Query 032899
Match_columns 131
No_of_seqs 131 out of 1030
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:19:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032899.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032899hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0193 Pth Peptidyl-tRNA hydr 100.0 2.3E-53 5E-58 330.0 11.4 115 17-131 1-116 (190)
2 cd02406 CRS2 Chloroplast RNA s 100.0 4E-53 8.6E-58 329.6 12.6 115 17-131 1-115 (191)
3 cd00462 PTH Peptidyl-tRNA hydr 100.0 6.8E-52 1.5E-56 317.8 12.5 112 20-131 1-112 (171)
4 TIGR00447 pth peptidyl-tRNA hy 100.0 1.4E-51 3E-56 320.1 12.9 114 18-131 1-115 (188)
5 PRK05426 peptidyl-tRNA hydrola 100.0 1.2E-50 2.6E-55 314.9 12.9 115 17-131 1-116 (189)
6 PF01195 Pept_tRNA_hydro: Pept 100.0 5.5E-49 1.2E-53 303.9 10.6 112 20-131 1-113 (184)
7 KOG2255 Peptidyl-tRNA hydrolas 100.0 5.6E-41 1.2E-45 262.2 9.7 115 17-131 38-152 (224)
8 PRK10466 hybD hydrogenase 2 ma 76.7 4 8.7E-05 30.6 3.8 30 18-51 2-31 (164)
9 cd06062 H2MP_MemB-H2up Endopep 73.7 4.9 0.00011 29.4 3.6 28 19-50 1-28 (146)
10 COG0680 HyaD Ni,Fe-hydrogenase 73.5 4 8.8E-05 31.0 3.1 31 17-51 2-32 (160)
11 TIGR00130 frhD coenzyme F420-r 69.4 6.2 0.00013 29.2 3.3 29 17-49 3-31 (153)
12 PF03418 Peptidase_A25: Germin 69.1 6.8 0.00015 33.7 3.8 29 15-47 94-122 (354)
13 TIGR00072 hydrog_prot hydrogen 68.9 5.3 0.00012 29.1 2.8 28 20-51 1-28 (145)
14 cd06064 H2MP_F420-Reduc Endope 66.8 6 0.00013 29.1 2.8 27 20-50 1-27 (150)
15 PRK10264 hydrogenase 1 maturat 65.5 12 0.00025 29.3 4.3 31 17-51 4-34 (195)
16 cd00518 H2MP Hydrogenase speci 64.6 7.5 0.00016 28.0 2.9 27 20-50 1-27 (139)
17 cd06066 H2MP_NAD-link-bidir En 62.6 8.8 0.00019 27.9 2.9 27 20-50 1-27 (139)
18 cd06067 H2MP_MemB-H2evol Endop 61.6 8.6 0.00019 27.8 2.7 27 20-50 1-27 (136)
19 PRK11544 hycI hydrogenase 3 ma 59.6 12 0.00025 27.9 3.2 28 18-49 2-29 (156)
20 cd06063 H2MP_Cyano-H2up This g 59.1 11 0.00024 27.6 3.0 27 19-49 1-27 (146)
21 TIGR00142 hycI hydrogenase mat 59.1 10 0.00023 27.7 2.8 28 19-50 1-28 (146)
22 PRK12362 germination protease; 58.3 13 0.00028 31.6 3.5 94 15-123 97-200 (318)
23 cd06070 H2MP_like-2 Putative [ 58.2 10 0.00023 27.5 2.7 25 20-48 1-25 (140)
24 PRK02858 germination protease; 56.6 8.1 0.00018 33.4 2.1 28 16-47 110-137 (369)
25 cd06068 H2MP_like-1 Putative [ 55.9 11 0.00024 27.4 2.5 27 20-50 1-27 (144)
26 TIGR01441 GPR GPR endopeptidas 51.5 11 0.00024 32.5 2.1 80 16-111 100-185 (358)
27 COG2179 Predicted hydrolase of 47.5 15 0.00033 28.6 2.2 29 85-113 95-123 (175)
28 PF14490 HHH_4: Helix-hairpin- 46.5 13 0.00029 25.3 1.5 25 31-55 45-71 (94)
29 COG2897 SseA Rhodanese-related 45.8 24 0.00052 29.3 3.2 31 80-110 69-99 (285)
30 COG2607 Predicted ATPase (AAA+ 42.2 16 0.00035 30.5 1.7 30 91-120 129-158 (287)
31 PF02789 Peptidase_M17_N: Cyto 39.5 29 0.00063 23.8 2.4 33 16-48 52-84 (126)
32 PF08282 Hydrolase_3: haloacid 38.8 27 0.00058 25.8 2.3 25 86-110 188-212 (254)
33 KOG2882 p-Nitrophenyl phosphat 37.7 28 0.0006 29.5 2.4 38 71-114 218-255 (306)
34 PF07431 DUF1512: Protein of u 35.9 1.9E+02 0.0042 25.0 7.2 67 37-105 184-253 (355)
35 KOG1486 GTP-binding protein DR 35.2 1.9E+02 0.004 24.7 6.8 72 32-105 148-219 (364)
36 PRK06437 hypothetical protein; 32.9 60 0.0013 20.8 2.9 29 85-113 19-47 (67)
37 COG5381 Uncharacterized protei 32.5 27 0.0006 27.1 1.5 22 30-51 56-77 (184)
38 COG4128 Zot Zonula occludens t 32.4 46 0.00099 28.8 2.9 41 83-123 36-76 (398)
39 PF13443 HTH_26: Cro/C1-type H 31.8 9.9 0.00021 23.3 -0.9 27 83-109 37-63 (63)
40 PRK10513 sugar phosphate phosp 31.6 31 0.00067 26.8 1.7 25 86-110 198-222 (270)
41 PRK10976 putative hydrolase; P 31.1 34 0.00074 26.6 1.8 26 85-110 191-216 (266)
42 PF11242 DUF2774: Protein of u 30.6 23 0.00049 23.3 0.6 24 80-103 7-30 (63)
43 TIGR01485 SPP_plant-cyano sucr 30.3 55 0.0012 25.4 2.9 27 85-111 168-194 (249)
44 PF09807 DUF2348: Uncharacteri 28.7 73 0.0016 25.6 3.4 97 2-112 34-146 (249)
45 smart00852 MoCF_biosynth Proba 28.1 35 0.00076 24.2 1.4 35 77-111 11-45 (135)
46 cd01896 DRG The developmentall 27.4 2.8E+02 0.0061 21.5 6.5 56 44-101 98-153 (233)
47 PF14681 UPRTase: Uracil phosp 26.8 88 0.0019 24.2 3.5 35 69-106 120-157 (207)
48 PTZ00397 macrophage migration 26.7 74 0.0016 22.1 2.8 29 84-112 77-105 (116)
49 PF13242 Hydrolase_like: HAD-h 26.5 53 0.0011 20.8 1.8 25 89-113 10-34 (75)
50 PRK15126 thiamin pyrimidine py 26.2 38 0.00083 26.5 1.4 26 85-110 189-214 (272)
51 PRK01158 phosphoglycolate phos 25.8 44 0.00096 25.2 1.6 26 86-111 159-184 (230)
52 TIGR02463 MPGP_rel mannosyl-3- 25.5 73 0.0016 24.0 2.8 26 85-110 180-205 (221)
53 TIGR02471 sucr_syn_bact_C sucr 25.2 52 0.0011 25.2 1.9 28 84-111 159-186 (236)
54 PF05116 S6PP: Sucrose-6F-phos 25.1 59 0.0013 25.7 2.2 27 85-111 166-192 (247)
55 COG4046 Uncharacterized protei 24.8 3.5E+02 0.0075 23.5 6.8 68 37-106 197-267 (368)
56 TIGR02667 moaB_proteo molybden 23.7 42 0.0009 25.2 1.1 31 81-111 19-49 (163)
57 COG0056 AtpA F0F1-type ATP syn 23.7 71 0.0015 28.8 2.6 24 85-111 241-264 (504)
58 cd06392 PBP1_iGluR_delta_1 N-t 23.5 98 0.0021 26.6 3.4 32 73-109 116-147 (400)
59 PRK08179 prfH peptide chain re 23.4 68 0.0015 25.4 2.3 27 103-129 95-123 (200)
60 cd01445 TST_Repeats Thiosulfat 23.0 1E+02 0.0022 22.2 3.0 22 88-109 82-103 (138)
61 TIGR01482 SPP-subfamily Sucros 23.0 63 0.0014 24.2 2.0 27 84-110 149-175 (225)
62 TIGR01683 thiS thiamine biosyn 22.7 1.3E+02 0.0029 18.6 3.2 28 86-113 13-40 (64)
63 PF07693 KAP_NTPase: KAP famil 22.4 83 0.0018 25.0 2.7 14 99-112 170-183 (325)
64 COG2344 AT-rich DNA-binding pr 22.1 63 0.0014 26.0 1.8 26 3-28 71-96 (211)
65 TIGR00013 taut 4-oxalocrotonat 21.8 1.1E+02 0.0025 18.4 2.7 22 91-112 27-48 (63)
66 COG4841 Uncharacterized protei 21.8 71 0.0015 22.6 1.8 24 107-130 14-40 (95)
67 PF05673 DUF815: Protein of un 21.6 1E+02 0.0023 25.2 3.1 30 90-119 95-124 (249)
68 cd05211 NAD_bind_Glu_Leu_Phe_V 21.5 1.1E+02 0.0025 23.9 3.2 34 5-49 12-45 (217)
69 cd00565 ThiS ThiaminS ubiquiti 21.2 1.4E+02 0.0029 18.6 3.0 29 86-114 14-42 (65)
70 KOG3731 Sulfatases [Carbohydra 21.2 78 0.0017 28.6 2.4 47 76-122 9-57 (541)
71 cd01614 EutN_CcmL Ethanolamine 21.2 2.2E+02 0.0048 19.4 4.2 44 68-125 19-62 (83)
72 KOG0076 GTP-binding ADP-ribosy 21.0 1E+02 0.0022 24.5 2.8 87 15-111 16-104 (197)
73 COG0035 Upp Uracil phosphoribo 20.7 1.6E+02 0.0036 23.6 3.9 36 68-107 122-160 (210)
74 COG0561 Cof Predicted hydrolas 20.6 68 0.0015 24.9 1.8 27 85-111 190-216 (264)
75 PRK02220 4-oxalocrotonate taut 20.5 1E+02 0.0022 18.6 2.3 20 92-111 28-47 (61)
76 TIGR00099 Cof-subfamily Cof su 20.4 59 0.0013 25.1 1.4 27 85-111 189-215 (256)
77 TIGR03072 release_prfH putativ 20.1 1E+02 0.0022 24.4 2.6 27 103-129 94-122 (200)
No 1
