Query 026620
Match_columns 236
No_of_seqs 139 out of 345
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 10:25:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026620.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026620hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3218 RNA polymerase, 25-kDa 100.0 1.6E-79 3.4E-84 529.1 20.0 200 36-236 6-208 (208)
2 PLN03111 DNA-directed RNA poly 100.0 1.6E-78 3.5E-83 528.1 20.6 204 32-236 1-206 (206)
3 PTZ00061 DNA-directed RNA poly 100.0 6.9E-77 1.5E-81 517.3 21.2 199 37-236 3-205 (205)
4 PRK09570 rpoH DNA-directed RNA 100.0 5.7E-38 1.2E-42 237.8 7.2 75 162-236 3-77 (79)
5 PF01191 RNA_pol_Rpb5_C: RNA p 100.0 4.1E-38 8.9E-43 236.1 6.2 74 163-236 1-74 (74)
6 COG2012 RPB5 DNA-directed RNA 100.0 3.1E-35 6.8E-40 221.4 7.4 79 158-236 2-80 (80)
7 PF03871 RNA_pol_Rpb5_N: RNA p 100.0 3E-30 6.6E-35 200.1 1.1 89 32-121 1-92 (93)
8 PF04471 Mrr_cat: Restriction 95.9 0.024 5.1E-07 42.8 5.7 76 85-162 36-112 (115)
9 PF13550 Phage-tail_3: Putativ 70.0 6.8 0.00015 31.4 3.9 55 175-234 104-159 (164)
10 PF13156 Mrr_cat_2: Restrictio 68.7 33 0.00071 28.5 7.7 91 69-161 16-110 (129)
11 TIGR00640 acid_CoA_mut_C methy 66.7 33 0.00071 28.0 7.4 87 46-150 19-105 (132)
12 KOG2754 Oligosaccharyltransfer 64.6 43 0.00094 32.9 8.7 153 48-227 41-201 (443)
13 cd02072 Glm_B12_BD B12 binding 60.9 48 0.001 27.3 7.3 76 46-139 16-91 (128)
14 PF03345 DDOST_48kD: Oligosacc 56.6 48 0.0011 32.6 7.7 98 46-166 14-115 (423)
15 COG4889 Predicted helicase [Ge 52.4 23 0.00049 38.8 4.9 80 85-166 61-155 (1518)
16 cd02071 MM_CoA_mut_B12_BD meth 51.3 70 0.0015 25.2 6.6 84 49-150 19-102 (122)
17 PF05273 Pox_RNA_Pol_22: Poxvi 49.4 28 0.00061 30.4 4.3 155 51-235 18-181 (185)
18 TIGR01501 MthylAspMutase methy 47.6 65 0.0014 26.7 6.1 74 46-137 18-91 (134)
19 PF01272 GreA_GreB: Transcript 46.7 30 0.00065 25.3 3.6 34 198-235 39-73 (77)
20 PRK05753 nucleoside diphosphat 46.1 35 0.00076 28.1 4.3 34 198-234 88-122 (137)
21 PRK02261 methylaspartate mutas 45.0 1.1E+02 0.0024 25.0 7.1 74 47-138 21-94 (137)
22 COG3400 Uncharacterized protei 44.2 41 0.00089 33.1 5.0 117 93-233 44-167 (471)
23 COG1787 Predicted endonuclease 42.3 59 0.0013 29.4 5.3 58 107-167 157-214 (217)
24 PF04225 OapA: Opacity-associa 41.9 14 0.00029 28.2 1.1 43 182-224 13-56 (85)
25 cd02067 B12-binding B12 bindin 41.6 1.6E+02 0.0035 22.6 7.5 85 47-150 17-102 (119)
26 PRK05892 nucleoside diphosphat 40.5 41 0.0009 28.4 4.0 36 196-235 116-152 (158)
27 PRK08485 DNA polymerase III su 38.8 69 0.0015 28.8 5.2 40 108-147 36-75 (206)
28 PRK01885 greB transcription el 36.9 50 0.0011 27.9 3.9 35 197-235 117-152 (157)
29 COG2002 AbrB Regulators of sta 36.4 33 0.0007 26.1 2.5 26 198-223 15-40 (89)
30 TIGR01462 greA transcription e 35.6 60 0.0013 26.9 4.1 34 198-235 114-148 (151)
31 TIGR03595 Obg_CgtA_exten Obg f 34.3 28 0.0006 25.6 1.7 14 207-220 50-63 (69)
32 COG0186 RpsQ Ribosomal protein 33.6 44 0.00096 26.2 2.8 26 194-222 42-69 (87)
33 TIGR01461 greB transcription e 33.3 67 0.0014 27.1 4.1 35 197-235 115-150 (156)
34 CHL00142 rps17 ribosomal prote 33.0 60 0.0013 25.1 3.4 37 195-235 38-74 (84)
35 PF13607 Succ_CoA_lig: Succiny 31.6 1.4E+02 0.0029 24.7 5.6 79 47-145 15-98 (138)
36 PRK08559 nusG transcription an 31.3 57 0.0012 27.2 3.3 31 176-222 76-106 (153)
37 COG2344 AT-rich DNA-binding pr 31.2 1.3E+02 0.0028 27.2 5.6 68 109-180 130-198 (211)
38 PF11513 TA0956: Thermoplasma 31.1 1.9E+02 0.0041 23.3 6.0 56 69-128 45-105 (110)
39 KOG1232 Proteins containing th 31.0 33 0.00071 34.0 2.0 62 11-73 332-404 (511)
40 PF09269 DUF1967: Domain of un 30.2 30 0.00066 25.3 1.3 12 208-219 51-62 (69)
41 PF05920 Homeobox_KN: Homeobox 30.2 21 0.00046 23.6 0.4 24 173-196 7-30 (40)
42 KOG0975 Branched chain aminotr 29.7 29 0.00063 33.8 1.5 67 5-74 241-316 (379)
43 PLN00045 photosystem I reactio 29.5 34 0.00074 27.4 1.6 16 208-223 37-52 (101)
44 PRK00226 greA transcription el 29.0 86 0.0019 26.1 4.0 35 197-235 118-153 (157)
45 cd02070 corrinoid_protein_B12- 28.9 3.1E+02 0.0067 23.4 7.6 77 47-141 100-178 (201)
46 PRK09539 tRNA-splicing endonuc 28.6 2.9E+02 0.0064 22.9 7.0 53 51-121 42-94 (124)
47 COG0250 NusG Transcription ant 28.5 76 0.0016 27.5 3.7 56 158-222 74-135 (178)
48 KOG4449 Translocase of outer m 28.3 38 0.00082 24.3 1.5 36 176-215 2-39 (53)
49 PRK03298 hypothetical protein; 28.0 97 0.0021 28.2 4.4 51 99-150 149-202 (224)
50 PF14085 DUF4265: Domain of un 27.9 90 0.0019 24.9 3.8 28 208-235 23-58 (117)
51 cd02069 methionine_synthase_B1 27.4 2.4E+02 0.0052 24.8 6.7 78 47-143 106-184 (213)
52 cd06573 PASTA PASTA domain. Th 27.2 1.1E+02 0.0023 19.3 3.5 21 171-192 2-22 (53)
53 TIGR01118 lacA galactose-6-pho 27.0 1.6E+02 0.0035 24.8 5.3 20 43-62 12-31 (141)
54 TIGR02370 pyl_corrinoid methyl 26.8 3E+02 0.0064 23.7 7.1 77 47-142 102-181 (197)
55 PF01568 Molydop_binding: Moly 26.6 91 0.002 23.3 3.5 27 197-223 30-56 (110)
56 TIGR03784 marine_sortase sorta 26.4 85 0.0018 27.0 3.6 28 205-235 103-130 (174)
57 PRK06437 hypothetical protein; 25.8 60 0.0013 23.4 2.2 41 182-222 23-63 (67)
58 PRK08621 galactose-6-phosphate 25.7 1.8E+02 0.0039 24.5 5.3 20 43-62 12-31 (142)
59 PF04023 FeoA: FeoA domain; I 25.5 53 0.0011 23.2 1.9 21 208-228 30-50 (74)
60 COG0782 Uncharacterized conser 25.4 1.1E+02 0.0023 25.8 4.0 35 196-234 110-145 (151)
61 PF04014 Antitoxin-MazE: Antid 25.3 72 0.0016 21.2 2.4 20 204-223 14-33 (47)
62 cd00988 PDZ_CTP_protease PDZ d 25.3 52 0.0011 23.4 1.8 19 199-218 20-38 (85)
