Query 027742
Match_columns 219
No_of_seqs 215 out of 1047
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 14:28:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027742.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027742hhsearch_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 3E-78 6.4E-83 512.3 20.3 187 18-206 2-189 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 9.5E-78 2.1E-82 511.7 21.7 190 17-207 1-190 (191)
3 TIGR00447 pth peptidyl-tRNA hy 100.0 9.1E-76 2E-80 498.5 22.2 186 18-205 1-188 (188)
4 PRK05426 peptidyl-tRNA hydrola 100.0 5E-74 1.1E-78 488.2 22.1 186 18-206 2-188 (189)
5 PF01195 Pept_tRNA_hydro: Pept 100.0 4.3E-73 9.4E-78 480.0 18.4 183 20-204 1-184 (184)
6 cd00462 PTH Peptidyl-tRNA hydr 100.0 1.5E-72 3.2E-77 472.7 19.7 171 20-192 1-171 (171)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 3E-56 6.5E-61 378.7 14.2 183 18-205 39-222 (224)
8 TIGR00130 frhD coenzyme F420-r 93.1 4.1 9E-05 33.2 13.6 133 17-183 3-146 (153)
9 PRK11544 hycI hydrogenase 3 ma 89.8 7.2 0.00016 32.0 11.1 134 19-195 3-146 (156)
10 PRK12362 germination protease; 89.3 12 0.00026 34.8 13.2 128 5-152 87-228 (318)
11 TIGR00072 hydrog_prot hydrogen 88.8 11 0.00024 30.3 12.9 126 20-182 1-139 (145)
12 COG0680 HyaD Ni,Fe-hydrogenase 88.4 14 0.00029 30.9 12.7 140 17-191 2-154 (160)
13 cd06070 H2MP_like-2 Putative [ 88.4 12 0.00025 30.1 11.7 84 20-139 1-96 (140)
14 TIGR00142 hycI hydrogenase mat 86.6 15 0.00033 29.5 14.6 132 20-192 2-142 (146)
15 cd06062 H2MP_MemB-H2up Endopep 85.1 18 0.00039 29.1 12.7 127 20-184 2-142 (146)
16 cd06064 H2MP_F420-Reduc Endope 82.3 25 0.00053 28.4 12.2 92 20-140 1-105 (150)
17 PRK10466 hybD hydrogenase 2 ma 79.6 33 0.00072 28.2 14.0 132 18-186 2-147 (164)
18 PF11775 CobT_C: Cobalamin bio 60.3 21 0.00045 31.6 5.4 89 83-178 115-206 (219)
19 PF06154 YagB_YeeU_YfjZ: YagB/ 58.4 18 0.00038 28.4 4.1 33 162-195 33-65 (103)
20 PRK10264 hydrogenase 1 maturat 55.4 1.3E+02 0.0029 25.7 15.0 137 18-192 5-157 (195)
21 PRK09256 hypothetical protein; 49.5 8.5 0.00018 31.5 1.1 25 106-130 3-29 (138)
22 cd06068 H2MP_like-1 Putative [ 48.5 17 0.00037 29.1 2.7 26 20-50 1-26 (144)
23 PF03418 Peptidase_A25: Germin 45.1 26 0.00056 33.2 3.6 132 15-171 94-248 (354)
24 cd00518 H2MP Hydrogenase speci 43.6 26 0.00057 27.7 3.1 88 20-139 1-98 (139)
25 cd06067 H2MP_MemB-H2evol Endop 43.1 25 0.00055 27.9 2.9 90 20-140 1-98 (136)
26 cd06066 H2MP_NAD-link-bidir En 42.7 27 0.00059 27.8 3.1 27 20-51 1-27 (139)
27 cd06063 H2MP_Cyano-H2up This g 42.3 30 0.00066 27.8 3.3 87 20-138 2-99 (146)
28 PF14490 HHH_4: Helix-hairpin- 41.9 16 0.00035 27.4 1.5 25 31-56 45-71 (94)
29 TIGR01651 CobT cobaltochelatas 40.2 54 0.0012 33.1 5.3 88 84-179 496-587 (600)
30 PRK02858 germination protease; 37.2 26 0.00057 33.3 2.4 114 16-152 110-240 (369)
31 TIGR01441 GPR GPR endopeptidas 36.8 27 0.00058 33.1 2.4 114 16-152 100-230 (358)
32 PF11458 Mistic: Membrane-inte 34.2 74 0.0016 24.0 3.9 25 168-192 2-26 (84)
33 PF06466 PCAF_N: PCAF (P300/CB 33.6 46 0.001 30.1 3.3 54 152-205 136-197 (252)
34 KOG1486 GTP-binding protein DR 31.8 1.8E+02 0.0039 27.1 6.8 72 32-106 148-219 (364)
35 cd00736 bacteriophage_lambda_l 29.3 91 0.002 26.1 4.2 42 164-205 81-122 (151)
36 PF06342 DUF1057: Alpha/beta h 27.8 2.8E+02 0.006 25.8 7.3 68 106-178 24-93 (297)
37 PRK10870 transcriptional repre 27.7 55 0.0012 27.2 2.7 38 163-200 137-175 (176)
38 COG2179 Predicted hydrolase of 26.7 46 0.001 28.6 2.0 29 86-114 95-123 (175)
39 PF13443 HTH_26: Cro/C1-type H 25.6 16 0.00035 24.6 -0.8 27 84-110 37-63 (63)
40 PF00472 RF-1: RF-1 domain; I 25.4 47 0.001 25.9 1.7 22 109-130 5-28 (113)
41 PF08282 Hydrolase_3: haloacid 25.4 51 0.0011 26.9 2.0 25 87-111 188-212 (254)
42 COG2897 SseA Rhodanese-related 24.6 76 0.0017 29.0 3.1 30 81-110 69-98 (285)
43 cd01614 EutN_CcmL Ethanolamine 23.5 1.7E+02 0.0038 21.9 4.4 44 69-126 19-62 (83)
44 PRK08179 prfH peptide chain re 23.1 60 0.0013 28.3 2.1 27 104-130 95-123 (200)
45 PF07431 DUF1512: Protein of u 22.9 3.5E+02 0.0075 25.8 7.2 66 39-106 185-253 (355)
46 PF12896 Apc4: Anaphase-promot 22.3 1E+02 0.0022 25.9 3.3 49 153-203 85-133 (210)
47 cd06392 PBP1_iGluR_delta_1 N-t 22.3 86 0.0019 29.7 3.2 33 74-111 116-148 (400)
48 PRK03604 moaC bifunctional mol 21.3 3E+02 0.0066 25.4 6.4 71 80-151 170-251 (312)
49 PF02318 FYVE_2: FYVE-type zin 20.9 1.9E+02 0.0042 22.5 4.4 36 167-203 1-36 (118)
50 PF13873 Myb_DNA-bind_5: Myb/S 20.7 2.3E+02 0.0051 19.8 4.5 24 167-190 3-26 (78)
51 PF11242 DUF2774: Protein of u 20.6 32 0.0007 24.8 -0.1 24 81-104 7-30 (63)
52 PRK10513 sugar phosphate phosp 20.5 56 0.0012 28.0 1.4 25 87-111 198-222 (270)
53 PF14681 UPRTase: Uracil phosp 20.5 1.3E+02 0.0028 25.7 3.6 36 70-108 120-158 (207)
54 PRK06437 hypothetical protein; 20.4 1.4E+02 0.0031 21.0 3.3 29 86-114 19-47 (67)
55 PRK10976 putative hydrolase; P 20.3 61 0.0013 27.8 1.6 25 87-111 192-216 (266)
56 TIGR03072 release_prfH putativ 20.2 89 0.0019 27.2 2.6 27 104-130 94-122 (200)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-78 Score=512.25 Aligned_cols=187 Identities=43% Similarity=0.772 Sum_probs=181.5
Q ss_pred CeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCC-CccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHh
Q 027742 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 96 (219)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~-~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~ 96 (219)
++|||||||||++|+.|||| ||||++|.||++++.++ +.++|.+.++++.+.+++|+|+||+||||+||++|.++++|
T Consensus 2 ~kLIVGLGNPG~~Y~~TRHN-vGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~l~kP~TyMNlSG~~V~~~~~f 80 (190)
T COG0193 2 MKLIVGLGNPGKKYAKTRHN-VGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASF 80 (190)
T ss_pred cEEEEECCCCchhhcccchh-HHHHHHHHHHHHhCCCCccccccCceeEEEEeCCcEEEEecCccceeCcHHHHHHHHHH
Confidence 78999999999999999999 99999999999999998 55789999999999999999999999999999999999999
Q ss_pred cCCCCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHH
Q 027742 97 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 176 (219)
Q Consensus 97 ~ki~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~ 176 (219)
|++++++++|||||||||+|++|+|.+||+|||||||||+++| ||++|+|||||||||+.+++|++|||++|+++|++.
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 027742 177 IDTALQEGVEVLKLLLSKGLTESARHFNTI 206 (219)
Q Consensus 177 l~~~i~~a~~~l~~~i~~~~~~amn~~n~~ 206 (219)
+++++++|+++++.+++.+++++||+||+.
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=9.5e-78 Score=511.69 Aligned_cols=190 Identities=65% Similarity=1.131 Sum_probs=181.7
Q ss_pred CCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHh
Q 027742 17 RPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 96 (219)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~ 96 (219)
.|+|||||||||++|++|||| |||+++|+||+++++++++.++.+.+++..+.+++++|+||+||||+||+||+++++|
T Consensus 1 ~~~LIvGLGNPG~~Y~~TRHN-iGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~ 79 (191)
T cd02406 1 TPWLIAGLGNPGNKYKGTRHN-VGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAY 79 (191)
T ss_pred CcEEEEEcCCCchhhCcCchh-HHHHHHHHHHHHcCCCccccccceEEEEEEECCeEEEEEeCCCchhcCHHHHHHHHHH
Confidence 478999999999999999999 9999999999999998766788899999999999999999999999999999999999
Q ss_pred cCCCCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHH
Q 027742 97 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 176 (219)
Q Consensus 97 ~ki~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~ 176 (219)
|++++++++|||||||||+|++|+|.+||+|||||||||+++|+||++|+|||||||||+.+.++++|||++|+++|++.