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-53 Score=329.98 Aligned_cols=115 Identities=46% Similarity=0.817 Sum_probs=110.4
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCC-CcceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHH
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISM-NTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~-~~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~ 95 (131)
.++|||||||||++|+.|||||||+++|.||++++.++ +.+++.+.++++.+++++|+|+||+||||+||++|.++++|
T Consensus 1 ~~kLIVGLGNPG~~Y~~TRHNvGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~l~kP~TyMNlSG~~V~~~~~f 80 (190)
T COG0193 1 MMKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASF 80 (190)
T ss_pred CcEEEEECCCCchhhcccchhHHHHHHHHHHHHhCCCCccccccCceeEEEEeCCcEEEEecCccceeCcHHHHHHHHHH
Confidence 36899999999999999999999999999999999998 46688899999999999999999999999999999999999
Q ss_pred cCCCCCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 96 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 96 ~ki~~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
|++++++++|||||||+|+|++|||.+||++||||+
T Consensus 81 y~i~~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGl 116 (190)
T COG0193 81 YKIKPEDILVVHDELDLPLGKVRLKLGGGAGGHNGL 116 (190)
T ss_pred hCCCHHHEEEEeeccCCCCceEEEEcCCCCCCcccH
Confidence 999999999999999999999999999999999995
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=4e-53 Score=329.58 Aligned_cols=115 Identities=70% Similarity=1.212 Sum_probs=109.9
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHc
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ 96 (131)
+|+|||||||||++|++|||||||+++|.||+++++++++.++++.++++.+.+++++|+||+||||+||++|+++++||
T Consensus 1 ~~~LIvGLGNPG~~Y~~TRHNiGf~vld~La~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~aV~~~~~~y 80 (191)
T cd02406 1 TPWLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYY 80 (191)
T ss_pred CcEEEEEcCCCchhhCcCchhHHHHHHHHHHHHcCCCccccccceEEEEEEECCeEEEEEeCCCchhcCHHHHHHHHHHh
Confidence 47899999999999999999999999999999999887666778888998999999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 97 ki~~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
+++++++||||||||||+|++|+|.+||++||||+
T Consensus 81 ki~~~~ilVihDdldl~~G~irlk~gGs~gGHNGl 115 (191)
T cd02406 81 KVPLRHILVIYDDMSLPNGVLRLQPKGGHGRHNGL 115 (191)
T ss_pred CCCHHHEEEEEECCCCCCCeEEEcCCCCCCCcCCH
Confidence 99999999999999999999999999999999996
No 3
>cd00462 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts.
Probab=100.00 E-value=6.8e-52 Score=317.78 Aligned_cols=112 Identities=56% Similarity=0.985 Sum_probs=107.6
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHcCCC
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ki~ 99 (131)
|||||||||++|++|||||||+++|+||++++.++.+.++.+.++++.+.+++++|+||+||||+||++|++++++|+++
T Consensus 1 LIvGLGNPG~~Y~~TRHNvGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~~i~ 80 (171)
T cd00462 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYKIP 80 (171)
T ss_pred CEEEECCCCcccCcCchHHHHHHHHHHHHHcCCCCCccccCEEEEEEEECCEEEEEEeCCcccccccHHHHHHHHhcCCC
Confidence 69999999999999999999999999999999888766667899999999999999999999999999999999999999
Q ss_pred CCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 100 LNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 100 ~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
++++||||||||+|+|++|+|++||++||||+
T Consensus 81 ~~~ilVihDdldl~~G~vrlk~~G~~gGHNGl 112 (171)
T cd00462 81 PEDILVIHDDLDLPLGKIRLKKGGGSGGHNGL 112 (171)
T ss_pred hhHEEEEEecCCCCCceEEEeCCCCCCCCCCH
Confidence 99999999999999999999999999999996
No 4
>TIGR00447 pth peptidyl-tRNA hydrolase. The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function.
Probab=100.00 E-value=1.4e-51 Score=320.08 Aligned_cols=114 Identities=46% Similarity=0.814 Sum_probs=108.0
Q ss_pred CeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCC-cceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHc
Q 032899 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (131)
Q Consensus 18 ~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~-~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ 96 (131)
|+|||||||||++|++|||||||+++|.||++++.+++ ..++.+.+++..+.+++++|+||+||||+||++|++++++|
T Consensus 1 ~~LIvGLGNPG~~Y~~TRHNiGf~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~ 80 (188)
T TIGR00447 1 IKLIVGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERGLLSGKKVILLKPLTYMNLSGEAVRALASFY 80 (188)
T ss_pred CEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCcCCcccccceEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHHh
Confidence 68999999999999999999999999999999998875 34567888888899999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 97 ki~~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
+++++++||||||||+|+|++|+|++||++||||+
T Consensus 81 ~i~~~~ilVihDdldl~~G~irlk~~G~~gGHNGl 115 (188)
T TIGR00447 81 RIKPAELLVVHDELDLPLGKVRLKMGGGAGGHNGL 115 (188)
T ss_pred CCChHHEEEEEecCCCCCceEEEecCCCCCCcCCH
Confidence 99999999999999999999999999999999996
No 5
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=1.2e-50 Score=314.95 Aligned_cols=115 Identities=48% Similarity=0.849 Sum_probs=108.2
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCC-cceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHH
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMN-TVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAY 95 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~-~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~ 95 (131)
+++|||||||||++|++|||||||+++|.||++++..+. ..++.+.+++..+++.+++|+||+||||+||++|++++++
T Consensus 1 ~~~LivGLGNPG~~Y~~TRHNvGf~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~ 80 (189)
T PRK05426 1 MMKLIVGLGNPGPEYANTRHNIGFMVVDELARRLGGSLKEKKKFKGLIAEGRINGEKVILLKPQTYMNLSGKAVAALANF 80 (189)
T ss_pred CcEEEEEeCCCchhhCcCchHHHHHHHHHHHHHcCCCCcccccccEEEEEEEECCeEEEEEeCCcchhcCcHHHHHHHHH
Confidence 368999999999999999999999999999999887654 4466788999999889999999999999999999999999
Q ss_pred cCCCCCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 96 YKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 96 ~ki~~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
|++++++++|||||+|+|+|++|+|.+||++||||+
T Consensus 81 ~~i~~~~ilVihDdldl~~G~~r~k~gGs~~GHNGl 116 (189)
T PRK05426 81 YKIPPEDILVIHDDLDLPPGKIRLKKGGGAGGHNGL 116 (189)
T ss_pred hCCCHHHEEEEEecCCCCCceEEEecCCCCCCcCCH
Confidence 999999999999999999999999999999999996
No 6
>PF01195 Pept_tRNA_hydro: Peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis [, ]. Bacterial PTH has been found to be evolutionary related to a yeast protein [].; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 3KJZ_A 3KK0_A 3P2J_A 3V2I_A 3TCN_A 3TD6_A 2Z2K_A 3TD2_A 2Z2J_B 2JRC_A ....