63 PF01963 TraB: TraB family; I 25.1 32 0.00069 29.8 0.8 15 48-62 244-258 (259)
64 cd02775 MopB_CT Molybdopterin- 24.7 95 0.0021 22.6 3.2 27 197-223 23-49 (101)
65 PRK08058 DNA polymerase III su 24.6 1.9E+02 0.0041 26.8 5.8 94 99-193 80-185 (329)
66 cd04459 Rho_CSD Rho_CSD: Rho p 24.5 41 0.0009 24.9 1.2 23 200-222 30-53 (68)
67 PRK05571 ribose-5-phosphate is 23.3 2.1E+02 0.0046 24.2 5.4 20 43-62 12-31 (148)
68 PRK06033 hypothetical protein; 23.1 57 0.0012 24.8 1.8 19 204-222 21-39 (83)
69 TIGR02480 fliN flagellar motor 23.1 59 0.0013 24.0 1.8 19 204-222 22-40 (77)
70 PF01939 DUF91: Protein of unk 22.9 1.3E+02 0.0028 27.3 4.2 58 98-158 149-210 (228)
71 PRK05610 rpsQ 30S ribosomal pr 22.4 1.3E+02 0.0027 23.2 3.5 37 195-235 41-77 (84)
72 COG1034 NuoG NADH dehydrogenas 22.2 84 0.0018 32.9 3.3 65 11-79 50-119 (693)
73 PF07653 SH3_2: Variant SH3 do 22.2 44 0.00094 22.6 0.9 12 209-220 16-27 (55)
74 cd02786 MopB_CT_3 The MopB_CT_ 22.1 1.3E+02 0.0028 22.9 3.6 27 197-223 31-57 (116)
75 PRK00276 infA translation init 21.7 1.2E+02 0.0025 22.2 3.1 23 211-234 47-71 (72)
76 PF08479 POTRA_2: POTRA domain 21.7 77 0.0017 22.8 2.2 52 11-63 6-57 (76)
77 cd01900 YchF YchF subfamily. 21.6 42 0.00091 30.8 0.9 24 177-200 244-267 (274)
78 PF14250 AbrB-like: AbrB-like 21.6 56 0.0012 24.8 1.4 32 189-220 31-62 (71)
79 PF01052 SpoA: Surface present 21.5 53 0.0011 23.7 1.2 19 204-222 22-40 (77)
80 PRK03972 ribosomal biogenesis 21.3 4.8E+02 0.011 23.4 7.5 121 110-235 34-188 (208)
81 cd02790 MopB_CT_Formate-Dh_H F 20.9 1.4E+02 0.0031 22.4 3.6 27 197-223 35-61 (116)
82 cd00989 PDZ_metalloprotease PD 20.9 72 0.0016 22.2 1.8 16 205-220 24-39 (79)
83 PF13167 GTP-bdg_N: GTP-bindin 20.5 1.4E+02 0.0031 23.4 3.6 53 109-165 41-93 (95)
84 cd02792 MopB_CT_Formate-Dh-Na- 20.5 1.2E+02 0.0027 23.1 3.2 28 196-223 34-61 (122)
85 smart00739 KOW KOW (Kyprides, 20.4 86 0.0019 17.9 1.8 17 211-228 2-18 (28)
86 cd02791 MopB_CT_Nitrate-R-NapA 20.4 1.2E+02 0.0027 23.1 3.2 28 196-223 34-61 (122)
87 KOG2776 Metallopeptidase [Gene 20.0 69 0.0015 31.3 2.0 14 208-221 100-113 (398)
No 1
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=100.00 E-value=1.6e-79 Score=529.06 Aligned_cols=200 Identities=46% Similarity=0.796 Sum_probs=197.7
Q ss_pred chhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecCCCccchhhH
Q 026620 36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVI 114 (236)
Q Consensus 36 ~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~-~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~I 114 (236)
+.|++|||++|||++|||+||||.|+++|++++|++|+++||+. |+|++|+|+|.|++||+++|+|||+++++||+|+|
T Consensus 6 e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~ 85 (208)
T KOG3218|consen 6 EEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTM 85 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHH
Confidence 68999999999999999999999999999999999999999997 99999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHHHhhhcCC
Q 026620 115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE 192 (236)
Q Consensus 115 r~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~ 192 (236)
|.++.+| .++|++++|+|+|+.+||+|++++..++ +.||+|+|+||+||||+|+|||||.+||+|||++||++|+++
T Consensus 86 k~~~~~~-~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~ 164 (208)
T KOG3218|consen 86 KTYVIQM-QSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLK 164 (208)
T ss_pred HHHHHHH-HhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCC
Confidence 9999999 8899999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred cccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620 193 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236 (236)
Q Consensus 193 ~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~ 236 (236)
++|||||+.+||+|||||||+||||||+|+|+|||+|++||+|+
T Consensus 165 e~qLPRIq~~DpvaRYyGLKrGqVVKI~r~setag~yitYR~v~ 208 (208)
T KOG3218|consen 165 ETQLPRIQKKDPVARYYGLKRGQVVKIIRRSETAGRYITYRCVV 208 (208)
T ss_pred cccCCeeeccChHHhhhccccCcEEEEEecCccCcceEEEEEeC
Confidence 99999999999999999999999999999999999999999996
No 2
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=1.6e-78 Score=528.09 Aligned_cols=204 Identities=52% Similarity=0.839 Sum_probs=200.3
Q ss_pred CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccch
Q 026620 32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKV 111 (236)
Q Consensus 32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgv 111 (236)
|+.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|++++.+||+++|+|||+++++||+
T Consensus 1 ~~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgv 80 (206)
T PLN03111 1 MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGV 80 (206)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCH
Confidence 46678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHHHhhh
Q 026620 112 NVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKY 189 (236)
Q Consensus 112 k~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y 189 (236)
|+||.|+++| +++|++++|||+|+++||+|++++.+++ ++||+|+|+||++|||+|+|||||++||+|||++||++|
T Consensus 81 k~ir~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y 159 (206)
T PLN03111 81 KTIKTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRY 159 (206)
T ss_pred HHHHHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHc
Confidence 9999999999 9999999999999999999999999995 899999999999999999999999999999999999999
Q ss_pred cCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620 190 SIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236 (236)