T Consensus 80 yki~~~~ilVihDdldl~~G~irlk~gGs~gGHNGlkSI~~~Lggt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~ 159 (191)
T cd02406 80 YKVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEHLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQ 159 (191)
T ss_pred hCCCHHHEEEEEECCCCCCCeEEEcCCCCCCCcCCHHHHHHHhCCCCCeEEEEEEeCCCCCCCchhhhhcCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999996578999999999999776789999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccHHHHHHhhhchh
Q 027742 177 IDTALQEGVEVLKLLLSKGLTESARHFNTIQ 207 (219)
Q Consensus 177 l~~~i~~a~~~l~~~i~~~~~~amn~~n~~~ 207 (219)
++++++.|+++++.|+.++++++||+||+.+
T Consensus 160 l~~~~~~a~~~~~~~~~~~~~~~~n~~n~~~ 190 (191)
T cd02406 160 IDTALEQGVDAVRTLVLKGFNGSAERFNLVQ 190 (191)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHhCCC
Confidence 9999999999999999999999999999653
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=9.1e-76 Score=498.55 Aligned_cols=186 Identities=44% Similarity=0.771 Sum_probs=178.2
Q ss_pred CeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCc-cccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHh
Q 027742 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNT-VHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 96 (219)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~-~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~ 96 (219)
|+|||||||||++|++|||| ||||++|+||++++.++++ .++.+.+++..+.+++++|+||+||||+||++|+++++|
T Consensus 1 ~~LIvGLGNPG~~Y~~TRHN-iGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~ 79 (188)
T TIGR00447 1 IKLIVGLGNPGKKYAGTRHN-AGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKPLTYMNLSGEAVRALASF 79 (188)
T ss_pred CEEEEEeCCCchhhCcCchH-HHHHHHHHHHHHcCcCCcccccceEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHH
Confidence 68999999999999999999 9999999999999998763 567788888889999999999999999999999999999
Q ss_pred cCCCCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHH
Q 027742 97 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 176 (219)
Q Consensus 97 ~ki~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~ 176 (219)
|+|+++++||||||||||+|++|+|++||+|||||||||+++| ||++|+|||||||||+++.++++|||++|+++|++.
T Consensus 80 ~~i~~~~ilVihDdldl~~G~irlk~~G~~gGHNGlkSI~~~l-gt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~e~~~ 158 (188)
T TIGR00447 80 YRIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGLKSIISHL-GTNNFNRLRIGIGSPGGSNKVVEFVLSKFTKSELPL 158 (188)
T ss_pred hCCChHHEEEEEecCCCCCceEEEecCCCCCCcCCHHHHHHHh-CCCCcceEEEEeCCCCCCCchhhhccCCCCHHHHHH
Confidence 9999999999999999999999999999999999999999999 689999999999999876789999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcc-HHHHHHhhhc
Q 027742 177 IDTALQEGVEVLKLLLSKG-LTESARHFNT 205 (219)
Q Consensus 177 l~~~i~~a~~~l~~~i~~~-~~~amn~~n~ 205 (219)
++++++.++++++.|++++ ++++||+||+
T Consensus 159 l~~~i~~~~~~~~~~~~~~~~~~~~n~~n~ 188 (188)
T TIGR00447 159 LEKALDKAVEALEMSFSEGAFLKAMNRFNS 188 (188)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHhhC
Confidence 9999999999999999999 9999999985
No 4
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=5e-74 Score=488.20 Aligned_cols=186 Identities=44% Similarity=0.801 Sum_probs=177.4
Q ss_pred CeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCC-ccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHh
Q 027742 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 96 (219)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~-~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~ 96 (219)
|||||||||||++|++|||| |||+++|.||++++..+. ..++.+.+++..+.+.+++|+||+||||+||++|.+++++
T Consensus 2 ~~LivGLGNPG~~Y~~TRHN-vGf~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~ 80 (189)
T PRK05426 2 MKLIVGLGNPGPEYANTRHN-IGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANF 80 (189)
T ss_pred cEEEEEeCCCchhhCcCchH-HHHHHHHHHHHHcCCCCcccccccEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHH
Confidence 79999999999999999999 999999999999887664 4567889999999889999999999999999999999999
Q ss_pred cCCCCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHH
Q 027742 97 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARER 176 (219)
Q Consensus 97 ~ki~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~ 176 (219)
|+|++++++|||||+|+|+|++|+|.+||+|||||||||+++| ||++|+|||||||||+ ..++++|||++|+++|++.
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 027742 177 IDTALQEGVEVLKLLLSKGLTESARHFNTI 206 (219)
Q Consensus 177 l~~~i~~a~~~l~~~i~~~~~~amn~~n~~ 206 (219)
++++++.|+++++.|++++++++||+||+.
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=4.3e-73 Score=479.98 Aligned_cols=183 Identities=44% Similarity=0.844 Sum_probs=163.2
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccc-cceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 98 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k-~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~k 98 (219)
|||||||||++|++|||| |||+++|+||++++.++.+.+ +.+.++...+.+.+++|+||+||||+||++|++++++|+
T Consensus 1 LivGLGNPG~~Y~~TRHN-vG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~KP~TyMN~SG~~V~~~~~~~~ 79 (184)
T PF01195_consen 1 LIVGLGNPGPKYENTRHN-VGFMVLDRLASRLGLSWKQKKKFKSLISEGSIKGEKVILLKPQTYMNLSGKAVKKILSFYK 79 (184)
T ss_dssp EEEE---SSTTTTTSGGG-HHHHHHHHHHHHTT---EEEGGGTEEEEEEEETTEEEEEEEESSTGGGHHHHHHHHHHHTT
T ss_pred CEEEcCCCChhhcCCCcC-chHHHHHHHHHHhCCCccccccceeEEEEEEEeeeeEEEEcCCCeEeCccHhHHHHHHHhC
Confidence 799999999999999999 999999999999999886654 788888999999999999999999999999999999999
Q ss_pred CCCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHH
Q 027742 99 LPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERID 178 (219)
Q Consensus 99 i~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~l~ 178 (219)
++++++||||||+|+|+|++|+|.+||+|||||||||+++| +|++|+|||||||||+...++++|||++|+++|++.++
T Consensus 80 i~~~~ilVihDdldl~~G~irlk~~Gs~~GHNGlkSI~~~L-gt~~f~RlrIGIGrp~~~~~v~~yVL~~f~~~E~~~l~ 158 (184)
T PF01195_consen 80 IPPENILVIHDDLDLPLGKIRLKKGGSSGGHNGLKSIIQHL-GTEDFPRLRIGIGRPPSKEDVADYVLSKFSPEERELLD 158 (184)
T ss_dssp --GGGEEEEEEETTSSTTEEEEEESS--TT-HHHHHHHHHC-TSSGSEEEEEEE--TSTTSGHHHHHTSB-HHHHHHHHH
T ss_pred CCcceEEEEEeccCCCCCeEEEccCCCCCCCCCHHHHHHHh-ccccceeEEEecCCCCCcchHHHHHhcCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999 68999999999999987778999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccHHHHHHhhh
Q 027742 179 TALQEGVEVLKLLLSKGLTESARHFN 204 (219)
Q Consensus 179 ~~i~~a~~~l~~~i~~~~~~amn~~n 204 (219)
++++.|+++++.|+++++++|||+||
T Consensus 159 ~~~~~a~~~l~~~i~~~~~~~mn~~n 184 (184)
T PF01195_consen 159 KVIPQAAEALEQIIEGGFEKAMNKFN 184 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHhC
Confidence 99999999999999999999999998
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=1.5e-72 Score=472.69 Aligned_cols=171 Identities=51% Similarity=0.938 Sum_probs=164.6
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
|||||||||++|++|||| ||||++|+||++++.++.+.++.+.+++..+.+++++|+||+||||+||++|.++++||++
T Consensus 1 LIvGLGNPG~~Y~~TRHN-vGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~~i 79 (171)
T cd00462 1 LIVGLGNPGPKYENTRHN-VGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYKI 79 (171)
T ss_pred CEEEECCCCcccCcCchH-HHHHHHHHHHHHcCCCCCccccCEEEEEEEECCEEEEEEeCCcccccccHHHHHHHHhcCC
Confidence 699999999999999999 9999999999999998877777899999999999999999999999999999999999999
Q ss_pred CCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHHH
Q 027742 100 PLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERIDT 179 (219)
Q Consensus 100 ~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~l~~ 179 (219)
+++++||||||||||+|++|+|++||+|||||||||+++| ||++|+|||||||||+.+.++++|||++|+++|++.+++
T Consensus 80 ~~~~ilVihDdldl~~G~vrlk~~G~~gGHNGlkSI~~~l-gt~~f~RlriGIGrP~~~~~v~~yVL~~f~~~E~~~l~~ 158 (171)
T cd00462 80 PPEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHL-GTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEE 158 (171)
T ss_pred ChhHEEEEEecCCCCCceEEEeCCCCCCCCCCHHHHHHHh-CCCCeeEEEEEeCCCCCCCChhhhhcCCCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999 689999999999999877799999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q 027742 180 ALQEGVEVLKLLL 192 (219)
Q Consensus 180 ~i~~a~~~l~~~i 192 (219)
+++.|+++++.|+
T Consensus 159 ~~~~~~~~~~~~~ 171 (171)
T cd00462 159 AIEKAADALEDIL 171 (171)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999998763
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-56 Score=378.69 Aligned_cols=183 Identities=56% Similarity=0.993 Sum_probs=164.8
Q ss_pred CeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhc
Q 027742 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 97 (219)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ 97 (219)
+|+|+||||||++|..|||| |||.++|.||++.+++..+.+.++..+-..+++..+++++|++|||.||++|.+++..|
T Consensus 39 ~wli~GLGNPg~~y~gTRHn-vG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y 117 (224)
T KOG2255|consen 39 PWLIVGLGNPGSKYVGTRHN-VGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALY 117 (224)
T ss_pred ceEEEecCCCcccccccchh-hHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhh
Confidence 58999999999999999999 99999999999999987766666777778899999999999999999999999999999
Q ss_pred CCCCCceEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHH-H
Q 027742 98 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE-R 176 (219)
Q Consensus 98 ki~~~~ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~-~ 176 (219)
+++.++++||||||++|+|++|+|++||++||||+||++++++|...|+||+||||||++++|+.+|||++|++.|++ .
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 999999999999999999999999999999999999999999877899999999999999999999999999999988 4
Q ss_pred HHHHHHHHHHHHHHHHhccHHHHHHhhhc
Q 027742 177 IDTALQEGVEVLKLLLSKGLTESARHFNT 205 (219)
Q Consensus 177 l~~~i~~a~~~l~~~i~~~~~~amn~~n~ 205 (219)
|+.. .+.+++++.+++..-.++||-
T Consensus 198 Let~----l~~~~~lil~~l~~~is~~~l 222 (224)
T KOG2255|consen 198 LETL----LEHVKTLILQGLQQSISRFNL 222 (224)
T ss_pred HHHH----HhhhHHHHHHHHHHhcccCcC
Confidence 4444 444555555666666666663
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=93.08 E-value=4.1 Score=33.20 Aligned_cols=133 Identities=17% Similarity=0.153 Sum_probs=69.0
Q ss_pred CCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHH-cCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHH
Q 027742 17 RPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAA 95 (219)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~-~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~ 95 (219)
...+|+|+|||-..= == +|..++++|+++ +..+ ..+.+ ++........+..