Probab=100.00 E-value=5.5e-49 Score=303.87 Aligned_cols=112 Identities=48% Similarity=0.883 Sum_probs=96.1
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcce-eeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHcCC
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKL 98 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~-~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ki 98 (131)
|||||||||++|++|||||||+++|+||++++.++.+.+ +++.++.+.+.+.+++|+||+||||+||++|++++++|++
T Consensus 1 LivGLGNPG~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~KP~TyMN~SG~~V~~~~~~~~i 80 (184)
T PF01195_consen 1 LIVGLGNPGPKYENTRHNVGFMVLDRLASRLGLSWKQKKKFKSLISEGSIKGEKVILLKPQTYMNLSGKAVKKILSFYKI 80 (184)
T ss_dssp EEEE---SSTTTTTSGGGHHHHHHHHHHHHTT---EEEGGGTEEEEEEEETTEEEEEEEESSTGGGHHHHHHHHHHHTT-
T ss_pred CEEEcCCCChhhcCCCcCchHHHHHHHHHHhCCCccccccceeEEEEEEEeeeeEEEEcCCCeEeCccHhHHHHHHHhCC
Confidence 799999999999999999999999999999998876543 6788888889999999999999999999999999999999
Q ss_pred CCCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 99 PLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 99 ~~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
++++++|||||+|+|+|++|+|++||++||||+
T Consensus 81 ~~~~ilVihDdldl~~G~irlk~~Gs~~GHNGl 113 (184)
T PF01195_consen 81 PPENILVIHDDLDLPLGKIRLKKGGSSGGHNGL 113 (184)
T ss_dssp -GGGEEEEEEETTSSTTEEEEEESS--TT-HHH
T ss_pred CcceEEEEEeccCCCCCeEEEccCCCCCCCCCH
Confidence 999999999999999999999999999999995
No 7
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.6e-41 Score=262.16 Aligned_cols=115 Identities=61% Similarity=1.106 Sum_probs=107.1
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHc
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYY 96 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ 96 (131)
.+|+|+||||||++|..||||+||.++|.||++.+++..+.+.++..+-+.+++.++++++|++|||.||++|.+++..|
T Consensus 38 k~wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y 117 (224)
T KOG2255|consen 38 KPWLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALY 117 (224)
T ss_pred CceEEEecCCCcccccccchhhHHHHHHHHHHHhCCcccccCcccccceeeecceeeEeeCcHhhhccccchhhhhHHhh
Confidence 46999999999999999999999999999999999886554445566677888999999999999999999999999999
Q ss_pred CCCCCcEEEEeccCCCCCceEEEecCCCCCCCCCC
Q 032899 97 KLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGC 131 (131)
Q Consensus 97 ki~~~~llVvhDdldl~~G~vrlk~~Gs~~GHNG~ 131 (131)
+++.++++||||||++|.|++|+|++||++|||||
T Consensus 118 ~i~~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgHNGv 152 (224)
T KOG2255|consen 118 KIPLRHIVVIHDELELPLGKLRLRPGGSHRGHNGV 152 (224)
T ss_pred cchheeEEEEeccccCcCceEEeccCCCccccccH
Confidence 99999999999999999999999999999999996
No 8
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=76.72 E-value=4 Score=30.60 Aligned_cols=30 Identities=23% Similarity=0.347 Sum_probs=22.9
Q ss_pred CeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcC
Q 032899 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQG 51 (131)
Q Consensus 18 ~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~ 51 (131)
+.+|+|+|||- .+-==+|..+++.|.+.+.
T Consensus 2 ~ilVlGiGN~l----~gDDGvG~~va~~L~~~~~ 31 (164)
T PRK10466 2 RILVLGVGNIL----LTDEAIGVRIVEALEQRYI 31 (164)
T ss_pred ceEEEEECchh----hccCcHHHHHHHHHHHhcC
Confidence 46899999993 1233499999999987654
No 9
>cd06062 H2MP_MemB-H2up Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.
Probab=73.68 E-value=4.9 Score=29.41 Aligned_cols=28 Identities=21% Similarity=0.400 Sum_probs=21.6
Q ss_pred eeEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 19 ~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
.+|+|+|||-. .-==+|..+++.|++++
T Consensus 1 ilV~GiGN~l~----gDDG~G~~va~~L~~~~ 28 (146)
T cd06062 1 ILVLGIGNILL----ADEGIGVHAVERLEENY 28 (146)
T ss_pred CEEEEECcccc----ccCcHHHHHHHHHHHhc
Confidence 37999999942 22349999999999874
No 10
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=73.48 E-value=4 Score=30.97 Aligned_cols=31 Identities=16% Similarity=0.219 Sum_probs=24.4
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcC
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQG 51 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~ 51 (131)
.+++|+|+|||= ..-==+|..+++.|++++.
T Consensus 2 ~~ilIlG~GN~L----~~DDG~Gv~vae~L~~~~~ 32 (160)
T COG0680 2 MRILILGVGNIL----MGDDGFGVRVAEKLKKRYK 32 (160)
T ss_pred CeEEEEeeCCcc----cccCcccHHHHHHHHHhcC
Confidence 468999999993 2344689999999999764
No 11
>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=69.36 E-value=6.2 Score=29.18 Aligned_cols=29 Identities=28% Similarity=0.281 Sum_probs=21.8
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHH
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~ 49 (131)
++.+|+|+|||-. .-==+|..++++|+++
T Consensus 3 ~~ilVlGiGN~l~----gDDGvG~~v~~~L~~~ 31 (153)
T TIGR00130 3 HEILVVGCGNILF----GDDGFGPAVIEYLKEN 31 (153)
T ss_pred ceEEEEEeCcccc----ccCcHhHHHHHHHHHh
Confidence 4578999999931 2224999999999863
No 12
>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=69.07 E-value=6.8 Score=33.72 Aligned_cols=29 Identities=28% Similarity=0.368 Sum_probs=18.9
Q ss_pred CCCCeeEEEecCCCcCcCcCcchHHHHHHHHHH
Q 032899 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (131)
Q Consensus 15 ~~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La 47 (131)
.....|||||||. .-|.-..|-.++|.+.
T Consensus 94 ~~~~iLVVGLGN~----~vTPDALGP~vv~~l~ 122 (354)
T PF03418_consen 94 KEASILVVGLGNW----NVTPDALGPRVVENLL 122 (354)
T ss_dssp TT--EEEEE-S-S----SSGGG-HHHHHHHT--
T ss_pred CCCeEEEEeCCCc----CCCccccchhhhhhhh
Confidence 3456899999996 6799999999999764
No 13
>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=68.91 E-value=5.3 Score=29.13 Aligned_cols=28 Identities=21% Similarity=0.322 Sum_probs=21.4
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHcC
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQG 51 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~ 51 (131)
+|+|+|||-. .-==+|..++++|++++.
T Consensus 1 lViGiGN~l~----~DDg~G~~v~~~L~~~~~ 28 (145)
T TIGR00072 1 LVLGIGNILR----GDDGFGPRVAERLEERYE 28 (145)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHHHhcC
Confidence 5899999932 223599999999998753
No 14
>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=66.85 E-value=6 Score=29.07 Aligned_cols=27 Identities=26% Similarity=0.309 Sum_probs=20.9
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
||+|+|||-. .-==+|..++++|++++
T Consensus 1 lViGiGN~l~----gDDgvG~~va~~l~~~~ 27 (150)
T cd06064 1 LVVGCGNILF----GDDGFGPAVIEELEKLE 27 (150)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcc
Confidence 5899999942 22349999999998764
No 15
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=65.52 E-value=12 Score=29.30 Aligned_cols=31 Identities=16% Similarity=0.211 Sum_probs=23.3
Q ss_pred CCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcC
Q 032899 17 RPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQG 51 (131)
Q Consensus 17 ~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~ 51 (131)
.+.+|+|+|||= ..-==+|..++++|++++.
T Consensus 4 ~rilVlGiGN~L----~gDDGvG~~va~~L~~~~~ 34 (195)
T PRK10264 4 QRVVVMGLGNLL----WADEGFGVRVAERLYAHYH 34 (195)
T ss_pred CCEEEEEeCccc----cccCcHHHHHHHHHHhhcC
Confidence 457999999992 1222499999999988754
No 16
>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=64.59 E-value=7.5 Score=28.01 Aligned_cols=27 Identities=26% Similarity=0.464 Sum_probs=20.9
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
+|+|+|||=. .-==+|..++++|+++.
T Consensus 1 lViGiGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd00518 1 LVLGIGNPLR----GDDGFGPAVAERLEERY 27 (139)
T ss_pred CEEEECCccc----ccCcHHHHHHHHHHhcC
Confidence 5899999931 22349999999999875
No 17
>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=62.59 E-value=8.8 Score=27.86 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=21.0
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
+|+|+|||=. .-==+|..++++|++++
T Consensus 1 lVlGvGN~l~----~DDGvG~~v~~~L~~~~ 27 (139)
T cd06066 1 LVIGYGNPLR----GDDGLGPAVAERIEEWL 27 (139)
T ss_pred CEEEeCCccc----cccchhHHHHHHHHhhC
Confidence 5899999931 23349999999999875
No 18
>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=61.55 E-value=8.6 Score=27.80 Aligned_cols=27 Identities=15% Similarity=0.315 Sum_probs=20.6
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
+|+|+|||-. .-==+|..++++|+++.
T Consensus 1 ~VlGiGN~L~----~DDgvG~~v~~~L~~~~ 27 (136)
T cd06067 1 VLLGVGNELR----GDDGAGPLLAEKLEDLP 27 (136)
T ss_pred CEEEeCcccc----ccCcHHHHHHHHHHhcC
Confidence 5899999932 22359999999998764
No 19
>PRK11544 hycI hydrogenase 3 maturation protease; Provisional
Probab=59.61 E-value=12 Score=27.93 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=21.2
Q ss_pred CeeEEEecCCCcCcCcCcchHHHHHHHHHHHH
Q 032899 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (131)
Q Consensus 18 ~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~ 49 (131)
+.+|+|+|||-.. -==+|..++++|++.
T Consensus 2 ~~lVlGiGN~L~g----DDGvG~~v~~~L~~~ 29 (156)
T PRK11544 2 TDVVLTVGNSMMG----DDGAGPLLAEKLAAA 29 (156)
T ss_pred cEEEEEeCccccc----cCcHHHHHHHHHhcc
Confidence 3589999999422 224999999999775
No 20
>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=59.14 E-value=11 Score=27.57 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=20.6
Q ss_pred eeEEEecCCCcCcCcCcchHHHHHHHHHHHH
Q 032899 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (131)
Q Consensus 19 ~livGLGNPG~~Y~~TRHNvG~~~ld~La~~ 49 (131)
.+|+|+|||-. .-==+|..++++|++.
T Consensus 1 ~lVlGiGN~L~----~DDG~G~~v~~~L~~~ 27 (146)
T cd06063 1 LTIIGCGNLNR----GDDGVGPILIRRLQAY 27 (146)
T ss_pred CEEEEECCccc----ccCcHHHHHHHHHhhc
Confidence 37999999932 2224999999999875
No 21
>TIGR00142 hycI hydrogenase maturation protease HycI. Hydrogenase maturation protease is a protease that is involved in the C-terminal processing of HycE,the large subunit of hydrogenase 3 from E.Coli. This protein seems to be found in E.Coli and in Archaea.