Q Consensus 190 ~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~ 236 (236)
+++++|||||+.+||+||||||++||||||+|+|+|||+|++||+|+
T Consensus 160 ~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv 206 (206)
T PLN03111 160 TVKETQLPRIQVSDPIARYYGLKRGQVVKIIRPSETAGRYVTYRCVV 206 (206)
T ss_pred CCCHHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCCceEEEEeC
Confidence 99999999999999999999999999999999999999999999996
No 3
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=6.9e-77 Score=517.29 Aligned_cols=199 Identities=38% Similarity=0.584 Sum_probs=194.0
Q ss_pred hhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecC-CCccchhhH
Q 026620 37 RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCG-PGIVKVNVI 114 (236)
Q Consensus 37 ~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~-~~r~~L~~~~~~~~~p~~~I~VfF~~-~~~vgvk~I 114 (236)
+++.||||+|||++|||+||||.|+++|+++|+++|+++||+. +.|++|+|++++.+||+++|+|||++ +++||+|+|
T Consensus 3 ~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~i 82 (205)
T PTZ00061 3 DSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKPI 82 (205)
T ss_pred HHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHHH
Confidence 6789999999999999999999999999999999999999887 47899999999999999999999998 579999999
Q ss_pred HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHHHhhhcCC
Q 026620 115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE 192 (236)
Q Consensus 115 r~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~ 192 (236)
|.|+++| +++|++++|||+|+++||+|++++.+++ ++||+|+|+||++|||+|+|||+|++||+|||++||++|+++
T Consensus 83 r~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~ 161 (205)
T PTZ00061 83 RELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK 161 (205)
T ss_pred HHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence 9999999 9999999999999999999999998886 899999999999999999999999999999999999999999
Q ss_pred cccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620 193 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236 (236)
Q Consensus 193 ~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~ 236 (236)
++|||||+.+||+||||||++||||||+|+|+|||+|++||+|+
T Consensus 162 ~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv 205 (205)
T PTZ00061 162 ESQLPRIQSADPVARYFGLSKGQVVKIIRPSETAGRYVTYRLVV 205 (205)
T ss_pred HHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCcceEEEEeC
Confidence 99999999999999999999999999999999999999999996
No 4
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=100.00 E-value=5.7e-38 Score=237.78 Aligned_cols=75 Identities=32% Similarity=0.589 Sum_probs=73.9
Q ss_pred eeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620 162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236 (236)
Q Consensus 162 l~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~ 236 (236)
.||||+|+|||+|++||+||+++||++|+++++|||||+.+||+|+||||++||||||+|+|+|||++++||+|+
T Consensus 3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv 77 (79)
T PRK09570 3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRKSPTAGEAVYYRLVV 77 (79)
T ss_pred ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEEEECCCCCCccEEEEEEe
Confidence 589999999999999999999999999999999999999999999999999999999999999999999999996
No 5
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=100.00 E-value=4.1e-38 Score=236.05 Aligned_cols=74 Identities=49% Similarity=0.793 Sum_probs=66.2
Q ss_pred eecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236 (236)
Q Consensus 163 ~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~ 236 (236)
||||+|+|||+|++||+||+++||++|+++++|||||+.+||+|||||+++||||||+|+|+|||++++||+||
T Consensus 1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv 74 (74)
T PF01191_consen 1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYLGAKPGDVVKIIRKSETAGEYVTYRLVV 74 (74)
T ss_dssp S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHTT--TTSEEEEEEEETTTSEEEEEEEEE
T ss_pred CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhcCCCCCCEEEEEecCCCCCCcEEEEEeC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999996
No 6
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=100.00 E-value=3.1e-35 Score=221.41 Aligned_cols=79 Identities=34% Similarity=0.543 Sum_probs=77.0
Q ss_pred eceeeeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620 158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236 (236)
Q Consensus 158 e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~ 236 (236)
++.+.||+++|+|||+|++||+||++++|++|+++++|||||+.+||+|+++|+++||||||+|+|+|||++++||+|+
T Consensus 2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~lgak~GdvVkIvRkS~TaGe~v~YR~Vv 80 (80)
T COG2012 2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKIVRKSPTAGESVYYRLVV 80 (80)
T ss_pred ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHccCCCCcEEEEEecCCCCCceEEEEEeC
Confidence 5678899999999999999999999999999999999999999999999999999999999999999999999999996
No 7
>PF03871 RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal domain; InterPro: IPR005571 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (IPR000783 from INTERPRO) [, , , ]. This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha []. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure []. This module is important for positioning the downstream DNA.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3H0G_Q 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E 1I50_E ....