T Consensus 3 ~~ilVlGiGN~l~gD----DG-vG~~v~~~L~~~~~~~~-----------------~~v~v------id~gt~~~~~l~~ 54 (153)
T TIGR00130 3 HEILVVGCGNILFGD----DG-FGPAVIEYLKENGVEKP-----------------DNVCL------IDAGTGAPHFVFT 54 (153)
T ss_pred ceEEEEEeCcccccc----Cc-HhHHHHHHHHHhCCCCC-----------------CCeEE------EECCCcHHHHHHH
Confidence 346899999995321 23 999999999863 2111 01111 2211111111112
Q ss_pred hcCCCCCceEEEeec--CCCCCceEEEec------CCC-CCCCCchhhHHHhhcCCCCccEEEE-eecCCCCCCCccccc
Q 027742 96 YYKLPLNRVLVFHDD--MGLPCGVLRLRH------NGG-HGGHNGLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFL 165 (219)
Q Consensus 96 ~~ki~~~~ilVihDD--ldlp~G~irlk~------gGs-~gGHNGLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yV 165 (219)
+..+...+.+||-|= .+.++|+++.-. ..+ +..+-|+..+++.+. .. .++.| ||- |.. -+..+|=
T Consensus 55 ~~~~~~~d~vIivDA~~~~~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~-~~--~~~~iiGi~-p~~-~~~~~~~ 129 (153)
T TIGR00130 55 LIPQSKWKKIIVVDIADFGAEPGTLRVLNVDELPNGRYMDAHGWSLAYPLHDLE-ER--IDIRVVGCQ-PKY-VSQPDVD 129 (153)
T ss_pred HhhhcCCCEEEEEEccCCCcCCCEEEEEchHHcCCCCCCCCccCCHHHHHHHhc-CC--CCEEEEEEE-EeE-ecCCCCC
Confidence 212334566777785 578999998742 212 344459999998773 22 45555 553 321 1111222
Q ss_pred cCcCCHHHHHHHHHHHHH
Q 027742 166 LQKFNAIARERIDTALQE 183 (219)
Q Consensus 166 L~~F~~~E~~~l~~~i~~ 183 (219)
-.+|++=++.++++++.
T Consensus 130 -~~LS~~v~~a~~~~~~~ 146 (153)
T TIGR00130 130 -IGLTEEVNKAIPRAVEI 146 (153)
T ss_pred -CCCCHHHHHHHHHHHHH
Confidence 25665555554444333
No 9
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=89.76 E-value=7.2 Score=32.03 Aligned_cols=134 Identities=17% Similarity=0.185 Sum_probs=71.3
Q ss_pred eEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcC
Q 027742 19 WLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYK 98 (219)
Q Consensus 19 ~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~k 98 (219)
.+|+|+|||-..=. .+|..++++|.+.. . . .+.++.-.| .|.-+-.+++.+
T Consensus 3 ~lVlGiGN~L~gDD-----GvG~~v~~~L~~~~-~--~----------------~v~vid~gt----~~~~~~~~i~~~- 53 (156)
T PRK11544 3 DVVLTVGNSMMGDD-----GAGPLLAEKLAAAP-K--G----------------GWVVIDGGS----APENDIVAIREL- 53 (156)
T ss_pred EEEEEeCccccccC-----cHHHHHHHHHhccC-C--C----------------CeEEEECCC----CHHHHHHHHHhc-
Confidence 48999999964322 29999999997642 1 0 111222222 122222222211
Q ss_pred CCCCceEEEee--cCCCCCceEEEecCC------CCCCCC-chhhHHHhhcCCCCccEEEE-eecCCCCCCCccccccCc
Q 027742 99 LPLNRVLVFHD--DMGLPCGVLRLRHNG------GHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQK 168 (219)
Q Consensus 99 i~~~~ilVihD--Dldlp~G~irlk~gG------s~gGHN-GLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yVL~~ 168 (219)
.+ +.+||.| +.+.++|+++.-... +...|. ||..++..+.+ ..+++.+ ||= |. ++ +| =..
T Consensus 54 -~~-d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~s~H~~~l~~~l~~l~~--~~p~v~iigI~-~~---~~-~~-g~~ 123 (156)
T PRK11544 54 -RP-ERLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKE--DVPEVIFLGIQ-PD---IV-GF-YYP 123 (156)
T ss_pred -CC-CEEEEEECCccCcCCCEEEEEchhhcccccCCCCCcCCHHHHHHHHhc--CCCcEEEEEEE-ee---ec-cC-CCC
Confidence 22 5566667 456799999873211 123444 78888888743 2345544 442 32 22 22 235
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 027742 169 FNAIARERIDTALQEGVEVLKLLLSKG 195 (219)
Q Consensus 169 F~~~E~~~l~~~i~~a~~~l~~~i~~~ 195 (219)
.|++=+ +.++++++.++.|..++
T Consensus 124 LS~~v~----~av~~~~~~l~~~~~~~ 146 (156)
T PRK11544 124 MTQPVK----DAVETVYQRLEGWEGNG 146 (156)
T ss_pred CCHHHH----HHHHHHHHHHHHhhccC
Confidence 555443 44556667777776543
No 10
>PRK12362 germination protease; Provisional
Probab=89.29 E-value=12 Score=34.84 Aligned_cols=128 Identities=19% Similarity=0.250 Sum_probs=75.0
Q ss_pred HHHHHHhccCCCCCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECC-eeEEEEeC----
Q 027742 5 RFLRRGFCTAVARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKP---- 79 (219)
Q Consensus 5 ~~~~~~~~~~~~~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~-~~v~L~KP---- 79 (219)
+.|+..+........|||||||. .-|--. .|-.+++.|.-.... ...+++..-.+ .+|.-+-|
T Consensus 87 ~~L~~ll~~~~~~~iLVvGLGN~----~vTpDa-LGP~Vv~~l~vTrhl-------~~~~~~~~~~~~~pV~AiaPGVmg 154 (318)
T PRK12362 87 KELKKLINLDKEMTVLVVGLGNW----NVTPDA-LGPKVVSKLMVTRHL-------KEYAPEEIDEGIRPVCAIAPGVLG 154 (318)
T ss_pred HHHHHHhCCCCCCcEEEEEcCCC----CcCccc-cchhhhhhhhhhhhh-------hhhcCchhcCCCCcceEecCCccc
Confidence 34455543234567899999996 358889 999999988643111 01111111111 23444444
Q ss_pred CCcccccchhHHHHHHhcCCCCCceEEEeecCC----CCCc-eEEEecCC---CCCCCCchhhHH-HhhcCCCCccEEEE
Q 027742 80 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMG----LPCG-VLRLRHNG---GHGGHNGLKSVM-NNFRGNREFARLRI 150 (219)
Q Consensus 80 ~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDld----lp~G-~irlk~gG---s~gGHNGLkSIi-~~L~gt~~f~RlrI 150 (219)
+|=||. ++.++.+.+.++ .+++|.-|-+- --+| +|.+...| |+|=.|==+.|. +.| | .+=+.|
T Consensus 155 ~TGiet-~Eii~gIv~k~k---pd~IIAIDALaar~~~Rl~~tIQisdtGI~PGSGVGN~R~~l~~etL-G---VPVIAI 226 (318)
T PRK12362 155 ITGIET-AEIIKGVVEKIK---PDLVIAIDALAARSVERVNTTIQISDTGISPGSGVGNKRMGINEETL-G---VPVIAI 226 (318)
T ss_pred ccchhH-HHHHHHHHHhcC---CCEEEEEeccccCCHHHccCeEEECCCCCCCCccCCCcccccCHHHc-C---CCEEEE
Confidence 566776 566777777665 36777778775 2467 88888776 444344333443 344 3 566666
Q ss_pred ee
Q 027742 151 GI 152 (219)
Q Consensus 151 GI 152 (219)
||
T Consensus 227 GV 228 (318)
T PRK12362 227 GV 228 (318)
T ss_pred cC
Confidence 66
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=88.79 E-value=11 Score=30.27 Aligned_cols=126 Identities=17% Similarity=0.184 Sum_probs=65.3
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
||+|+|||-..=. .+|..++++|++++.... .+-++.- |...-.++.+..