Probab=59.10 E-value=10 Score=27.68 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=21.0
Q ss_pred eeEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 19 ~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
.+|+|+|||-.. -==+|..++++|.+.+
T Consensus 1 ~lVlGiGN~l~~----DDG~G~~v~~~L~~~~ 28 (146)
T TIGR00142 1 LVLLCVGNELMG----DDGAGPYLAEKCAAAP 28 (146)
T ss_pred CEEEEeCccccc----cCcHHHHHHHHHHhcc
Confidence 379999999422 2249999999998753
No 22
>PRK12362 germination protease; Provisional
Probab=58.30 E-value=13 Score=31.61 Aligned_cols=94 Identities=18% Similarity=0.220 Sum_probs=56.1
Q ss_pred CCCCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECC-eeEEEEeC----CchhhcchhhH
Q 032899 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGD-APVLLAKP----QTYMNLSGEST 89 (131)
Q Consensus 15 ~~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~-~~v~l~kP----~tyMN~SG~~v 89 (131)
.....|||||||. .-|--..|-.+++.|.-.... ..++++..-.+ .+|.-.-| +|=||.+ +.+
T Consensus 97 ~~~~iLVvGLGN~----~vTpDaLGP~Vv~~l~vTrhl-------~~~~~~~~~~~~~pV~AiaPGVmg~TGiet~-Eii 164 (318)
T PRK12362 97 KEMTVLVVGLGNW----NVTPDALGPKVVSKLMVTRHL-------KEYAPEEIDEGIRPVCAIAPGVLGITGIETA-EII 164 (318)
T ss_pred CCCcEEEEEcCCC----CcCccccchhhhhhhhhhhhh-------hhhcCchhcCCCCcceEecCCcccccchhHH-HHH
Confidence 4467899999996 568999999999988753111 01111101112 34444444 4555543 445
Q ss_pred HHHHHHcCCCCCcEEEEeccCC----CCCc-eEEEecCC
Q 032899 90 GPLAAYYKLPLNRVLVFHDDMG----LPCG-VLRLRHNG 123 (131)
Q Consensus 90 ~~~~~~~ki~~~~llVvhDdld----l~~G-~vrlk~~G 123 (131)
+.+.++++ .++||.-|-+- -.+| +|++...|
T Consensus 165 ~gIv~k~k---pd~IIAIDALaar~~~Rl~~tIQisdtG 200 (318)
T PRK12362 165 KGVVEKIK---PDLVIAIDALAARSVERVNTTIQISDTG 200 (318)
T ss_pred HHHHHhcC---CCEEEEEeccccCCHHHccCeEEECCCC
Confidence 55655543 57888888776 3466 77776555
No 23
>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=58.18 E-value=10 Score=27.49 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=19.3
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHH
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAE 48 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~ 48 (131)
||+|+|||=. .-==+|..+++.|++
T Consensus 1 lVlGiGN~l~----~DDg~G~~v~~~L~~ 25 (140)
T cd06070 1 LIIGVGNRLY----GDDGFGSCLAEALEQ 25 (140)
T ss_pred CEEEECchhc----ccCcHHHHHHHHHhh
Confidence 5899999931 222499999999987
No 24
>PRK02858 germination protease; Provisional
Probab=56.58 E-value=8.1 Score=33.42 Aligned_cols=28 Identities=29% Similarity=0.361 Sum_probs=23.1
Q ss_pred CCCeeEEEecCCCcCcCcCcchHHHHHHHHHH
Q 032899 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFA 47 (131)
Q Consensus 16 ~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La 47 (131)
....|||||||- .-|.-..|-.+++.|.
T Consensus 110 ~~~vLVVGLGN~----~VTPDALGP~vv~~l~ 137 (369)
T PRK02858 110 EASCLIVGLGNW----NVTPDALGPLVVENVL 137 (369)
T ss_pred CCcEEEEeCCCc----CCCccccChheeccee
Confidence 356899999995 6788899999998655
No 25
>cd06068 H2MP_like-1 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=55.94 E-value=11 Score=27.41 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.3
Q ss_pred eEEEecCCCcCcCcCcchHHHHHHHHHHHHc
Q 032899 20 LFVGLGNPGDKYKGTRHNVGFEMIDAFAESQ 50 (131)
Q Consensus 20 livGLGNPG~~Y~~TRHNvG~~~ld~La~~~ 50 (131)
||+|+|||-.. -==+|..++++|+++.
T Consensus 1 lViGiGN~l~~----DDGvG~~v~~~L~~~~ 27 (144)
T cd06068 1 LVAGVGNIFLG----DDGFGVEVARRLRPRQ 27 (144)
T ss_pred CEEEECccccc----cCcHHHHHHHHHhccC
Confidence 68999999422 2239999999998753
No 26
>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=51.49 E-value=11 Score=32.52 Aligned_cols=80 Identities=19% Similarity=0.248 Sum_probs=44.7
Q ss_pred CCCeeEEEecCCCcCcCcCcchHHHHHHHHHHH-HcCCCCCcceeeeEEEEEEECC-eeEEEEeCCchhhcch----hhH
Q 032899 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAE-SQGISMNTVHCKATFGQGFVGD-APVLLAKPQTYMNLSG----EST 89 (131)
Q Consensus 16 ~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~-~~~~~~~~~~~~~~~~~~~~~~-~~v~l~kP~tyMN~SG----~~v 89 (131)
....|||||||- .-|.-..|-.+++.|.- ++-..+..... -++ ..|.-+-| --|=..| +.|
T Consensus 100 ~~~iLVVGLGN~----~VTPDALGP~vv~~l~VTRHL~~~~p~~~--------~~g~r~VsaiaP-GVmg~TGiET~EII 166 (358)
T TIGR01441 100 DMTCLVVGLGNW----NVTPDALGPKVVENLLVTRHLFKLIPESV--------DEGIRPVSAVAP-GVMGITGIETSDII 166 (358)
T ss_pred CCcEEEEeCCCc----CCCccccChheecceeeehhhhhhcchhh--------ccCCceeeEEcC-CccccccccHHHHH
Confidence 356899999995 66888999999887652 21111110000 112 23444444 3444444 456
Q ss_pred HHHHHHcCCCCCcEEEEeccCC
Q 032899 90 GPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 90 ~~~~~~~ki~~~~llVvhDdld 111 (131)
+.+.+..| .++||+-|-|-
T Consensus 167 kgiVek~k---PD~VIaIDALA 185 (358)
T TIGR01441 167 RGIIEQIK---PDFVIAIDALA 185 (358)
T ss_pred HHHHHhhC---CCEEEEechhh
Confidence 66655433 46777777653
No 27
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=47.45 E-value=15 Score=28.65 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=25.5
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCCCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdldl~ 113 (131)
++.++.++++.++++++++++|-|.|=.+
T Consensus 95 ~~~~fr~Al~~m~l~~~~vvmVGDqL~TD 123 (175)
T COG2179 95 FGRAFRRALKEMNLPPEEVVMVGDQLFTD 123 (175)
T ss_pred cHHHHHHHHHHcCCChhHEEEEcchhhhh
Confidence 67888999999999999999999988544
No 28
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=46.52 E-value=13 Score=25.28 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=19.5
Q ss_pred cCcCc--chHHHHHHHHHHHHcCCCCC
Q 032899 31 YKGTR--HNVGFEMIDAFAESQGISMN 55 (131)
Q Consensus 31 Y~~TR--HNvG~~~ld~La~~~~~~~~ 55 (131)
|.-.. --+||..+|.+|.++|++..
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 77676 67999999999999998654
No 29
>COG2897 SseA Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]
Probab=45.84 E-value=24 Score=29.34 Aligned_cols=31 Identities=23% Similarity=0.091 Sum_probs=27.1
Q ss_pred chhhcchhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 80 TYMNLSGESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 80 tyMN~SG~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
.=|=.+.+.+.++++..+|..++.||+|||-
T Consensus 69 ~~~lp~~e~fa~~~~~~GI~~d~tVVvYdd~ 99 (285)
T COG2897 69 PHMLPSPEQFAKLLGELGIRNDDTVVVYDDG 99 (285)
T ss_pred CCCCCCHHHHHHHHHHcCCCCCCEEEEECCC
Confidence 4566778889999999999999999999993
No 30
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=42.19 E-value=16 Score=30.47 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=23.9
Q ss_pred HHHHHcCCCCCcEEEEeccCCCCCceEEEe
Q 032899 91 PLAAYYKLPLNRVLVFHDDMGLPCGVLRLR 120 (131)
Q Consensus 91 ~~~~~~ki~~~~llVvhDdldl~~G~vrlk 120 (131)
.++...+..++..||.+|||+.+-|.-..|
T Consensus 129 ~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK 158 (287)
T COG2607 129 DLVELLRARPEKFILFCDDLSFEEGDDAYK 158 (287)
T ss_pred HHHHHHhcCCceEEEEecCCCCCCCchHHH
Confidence 345555667889999999999999987665
No 31
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=39.46 E-value=29 Score=23.79 Aligned_cols=33 Identities=24% Similarity=0.319 Sum_probs=19.8
Q ss_pred CCCeeEEEecCCCcCcCcCcchHHHHHHHHHHH
Q 032899 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAE 48 (131)
Q Consensus 16 ~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~ 48 (131)
..++++||||+....=..+--.++-.++..+.+
T Consensus 52 ~~~v~lvGlG~~~~~~~~~~r~a~~~~~~~l~~ 84 (126)
T PF02789_consen 52 AKRVLLVGLGKKEKLTAESLRKAGAAAARALKK 84 (126)
T ss_dssp CSEEEEEEEESCTGBCHHHHHHHHHHHHHHHHH
T ss_pred ccEEEEEECCCcCcCCHHHHHHHHHHHHHHHhh
Confidence 356899999999753222333445555555554
No 32
>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=38.79 E-value=27 Score=25.83 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=22.8
Q ss_pred hhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 86 G~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
|.+++.+++.+++++++++++=|+.