Probab=99.96 E-value=3e-30 Score=200.11 Aligned_cols=89 Identities=42% Similarity=0.722 Sum_probs=74.6
Q ss_pred CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCC---CCCCCceEEEeecCCCCCCcEEEEecCCCc
Q 026620 32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKRILVVFCGPGI 108 (236)
Q Consensus 32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~---~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~ 108 (236)
|| +++|++||||||||++|||+||||.|++.|+++|+++|+++|++ .|+|++|+|++.+.+||+++|+|||+++++
T Consensus 1 m~-~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~k 79 (93)
T PF03871_consen 1 MD-DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPK 79 (93)
T ss_dssp ---TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSC
T ss_pred Cc-cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCC
Confidence 45 44899999999999999999999999999999999999999988 799999999999999999999999999999
Q ss_pred cchhhHHHHHHHH
Q 026620 109 VKVNVIRSIISQI 121 (236)
Q Consensus 109 vgvk~Ir~~~~~~ 121 (236)
||+|+||+|+++|
T Consensus 80 vgvk~Ir~~~~~m 92 (93)
T PF03871_consen 80 VGVKTIRKYCERM 92 (93)
T ss_dssp ESCCCCHHHCHHH
T ss_pred cCHHHHHHHHHhc
Confidence 9999999999988
No 8
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=95.86 E-value=0.024 Score=42.75 Aligned_cols=76 Identities=21% Similarity=0.270 Sum_probs=41.5
Q ss_pred eEEEeecCCCCCCcEEEEecC-CCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhccceEeeeeeceee
Q 026620 85 LRISISHQSDPSKRILVVFCG-PGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLL 162 (236)
Q Consensus 85 L~~~~~~~~~p~~~I~VfF~~-~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~~~IEiF~e~eLl 162 (236)
..+.+.........++|.+.. ..+++.+.|++++..+ ...+...++||+.+.+|+.|++.+.... .|+++.-++|+
T Consensus 36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~~-~I~l~d~~~L~ 112 (115)
T PF04471_consen 36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKFK-NIELIDGEDLQ 112 (115)
T ss_dssp EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH---------------
T ss_pred EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhhc-ccccccccccc
Confidence 344444433232456666644 3689999999999999 8889999999999999999999887643 67777766653
No 9
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=70.00 E-value=6.8 Score=31.43 Aligned_cols=55 Identities=15% Similarity=0.248 Sum_probs=34.1
Q ss_pred eecChHHHHHHHhhhcCCcccCCc-cccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEE
Q 026620 175 QVLTDQEKEKLLKKYSIEEKQLPR-MLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRC 234 (236)
Q Consensus 175 ~~Ls~eEk~~ll~~y~i~~~qLP~-I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~ 234 (236)
-++++.+++.+-+++- ....-++ -...-=-..++.++|||||.|.-+ |....+|+
T Consensus 104 ~v~~~~qA~r~a~~~l-~~~~~~r~t~~f~~~~~~~~l~pGDvi~l~~~----~~~~~~RI 159 (164)
T PF13550_consen 104 GVTDASQAQRLAERLL-RRSRYERRTVSFTLPPDGLALEPGDVIALSDD----GRDMRFRI 159 (164)
T ss_pred eECCHHHHHHHHHHHH-HHhhccceEEEEEEChhhccCCCCCEEEEEeC----CCceEEEE
Confidence 4567788776655533 3333333 222221234588999999999988 56677776
No 10
>PF13156 Mrr_cat_2: Restriction endonuclease
Probab=68.66 E-value=33 Score=28.51 Aligned_cols=91 Identities=18% Similarity=0.245 Sum_probs=59.2
Q ss_pred HHHHHHHhCC-CCCCCceEEEeecCCCCCC-cEEEEecC-CCccchhhHHHHHHHHhhcCCCcEEEEEEc-CCCCHHHHH
Q 026620 69 VQDFRAIYGQ-DPDVDRLRISISHQSDPSK-RILVVFCG-PGIVKVNVIRSIISQIVNRDTLTGLILILQ-NQITSQATK 144 (236)
Q Consensus 69 l~eF~~~y~~-~~~r~~L~~~~~~~~~p~~-~I~VfF~~-~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q-~~lt~~Ark 144 (236)
..+|-.+++. .+|. -+-+++...++..- +|-+-|.. +.+|..+.|..|+... ....+.+.|||.- .++++.|.+
T Consensus 16 w~dwp~~~~~~~~Dt-GIDLVA~~~~~g~~~AIQCKfY~~~~~I~k~didSF~s~s-gk~~f~~rliisTt~~~s~nAe~ 93 (129)
T PF13156_consen 16 WSDWPERYGWGGKDT-GIDLVARTRDGGEYWAIQCKFYDPDHTIQKSDIDSFFSAS-GKSRFSRRLIISTTDKWSKNAEK 93 (129)
T ss_pred hhhhhHhhCCCCCCC-CEeEEEEEcCCCcEEEEEEEeeCCCceEcHHHhhHHHHhc-CCccccCcEEEEcCcHhhHHHHH
Confidence 4566655533 2333 35566665554433 67666655 4799999999999998 7677777777754 479999999
Q ss_pred HhhhccceEeeeeecee
Q 026620 145 AVGLFQFKVEMFQITDL 161 (236)
Q Consensus 145 ~l~~~~~~IEiF~e~eL 161 (236)
++..-...+..+...+|
T Consensus 94 ~l~~q~~pv~ri~l~dl 110 (129)
T PF13156_consen 94 ALENQSIPVSRIGLSDL 110 (129)
T ss_pred HHHcCCCCeEEEcHHHH
Confidence 88765433444444444
No 11
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=66.70 E-value=33 Score=28.03 Aligned_cols=87 Identities=8% Similarity=0.139 Sum_probs=55.3
Q ss_pred HHHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 026620 46 RRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (236)
Q Consensus 46 rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~e 125 (236)
.+-+.-||++-||.|.+.....|.++|.+..-+. ++ =.|..|.-..-.+..++.+++.+ .++
T Consensus 19 ~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~--------------~a---dii~iSsl~~~~~~~~~~~~~~L-~~~ 80 (132)
T TIGR00640 19 AKVIATAYADLGFDVDVGPLFQTPEEIARQAVEA--------------DV---HVVGVSSLAGGHLTLVPALRKEL-DKL 80 (132)
T ss_pred HHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc--------------CC---CEEEEcCchhhhHHHHHHHHHHH-Hhc
Confidence 3556679999999999988889999998775221 11 01111222223445688888888 777
Q ss_pred CCcEEEEEEcCCCCHHHHHHhhhcc
Q 026620 126 TLTGLILILQNQITSQATKAVGLFQ 150 (236)
Q Consensus 126 n~~~~IiV~q~~lt~~Ark~l~~~~ 150 (236)
+.....+++.+.+.+.-...+.+++
T Consensus 81 g~~~i~vivGG~~~~~~~~~l~~~G 105 (132)
T TIGR00640 81 GRPDILVVVGGVIPPQDFDELKEMG 105 (132)
T ss_pred CCCCCEEEEeCCCChHhHHHHHHCC
Confidence 7755555566656554455566555
No 12
>KOG2754 consensus Oligosaccharyltransferase, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=64.64 E-value=43 Score=32.94 Aligned_cols=153 Identities=15% Similarity=0.243 Sum_probs=77.3
Q ss_pred HHHHHhcCCCcccCcc---ccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhc
Q 026620 48 TVLEMLKDRGYAVALS---EINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNR 124 (236)
Q Consensus 48 Tv~eMl~DRGY~v~~~---el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~ 124 (236)
+-++-|.||||.+.-. +-.+++..+-++- .+.|-+.++ .... | ...+.+|.|-+|+ +.