T Consensus 1 lViGiGN~l~~DD-----g~G~~v~~~L~~~~~~~~-----------------~v~~id~-------g~~~~~l~~~l~- 50 (145)
T TIGR00072 1 LVLGIGNILRGDD-----GFGPRVAERLEERYEFPP-----------------GVEVLDG-------GTLGLELLDAIE- 50 (145)
T ss_pred CEEEECchhcccC-----cHHHHHHHHHHHhcCCCC-----------------CeEEEEC-------CCCHHHHHHHHh-
Confidence 5899999943211 399999999988653210 0111111 111123333332
Q ss_pred CCCceEEEeecC--CCCCceEEEec--------CCC-CCCCCchhhHHHhhcCCCCcc-EEEE-eecCCCCCCCcccccc
Q 027742 100 PLNRVLVFHDDM--GLPCGVLRLRH--------NGG-HGGHNGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKAFLL 166 (219)
Q Consensus 100 ~~~~ilVihDDl--dlp~G~irlk~--------gGs-~gGHNGLkSIi~~L~gt~~f~-RlrI-GIGrP~~~~~v~~yVL 166 (219)
..+.+|+.|=. +.++|+++.-. .++ +..+-|+..+++.+.-....+ ++.+ ||= |. ++ +|-
T Consensus 51 -~~d~viiVDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~g~~p~~~~lvgi~-~~---~~-~~g- 123 (145)
T TIGR00072 51 -GADRVIVVDAVDSGAEPGTVRRLPGEDLPAFLGGKLSTHQLGLSEVLALLELLGALPPEVVLLGIQ-PE---SL-EFG- 123 (145)
T ss_pred -CCCEEEEEEccCCCcCCceEEEEchhhccccccCCCCcCcCCHHHHHHHHHHcCCCCCeEEEEEEE-ee---ec-ccC-
Confidence 24566677865 55999988632 123 333448888887663112333 4444 552 21 22 222
Q ss_pred CcCCHHHHHHHHHHHH
Q 027742 167 QKFNAIARERIDTALQ 182 (219)
Q Consensus 167 ~~F~~~E~~~l~~~i~ 182 (219)
..+|++=++.++++++
T Consensus 124 ~~LS~~v~~~~~~~~~ 139 (145)
T TIGR00072 124 LGLSPEVAAAVPAAVE 139 (145)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 3566655555444433
No 12
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=88.43 E-value=14 Score=30.92 Aligned_cols=140 Identities=17% Similarity=0.168 Sum_probs=81.4
Q ss_pred CCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCC-cccccchhHHHHHH
Q 027742 17 RPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQT-YMNLSGESTGPLAA 95 (219)
Q Consensus 17 ~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~T-yMN~SG~aV~~~~~ 95 (219)
.+.+|+|+|||=.. -=- +|-.++++|.+++...- +|-++.-.| -+|+.+
T Consensus 2 ~~ilIlG~GN~L~~----DDG-~Gv~vae~L~~~~~~~~-----------------~v~vid~Gt~~~~l~~-------- 51 (160)
T COG0680 2 MRILILGVGNILMG----DDG-FGVRVAEKLKKRYKPPE-----------------NVEVIDGGTAGPNLLG-------- 51 (160)
T ss_pred CeEEEEeeCCcccc----cCc-ccHHHHHHHHHhcCCCC-----------------CeEEEEcCCCcHHHHH--------
Confidence 35789999999432 334 99999999998753210 122222211 133322
Q ss_pred hcCCCCCceEEEeecCCC--CCceEEEec------CCCCC---CCC-chhhHHHhhcCCCCccEEEEeecCCCCCCCccc
Q 027742 96 YYKLPLNRVLVFHDDMGL--PCGVLRLRH------NGGHG---GHN-GLKSVMNNFRGNREFARLRIGIGRPPGQMDPKA 163 (219)
Q Consensus 96 ~~ki~~~~ilVihDDldl--p~G~irlk~------gGs~g---GHN-GLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~ 163 (219)
.+...+-++|.|=++. .+|++++-. ...+. .|+ ++..+++.+.-..++...-+|+.-|+. ...+
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 688888777433456778888886542 2112
Q ss_pred cccCcCCHHHHHHHHHHHHHHHHHHHHH
Q 027742 164 FLLQKFNAIARERIDTALQEGVEVLKLL 191 (219)
Q Consensus 164 yVL~~F~~~E~~~l~~~i~~a~~~l~~~ 191 (219)
+-..+|++=++.++.+++.+.+.++.+
T Consensus 128 -~~~~lS~ev~~a~~~av~~i~~~l~~~ 154 (160)
T COG0680 128 -FGGGLSPEVEEAVDKAVERILEELREW 154 (160)
T ss_pred -cccccCHHHHHHHHHHHHHHHHHHHhh
Confidence 225666666666666666666655543
No 13
>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=88.38 E-value=12 Score=30.05 Aligned_cols=84 Identities=18% Similarity=0.200 Sum_probs=50.6
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
||+|+|||=..=. = +|..++++|++ .+ +-++.- |.....++.++
T Consensus 1 lVlGiGN~l~~DD----g-~G~~v~~~L~~-~~---------------------v~vi~~-------g~~~~~ll~~i-- 44 (140)
T cd06070 1 LIIGVGNRLYGDD----G-FGSCLAEALEQ-CG---------------------APVFDG-------GLDGFGLLSHL-- 44 (140)
T ss_pred CEEEECchhcccC----c-HHHHHHHHHhh-CC---------------------CEEEEC-------CCcHHHHHHHH--
Confidence 6899999953222 2 99999999976 11 111111 22223344433
Q ss_pred CCCceEEEeecCC--CCCceEEEecC---------CCCCCCC-chhhHHHhh
Q 027742 100 PLNRVLVFHDDMG--LPCGVLRLRHN---------GGHGGHN-GLKSVMNNF 139 (219)
Q Consensus 100 ~~~~ilVihDDld--lp~G~irlk~g---------Gs~gGHN-GLkSIi~~L 139 (219)
...+.+||.|=++ .++|.++++.. .+...|+ |+.++.+.+
T Consensus 45 ~~~d~viiVDA~~~~~~pG~~~~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~ 96 (140)
T cd06070 45 ENYDIVIFIDVAVIDEDVGVFKITPEPASVAEQISFETDAHRLGPAHLLLLL 96 (140)
T ss_pred cCCCEEEEEEeecCCCCCeEEEEecCchhccccccCCCCCCcCCHHHHHHHH
Confidence 2356666777654 68998888543 2224566 999987665
No 14
>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=86.56 E-value=15 Score=29.53 Aligned_cols=132 Identities=14% Similarity=0.132 Sum_probs=70.0
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
+|+|+|||-..=. .+|..++++|.+.+.. . .+.++.-.| .|.-.-.+++.++
T Consensus 2 lVlGiGN~l~~DD-----G~G~~v~~~L~~~~~~---~---------------~v~v~d~gt----~~~~~~~~~~~~~- 53 (146)
T TIGR00142 2 VLLCVGNELMGDD-----GAGPYLAEKCAAAPKE---E---------------NWVVINAGT----VPENFTVAIRELR- 53 (146)
T ss_pred EEEEeCccccccC-----cHHHHHHHHHHhccCC---C---------------CEEEEECCC----ChHHHHHHHHhcC-
Confidence 6999999964322 2999999999865311 0 122222222 1222222222222
Q ss_pred CCCceEEEeecC--CCCCceEEEecC-----CCCCCCC-chhhHHHhhcCCCCccEEEE-eecCCCCCCCccccccCcCC
Q 027742 100 PLNRVLVFHDDM--GLPCGVLRLRHN-----GGHGGHN-GLKSVMNNFRGNREFARLRI-GIGRPPGQMDPKAFLLQKFN 170 (219)
Q Consensus 100 ~~~~ilVihDDl--dlp~G~irlk~g-----Gs~gGHN-GLkSIi~~L~gt~~f~RlrI-GIGrP~~~~~v~~yVL~~F~ 170 (219)
.+.++|.|-. +.++|+++.-.. .+..-|. |+..+++.+.+ .--.++.+ ||- |. ++ +|- ...|
T Consensus 54 --~d~viivDA~~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~ll~~~~~-~~~~~~~ligi~-~~---~~-~~g-~~LS 124 (146)
T TIGR00142 54 --PTHILIVDATDMGLNPGEVRIIDDDIIEMYSMSTHNMPLSYLVDYLKE-DINGEIIFLGIQ-PD---IV-GFY-YPMS 124 (146)
T ss_pred --CCEEEEEECcccCCCCCeEEEEChhhccccccCcCcCCHHHHHHHHHh-cCCCeEEEEEEe-ee---ee-ecC-CCCC
Confidence 3566666764 569999887432 1223454 99998877732 21235554 553 32 23 333 4666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 027742 171 AIARERIDTALQEGVEVLKLLL 192 (219)
Q Consensus 171 ~~E~~~l~~~i~~a~~~l~~~i 192 (219)
++=++.++ ++++.+..++
T Consensus 125 ~~v~~a~~----~~~~~i~~~i 142 (146)
T TIGR00142 125 QPVKDAVE----TLYQRLIGWE 142 (146)
T ss_pred HHHHHHHH----HHHHHHHHHH
Confidence 65555444 4444444444
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=85.14 E-value=18 Score=29.06 Aligned_cols=127 Identities=20% Similarity=0.241 Sum_probs=67.7
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
+|+|+|||-..=. .+|..++++|++.+..+.. +-+ ++. |.....++..+.
T Consensus 2 lV~GiGN~l~gDD-----G~G~~va~~L~~~~~~~~~-----------------v~v------i~~-~~~~~~l~~~l~- 51 (146)
T cd06062 2 LVLGIGNILLADE-----GIGVHAVERLEENYSFPEN-----------------VEL------IDG-GTLGLELLPYIE- 51 (146)
T ss_pred EEEEECccccccC-----cHHHHHHHHHHHhcCCCCC-----------------eEE------EEC-CCCHHHHHHHHh-
Confidence 7999999953211 3999999999887533210 111 111 222223333322
Q ss_pred CCCceEEEeec--CCCCCceEEEecC---------CCCCCCCchhhHHHhhc--CCCCccEEEE-eecCCCCCCCccccc
Q 027742 100 PLNRVLVFHDD--MGLPCGVLRLRHN---------GGHGGHNGLKSVMNNFR--GNREFARLRI-GIGRPPGQMDPKAFL 165 (219)
Q Consensus 100 ~~~~ilVihDD--ldlp~G~irlk~g---------Gs~gGHNGLkSIi~~L~--gt~~f~RlrI-GIGrP~~~~~v~~yV 165 (219)
..+.+|+.|= .+.++|+++.-.. ..+..+-|+..+++.+. +. .-.++.| ||= |. ++ +|-
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 3477777786 4779999876421 22445556888776642 11 1124443 442 21 22 222
Q ss_pred cCcCCHHHHHHHHHHHHHH
Q 027742 166 LQKFNAIARERIDTALQEG 184 (219)
Q Consensus 166 L~~F~~~E~~~l~~~i~~a 184 (219)
..+|++=++.++++++.+
T Consensus 125 -~~LS~~v~~av~~~~~~i 142 (146)
T cd06062 125 -LELSPEVAAALPTAIEAV 142 (146)
T ss_pred -CCCCHHHHHHHHHHHHHH
Confidence 367766666655554443
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=82.26 E-value=25 Score=28.41 Aligned_cols=92 Identities=17% Similarity=0.196 Sum_probs=53.8
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHH-HHhcC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPL-AAYYK 98 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~-~~~~k 98 (219)
||+|+|||-..= == +|..++++|++++... ..+.++. .|.....+ ..+..
T Consensus 1 lViGiGN~l~gD----Dg-vG~~va~~l~~~~~~~-----------------~~v~vid-------~g~~~~~~~~~~~~ 51 (150)
T cd06064 1 LVVGCGNILFGD----DG-FGPAVIEELEKLELLP-----------------DNVQVID-------AGTGAPHLLFTLLD 51 (150)
T ss_pred CEEEECCccccc----Cc-HHHHHHHHHHhccCCC-----------------CCEEEEE-------CCCcHHHHHHHHHh
Confidence 689999996331 22 9999999998754211 0122222 23322121 11111
Q ss_pred -CCCCceEEEeecC--CCCCceEEEecC---------CCCCCCCchhhHHHhhc
Q 027742 99 -LPLNRVLVFHDDM--GLPCGVLRLRHN---------GGHGGHNGLKSVMNNFR 140 (219)
Q Consensus 99 -i~~~~ilVihDDl--dlp~G~irlk~g---------Gs~gGHNGLkSIi~~L~ 140 (219)
....+.+||.|=+ +.++|+++.... ..+-.+-|+..+++.+.