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 6789999999999999999999975
No 33
>KOG2882 consensus p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]
Probab=37.71 E-value=28 Score=29.47 Aligned_cols=38 Identities=24% Similarity=0.419 Sum_probs=31.9
Q ss_pred eeEEEEeCCchhhcchhhHHHHHHHcCCCCCcEEEEeccCCCCC
Q 032899 71 APVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPC 114 (131)
Q Consensus 71 ~~v~l~kP~tyMN~SG~~v~~~~~~~ki~~~~llVvhDdldl~~ 114 (131)
+.+++=||.++|= ..+.+.|++.|++++.|-|-||.+.
T Consensus 218 ~P~v~GKP~~~m~------~~l~~~~~i~psRt~mvGDRL~TDI 255 (306)
T KOG2882|consen 218 QPIVLGKPSTFMF------EYLLEKFNIDPSRTCMVGDRLDTDI 255 (306)
T ss_pred CCeecCCCCHHHH------HHHHHHcCCCcceEEEEcccchhhh
Confidence 4688999999883 2468899999999999999998764
No 34
>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=35.90 E-value=1.9e+02 Score=25.02 Aligned_cols=67 Identities=9% Similarity=0.070 Sum_probs=45.5
Q ss_pred hHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeC---CchhhcchhhHHHHHHHcCCCCCcEEE
Q 032899 37 NVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKP---QTYMNLSGESTGPLAAYYKLPLNRVLV 105 (131)
Q Consensus 37 NvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP---~tyMN~SG~~v~~~~~~~ki~~~~llV 105 (131)
.+|=+++-.|...... + ..-..-.+++..+++++++++|+ .+=.=.=|++|..+.+..+-.++.+|-
T Consensus 184 gaGPLVA~~l~~~~~~-~-~~~~dtv~~e~~~egRrv~viKA~GPGstVGrpgeave~i~~~~~~k~~~IIT 253 (355)
T PF07431_consen 184 GAGPLVAGRLMENCSK-W-EIAKDTVIAECEFEGRRVYVIKAEGPGSTVGRPGEAVEYIVEKLGGKVDLIIT 253 (355)
T ss_pred CcchHHHHHHHhcCcc-c-ccccccEEEEEEECCcEEEEEeccCCCccCCChHHHHHHHHHHhcCCccEEEE
Confidence 4677788877775443 1 12234577888999999999995 444445567888898887655555443
No 35
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=35.23 E-value=1.9e+02 Score=24.73 Aligned_cols=72 Identities=19% Similarity=0.181 Sum_probs=55.1
Q ss_pred CcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHcCCCCCcEEE
Q 032899 32 KGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLV 105 (131)
Q Consensus 32 ~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ki~~~~llV 105 (131)
..|+|+.-...++.=.+..|+++.+.+..-++.....++-++-.--|.|-||. +.+..++..|++.-.++++
T Consensus 148 Datk~e~qr~~le~ELe~vGiRLNk~~Pniy~k~kk~gGi~f~~T~~lT~~~e--k~i~~ILheykI~Naevl~ 219 (364)
T KOG1486|consen 148 DATKSEDQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPLTHCDE--KLIYTILHEYKIHNAEVLF 219 (364)
T ss_pred cCCcchhHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeeccccccH--HHHHHHHHHHeeccceEEE
Confidence 45888888888888778889988776666667776777778888888887665 6788899999986655554
No 36
>PRK06437 hypothetical protein; Provisional
Probab=32.93 E-value=60 Score=20.81 Aligned_cols=29 Identities=7% Similarity=-0.011 Sum_probs=23.8
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCCCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdldl~ 113 (131)
.+.+++.+++.++++++.+.|..|.--+|
T Consensus 19 ~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~ 47 (67)
T PRK06437 19 HELTVNDIIKDLGLDEEEYVVIVNGSPVL 47 (67)
T ss_pred CCCcHHHHHHHcCCCCccEEEEECCEECC
Confidence 34678999999999999998888876665
No 37
>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.50 E-value=27 Score=27.07 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=17.7
Q ss_pred CcCcCcchHHHHHHHHHHHHcC
Q 032899 30 KYKGTRHNVGFEMIDAFAESQG 51 (131)
Q Consensus 30 ~Y~~TRHNvG~~~ld~La~~~~ 51 (131)
.|..-|||||+++-+.+.+...
T Consensus 56 dy~evrhsvgYl~NELiENAVK 77 (184)
T COG5381 56 DYDEVRHSVGYLANELIENAVK 77 (184)
T ss_pred cHHHHhhhHHHHHHHHHHhhhc
Confidence 4999999999998887766543
No 38
>COG4128 Zot Zonula occludens toxin [General function prediction only]
Probab=32.37 E-value=46 Score=28.77 Aligned_cols=41 Identities=15% Similarity=0.166 Sum_probs=34.1
Q ss_pred hcchhhHHHHHHHcCCCCCcEEEEeccCCCCCceEEEecCC
Q 032899 83 NLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNG 123 (131)
Q Consensus 83 N~SG~~v~~~~~~~ki~~~~llVvhDdldl~~G~vrlk~~G 123 (131)
|.-|-.+..+.+.|+-.+.+++|+.||++.+=+....+.-+
T Consensus 36 NVrGl~ler~~~~~pd~~~~i~I~n~D~~~~d~~~~m~~~~ 76 (398)
T COG4128 36 NVRGLQLERITERYPDATGEIIIVNDDVLKADFFPFMGGEG 76 (398)
T ss_pred ecccccHHHHHHhccCCCCceEEEeccccCcccchhhccee
Confidence 77888888999999999999999999999987766555433
No 39
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=31.76 E-value=9.9 Score=23.28 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=17.4
Q ss_pred hcchhhHHHHHHHcCCCCCcEEEEecc
Q 032899 83 NLSGESTGPLAAYYKLPLNRVLVFHDD 109 (131)
Q Consensus 83 N~SG~~v~~~~~~~ki~~~~llVvhDd 109 (131)
+.|-..+.++++++++++++++...+|
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 445677888999999999888876655
No 40
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=31.65 E-value=31 Score=26.81 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=22.8
Q ss_pred hhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 86 GESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 86 G~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
|.+++.+++.+++++++++++=|..
T Consensus 198 g~al~~l~~~~gi~~~~v~afGD~~ 222 (270)
T PRK10513 198 GTGVKSLAEHLGIKPEEVMAIGDQE 222 (270)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCch
Confidence 6889999999999999999999875
No 41
>PRK10976 putative hydrolase; Provisional
Probab=31.10 E-value=34 Score=26.59 Aligned_cols=26 Identities=23% Similarity=0.379 Sum_probs=23.2
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
-|.+++.+++.+++++++++++=|..
T Consensus 191 Kg~al~~l~~~lgi~~~~viafGD~~ 216 (266)
T PRK10976 191 KGHALEAVAKKLGYSLKDCIAFGDGM 216 (266)
T ss_pred hHHHHHHHHHHcCCCHHHeEEEcCCc
Confidence 37889999999999999999999864
No 42
>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=30.58 E-value=23 Score=23.32 Aligned_cols=24 Identities=21% Similarity=0.213 Sum_probs=20.5
Q ss_pred chhhcchhhHHHHHHHcCCCCCcE
Q 032899 80 TYMNLSGESTGPLAAYYKLPLNRV 103 (131)
Q Consensus 80 tyMN~SG~~v~~~~~~~ki~~~~l 103 (131)
-||..||....+|++.+++.+.++
T Consensus 7 hflhE~g~~FveIAr~~~i~a~e~ 30 (63)
T PF11242_consen 7 HFLHESGLSFVEIARKIGITAKEV 30 (63)
T ss_pred hhHHHcCCcHHHHHHHhCCCHHHH
Confidence 489999999999999999877653
No 43
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=30.29 E-value=55 Score=25.40 Aligned_cols=27 Identities=19% Similarity=0.173 Sum_probs=23.6
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
.|.+++.+++.+++++++++++=|..+
T Consensus 168 K~~al~~l~~~~~i~~~~~i~~GD~~N 194 (249)
T TIGR01485 168 KGQALQYLLQKLAMEPSQTLVCGDSGN 194 (249)
T ss_pred hHHHHHHHHHHcCCCccCEEEEECChh
Confidence 478899999999999999999998754
No 44
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=28.69 E-value=73 Score=25.60 Aligned_cols=97 Identities=15% Similarity=0.229 Sum_probs=50.6
Q ss_pred hHhHHHHhhhccCCCCCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEE---------ECCee
Q 032899 2 LINRFLRRGFCTAVARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGF---------VGDAP 72 (131)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~---------~~~~~ 72 (131)
++..|+++.+. +..+.++|++-||=.-|. ..++++|+.+...+-++.+.-.+ +.+..
