.|..|+.+++.++++++.+.|.++.--+|
T Consensus 19 ~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 19 HELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 45678999999999999999998877666
Done!