T Consensus 52 ~~~~~d~viivDA~~~g~~pG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~ 105 (150)
T cd06064 52 EESKPKKIIIVDAIDFGLEPGTLKKISVDELPPGKYYDFDAHSWPLADPLHELK 105 (150)
T ss_pred ccCCCCEEEEEEecCCCCCCCeEEEEehhhcccccCCCcCCCcCCHHHHHHHHH
Confidence 1225677778874 779999887432 12456679999998774
No 17
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=79.57 E-value=33 Score=28.21 Aligned_cols=132 Identities=19% Similarity=0.246 Sum_probs=66.4
Q ss_pred CeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhc
Q 027742 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 97 (219)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ 97 (219)
..+|+|+|||-.. -== +|..++++|.+.+..+. .+. +++. |.....++.++
T Consensus 2 ~ilVlGiGN~l~g----DDG-vG~~va~~L~~~~~~~~-----------------~v~------vid~-gt~~~~ll~~l 52 (164)
T PRK10466 2 RILVLGVGNILLT----DEA-IGVRIVEALEQRYILPD-----------------YVE------ILDG-GTAGMELLGDM 52 (164)
T ss_pred ceEEEEECchhhc----cCc-HHHHHHHHHHHhcCCCC-----------------CeE------EEec-cccHHHHHHHH
Confidence 3589999999532 223 99999999987653311 111 1111 22223344433
Q ss_pred CCCCCceEEEeecC--CCC-CceEEEecC--------CCCCCC-CchhhHHHhhcCCCCcc-EEEE-eecCCCCCCCccc
Q 027742 98 KLPLNRVLVFHDDM--GLP-CGVLRLRHN--------GGHGGH-NGLKSVMNNFRGNREFA-RLRI-GIGRPPGQMDPKA 163 (219)
Q Consensus 98 ki~~~~ilVihDDl--dlp-~G~irlk~g--------Gs~gGH-NGLkSIi~~L~gt~~f~-RlrI-GIGrP~~~~~v~~ 163 (219)
. ..+.+||.|=. +.+ +|+++.-.. .+...| -|+..+...+.-..+.+ ++.+ ||- |. ++ +
T Consensus 53 ~--~~d~vIiVDA~~~g~~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~L~~~~~~g~~p~~v~lvgie-p~---~~-~ 125 (164)
T PRK10466 53 A--NRDHLIIADAIVSKKNAPGTIMVLRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVI-PE---SL-E 125 (164)
T ss_pred h--CCCEEEEEEecCCCCCCCCEEEEEchhhccccccCCCCcccCCHHHHHHHHHHcCCCCCeEEEEEEE-Ee---ec-c
Confidence 2 34667777865 434 999876321 111234 45666665432111233 4444 774 32 11 2
Q ss_pred cccCcCCHHHHHHHHHHHHHHHH
Q 027742 164 FLLQKFNAIARERIDTALQEGVE 186 (219)
Q Consensus 164 yVL~~F~~~E~~~l~~~i~~a~~ 186 (219)
|= ..+|++=++.++++++.+.+
T Consensus 126 ~g-~~LS~~V~~av~~~~~~i~~ 147 (164)
T PRK10466 126 PH-IGLTPTVEAMIEPALEQVLA 147 (164)
T ss_pred CC-CCCCHHHHHHHHHHHHHHHH
Confidence 32 35665555544444444333
No 18
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=60.28 E-value=21 Score=31.62 Aligned_cols=89 Identities=21% Similarity=0.295 Sum_probs=50.7
Q ss_pred ccccchhHHHHHHhcC-CCC-Cce-EEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCC
Q 027742 83 MNLSGESTGPLAAYYK-LPL-NRV-LVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQM 159 (219)
Q Consensus 83 MN~SG~aV~~~~~~~k-i~~-~~i-lVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~ 159 (219)
=|..|+|+..+.+... .+. .+| +||.|= -|...-.+..+++.-=++=||.+++......+.-=+.||||.
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 4899999987766443 332 244 566663 455444444444444345588888888422356668999985
Q ss_pred CccccccCcCCHHHHHHHH
Q 027742 160 DPKAFLLQKFNAIARERID 178 (219)
Q Consensus 160 ~v~~yVL~~F~~~E~~~l~ 178 (219)
|+..|=-....-...+.|.
T Consensus 188 D~~~yY~~~~~i~~~e~l~ 206 (219)
T PF11775_consen 188 DVSRYYRRAVTIDDVEELG 206 (219)
T ss_pred CchhhcccceecCCHHHHH
Confidence 3433443333333444443
No 19
>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=58.42 E-value=18 Score=28.44 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=25.0
Q ss_pred cccccCcCCHHHHHHHHHHHHHHHHHHHHHHhcc
Q 027742 162 KAFLLQKFNAIARERIDTALQEGVEVLKLLLSKG 195 (219)
Q Consensus 162 ~~yVL~~F~~~E~~~l~~~i~~a~~~l~~~i~~~ 195 (219)
++++ +.||++|...|+++++...+-+|..+..|
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 3444 89999999999999999999999888643
No 20
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=55.36 E-value=1.3e+02 Score=25.69 Aligned_cols=137 Identities=20% Similarity=0.241 Sum_probs=77.5
Q ss_pred CeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhc
Q 027742 18 PWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 97 (219)
Q Consensus 18 ~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ 97 (219)
..+|+|+|||=.. -= .+|..++++|.+++..+. .+.++.- |.....++.+.
T Consensus 5 rilVlGiGN~L~g----DD-GvG~~va~~L~~~~~~~~-----------------~V~vid~-------Gt~g~~ll~~i 55 (195)
T PRK10264 5 RVVVMGLGNLLWA----DE-GFGVRVAERLYAHYHWPE-----------------YVEIVDG-------GTQGLNLLGYV 55 (195)
T ss_pred CEEEEEeCccccc----cC-cHHHHHHHHHHhhcCCCC-----------------CeEEEEC-------CCCHHHHHHHH
Confidence 4689999999422 12 399999999987654321 0111111 11112333333
Q ss_pred CCCCCceEEEeecC--CCCCceEEEecCC---------C-CCCCCchhhHHHh--hcCCCCcc-EEE-EeecCCCCCCCc
Q 027742 98 KLPLNRVLVFHDDM--GLPCGVLRLRHNG---------G-HGGHNGLKSVMNN--FRGNREFA-RLR-IGIGRPPGQMDP 161 (219)
Q Consensus 98 ki~~~~ilVihDDl--dlp~G~irlk~gG---------s-~gGHNGLkSIi~~--L~gt~~f~-Rlr-IGIGrP~~~~~v 161 (219)
. ..+.+||.|=+ +.++|+++.-... + +-.+-|+..++.. +.| +.+ ++. |||= |. ++
T Consensus 56 ~--~~d~vIiVDAv~~g~~PGtv~~~~~~~~~~~~~~~~~S~H~~~l~~~L~l~~l~g--~~P~~v~iiGie-p~---~~ 127 (195)
T PRK10264 56 E--SASHLLILDAIDYGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSEVLALADIRG--HLPAHIALVGLQ-PA---ML 127 (195)
T ss_pred c--CCCEEEEEECCccCCCCCeEEEEehhhcccccccCCcCcccCCHHHHHHHHHHcC--CCCCeEEEEEEE-Ee---Ee
Confidence 2 24566777854 5689998874311 1 2233588888753 322 343 566 4774 32 12
Q ss_pred cccccCcCCHHHHHHHHHHHHHHHHHHHHHH
Q 027742 162 KAFLLQKFNAIARERIDTALQEGVEVLKLLL 192 (219)
Q Consensus 162 ~~yVL~~F~~~E~~~l~~~i~~a~~~l~~~i 192 (219)
.+ .=-..|++=++.++++++.+.+.++.|.
T Consensus 128 ~~-~g~~LSp~V~~av~~~v~~i~~~l~~~~ 157 (195)
T PRK10264 128 DD-YGGSLSELAREQLPAAEQAALAQLAAWG 157 (195)
T ss_pred cC-CCCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 11 2247787777788888777777776665
No 21
>PRK09256 hypothetical protein; Provisional
Probab=49.45 E-value=8.5 Score=31.54 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=20.7
Q ss_pred EEeecCCCCCceEEEe--cCCCCCCCC
Q 027742 106 VFHDDMGLPCGVLRLR--HNGGHGGHN 130 (219)
Q Consensus 106 VihDDldlp~G~irlk--~gGs~gGHN 130 (219)
-|.+|+++|...++++ .++|.||+|
T Consensus 3 ~~~~~~~i~~~~l~~~~~RSSGPGGQ~ 29 (138)
T PRK09256 3 RITRRLVIPENELEWRFIRASGPGGQN 29 (138)
T ss_pred ccCccCccCHHHeEEEEEEcCCCCccc
Confidence 3678899999888776 688999987
No 22
>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=48.47 E-value=17 Score=29.12 Aligned_cols=26 Identities=23% Similarity=0.230 Sum_probs=20.5
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHH
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAES 50 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~ 50 (219)
||+|+|||-..=. .+|..++++|+++
T Consensus 1 lViGiGN~l~~DD-----GvG~~v~~~L~~~ 26 (144)
T cd06068 1 LVAGVGNIFLGDD-----GFGVEVARRLRPR 26 (144)
T ss_pred CEEEECccccccC-----cHHHHHHHHHhcc
Confidence 6899999964322 2999999999865
No 23
>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=45.06 E-value=26 Score=33.17 Aligned_cols=132 Identities=21% Similarity=0.350 Sum_probs=48.9
Q ss_pred CCCCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCC-CCCccccceEEEEEEECC-eeEEEEeCCCccccc----ch
Q 027742 15 VARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGI-SMNTVHCKATFGQGFVGD-APVLLAKPQTYMNLS----GE 88 (219)
Q Consensus 15 ~~~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~-~~~~~k~~~~~~~~~~~~-~~v~L~KP~TyMN~S----G~ 88 (219)
.....|||||||. .-|--. +|-.++|.+.-.-.+ .+..... ..+ ..|.-+-| --|=.. ++
T Consensus 94 ~~~~iLVVGLGN~----~vTPDA-LGP~vv~~l~VTRHL~~~~pe~~--------~~g~r~VsaiaP-GVmg~TGiET~e 159 (354)
T PF03418_consen 94 KEASILVVGLGNW----NVTPDA-LGPRVVENLLVTRHLFELQPEEV--------DEGYRPVSAIAP-GVMGQTGIETAE 159 (354)
T ss_dssp TT--EEEEE-S-S----SSGGG--HHHHHHHT----HHHHHHS--SS---------SS---EEEE-S-GGG---SS-HHH
T ss_pred CCCeEEEEeCCCc----CCCccc-cchhhhhhhhhhhhhhhhCchhh--------ccCcceeeEEcC-CccccccccHHH
Confidence 3456799999996 368899 999999976422111 0000000 111 23455555 223333 45
Q ss_pred hHHHHHHhcCCCCCceEEEeecCC-----CCCceEEEecCC-----CCCCC-CchhhHHHhhcCCCCccEEEEeecCCCC
Q 027742 89 STGPLAAYYKLPLNRVLVFHDDMG-----LPCGVLRLRHNG-----GHGGH-NGLKSVMNNFRGNREFARLRIGIGRPPG 157 (219)
Q Consensus 89 aV~~~~~~~ki~~~~ilVihDDld-----lp~G~irlk~gG-----s~gGH-NGLkSIi~~L~gt~~f~RlrIGIGrP~~ 157 (219)
.|+.+++..| -+++|.-|-|- -=--+|++..-| |-|-| ++|-. +.| | .+=+.||| |.-
T Consensus 160 Ii~gvv~~~k---Pd~VIaIDALAaRs~~Rl~~TIQisDTGI~PGSGVGN~R~~l~~--etL-G---vPVIAIGV--PTV 228 (354)
T PF03418_consen 160 IIKGVVEKIK---PDLVIAIDALAARSLERLNTTIQISDTGIHPGSGVGNHRKELNE--ETL-G---VPVIAIGV--PTV 228 (354)
T ss_dssp HHHHHHHHH-----SEEEEEEEE--SSGGGSSSEEEEETT-B-S-SSSS----BSSS-----------------------
T ss_pred HHHHHHHhhC---CCEEEEehhhhcCchhhccCeEEecCCCcCCCCCcCcccccCCH--HHc-C---CCEEEEcC--Cee
Confidence 5666666554 26677778653 234456766544 33444 33321 333 2 44555555 531
Q ss_pred ------CCCccccccCcCCH
Q 027742 158 ------QMDPKAFLLQKFNA 171 (219)
Q Consensus 158 ------~~~v~~yVL~~F~~ 171 (219)
-.|..++++..|..