T Consensus 34 Llh~~L~~~Lk--~~~~V~fv~~~q~~~HY~------------~v~~KLG~NL~~~~~~gql~fiD~l~~~~~~l~~~~~ 99 (249)
T PF09807_consen 34 LLHHFLSQYLK--AGCKVCFVAFSQSFSHYN------------NVAQKLGVNLSAAKEKGQLVFIDGLKSSLDLLFDEDS 99 (249)
T ss_pred HHHHHHHHHhc--CCCcEEEEEccCCHHHHH------------HHHHhhEecchHhccCCcEEEeehhhhhhhhhhcccc
Confidence 45667777766 556788999999854442 45567777664332222111110 00000
Q ss_pred EEEEeCCchhhcchh-hHHHHHHH----cCC--CCCcEEEEeccCCC
Q 032899 73 VLLAKPQTYMNLSGE-STGPLAAY----YKL--PLNRVLVFHDDMGL 112 (131)
Q Consensus 73 v~l~kP~tyMN~SG~-~v~~~~~~----~ki--~~~~llVvhDdldl 112 (131)
----+|..|+..++. .+.++.++ .+- ..+..+||-||++.
T Consensus 100 ~~~~~~~~~l~~~~~~~L~~L~~~I~~~l~~~~~~~~~~liIDdls~ 146 (249)
T PF09807_consen 100 SDEPNPLKFLREDNASSLRSLYEFIQEALSPADSNGSVVLIIDDLSV 146 (249)
T ss_pred ccCCccccccccCCcchHHHHHHHHHHHHhhccCCCCeEEEEeCHHH
Confidence 001124567776662 34444332 221 23468999999874
No 45
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=28.13 E-value=35 Score=24.17 Aligned_cols=35 Identities=14% Similarity=0.215 Sum_probs=28.0
Q ss_pred eCCchhhcchhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 77 KPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 77 kP~tyMN~SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
.+.+.=|.+|..+.++++.++.......++-||.+
T Consensus 11 ~~~~~~d~~~~~l~~~l~~~G~~~~~~~~v~Dd~~ 45 (135)
T smart00852 11 SGGQIYDSNGPALAELLTELGIEVTRYVIVPDDKE 45 (135)
T ss_pred cCCCcccCcHHHHHHHHHHCCCeEEEEEEeCCCHH
Confidence 34455599999999999999988777878888855
No 46
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=27.39 E-value=2.8e+02 Score=21.54 Aligned_cols=56 Identities=18% Similarity=0.194 Sum_probs=28.2
Q ss_pred HHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeCCchhhcchhhHHHHHHHcCCCCC
Q 032899 44 DAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLN 101 (131)
Q Consensus 44 d~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ki~~~ 101 (131)
....++.|+.+.+....-.+.....++-.+.-.-+ -.+.+-+.|+++++.|++...
T Consensus 98 ~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~~~--~~~~~~~~v~~~l~~~~i~~~ 153 (233)
T cd01896 98 ERELEGVGIRLNKRPPNITIKKKKKGGINITSTVP--LTKLDEKTIKAILREYKIHNA 153 (233)
T ss_pred HHHHHHcCceecCCCCeEEEEEEecCCEEEeccCC--CCCCCHHHHHHHHHHhCeeeE
Confidence 33444456544332222222332333333332233 344466889999999998543
No 47
>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=26.79 E-value=88 Score=24.24 Aligned_cols=35 Identities=20% Similarity=0.304 Sum_probs=24.8
Q ss_pred CCeeEEEEeCCchhhcchhhHHHHH---HHcCCCCCcEEEE
Q 032899 69 GDAPVLLAKPQTYMNLSGESTGPLA---AYYKLPLNRVLVF 106 (131)
Q Consensus 69 ~~~~v~l~kP~tyMN~SG~~v~~~~---~~~ki~~~~llVv 106 (131)
.+.+|+|+-| |-.+|.++..+. +.++.++++++++
T Consensus 120 ~~~~VillDp---mlaTG~s~~~ai~~L~~~G~~~~~I~~v 157 (207)
T PF14681_consen 120 ENRKVILLDP---MLATGGSAIAAIEILKEHGVPEENIIIV 157 (207)
T ss_dssp TTSEEEEEES---EESSSHHHHHHHHHHHHTTG-GGEEEEE
T ss_pred cCCEEEEEec---cccchhhHHHHHHHHHHcCCCcceEEEE
Confidence 4578999999 888998877644 4456677777665
No 48
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=26.75 E-value=74 Score=22.09 Aligned_cols=29 Identities=24% Similarity=0.238 Sum_probs=20.6
Q ss_pred cchhhHHHHHHHcCCCCCcEEEEeccCCC
Q 032899 84 LSGESTGPLAAYYKLPLNRVLVFHDDMGL 112 (131)
Q Consensus 84 ~SG~~v~~~~~~~ki~~~~llVvhDdldl 112 (131)
++......+.+..+++++++.|...|++-
T Consensus 77 l~~~i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 77 IAAAITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred HHHHHHHHHHHHhCcCcccEEEEEEECCh
Confidence 33333334566789999999999998864
No 49
>PF13242 Hydrolase_like: HAD-hyrolase-like; PDB: 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A 2HX1_D 2X4D_A 3HLT_C 3L1U_B ....
Probab=26.51 E-value=53 Score=20.81 Aligned_cols=25 Identities=8% Similarity=0.052 Sum_probs=20.3
Q ss_pred HHHHHHHcCCCCCcEEEEeccCCCC
Q 032899 89 TGPLAAYYKLPLNRVLVFHDDMGLP 113 (131)
Q Consensus 89 v~~~~~~~ki~~~~llVvhDdldl~ 113 (131)
+..+++.++++++++++|=|.+..+
T Consensus 10 ~~~a~~~~~~~~~~~~~VGD~~~~D 34 (75)
T PF13242_consen 10 LEQALKRLGVDPSRCVMVGDSLETD 34 (75)
T ss_dssp HHHHHHHHTSGGGGEEEEESSTTTH
T ss_pred HHHHHHHcCCCHHHEEEEcCCcHhH
Confidence 4567888899999999999995543
No 50
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=26.25 E-value=38 Score=26.52 Aligned_cols=26 Identities=27% Similarity=0.409 Sum_probs=23.3
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
-|.+++.+++.+++++++++++=|..
T Consensus 189 Kg~al~~l~~~~gi~~~~v~afGD~~ 214 (272)
T PRK15126 189 KGAALAVLSQHLGLSLADCMAFGDAM 214 (272)
T ss_pred hHHHHHHHHHHhCCCHHHeEEecCCH
Confidence 57899999999999999999999864
No 51
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=25.82 E-value=44 Score=25.16 Aligned_cols=26 Identities=19% Similarity=0.202 Sum_probs=23.4
Q ss_pred hhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 86 GESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 86 G~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
|.++..+++.+++++++++++=|..+
T Consensus 159 g~al~~l~~~~~i~~~~~i~~GD~~N 184 (230)
T PRK01158 159 GTGLKKLAELMGIDPEEVAAIGDSEN 184 (230)
T ss_pred HHHHHHHHHHhCCCHHHEEEECCchh
Confidence 88999999999999999999998753
No 52
>TIGR02463 MPGP_rel mannosyl-3-phosphoglycerate phosphatase-related protein. This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbor-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (TIGR02460). Members of this family are like to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate.
Probab=25.54 E-value=73 Score=23.95 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=23.1
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
-|.++..+++.+++++++++.+=|..
T Consensus 180 Kg~al~~l~~~lgi~~~~vi~~GD~~ 205 (221)
T TIGR02463 180 KGKAANWLKATYNQPDVKTLGLGDGP 205 (221)
T ss_pred HHHHHHHHHHHhCCCCCcEEEECCCH
Confidence 67889999999999999999998864
No 53
>TIGR02471 sucr_syn_bact_C sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial. Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by TIGR02472.
Probab=25.22 E-value=52 Score=25.23 Aligned_cols=28 Identities=29% Similarity=0.341 Sum_probs=24.0
Q ss_pred cchhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 84 LSGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 84 ~SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
..|.+++.+++.+++++++++.+=|+.+
T Consensus 159 ~K~~al~~l~~~~g~~~~~~i~~GD~~n 186 (236)
T TIGR02471 159 SKGLALRYLSYRWGLPLEQILVAGDSGN 186 (236)
T ss_pred ChHHHHHHHHHHhCCCHHHEEEEcCCcc
Confidence 3578899999999999999999998754
No 54
>PF05116 S6PP: Sucrose-6F-phosphate phosphohydrolase; InterPro: IPR006380 This family of sequences represent sucrose phosphate phosphohydrolase (SPP) from plants and cyanobacteria []. SPP is a member of the Class IIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.; PDB: 1TJ5_A 2B1Q_A 1TJ4_A 1S2O_A 1U2T_A 2D2V_A 1TJ3_A 1U2S_A 2B1R_A 3GYG_B ....