T Consensus 41 vFl~sLkdRgf~L~~~~a~dssl~L~~Ygq~L-----yDnlIifap-~~e~-------f--gg~is~k~l~~Fv----d~ 101 (443)
T KOG2754|consen 41 VFLKSLKDRGFKLTYKLADDSSLALFKYGQRL-----YDNLIIFAP-SVEN-------F--GGSISVKSLAKFV----DS 101 (443)
T ss_pred hhhhhHHhcCceeEEEecCCchhHHHHhhhHh-----hccEEEecC-chhh-------c--CCCCCHHHHHHHH----hC
Confidence 4468899999999632 2234455443331 122333322 1110 1 2467888888886 33
Q ss_pred CCCcEEEEEEcCC-CCHHHHHHhhhccceEeeeeeceeeeecccccc---cCceeecChHHHHHHHhhhcCCcccC-Ccc
Q 026620 125 DTLTGLILILQNQ-ITSQATKAVGLFQFKVEMFQITDLLVNITKHVL---KPKHQVLTDQEKEKLLKKYSIEEKQL-PRM 199 (236)
Q Consensus 125 en~~~~IiV~q~~-lt~~Ark~l~~~~~~IEiF~e~eLl~nit~H~l---VPkH~~Ls~eEk~~ll~~y~i~~~qL-P~I 199 (236)
.+ -+||..+. +....|....+.+ +|.=++.-..++=..|.. --.|.++.. ..-++..|-+....- --|
T Consensus 102 gG---nvlv~ass~~~d~iRe~~~E~g--~~~~e~~~~ViDH~~~d~s~~sgdhtli~~--~nl~~~~~Ivg~~~~~~pi 174 (443)
T KOG2754|consen 102 GG---NVLVAASSAIGDAIREFASECG--IEFDEEGAAVIDHHNYDVSSDSGDHTLIVA--DNLLKAPYIVGKSKRAAPI 174 (443)
T ss_pred CC---cEEEEcCCcccHHHHHHHHHhC--cccCcccceeeeeeeccccCCCCCeEEEee--cccccCceeeccccccCCe
Confidence 32 34555554 4333333334333 332222222222222221 236777766 445556666654431 111
Q ss_pred ccCCchhhhcCCCCCCEEEEEecCCCCc
Q 026620 200 LKKDAIAQYYGLERGQVVKVTYSGEITE 227 (236)
Q Consensus 200 ~~~DPvary~g~~~GdVvkI~R~s~tag 227 (236)
+- -=+.-++|-..-+|++|-|.|+||=
T Consensus 175 Lf-rgig~~l~~~n~lvl~IL~a~~TsY 201 (443)
T KOG2754|consen 175 LF-RGIGHVLGPTNPLVLPILRASPTSY 201 (443)
T ss_pred ee-ecchhhcCCCCcceeeeecCCCcce
Confidence 11 1134566667889999999998874
No 13
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=60.86 E-value=48 Score=27.35 Aligned_cols=76 Identities=11% Similarity=0.128 Sum_probs=50.6
Q ss_pred HHHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 026620 46 RRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (236)
Q Consensus 46 rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~e 125 (236)
.+-+.-||++.||.|-+--...+.++|.+..-+. +.+-+.++ .--.-.+..++++++.+ .++
T Consensus 16 kniv~~~L~~~GfeVidLG~~v~~e~~v~aa~~~-~adiVglS----------------~L~t~~~~~~~~~~~~l-~~~ 77 (128)
T cd02072 16 NKILDHAFTEAGFNVVNLGVLSPQEEFIDAAIET-DADAILVS----------------SLYGHGEIDCKGLREKC-DEA 77 (128)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEe----------------ccccCCHHHHHHHHHHH-HHC
Confidence 3455669999999999998999999999875221 11112222 11123446688888888 888
Q ss_pred CCcEEEEEEcCCCC
Q 026620 126 TLTGLILILQNQIT 139 (236)
Q Consensus 126 n~~~~IiV~q~~lt 139 (236)
++....+++.+.+.
T Consensus 78 gl~~v~vivGG~~~ 91 (128)
T cd02072 78 GLKDILLYVGGNLV 91 (128)
T ss_pred CCCCCeEEEECCCC
Confidence 88556666777653
No 14
>PF03345 DDOST_48kD: Oligosaccharyltransferase 48 kDa subunit beta; InterPro: IPR005013 During N-linked glycosylation of proteins, oligosaccharide chains are assembled on the carrier molecule dolichyl pyrophosphate in the following order: 2 molecules of N-acetylglucosamine (GlcNAc), 9 molecules of mannose, and 3 molecules of glucose. These 14-residue oligosaccharide cores are then transferred to asparagine residues on nascent polypeptide chains in the endoplasmic reticulum (ER). As proteins progress through the Golgi apparatus, the oligosaccharide cores are modified by trimming and extension to generate a diverse array of glycosylated proteins [, ]. The oligosaccharyl transferase complex (OST complex) 2.4.1.119 from EC transfers 14-sugar branched oligosaccharides from dolichyl pyrophosphate to asparagine residues []. The complex contains nine protein subunits: Ost1p, Ost2p, Ost3p, Ost4p, Ost5p, Ost6p, Stt3p, Swp1p, and Wbp1p, all of which are integral membrane proteins of the ER. The OST complex interacts with the Sec61p pore complex [] involved in protein import into the ER. This entry represents subunits OST3 and OST6. OST3 is homologous to OST6 [], and several lines of evidence indicate that they are alternative members of the OST complex. Disruption of both OST3 and OST6 causes severe underglycosylation of soluble and membrane-bound glycoproteins and a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation []. This entry also includes the magnesium transporter protein 1, also known as OST3 homologue B, which might be involved in N-glycosylation through its association with the oligosaccharyl transferase (OST) complex. Wbp1p is the beta subunit of the OST complex, one of the original six subunits purified []. Wbp1 is essential [, ], but conditional mutants have decreased transferase activity [, ]. Wbp1p is homologous to mammalian OST48 [].; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0018279 protein N-linked glycosylation via asparagine, 0005789 endoplasmic reticulum membrane
Probab=56.58 E-value=48 Score=32.57 Aligned_cols=98 Identities=16% Similarity=0.275 Sum_probs=52.5
Q ss_pred HHHHHHHhcCCCcccCcc---ccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHh
Q 026620 46 RRTVLEMLKDRGYAVALS---EINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIV 122 (236)
Q Consensus 46 rrTv~eMl~DRGY~v~~~---el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~ 122 (236)
..+.++.|++|||.+.=. +-.++|..+ |+. ..+.|-+..+. ... | .+.++.+.|-+|+
T Consensus 14 yS~Ff~~L~~rg~~l~~~~~~d~~l~L~~~----ge~-~YD~LIif~~~-~k~-------~--g~~ls~~~ll~Fv---- 74 (423)
T PF03345_consen 14 YSTFFNSLKERGYELTFKSADDESLSLFKY----GER-LYDHLIIFPPS-VKE-------F--GGSLSPKTLLDFV---- 74 (423)
T ss_pred HHHHHHHHHhCCCEEEEecCCCCCcchhhC----Chh-hcceEEEeCCc-ccc-------c--CCCCCHHHHHHHH----
Confidence 678899999999999622 222333333 332 23334332211 111 1 1346667776665
Q ss_pred hcCCCcEEEEEEcCC-CCHHHHHHhhhccceEeeeeeceeeeecc
Q 026620 123 NRDTLTGLILILQNQ-ITSQATKAVGLFQFKVEMFQITDLLVNIT 166 (236)
Q Consensus 123 ~~en~~~~IiV~q~~-lt~~Ark~l~~~~~~IEiF~e~eLl~nit 166 (236)
+.. ...++++... ++...|..+.+++ ||+=...-.+++-.