T Consensus 229 VdA~tI~~Dtid~~~~~~~~ 248 (354)
T PF03418_consen 229 VDAATIVNDTIDYLLKHFGR 248 (354)
T ss_dssp EEEEEEE--EES---HHHHT
T ss_pred echHHHHHHHHHHHHHHHHH
Confidence 02445777776644
No 24
>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=43.56 E-value=26 Score=27.71 Aligned_cols=88 Identities=18% Similarity=0.175 Sum_probs=51.4
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
+|+|+|||=..= == +|..++++|.++... ..+-++.- |...-.++....
T Consensus 1 lViGiGN~l~~D----DG-vG~~v~~~L~~~~~~------------------~~v~~id~-------gt~~~~l~~~l~- 49 (139)
T cd00518 1 LVLGIGNPLRGD----DG-FGPAVAERLEERYLP------------------PGVEVIDG-------GTLGLELLDLLE- 49 (139)
T ss_pred CEEEECCccccc----Cc-HHHHHHHHHHhcCCC------------------CCeEEEEC-------CCCHHHHHHHHh-
Confidence 589999995321 23 999999999876420 01112111 111223333322
Q ss_pred CCCceEEEeecCC--CCCceEEEec------CCC-CCCCC-chhhHHHhh
Q 027742 100 PLNRVLVFHDDMG--LPCGVLRLRH------NGG-HGGHN-GLKSVMNNF 139 (219)
Q Consensus 100 ~~~~ilVihDDld--lp~G~irlk~------gGs-~gGHN-GLkSIi~~L 139 (219)
..+.+||.|=.+ .++|+++.-. ..+ ...|. |+..+++.+
T Consensus 50 -~~d~viiVDA~~~~~~pG~i~~~~~~~~~~~~~~~s~H~~~l~~~l~~~ 98 (139)
T cd00518 50 -GADRVIIVDAVDSGGEPGTVRRLEPEELPAYLSALSTHQLGLAELLALL 98 (139)
T ss_pred -cCCeEEEEECccCCCCCCeEEEEchhhcccccCCCCCccCCHHHHHHHH
Confidence 256677778764 6999988732 112 13455 999998877
No 25
>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=43.07 E-value=25 Score=27.90 Aligned_cols=90 Identities=17% Similarity=0.170 Sum_probs=50.3
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
+|+|+|||-..= == +|..++++|.++. . . .+-++.-.| .|..+ +.....
T Consensus 1 ~VlGiGN~L~~D----Dg-vG~~v~~~L~~~~-~--~----------------~v~vid~gt----~~~~~---~~~l~~ 49 (136)
T cd06067 1 VLLGVGNELRGD----DG-AGPLLAEKLEDLP-N--P----------------NWLVIDGGT----VPENF---TGKIRE 49 (136)
T ss_pred CEEEeCcccccc----Cc-HHHHHHHHHHhcC-C--C----------------CEEEEECCC----CHHHH---HHHHHh
Confidence 589999995332 23 9999999998753 1 0 111122111 22222 221111
Q ss_pred CCCceEEEeecC--CCCCceEEEecCC------CCCCCCchhhHHHhhc
Q 027742 100 PLNRVLVFHDDM--GLPCGVLRLRHNG------GHGGHNGLKSVMNNFR 140 (219)
Q Consensus 100 ~~~~ilVihDDl--dlp~G~irlk~gG------s~gGHNGLkSIi~~L~ 140 (219)
...+.+||.|=. +.++|+++.-... .+..+-|+..+.+.+.
T Consensus 50 ~~~d~vIiVDAv~~g~~PG~v~~~~~~~~~~~~~s~H~~~l~~~L~~~~ 98 (136)
T cd06067 50 EKPDLIVIVDAADMGLEPGEIRIIDPEEIAEYFFSTHTLPLSILIDYLR 98 (136)
T ss_pred cCCCEEEEEECCccCcCCCEEEEEchhhcccccCCCCcCCHHHHHHHHH
Confidence 124566677875 4599999874321 2334448888887763
No 26
>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=42.68 E-value=27 Score=27.82 Aligned_cols=27 Identities=26% Similarity=0.386 Sum_probs=20.9
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHc
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQ 51 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~ 51 (219)
||+|+|||=..= == +|..++++|++++
T Consensus 1 lVlGvGN~l~~D----DG-vG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPLRGD----DG-LGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCccccc----cc-hhHHHHHHHHhhC
Confidence 589999995322 23 9999999998764
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=42.27 E-value=30 Score=27.78 Aligned_cols=87 Identities=15% Similarity=0.068 Sum_probs=48.6
Q ss_pred EEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCC
Q 027742 20 LFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 99 (219)
Q Consensus 20 LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki 99 (219)
||+|+|||-..=. = +|..++++|++.. .+ . .+.++-- |.....++...
T Consensus 2 lVlGiGN~L~~DD----G-~G~~v~~~L~~~~-~~--~---------------~v~~id~-------gt~~~~l~~~l-- 49 (146)
T cd06063 2 TIIGCGNLNRGDD----G-VGPILIRRLQAYL-LP--P---------------HVRLVDC-------GTAGMEVMFRA-- 49 (146)
T ss_pred EEEEECCcccccC----c-HHHHHHHHHhhcC-CC--C---------------CeEEEEC-------CCCHHHHHHHh--
Confidence 7999999953322 2 9999999998642 11 0 0111111 12222333322
Q ss_pred CCCceEEEeecC--CCCCceEEEe------c---CCCCCCCCchhhHHHh
Q 027742 100 PLNRVLVFHDDM--GLPCGVLRLR------H---NGGHGGHNGLKSVMNN 138 (219)
Q Consensus 100 ~~~~ilVihDDl--dlp~G~irlk------~---gGs~gGHNGLkSIi~~ 138 (219)
...+.+||.|=. +.++|+++.- . ...+..+=|+.++++.
T Consensus 50 ~~~d~vIiVDA~~~g~~PG~v~~~~~~~~~~~~~~~~s~H~~~l~~~l~~ 99 (146)
T cd06063 50 RGAKQLIIIDASSTGSEPGAVFEVPGEELEALPEPSYNLHDFRWDHALAA 99 (146)
T ss_pred cCCCEEEEEEeCCCCCCCCeEEEEcchhccccccCCcCcccCCHHHHHHH
Confidence 234667777875 5699998752 1 1223445578887653
No 28
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=41.93 E-value=16 Score=27.39 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=19.6
Q ss_pred CCCCc--chHHHHHHHHHHHHHcCCCCC
Q 027742 31 YKGTR--HNQVGFEMIDAFAESQGISMN 56 (219)
Q Consensus 31 Y~~TR--HN~vGf~vld~La~~~~~~~~ 56 (219)
|.-.. -. +||..+|.+|.++|+...
T Consensus 45 Y~L~~~i~g-i~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDG-IGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSS-SBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccC-CCHHHHHHHHHHcCCCCC
Confidence 77777 67 999999999999998754
No 29
>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=40.24 E-value=54 Score=33.14 Aligned_cols=88 Identities=20% Similarity=0.272 Sum_probs=52.7
Q ss_pred cccchhHHHHHHhcCCCCC--c-eEEEeecCCCCCceEEEecCCCCCCCCchhhHHHhhcCCC-CccEEEEeecCCCCCC
Q 027742 84 NLSGESTGPLAAYYKLPLN--R-VLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNNFRGNR-EFARLRIGIGRPPGQM 159 (219)
Q Consensus 84 N~SG~aV~~~~~~~ki~~~--~-ilVihDDldlp~G~irlk~gGs~gGHNGLkSIi~~L~gt~-~f~RlrIGIGrP~~~~ 159 (219)
|..|+|+..++...--.++ + ++||.|= -|...-.+....+.-=++=||.+|+.. .++ ..-=+.||||..
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 NIDGEALMWAHQRLIARPEQRRILMMISDG--APVDDSTLSVNPGNYLERHLRAVIEEI-ETRSPVELLAIGIGHD---- 568 (600)
T ss_pred CCchHHHHHHHHHHhcCcccceEEEEEeCC--CcCCccccccCchhHHHHHHHHHHHHH-hccCCceEEEeecccc----
Confidence 8889999887765443333 3 4677774 344333333333444455699999998 453 566699999963
Q ss_pred CccccccCcCCHHHHHHHHH
Q 027742 160 DPKAFLLQKFNAIARERIDT 179 (219)
Q Consensus 160 ~v~~yVL~~F~~~E~~~l~~ 179 (219)
|..|--.-++-.+.+.|..
T Consensus 569 -v~r~Y~~~v~i~~~~eL~~ 587 (600)
T TIGR01651 569 -VTRYYRRAVTIVDAEELAG 587 (600)
T ss_pred -HHHHccccceecCHHHHHH
Confidence 5444444444444454543
No 30
>PRK02858 germination protease; Provisional
Probab=37.23 E-value=26 Score=33.29 Aligned_cols=114 Identities=18% Similarity=0.279 Sum_probs=59.1
Q ss_pred CCCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHHcCC-CCCccccceEEEEEEECC-eeEEEEeC----CCcccccchh
Q 027742 16 ARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAESQGI-SMNTVHCKATFGQGFVGD-APVLLAKP----QTYMNLSGES 89 (219)
Q Consensus 16 ~~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~~~~-~~~~~k~~~~~~~~~~~~-~~v~L~KP----~TyMN~SG~a 89 (219)
....|||||||- .-|--. .|-.+++.|.-.-.+ ....... -.+ ..|.-+-| +|=| .+++.