Probab=25.08 E-value=59 Score=25.72 Aligned_cols=27 Identities=26% Similarity=0.330 Sum_probs=22.3
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
.|.||+.+++.+++++++++++=|.-+
T Consensus 166 K~~Al~~L~~~~~~~~~~vl~aGDSgN 192 (247)
T PF05116_consen 166 KGAALRYLMERWGIPPEQVLVAGDSGN 192 (247)
T ss_dssp HHHHHHHHHHHHT--GGGEEEEESSGG
T ss_pred HHHHHHHHHHHhCCCHHHEEEEeCCCC
Confidence 688999999999999999999988754
No 55
>COG4046 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.82 E-value=3.5e+02 Score=23.46 Aligned_cols=68 Identities=6% Similarity=0.043 Sum_probs=46.2
Q ss_pred hHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEEEeCCchhh---cchhhHHHHHHHcCCCCCcEEEE
Q 032899 37 NVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMN---LSGESTGPLAAYYKLPLNRVLVF 106 (131)
Q Consensus 37 NvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l~kP~tyMN---~SG~~v~~~~~~~ki~~~~llVv 106 (131)
++|=++.-.|..+- ..+. ......+++..+.++++.++||.--|- .=|+++.++.+.++-.+..++-|
T Consensus 197 saGPlvA~~L~~~~-~~~e-~~~etV~~e~e~eGRkl~IvKa~GpgstvGr~g~AvE~vv~~~g~~~k~IItI 267 (368)
T COG4046 197 SAGPLVAARLIGNR-DVRE-HEKETVYAEKELEGRKLYIVKAEGPGSTVGRLGEAVEEVVERLGAVPKEIITI 267 (368)
T ss_pred CcchHHHHHHHhcc-cccc-ccccceEEEEeecCcEEEEEecCCCCcccCChHHHHHHHHHHhccCcceEEEe
Confidence 67888888888764 2222 122346778899999999999765554 44578888888886555544443
No 56
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=23.68 E-value=42 Score=25.16 Aligned_cols=31 Identities=16% Similarity=-0.008 Sum_probs=27.2
Q ss_pred hhhcchhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 81 YMNLSGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 81 yMN~SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
.-|.+|..+..+++.++.+....-+|-||.+
T Consensus 19 ~~d~n~~~l~~~L~~~G~~v~~~~iv~Dd~~ 49 (163)
T TIGR02667 19 EDDTSGQYLVERLTEAGHRLADRAIVKDDIY 49 (163)
T ss_pred cCCCcHHHHHHHHHHCCCeEEEEEEcCCCHH
Confidence 3599999999999999998888889999966
No 57
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=23.67 E-value=71 Score=28.80 Aligned_cols=24 Identities=25% Similarity=0.459 Sum_probs=16.5
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
+|-++.+ +|.-.-++.|||+|||.
T Consensus 241 ~g~a~aE---~f~~~G~dvLIVyDDLs 264 (504)
T COG0056 241 AGCAMAE---YFRDNGKDVLIVYDDLS 264 (504)
T ss_pred hhhHHHH---HHHhcCCeEEEEecCch
Confidence 5555544 44444589999999985
No 58
>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=23.46 E-value=98 Score=26.59 Aligned_cols=32 Identities=25% Similarity=0.417 Sum_probs=24.8
Q ss_pred EEEEeCCchhhcchhhHHHHHHHcCCCCCcEEEEecc
Q 032899 73 VLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDD 109 (131)
Q Consensus 73 v~l~kP~tyMN~SG~~v~~~~~~~ki~~~~llVvhDd 109 (131)
.++++|..+.| .|+..+.++|++ .++++||||
T Consensus 116 ~~~lrp~~~~~---~Ai~dlV~~~~W--~~v~~iYD~ 147 (400)
T cd06392 116 TLAARPPVRLN---DVMLKLVTELRW--QKFIVFYDS 147 (400)
T ss_pred eEEecCchHHH---HHHHHHHHhCCC--cEEEEEEEC
Confidence 47788853333 399999999988 789999975
No 59
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=23.41 E-value=68 Score=25.40 Aligned_cols=27 Identities=22% Similarity=0.412 Sum_probs=21.6
Q ss_pred EEEEeccCCCCCceEEEe--cCCCCCCCC
Q 032899 103 VLVFHDDMGLPCGVLRLR--HNGGHGGHN 129 (131)
Q Consensus 103 llVvhDdldl~~G~vrlk--~~Gs~~GHN 129 (131)
+.|+-.+++++...+++. +.++++|+|
T Consensus 95 V~v~~~~~~i~~~dl~~~~~RssGpGGQ~ 123 (200)
T PRK08179 95 IGRFSADEEEQSDEIRFETLRSSGPGGQH 123 (200)
T ss_pred EEEeCCcCccCHHHeEEEEEEccCCcccc
Confidence 556677889999999976 577899986
No 60
>cd01445 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.
Probab=22.99 E-value=1e+02 Score=22.19 Aligned_cols=22 Identities=14% Similarity=0.187 Sum_probs=18.6
Q ss_pred hHHHHHHHcCCCCCcEEEEecc
Q 032899 88 STGPLAAYYKLPLNRVLVFHDD 109 (131)
Q Consensus 88 ~v~~~~~~~ki~~~~llVvhDd 109 (131)
-+.++++..++.++.-||++|+
T Consensus 82 ~~~~~~~~~GI~~~~~vVvY~~ 103 (138)
T cd01445 82 EFAAMFEAKGIDLDKHLIATDG 103 (138)
T ss_pred HHHHHHHHcCCCCCCeEEEECC
Confidence 4667788889999999999996
No 61
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=22.98 E-value=63 Score=24.16 Aligned_cols=27 Identities=19% Similarity=0.134 Sum_probs=23.2
Q ss_pred cchhhHHHHHHHcCCCCCcEEEEeccC
Q 032899 84 LSGESTGPLAAYYKLPLNRVLVFHDDM 110 (131)
Q Consensus 84 ~SG~~v~~~~~~~ki~~~~llVvhDdl 110 (131)
..|.++..+++.+++++++++.+=|..
T Consensus 149 ~K~~~i~~l~~~~~i~~~~~i~~GD~~ 175 (225)
T TIGR01482 149 NKGVAVKKLKEKLGIKPGETLVCGDSE 175 (225)
T ss_pred CHHHHHHHHHHHhCCCHHHEEEECCCH
Confidence 456889999999999999999998853
No 62
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=22.72 E-value=1.3e+02 Score=18.60 Aligned_cols=28 Identities=25% Similarity=0.205 Sum_probs=22.1
Q ss_pred hhhHHHHHHHcCCCCCcEEEEeccCCCC
Q 032899 86 GESTGPLAAYYKLPLNRVLVFHDDMGLP 113 (131)
Q Consensus 86 G~~v~~~~~~~ki~~~~llVvhDdldl~ 113 (131)
+.++..+++.++++++.+.|..+.-=+|
T Consensus 13 ~~tv~~ll~~l~~~~~~v~v~vN~~iv~ 40 (64)
T TIGR01683 13 GLTLAALLESLGLDPRRVAVAVNGEIVP 40 (64)
T ss_pred CCcHHHHHHHcCCCCCeEEEEECCEEcC
Confidence 4578899999999988888887775554
No 63
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=22.35 E-value=83 Score=24.99 Aligned_cols=14 Identities=21% Similarity=0.494 Sum_probs=11.7
Q ss_pred CCCcEEEEeccCCC
Q 032899 99 PLNRVLVFHDDMGL 112 (131)
Q Consensus 99 ~~~~llVvhDdldl 112 (131)
...++||+-||||.
T Consensus 170 ~~~~iViiIDdLDR 183 (325)
T PF07693_consen 170 SKKRIVIIIDDLDR 183 (325)
T ss_pred CCceEEEEEcchhc
Confidence 45679999999995
No 64
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=22.14 E-value=63 Score=25.98 Aligned_cols=26 Identities=23% Similarity=0.411 Sum_probs=17.2
Q ss_pred HhHHHHhhhccCCCCCeeEEEecCCC
Q 032899 3 INRFLRRGFCTAVARPWLFVGLGNPG 28 (131)
Q Consensus 3 ~~~~~~~~~~~~~~~~~livGLGNPG 28 (131)
+.+|+...+...+-.-.+|||.||-|
T Consensus 71 L~~ff~~~Lg~~~~tnviiVG~GnlG 96 (211)
T COG2344 71 LRDFFDDLLGQDKTTNVIIVGVGNLG 96 (211)
T ss_pred HHHHHHHHhCCCcceeEEEEccChHH
Confidence 34556666665444456899999975
No 65
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=21.83 E-value=1.1e+02 Score=18.42 Aligned_cols=22 Identities=23% Similarity=0.308 Sum_probs=17.5
Q ss_pred HHHHHcCCCCCcEEEEeccCCC
Q 032899 91 PLAAYYKLPLNRVLVFHDDMGL 112 (131)
Q Consensus 91 ~~~~~~ki~~~~llVvhDdldl 112 (131)
.+.+.++.+++++.|+-+|++-
T Consensus 27 ~l~~~lg~~~~~v~V~i~e~~~ 48 (63)
T TIGR00013 27 AMAETLGANLESIVVIIDEMPK 48 (63)
T ss_pred HHHHHhCCCcccEEEEEEEcCH
Confidence 3566778999999999888764
No 66
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.78 E-value=71 Score=22.57 Aligned_cols=24 Identities=25% Similarity=0.475 Sum_probs=18.4
Q ss_pred eccCCCCCce-EEE--ecCCCCCCCCC
Q 032899 107 HDDMGLPCGV-LRL--RHNGGHGGHNG 130 (131)
Q Consensus 107 hDdldl~~G~-vrl--k~~Gs~~GHNG 130 (131)
+||++|+=|. ||+ |.||++.+|-|
T Consensus 14 k~E~~l~~g~~vrffvRyGG~~~~~~G 40 (95)
T COG4841 14 KEELDLEEGNKVRFFVRYGGCSSLQQG 40 (95)
T ss_pred HHhcCCCCCCEEEEEEEEcCcccccCC
Confidence 4889999884 554 78998877776
No 67
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=21.55 E-value=1e+02 Score=25.24 Aligned_cols=30 Identities=17% Similarity=0.241 Sum_probs=21.4
Q ss_pred HHHHHHcCCCCCcEEEEeccCCCCCceEEE
Q 032899 90 GPLAAYYKLPLNRVLVFHDDMGLPCGVLRL 119 (131)
Q Consensus 90 ~~~~~~~ki~~~~llVvhDdldl~~G~vrl 119 (131)
.++++..+-.+...||++|||..+-+.-..