T Consensus 75 d~G--gNilv~~s~~~~~~~ir~~~~E~g--i~~~~~~~~viDHf 115 (423)
T PF03345_consen 75 DNG--GNILVAGSSDAIPDSIREFANELG--IEFDPKGSKVIDHF 115 (423)
T ss_pred hCC--CcEEEEeCCCcCcHHHHHHHHHCC--eEECCCCCEEEcCC
Confidence 322 3355566666 7777888888776 44433333444433
No 15
>COG4889 Predicted helicase [General function prediction only]
Probab=52.45 E-value=23 Score=38.77 Aligned_cols=80 Identities=18% Similarity=0.240 Sum_probs=63.5
Q ss_pred eEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--------------
Q 026620 85 LRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-------------- 150 (236)
Q Consensus 85 L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~-------------- 150 (236)
+.+++...++.-..|.+-|.. .+++...|..|++.+ ..-++.+++||.-...++.|.+++.+..
T Consensus 61 idlva~~d~g~ytaiQcKFy~-nslak~di~sF~t~l-gkt~f~~gliiSTtdw~sNA~~aieq~~~~~~~Iglsei~es 138 (1518)
T COG4889 61 IDLVAREDNGNYTAIQCKFYQ-NSLAKGDIDSFFTAL-GKTGFKNGLIISTTDWTSNAEKAIEQQRSPGMRIGLSEIAES 138 (1518)
T ss_pred eeEEEEccCCCeEEEEeeeec-cccccccccHHHHHh-ccccccCceEEEecccchhHHHHHHhhhCccceecHHHHhcC
Confidence 455665544444667777765 689999999999999 8889999999987789999999987653
Q ss_pred -ceEeeeeeceeeeecc
Q 026620 151 -FKVEMFQITDLLVNIT 166 (236)
Q Consensus 151 -~~IEiF~e~eLl~nit 166 (236)
...++|...||..|++
T Consensus 139 ~IDW~~f~p~e~~~nl~ 155 (1518)
T COG4889 139 PIDWDIFDPTELQDNLP 155 (1518)
T ss_pred CCChhhcCccccccccc
Confidence 3457888899999987
No 16
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=51.29 E-value=70 Score=25.19 Aligned_cols=84 Identities=11% Similarity=0.132 Sum_probs=50.3
Q ss_pred HHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCc
Q 026620 49 VLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLT 128 (236)
Q Consensus 49 v~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en~~ 128 (236)
+.-|++..||.|..--...+.++|.+.-.+. +| +-|.+.+.. .-....++++++.+ .+.+..
T Consensus 19 ~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~--------------~~-d~V~iS~~~--~~~~~~~~~~~~~L-~~~~~~ 80 (122)
T cd02071 19 IARALRDAGFEVIYTGLRQTPEEIVEAAIQE--------------DV-DVIGLSSLS--GGHMTLFPEVIELL-RELGAG 80 (122)
T ss_pred HHHHHHHCCCEEEECCCCCCHHHHHHHHHHc--------------CC-CEEEEcccc--hhhHHHHHHHHHHH-HhcCCC
Confidence 3458999999999877788899997664211 11 112222222 34455688899988 777665
Q ss_pred EEEEEEcCCCCHHHHHHhhhcc
Q 026620 129 GLILILQNQITSQATKAVGLFQ 150 (236)
Q Consensus 129 ~~IiV~q~~lt~~Ark~l~~~~ 150 (236)
...+++.+...+.-...+.+++
T Consensus 81 ~i~i~~GG~~~~~~~~~~~~~G 102 (122)
T cd02071 81 DILVVGGGIIPPEDYELLKEMG 102 (122)
T ss_pred CCEEEEECCCCHHHHHHHHHCC
Confidence 5555555554443233344444
No 17
>PF05273 Pox_RNA_Pol_22: Poxvirus RNA polymerase 22 kDa subunit; InterPro: IPR007937 Vaccinia viral RNA synthesis is carried out by a virus coded, multi-subunit, eukaryotic-like RNA polymerase. RNA polymerase subunits are synthesized throughout infection and the assembled RNA polymerase is packaged into nascent virions late in infection. The RNA polymerase exists in two different forms, one specific for early genes and one specific for late genes. Both forms of the RNA polymerase have in common eight subunits, ranging in size from 147 to 7 kDa This family consists of several poxvirus DNA-dependent RNA polymerase 22 kDa subunits.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=49.44 E-value=28 Score=30.44 Aligned_cols=155 Identities=24% Similarity=0.334 Sum_probs=98.9
Q ss_pred HHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEE--EeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCc
Q 026620 51 EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRI--SISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLT 128 (236)
Q Consensus 51 eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~--~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en~~ 128 (236)
|.++ .-|.+...+ -..+|.-....++|.- .+.|+-|.+..+|=.|.+ ++|.-.++. ..+.
T Consensus 18 Ei~r-~PyavIsk~-------~~~~Y~~~v~YgDlvt~itv~hkid~~~tVfQvFnE-ssV~YsP~e---------~DYG 79 (185)
T PF05273_consen 18 EILR-DPYAVISKD-------ILSRYDTDVEYGDLVTIITVTHKIDSSKTVFQVFNE-SSVNYSPLE---------DDYG 79 (185)
T ss_pred HHhc-CCceeeeHH-------HHhhheeeeeeCcEEEEEEEEEEccCCceeeeeecc-cceeecccc---------ccCC
Confidence 3443 456665543 3445555455555543 445677777777777754 445555543 3344
Q ss_pred EEEEEEcCCCCHHHHHHhhhccceEeeeeeceeeeecccccccCceeecChHHHHHHHhhhcCCcc-----cCCccccCC
Q 026620 129 GLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEK-----QLPRMLKKD 203 (236)
Q Consensus 129 ~~IiV~q~~lt~~Ark~l~~~~~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~-----qLP~I~~~D 203 (236)
--||++.-..+. =.-|...-|-+++-.-.+-|++..|+++|..-+-.-..+.+. .||||+.+.