T Consensus 110 ~~~vLVVGLGN~----~VTPDA-LGP~vv~~l~VTRHL~~~~p~~~--------~~g~r~VsAiaPGVmg~TGi-ET~EI 175 (369)
T PRK02858 110 EASCLIVGLGNW----NVTPDA-LGPLVVENVLVTRHLFQLQPESV--------EEGFRPVSAIAPGVMGITGI-ETSDI 175 (369)
T ss_pred CCcEEEEeCCCc----CCCccc-cChheecceeeehhhhhhcchhh--------ccCCceeeEEcCCcccccch-hHHHH
Confidence 456899999995 468888 999999866521111 1000000 011 23444444 2333 34555
Q ss_pred HHHHHHhcCCCCCceEEEeecCCC-----CCceEEEecCC-----CCCCCCchhhHH-HhhcCCCCccEEEEee
Q 027742 90 TGPLAAYYKLPLNRVLVFHDDMGL-----PCGVLRLRHNG-----GHGGHNGLKSVM-NNFRGNREFARLRIGI 152 (219)
Q Consensus 90 V~~~~~~~ki~~~~ilVihDDldl-----p~G~irlk~gG-----s~gGHNGLkSIi-~~L~gt~~f~RlrIGI 152 (219)
|+.+++..| | +++|.-|-|-- =-=+|++..-| |-|-|. +.|. +.| | .+=+.|||
T Consensus 176 IkgIVek~K--P-D~VIaIDALAaRs~~Rln~TIQIsDTGI~PGSGVGN~R--~~l~~etL-G---VPVIAIGV 240 (369)
T PRK02858 176 IYGIIEKTK--P-DFVIAIDALAARSIERVNTTIQISDTGIHPGSGVGNKR--KELSKETL-G---IPVIAIGV 240 (369)
T ss_pred HHHHHHhhC--C-CEEEEechhhcCchhhccCeEEecCCCcCCCCCcCccc--cccCHHHc-C---CCEEEEcC
Confidence 666766544 3 66677786532 22345665444 333332 3333 344 3 46666665
No 31
>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=36.83 E-value=27 Score=33.14 Aligned_cols=114 Identities=18% Similarity=0.276 Sum_probs=59.9
Q ss_pred CCCeEEEeecCcCCCCCCCcchHHHHHHHHHHHHH-cCCCCCccccceEEEEEEECC-eeEEEEeC----CCcccccchh
Q 027742 16 ARPWLFVGLGNPGDKYKGTRHNQVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGD-APVLLAKP----QTYMNLSGES 89 (219)
Q Consensus 16 ~~~~LIvGLGNPG~~Y~~TRHN~vGf~vld~La~~-~~~~~~~~k~~~~~~~~~~~~-~~v~L~KP----~TyMN~SG~a 89 (219)
....|||||||- .-|--. .|-.+++.|.-. +=......+. -.+ ..|.-+-| +|=| .+++.
T Consensus 100 ~~~iLVVGLGN~----~VTPDA-LGP~vv~~l~VTRHL~~~~p~~~--------~~g~r~VsaiaPGVmg~TGi-ET~EI 165 (358)
T TIGR01441 100 DMTCLVVGLGNW----NVTPDA-LGPKVVENLLVTRHLFKLIPESV--------DEGIRPVSAVAPGVMGITGI-ETSDI 165 (358)
T ss_pred CCcEEEEeCCCc----CCCccc-cChheecceeeehhhhhhcchhh--------ccCCceeeEEcCCccccccc-cHHHH
Confidence 456899999995 468888 999998877521 1111110011 011 23444445 3334 34566
Q ss_pred HHHHHHhcCCCCCceEEEeecCCC-----CCceEEEecCC-----CCCCCCchhhHH-HhhcCCCCccEEEEee
Q 027742 90 TGPLAAYYKLPLNRVLVFHDDMGL-----PCGVLRLRHNG-----GHGGHNGLKSVM-NNFRGNREFARLRIGI 152 (219)
Q Consensus 90 V~~~~~~~ki~~~~ilVihDDldl-----p~G~irlk~gG-----s~gGHNGLkSIi-~~L~gt~~f~RlrIGI 152 (219)
|+.+++..| | +++|.-|-|-- =-=+|++..-| |-|-|. +.|. +.| | .+=+.|||
T Consensus 166 IkgiVek~k--P-D~VIaIDALAaRs~~Rln~TIQIsDTGI~PGSGVGN~R--~~l~~etL-G---VPVIAIGV 230 (358)
T TIGR01441 166 IRGIIEQIK--P-DFVIAIDALAARKMERVNSTIQISDTGIHPGSGVGNKR--KELSKKTL-G---VPVIAVGV 230 (358)
T ss_pred HHHHHHhhC--C-CEEEEechhhcCchhhccCeEEecCCCcCCCCCcCccc--cccCHHHc-C---CCEEEEcC
Confidence 677766544 3 66667786532 22345665444 333332 3333 344 3 56677766
No 32
>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=34.19 E-value=74 Score=23.95 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=19.8
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHH
Q 027742 168 KFNAIARERIDTALQEGVEVLKLLL 192 (219)
Q Consensus 168 ~F~~~E~~~l~~~i~~a~~~l~~~i 192 (219)
+.+.+|++.|..+|++..+.+..|+
T Consensus 2 KVt~~EkeQLS~AID~mnEGLD~fI 26 (84)
T PF11458_consen 2 KVTDQEKEQLSTAIDRMNEGLDTFI 26 (84)
T ss_pred CCchHHHHHHHHHHHHHHhhHHHHH
Confidence 4577899999999988877776665
No 33
>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=33.64 E-value=46 Score=30.12 Aligned_cols=54 Identities=17% Similarity=0.230 Sum_probs=33.6
Q ss_pred ecCCCCC-CC----ccccccCcCC---HHHHHHHHHHHHHHHHHHHHHHhccHHHHHHhhhc
Q 027742 152 IGRPPGQ-MD----PKAFLLQKFN---AIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 205 (219)
Q Consensus 152 IGrP~~~-~~----v~~yVL~~F~---~~E~~~l~~~i~~a~~~l~~~i~~~~~~amn~~n~ 205 (219)
+|.||.. .+ |.+||+.+|+ +.|.+.+-++-....-.+..|--+..+.-.+..+.
T Consensus 136 lG~PPFE~PsI~k~V~nfv~~kf~~l~~~E~q~m~elakmFL~~lN~W~le~ps~~~~~~~~ 197 (252)
T PF06466_consen 136 LGKPPFEKPSIEKAVTNFVLYKFSHLPQKEWQTMYELAKMFLHCLNHWKLEAPSQRRQRSNA 197 (252)
T ss_pred CCCCCCCCccHHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHHHhhccCCChHHHHhhcCc
Confidence 3566643 23 4589999985 56777766555555556666655666666666554
No 34
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=31.77 E-value=1.8e+02 Score=27.11 Aligned_cols=72 Identities=19% Similarity=0.181 Sum_probs=58.1
Q ss_pred CCCcchHHHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeCCCcccccchhHHHHHHhcCCCCCceEE
Q 027742 32 KGTRHNQVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLV 106 (219)
Q Consensus 32 ~~TRHN~vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilV 106 (219)
.-|+|+ .-...++.=.+..|+.+.+.+.+-++.....+|-++-.--|.|-||. +.+..++..|+|...++++
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 DATKSE-DQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPLTHCDE--KLIYTILHEYKIHNAEVLF 219 (364)
T ss_pred cCCcch-hHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeeccccccH--HHHHHHHHHHeeccceEEE
Confidence 358888 77888888888899998887777677777777888888889887765 7788999999998777764
No 35
>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=29.32 E-value=91 Score=26.05 Aligned_cols=42 Identities=12% Similarity=0.201 Sum_probs=31.4
Q ss_pred cccCcCCHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHhhhc
Q 027742 164 FLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHFNT 205 (219)
Q Consensus 164 yVL~~F~~~E~~~l~~~i~~a~~~l~~~i~~~~~~amn~~n~ 205 (219)
+=|..|+|+.++.+.-.+-+...++..+.+..++.||+++..
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 335899999998876543344447888888889999998764
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=27.76 E-value=2.8e+02 Score=25.81 Aligned_cols=68 Identities=22% Similarity=0.338 Sum_probs=46.5
Q ss_pred EEeecCCCC--CceEEEecCCCCCCCCchhhHHHhhcCCCCccEEEEeecCCCCCCCccccccCcCCHHHHHHHH
Q 027742 106 VFHDDMGLP--CGVLRLRHNGGHGGHNGLKSVMNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERID 178 (219)
Q Consensus 106 VihDDldlp--~G~irlk~gGs~gGHNGLkSIi~~L~gt~~f~RlrIGIGrP~~~~~v~~yVL~~F~~~E~~~l~ 178 (219)
|..|++.-+ +|+| +-.-||.|.||-.|=|...|. . .=.|+ |||--|..+ .+..|--..++.+|+...-
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 6655 668899999999999999983 2 22343 788888653 4455666778888887553
No 37
>PRK10870 transcriptional repressor MprA; Provisional
Probab=27.73 E-value=55 Score=27.22 Aligned_cols=38 Identities=11% Similarity=0.229 Sum_probs=28.2
Q ss_pred ccccCcCCHHHHHHHHHHHHHHHHHHHHHHhcc-HHHHH
Q 027742 163 AFLLQKFNAIARERIDTALQEGVEVLKLLLSKG-LTESA 200 (219)
Q Consensus 163 ~yVL~~F~~~E~~~l~~~i~~a~~~l~~~i~~~-~~~am 200 (219)
+-+++.++++|++.+...+.+..+.++..-++| +-+||
T Consensus 137 ~~~~~~ls~~e~~~l~~~L~kl~~~l~~~~~~~~~~~~~ 175 (176)
T PRK10870 137 HQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAM 175 (176)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHhhCCCchhhhhc
Confidence 556788899999888888888888777665544 55554
No 38
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=26.69 E-value=46 Score=28.56 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=25.2
Q ss_pred cchhHHHHHHhcCCCCCceEEEeecCCCC
Q 027742 86 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 114 (219)
Q Consensus 86 SG~aV~~~~~~~ki~~~~ilVihDDldlp 114 (219)
++.++.++++.++++++++++|-|.|=..
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL~TD 123 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQLFTD 123 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchhhhh
Confidence 47889999999999999999999988433
No 39
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.60 E-value=16 Score=24.56 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=18.3
Q ss_pred cccchhHHHHHHhcCCCCCceEEEeec
Q 027742 84 NLSGESTGPLAAYYKLPLNRVLVFHDD 110 (219)
Q Consensus 84 N~SG~aV~~~~~~~ki~~~~ilVihDD 110 (219)
+.|-..+..+++++++++++++...+|
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 456678889999999999999887765
No 40
>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=25.39 E-value=47 Score=25.93 Aligned_cols=22 Identities=27% Similarity=0.634 Sum_probs=16.8
Q ss_pred ecCCCCCceEEEe--cCCCCCCCC
Q 027742 109 DDMGLPCGVLRLR--HNGGHGGHN 130 (219)
Q Consensus 109 DDldlp~G~irlk--~gGs~gGHN 130 (219)
.++++|...+.+. .++|+||+|
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 4677888888776 688999986
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=25.37 E-value=51 Score=26.91 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=23.0
Q ss_pred chhHHHHHHhcCCCCCceEEEeecC
Q 027742 87 GESTGPLAAYYKLPLNRVLVFHDDM 111 (219)
Q Consensus 87 G~aV~~~~~~~ki~~~~ilVihDDl 111 (219)
|.++..+++.+++++++++++=|+.