T Consensus 95 ~~l~~~l~~~~~kFIlf~DDLsFe~~d~~y 124 (249)
T PF05673_consen 95 PELLDLLRDRPYKFILFCDDLSFEEGDTEY 124 (249)
T ss_pred HHHHHHHhcCCCCEEEEecCCCCCCCcHHH
Confidence 344555455568999999999988776443
No 68
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=21.53 E-value=1.1e+02 Score=23.92 Aligned_cols=34 Identities=24% Similarity=0.258 Sum_probs=23.3
Q ss_pred HHHHhhhccCCCCCeeEEEecCCCcCcCcCcchHHHHHHHHHHHH
Q 032899 5 RFLRRGFCTAVARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAES 49 (131)
Q Consensus 5 ~~~~~~~~~~~~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~ 49 (131)
..+++.....+..+.+|.|+|| ||..++..|.+.
T Consensus 12 ~~~~~~~~~l~g~~vaIqGfGn-----------VG~~~a~~L~~~ 45 (217)
T cd05211 12 AAMKHLGDSLEGLTVAVQGLGN-----------VGWGLAKKLAEE 45 (217)
T ss_pred HHHHHcCCCcCCCEEEEECCCH-----------HHHHHHHHHHHc
Confidence 3444444334556789999996 788888888774
No 69
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=21.20 E-value=1.4e+02 Score=18.59 Aligned_cols=29 Identities=21% Similarity=0.123 Sum_probs=21.9
Q ss_pred hhhHHHHHHHcCCCCCcEEEEeccCCCCC
Q 032899 86 GESTGPLAAYYKLPLNRVLVFHDDMGLPC 114 (131)
Q Consensus 86 G~~v~~~~~~~ki~~~~llVvhDdldl~~ 114 (131)
+.++..+++.++++++.+.|..+.--+|.
T Consensus 14 ~~tv~~ll~~l~~~~~~i~V~vNg~~v~~ 42 (65)
T cd00565 14 GATLAELLEELGLDPRGVAVALNGEIVPR 42 (65)
T ss_pred CCCHHHHHHHcCCCCCcEEEEECCEEcCH
Confidence 56788999999999888888777654433
No 70
>KOG3731 consensus Sulfatases [Carbohydrate transport and metabolism]
Probab=21.20 E-value=78 Score=28.63 Aligned_cols=47 Identities=23% Similarity=0.155 Sum_probs=30.3
Q ss_pred EeCCchhhcchhhHHHHHHHc-C-CCCCcEEEEeccCCCCCceEEEecC
Q 032899 76 AKPQTYMNLSGESTGPLAAYY-K-LPLNRVLVFHDDMGLPCGVLRLRHN 122 (131)
Q Consensus 76 ~kP~tyMN~SG~~v~~~~~~~-k-i~~~~llVvhDdldl~~G~vrlk~~ 122 (131)
.-+.|||=++.....-..... + .+|.-++|+.||.|.++|.+.+...
T Consensus 9 ~~~it~~L~l~~~~~v~~~~~a~~~~PNvIlvLTDDqD~eLGsm~vm~k 57 (541)
T KOG3731|consen 9 GSMITLMLLLNLWKYVALSDGAGRLPPNVILVLTDDQDVELGSMAVMFK 57 (541)
T ss_pred cchHHHHHHHhhhHHhhhccccCCCCCCEEEEEccCcchhcccccccch
Confidence 345677766654432222111 1 3467789999999999999887654
No 71
>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=21.17 E-value=2.2e+02 Score=19.39 Aligned_cols=44 Identities=25% Similarity=0.375 Sum_probs=34.8
Q ss_pred ECCeeEEEEeCCchhhcchhhHHHHHHHcCCCCCcEEEEeccCCCCCceEEEecCCCC
Q 032899 68 VGDAPVLLAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGH 125 (131)
Q Consensus 68 ~~~~~v~l~kP~tyMN~SG~~v~~~~~~~ki~~~~llVvhDdldl~~G~vrlk~~Gs~ 125 (131)
+.+.++++++|. +..|+ +..+.+|..|.+.--.|+.-+-..||+
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 567789999995 33332 567899999999999999998877764
No 72
>KOG0076 consensus GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.96 E-value=1e+02 Score=24.52 Aligned_cols=87 Identities=15% Similarity=0.193 Sum_probs=51.4
Q ss_pred CCCCeeEEEecCCCcCcCcCcchHHHHHHHHHHHHcCCCCCcceeeeEEEEEEECCeeEEE-EeCCchhhcchh-hHHHH
Q 032899 15 VARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLL-AKPQTYMNLSGE-STGPL 92 (131)
Q Consensus 15 ~~~~~livGLGNPG~~Y~~TRHNvG~~~ld~La~~~~~~~~~~~~~~~~~~~~~~~~~v~l-~kP~tyMN~SG~-~v~~~ 92 (131)
.....+|.||-|-|+. .+++++.+.+.-.+.-....-..++.-+....+-+ -.|..|-.+-|+ +.+.+
T Consensus 16 e~y~vlIlgldnAGKt----------tfLe~~Kt~~~~~~~~l~~~ki~~tvgLnig~i~v~~~~l~fwdlgGQe~lrSl 85 (197)
T KOG0076|consen 16 EDYSVLILGLDNAGKT----------TFLEALKTDFSKAYGGLNPSKITPTVGLNIGTIEVCNAPLSFWDLGGQESLRSL 85 (197)
T ss_pred hhhhheeeccccCCch----------hHHHHHHHHHHhhhcCCCHHHeecccceeecceeeccceeEEEEcCChHHHHHH
Confidence 4455789999999976 56888887765322111000111221122222222 457889999995 66778
Q ss_pred HHHcCCCCCcEEEEeccCC
Q 032899 93 AAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 93 ~~~~ki~~~~llVvhDdld 111 (131)
++.|-....-++-+.|-.|
T Consensus 86 w~~yY~~~H~ii~viDa~~ 104 (197)
T KOG0076|consen 86 WKKYYWLAHGIIYVIDATD 104 (197)
T ss_pred HHHHHHHhceeEEeecCCC
Confidence 7776555556777777766
No 73
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=20.67 E-value=1.6e+02 Score=23.56 Aligned_cols=36 Identities=17% Similarity=0.187 Sum_probs=25.7
Q ss_pred ECCeeEEEEeCCchhhcchhhHHHH---HHHcCCCCCcEEEEe
Q 032899 68 VGDAPVLLAKPQTYMNLSGESTGPL---AAYYKLPLNRVLVFH 107 (131)
Q Consensus 68 ~~~~~v~l~kP~tyMN~SG~~v~~~---~~~~ki~~~~llVvh 107 (131)
+.+..++++-| |..+|.++-.+ ++.++ .++++.+++
T Consensus 122 ~~~~~viv~DP---MLATG~s~i~ai~~L~~~G-~~~~I~~v~ 160 (210)
T COG0035 122 IDERTVIVLDP---MLATGGSAIAAIDLLKKRG-GPKNIKVVS 160 (210)
T ss_pred ccCCeEEEECc---hhhccHhHHHHHHHHHHhC-CCceEEEEE
Confidence 45667899988 99999876543 44455 778876654
No 74
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=20.64 E-value=68 Score=24.89 Aligned_cols=27 Identities=26% Similarity=0.386 Sum_probs=23.3
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
-|.+++.+++.+++++++++.+-|..+
T Consensus 190 K~~al~~l~~~lgi~~~~v~afGD~~N 216 (264)
T COG0561 190 KGYALQRLAKLLGIKLEEVIAFGDSTN 216 (264)
T ss_pred hHHHHHHHHHHhCCCHHHeEEeCCccc
Confidence 467899999999999999999998753
No 75
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=20.48 E-value=1e+02 Score=18.57 Aligned_cols=20 Identities=15% Similarity=0.298 Sum_probs=16.2
Q ss_pred HHHHcCCCCCcEEEEeccCC
Q 032899 92 LAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 92 ~~~~~ki~~~~llVvhDdld 111 (131)
+.+.++++++++.|+-+|++
T Consensus 28 l~~~~~~p~~~v~V~i~e~~ 47 (61)
T PRK02220 28 VSKNTGAPAEHIHVIINEMS 47 (61)
T ss_pred HHHHhCcChhhEEEEEEEeC
Confidence 55677899999999888865
No 76
>TIGR00099 Cof-subfamily Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences.
Probab=20.44 E-value=59 Score=25.11 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=23.7
Q ss_pred chhhHHHHHHHcCCCCCcEEEEeccCC
Q 032899 85 SGESTGPLAAYYKLPLNRVLVFHDDMG 111 (131)
Q Consensus 85 SG~~v~~~~~~~ki~~~~llVvhDdld 111 (131)
-|.+++.+++.+++++++++++=|+.+
T Consensus 189 K~~~i~~~~~~~~~~~~~~~~~GD~~n 215 (256)
T TIGR00099 189 KGSALQSLAEALGISLEDVIAFGDGMN 215 (256)
T ss_pred hHHHHHHHHHHcCCCHHHEEEeCCcHH
Confidence 478899999999999999999999754
No 77
>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=20.14 E-value=1e+02 Score=24.41 Aligned_cols=27 Identities=22% Similarity=0.384 Sum_probs=20.8
Q ss_pred EEEEeccCCCCCceEEEe--cCCCCCCCC
Q 032899 103 VLVFHDDMGLPCGVLRLR--HNGGHGGHN 129 (131)
Q Consensus 103 llVvhDdldl~~G~vrlk--~~Gs~~GHN 129 (131)
+.|+-.+++++...+++. +++|++|+|
T Consensus 94 V~v~~~~~~i~~~dl~~~~~RssGpGGQ~ 122 (200)
T TIGR03072 94 VQRFSASEEATEDEIRFETLRSSGPGGQH 122 (200)
T ss_pred EEEecCccccChhheEEEEEECCCCCccc
Confidence 445557889999999986 577888876
Done!