T Consensus 80 ePIiiTs~lq~g------------HnKfPi~~lyIDvVaSDlFP~F~Rlt~~e~~vv~svl~~gd~kE~~lkLPkmleTE 147 (185)
T PF05273_consen 80 EPIIITSFLQPG------------HNKFPINMLYIDVVASDLFPKFVRLTPDEIAVVNSVLQIGDRKEQSLKLPKMLETE 147 (185)
T ss_pred CcEEEEeccccc------------ccccceeeEEeeeeecccccccccCChhhhhHhhhhhccCCCccceeecchhhhhh
Confidence 457776432222 122777788899999999999999999998876555555333 499999999
Q ss_pred chhhhcCCC--CCCEEEEEecCCCCcceeEEEEe
Q 026620 204 AIAQYYGLE--RGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 204 Pvary~g~~--~GdVvkI~R~s~tag~~v~YR~V 235 (236)
=+|+.|--+ |=-+|+--|+--.+|--++=|-|
T Consensus 148 l~~KILyh~d~PLKiVRf~rnNm~TGvEi~DRsv 181 (185)
T PF05273_consen 148 LVAKILYHKDIPLKIVRFFRNNMVTGVEIADRSV 181 (185)
T ss_pred hhheeeccCCCcceeeeeeccCceeeeEEecceE
Confidence 999877443 33455556666777766666655
No 18
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=47.63 E-value=65 Score=26.73 Aligned_cols=74 Identities=11% Similarity=0.116 Sum_probs=49.2
Q ss_pred HHHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 026620 46 RRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (236)
Q Consensus 46 rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~e 125 (236)
.+-+.-||++.||.|-+--...|.++|.+..-+. +.+-+-++.- . .-.+..++.+++.+ .++
T Consensus 18 k~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~-~adiVglS~l--------------~--~~~~~~~~~~~~~l-~~~ 79 (134)
T TIGR01501 18 NKILDHAFTNAGFNVVNLGVLSPQEEFIKAAIET-KADAILVSSL--------------Y--GHGEIDCKGLRQKC-DEA 79 (134)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEecc--------------c--ccCHHHHHHHHHHH-HHC
Confidence 4667789999999999988889999999875221 1112222211 0 12334578888888 888
Q ss_pred CCcEEEEEEcCC
Q 026620 126 TLTGLILILQNQ 137 (236)
Q Consensus 126 n~~~~IiV~q~~ 137 (236)
++....+++.+.
T Consensus 80 gl~~~~vivGG~ 91 (134)
T TIGR01501 80 GLEGILLYVGGN 91 (134)
T ss_pred CCCCCEEEecCC
Confidence 886655666665
No 19
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=46.75 E-value=30 Score=25.33 Aligned_cols=34 Identities=18% Similarity=0.363 Sum_probs=25.6
Q ss_pred ccccCCchhhh-cCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 198 RMLKKDAIAQY-YGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 198 ~I~~~DPvary-~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
+|+..-|+++. +|.+.||.|.+.-+. ....|++.
T Consensus 39 ~IS~~SPLG~ALlG~~~Gd~v~~~~~~----g~~~~~I~ 73 (77)
T PF01272_consen 39 KISIDSPLGKALLGKKVGDEVEVELPG----GERKYEIL 73 (77)
T ss_dssp EEETTSHHHHHHTT-BTT-EEEEEETT----BEEEEEEE
T ss_pred EEEecCHHHHHhcCCCCCCEEEEEeCC----ceEEEEEE
Confidence 89999999886 599999999998876 35556653
No 20
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=46.14 E-value=35 Score=28.12 Aligned_cols=34 Identities=15% Similarity=0.243 Sum_probs=26.3
Q ss_pred ccccCCchhhh-cCCCCCCEEEEEecCCCCcceeEEEE
Q 026620 198 RMLKKDAIAQY-YGLERGQVVKVTYSGEITESHVTYRC 234 (236)
Q Consensus 198 ~I~~~DPvary-~g~~~GdVvkI~R~s~tag~~v~YR~ 234 (236)
+|+..-|+++. +|.+.||+|.+.-++ |....|++
T Consensus 88 ~ISi~SPlG~ALlG~~~Gd~v~v~~p~---G~~~~~~I 122 (137)
T PRK05753 88 QLSVLAPVGAALLGLSVGQSIDWPLPG---GKETHLEV 122 (137)
T ss_pred cCcccCHHHHHHcCCCCCCEEEEECCC---CCEEEEEE
Confidence 88999999986 599999999998664 43344544
No 21
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=45.01 E-value=1.1e+02 Score=25.01 Aligned_cols=74 Identities=16% Similarity=0.124 Sum_probs=47.6
Q ss_pred HHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCC
Q 026620 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDT 126 (236)
Q Consensus 47 rTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en 126 (236)
+-+.-||++.||.|..--...+.++|.+.-.+. +| +-+.+.+.. .-....++++++.+ .+.+
T Consensus 21 ~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~--------------~~-d~V~lS~~~--~~~~~~~~~~~~~L-~~~~ 82 (137)
T PRK02261 21 KILDRALTEAGFEVINLGVMTSQEEFIDAAIET--------------DA-DAILVSSLY--GHGEIDCRGLREKC-IEAG 82 (137)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc--------------CC-CEEEEcCcc--ccCHHHHHHHHHHH-HhcC
Confidence 344569999999999988888999998764211 11 112222222 23556778888888 7776
Q ss_pred CcEEEEEEcCCC
Q 026620 127 LTGLILILQNQI 138 (236)
Q Consensus 127 ~~~~IiV~q~~l 138 (236)
.....+++.+.+
T Consensus 83 ~~~~~i~vGG~~ 94 (137)
T PRK02261 83 LGDILLYVGGNL 94 (137)
T ss_pred CCCCeEEEECCC
Confidence 655556666665
No 22
>COG3400 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.24 E-value=41 Score=33.08 Aligned_cols=117 Identities=22% Similarity=0.263 Sum_probs=64.8
Q ss_pred CCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeece-eeee----c
Q 026620 93 SDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITD-LLVN----I 165 (236)
Q Consensus 93 ~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~e-Ll~n----i 165 (236)
+.|+.--++||..++. ...+ +.+ ..+-.+..|++-+-.-|-...+++++.. +.+|+---.+ |-.| =
T Consensus 44 ~~~e~~~fh~fdaTs~---~rl~---~~~-n~~~~~Afi~~qd~~et~~i~k~lr~~f~n~e~ei~~~~~~l~~Nee~~d 116 (471)
T COG3400 44 NYPETFAFHCFDATSS---FRLL---QVL-NDEVSDAFIIIQDFKETRIIHKILRTHFKNMEVEISVKRDELENNEENKD 116 (471)
T ss_pred cCcceEEEEEeCCccH---HHHH---HHh-hhHhhhhheehhhHHHHHHHHHHHHHhccCcEEEEEEEeCCCccchhhcc
Confidence 4455667888876543 2333 334 3333333444444445666667777433 5666644433 6666 2
Q ss_pred ccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEE
Q 026620 166 TKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 233 (236)
Q Consensus 166 t~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR 233 (236)
++-.|+- +...|-.++. .-||-|-.+ ++++||.+|.++.|+=+ +|.-..||
T Consensus 117 ~k~~lid--------~~~vL~~~F~---~~Lp~I~~t---p~~iGLgkGEImEI~vp---~gSifaYr 167 (471)
T COG3400 117 EKLILID--------EFEVLANKFI---SRLPNIPST---PREIGLGKGEIMEIDVP---FGSIFAYR 167 (471)
T ss_pred cceeecc--------hHHHHHHHHH---HhcCCcccc---chhcccccceEEEEecC---CCchhhhh
Confidence 3333332 3333333332 447877655 68999999999999754 45444454
No 23
>COG1787 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]
Probab=42.30 E-value=59 Score=29.43 Aligned_cols=58 Identities=17% Similarity=0.111 Sum_probs=47.8
Q ss_pred CccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhccceEeeeeeceeeeeccc
Q 026620 107 GIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITK 167 (236)
Q Consensus 107 ~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~~~IEiF~e~eLl~nit~ 167 (236)
.+|+.+.|+++.... -..++..+++|+.++.|-.|++... . ..+|++.-.++..++..