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 7889999999999999999999875
No 42
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=24.57 E-value=76 Score=29.03 Aligned_cols=30 Identities=23% Similarity=0.133 Sum_probs=27.2
Q ss_pred CcccccchhHHHHHHhcCCCCCceEEEeec
Q 027742 81 TYMNLSGESTGPLAAYYKLPLNRVLVFHDD 110 (219)
Q Consensus 81 TyMN~SG~aV~~~~~~~ki~~~~ilVihDD 110 (219)
.=|=.|.+...+++...+|..++.||+|||
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd 98 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDD 98 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECC
Confidence 467778889999999999999999999999
No 43
>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=23.54 E-value=1.7e+02 Score=21.92 Aligned_cols=44 Identities=25% Similarity=0.375 Sum_probs=35.7
Q ss_pred ECCeeEEEEeCCCcccccchhHHHHHHhcCCCCCceEEEeecCCCCCceEEEecCCCC
Q 027742 69 VGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGH 126 (219)
Q Consensus 69 ~~~~~v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDldlp~G~irlk~gGs~ 126 (219)
+.+.++++++|. +..|+ +..+.+|..|.++--.|..-+--.||+
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 467899999996 44443 567889999999999999999887764
No 44
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=23.08 E-value=60 Score=28.25 Aligned_cols=27 Identities=22% Similarity=0.412 Sum_probs=21.8
Q ss_pred eEEEeecCCCCCceEEEe--cCCCCCCCC
Q 027742 104 VLVFHDDMGLPCGVLRLR--HNGGHGGHN 130 (219)
Q Consensus 104 ilVihDDldlp~G~irlk--~gGs~gGHN 130 (219)
+.|+-.+++++...+++. +++|+||+|
T Consensus 95 V~v~~~~~~i~~~dl~~~~~RssGpGGQ~ 123 (200)
T PRK08179 95 IGRFSADEEEQSDEIRFETLRSSGPGGQH 123 (200)
T ss_pred EEEeCCcCccCHHHeEEEEEEccCCcccc
Confidence 456667889999999976 688999995
No 45
>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=22.86 E-value=3.5e+02 Score=25.80 Aligned_cols=66 Identities=9% Similarity=0.056 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHcCCCCCccccceEEEEEEECCeeEEEEeC---CCcccccchhHHHHHHhcCCCCCceEE
Q 027742 39 VGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKP---QTYMNLSGESTGPLAAYYKLPLNRVLV 106 (219)
Q Consensus 39 vGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~KP---~TyMN~SG~aV~~~~~~~ki~~~~ilV 106 (219)
+|=+++-.|...... ...-++..+++..+.|.+++++|+ ..=.=.=|+||..+.+.++-.++.|+-
T Consensus 185 aGPLVA~~l~~~~~~--~~~~~dtv~~e~~~egRrv~viKA~GPGstVGrpgeave~i~~~~~~k~~~IIT 253 (355)
T PF07431_consen 185 AGPLVAGRLMENCSK--WEIAKDTVIAECEFEGRRVYVIKAEGPGSTVGRPGEAVEYIVEKLGGKVDLIIT 253 (355)
T ss_pred cchHHHHHHHhcCcc--cccccccEEEEEEECCcEEEEEeccCCCccCCChHHHHHHHHHHhcCCccEEEE
Confidence 777888887765543 222345677888999999999995 444555688999999988666666654
No 46
>PF12896 Apc4: Anaphase-promoting complex, cyclosome, subunit 4; InterPro: IPR024790 Apc4 is one of the larger of the subunits of the anaphase-promoting complex (APC) or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [, ]. Results in Caenorhabditis elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle. The APC is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism []. This entry represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits.
Probab=22.32 E-value=1e+02 Score=25.87 Aligned_cols=49 Identities=18% Similarity=0.302 Sum_probs=39.9
Q ss_pred cCCCCCCCccccccCcCCHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHhh
Q 027742 153 GRPPGQMDPKAFLLQKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHF 203 (219)
Q Consensus 153 GrP~~~~~v~~yVL~~F~~~E~~~l~~~i~~a~~~l~~~i~~~~~~amn~~ 203 (219)
|.+. +.+.+|....+++.-.++++++++.+.+.+..++.+.+..|+.++
T Consensus 85 G~~s--~~l~~fL~~~l~erglKr~~k~~~~~y~~i~~l~~~~l~pa~erl 133 (210)
T PF12896_consen 85 GHAS--PALKQFLVNQLGERGLKRWEKAVDSAYSSIRKLLFEHLIPALERL 133 (210)
T ss_pred cCCC--HHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4443 367899999999999999999999999999988887777666554
No 47
>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=22.32 E-value=86 Score=29.70 Aligned_cols=33 Identities=24% Similarity=0.384 Sum_probs=25.6
Q ss_pred EEEEeCCCcccccchhHHHHHHhcCCCCCceEEEeecC
Q 027742 74 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDM 111 (219)
Q Consensus 74 v~L~KP~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDl 111 (219)
.++++|..+.| .|+..++.+|+. .++++||||=
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 47888863333 399999999987 6999999753
No 48
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional
Probab=21.30 E-value=3e+02 Score=25.42 Aligned_cols=71 Identities=13% Similarity=0.087 Sum_probs=54.2
Q ss_pred CCcccccchhHHHHHHhcCCCCCceEEEeecCC--------C--CCceEEEecCC-CCCCCCchhhHHHhhcCCCCccEE
Q 027742 80 QTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMG--------L--PCGVLRLRHNG-GHGGHNGLKSVMNNFRGNREFARL 148 (219)
Q Consensus 80 ~TyMN~SG~aV~~~~~~~ki~~~~ilVihDDld--------l--p~G~irlk~gG-s~gGHNGLkSIi~~L~gt~~f~Rl 148 (219)
...=|.+|..+..+++.++......-++-||.+ + .--.+=+--|| |.+-..=....++.+ +..+|+.+
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 027742 149 RIG 151 (219)
Q Consensus 149 rIG 151 (219)
+..
T Consensus 249 ae~ 251 (312)
T PRK03604 249 AEA 251 (312)
T ss_pred HHH
Confidence 754
No 49
>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=20.90 E-value=1.9e+02 Score=22.45 Aligned_cols=36 Identities=19% Similarity=0.195 Sum_probs=23.5
Q ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHhh
Q 027742 167 QKFNAIARERIDTALQEGVEVLKLLLSKGLTESARHF 203 (219)
Q Consensus 167 ~~F~~~E~~~l~~~i~~a~~~l~~~i~~~~~~amn~~ 203 (219)
|..|++|++.|.+++.++.+ ++..-++-+.+..+++
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 46789999999999998766 3333334455555554
No 50
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=20.71 E-value=2.3e+02 Score=19.77 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=17.7
Q ss_pred CcCCHHHHHHHHHHHHHHHHHHHH
Q 027742 167 QKFNAIARERIDTALQEGVEVLKL 190 (219)
Q Consensus 167 ~~F~~~E~~~l~~~i~~a~~~l~~ 190 (219)
.+||++|.+.|-+.+..-.+.++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~ 26 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILEN 26 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhc
Confidence 479999999887777665555544
No 51
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=20.61 E-value=32 Score=24.80 Aligned_cols=24 Identities=21% Similarity=0.213 Sum_probs=20.8
Q ss_pred CcccccchhHHHHHHhcCCCCCce
Q 027742 81 TYMNLSGESTGPLAAYYKLPLNRV 104 (219)
Q Consensus 81 TyMN~SG~aV~~~~~~~ki~~~~i 104 (219)
-||..||....++++.++|.+.++
T Consensus 7 hflhE~g~~FveIAr~~~i~a~e~ 30 (63)
T PF11242_consen 7 HFLHESGLSFVEIARKIGITAKEV 30 (63)
T ss_pred hhHHHcCCcHHHHHHHhCCCHHHH
Confidence 478999999999999999987654
No 52
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=20.53 E-value=56 Score=28.02 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=22.7
Q ss_pred chhHHHHHHhcCCCCCceEEEeecC
Q 027742 87 GESTGPLAAYYKLPLNRVLVFHDDM 111 (219)
Q Consensus 87 G~aV~~~~~~~ki~~~~ilVihDDl 111 (219)
|.++..+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 7889999999999999999999865
No 53
>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=20.46 E-value=1.3e+02 Score=25.67 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=26.8
Q ss_pred CCeeEEEEeCCCcccccchhHHHHHH---hcCCCCCceEEEe
Q 027742 70 GDAPVLLAKPQTYMNLSGESTGPLAA---YYKLPLNRVLVFH 108 (219)
Q Consensus 70 ~~~~v~L~KP~TyMN~SG~aV~~~~~---~~ki~~~~ilVih 108 (219)
.+.+|+|+-| |-.+|.++..+++ .+++++++|++++
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 8889998866544 5567888887764
No 54
>PRK06437 hypothetical protein; Provisional
Probab=20.41 E-value=1.4e+02 Score=20.95 Aligned_cols=29 Identities=7% Similarity=-0.011 Sum_probs=24.6
Q ss_pred cchhHHHHHHhcCCCCCceEEEeecCCCC
Q 027742 86 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 114 (219)
Q Consensus 86 SG~aV~~~~~~~ki~~~~ilVihDDldlp 114 (219)
.|.+|+.+++.++++++.+.|+++.--+|
T Consensus 19 ~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 19 HELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 45679999999999999999998877666
No 55
>PRK10976 putative hydrolase; Provisional
Probab=20.28 E-value=61 Score=27.82 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=22.7
Q ss_pred chhHHHHHHhcCCCCCceEEEeecC
Q 027742 87 GESTGPLAAYYKLPLNRVLVFHDDM 111 (219)
Q Consensus 87 G~aV~~~~~~~ki~~~~ilVihDDl 111 (219)
|.+++.+++.++|++++++++=|..
T Consensus 192 g~al~~l~~~lgi~~~~viafGD~~ 216 (266)
T PRK10976 192 GHALEAVAKKLGYSLKDCIAFGDGM 216 (266)
T ss_pred HHHHHHHHHHcCCCHHHeEEEcCCc
Confidence 8889999999999999999998864
No 56
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=20.22 E-value=89 Score=27.21 Aligned_cols=27 Identities=22% Similarity=0.384 Sum_probs=20.8
Q ss_pred eEEEeecCCCCCceEEEe--cCCCCCCCC
Q 027742 104 VLVFHDDMGLPCGVLRLR--HNGGHGGHN 130 (219)
Q Consensus 104 ilVihDDldlp~G~irlk--~gGs~gGHN 130 (219)
+.|+-.+++++...+++. +++|+||+|
T Consensus 94 V~v~~~~~~i~~~dl~~~~~RssGpGGQ~ 122 (200)
T TIGR03072 94 VQRFSASEEATEDEIRFETLRSSGPGGQH 122 (200)
T ss_pred EEEecCccccChhheEEEEEECCCCCccc
Confidence 445556888999999986 678999965
Done!