T Consensus 157 ~aV~~kaiqEivask-~~Y~~eka~vvTn~~yt~~aqkla~-~-nsv~l~~r~~~~~f~~~ 214 (217)
T COG1787 157 SAVSKKAIQEIVASK-AYYGCEKAKVVTNGSYTYAAQKLAQ-A-NSVELIDRDELSEFIRE 214 (217)
T ss_pred HhhhHHHHHHHHHhh-hccCcceEEEecCCccchhHHHHHH-h-hcceEEecchHHhhhcc
Confidence 578999999999887 7889999999999999997777532 2 47899999988887764
No 24
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=41.86 E-value=14 Score=28.22 Aligned_cols=43 Identities=16% Similarity=0.302 Sum_probs=29.1
Q ss_pred HHHHHhhhcCCcccCCccccCCchhhhc-CCCCCCEEEEEecCC
Q 026620 182 KEKLLKKYSIEEKQLPRMLKKDAIAQYY-GLERGQVVKVTYSGE 224 (236)
Q Consensus 182 k~~ll~~y~i~~~qLP~I~~~DPvary~-g~~~GdVvkI~R~s~ 224 (236)
-..+++++++....|=+|...|+-++.| .++|||-+.+.-.+.
T Consensus 13 Ls~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~~ 56 (85)
T PF04225_consen 13 LSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDED 56 (85)
T ss_dssp HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-TT
T ss_pred HHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEECCC
Confidence 4568999999999999999999666544 799999999987764
No 25
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=41.63 E-value=1.6e+02 Score=22.57 Aligned_cols=85 Identities=14% Similarity=0.223 Sum_probs=49.1
Q ss_pred HHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCC
Q 026620 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDT 126 (236)
Q Consensus 47 rTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en 126 (236)
+-+..+|+..||.|..-..+++.++|.+.... .+|. +.+ ++....-....++.+++.+ .+.+
T Consensus 17 ~~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~--------------~~pd--vV~-iS~~~~~~~~~~~~~i~~l-~~~~ 78 (119)
T cd02067 17 NIVARALRDAGFEVIDLGVDVPPEEIVEAAKE--------------EDAD--AIG-LSGLLTTHMTLMKEVIEEL-KEAG 78 (119)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHH--------------cCCC--EEE-EeccccccHHHHHHHHHHH-HHcC
Confidence 34567899999999887777889999866421 1221 111 2222233457788888888 5555
Q ss_pred C-cEEEEEEcCCCCHHHHHHhhhcc
Q 026620 127 L-TGLILILQNQITSQATKAVGLFQ 150 (236)
Q Consensus 127 ~-~~~IiV~q~~lt~~Ark~l~~~~ 150 (236)
- +-.|+|.....+... +.+.+.+
T Consensus 79 ~~~~~i~vGG~~~~~~~-~~~~~~G 102 (119)
T cd02067 79 LDDIPVLVGGAIVTRDF-KFLKEIG 102 (119)
T ss_pred CCCCeEEEECCCCChhH-HHHHHcC
Confidence 4 333445444444322 3444444
No 26
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=40.54 E-value=41 Score=28.44 Aligned_cols=36 Identities=11% Similarity=0.137 Sum_probs=28.5
Q ss_pred CCccccCCchhhh-cCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 196 LPRMLKKDAIAQY-YGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 196 LP~I~~~DPvary-~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
.-+|+..-|+++. +|.+.||.|.+.-++. ...|+++
T Consensus 116 ~~~IS~~SPlG~ALlGk~vGD~v~v~~p~g----~~~~eI~ 152 (158)
T PRK05892 116 AETLTADSPLGQALAGHQAGDTVTYSTPQG----PAQVELL 152 (158)
T ss_pred CCEEccCCHHHHHHhCCCCCCEEEEEcCCC----cEEEEEE
Confidence 4589999999996 5999999999987663 2566654
No 27
>PRK08485 DNA polymerase III subunit delta'; Validated
Probab=38.77 E-value=69 Score=28.76 Aligned_cols=40 Identities=15% Similarity=0.170 Sum_probs=28.3
Q ss_pred ccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhh
Q 026620 108 IVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVG 147 (236)
Q Consensus 108 ~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~ 147 (236)
.+|+..+|++++.+.-..+-.+.||.--..+|..|..++-
T Consensus 36 ~i~Vd~iReii~~~~~~~~~~k~iI~~a~~l~~~A~NaLL 75 (206)
T PRK08485 36 EFKIEDAKEVIAEAYIAESEEKIIVIAAPSYGIEAQNALL 75 (206)
T ss_pred CCCHHHHHHHHHHHhhCCCCcEEEEEchHhhCHHHHHHHH
Confidence 6999999999998733333445555555678888777664
No 28
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=36.94 E-value=50 Score=27.89 Aligned_cols=35 Identities=14% Similarity=0.073 Sum_probs=27.9
Q ss_pred CccccCCchhhhc-CCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 197 PRMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 197 P~I~~~DPvary~-g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
-+|+..-|+++.| |.+.||.|.+.-++.+ ..|+++
T Consensus 117 ~~IS~~SPlG~ALlGk~vGd~v~v~~p~g~----~~~eI~ 152 (157)
T PRK01885 117 GYISIDSPMARALLKKEVGDEVTVNTPAGE----AEWYVN 152 (157)
T ss_pred CeEeccCHHHHHHhCCCCCCEEEEEcCCCc----EEEEEE
Confidence 4899999999865 9999999999877642 456654
No 29
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=36.38 E-value=33 Score=26.12 Aligned_cols=26 Identities=19% Similarity=0.512 Sum_probs=20.8
Q ss_pred ccccCCchhhhcCCCCCCEEEEEecC
Q 026620 198 RMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 198 ~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
+|----++-+.||+++||++.|+...
T Consensus 15 qIvIPkeiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 15 QIVIPKEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred eEEecHHHHHHhCCCCCCEEEEEEeC
Confidence 34444578899999999999998765
No 30
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=35.65 E-value=60 Score=26.93 Aligned_cols=34 Identities=18% Similarity=0.274 Sum_probs=27.5
Q ss_pred ccccCCchhhh-cCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 198 RMLKKDAIAQY-YGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 198 ~I~~~DPvary-~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
+|+..-|+++. +|.+.||.|.+.-++.. ..|+++
T Consensus 114 ~IS~~SPlG~ALlG~~~Gd~v~v~~p~g~----~~~~I~ 148 (151)
T TIGR01462 114 KISIDSPLGKALIGKKVGDVVEVQTPKGE----KEYEIL 148 (151)
T ss_pred eecCCCHHHHHHcCCCCCCEEEEEeCCCc----EEEEEE
Confidence 89999999986 49999999999876632 566654
No 31
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=34.31 E-value=28 Score=25.58 Aligned_cols=14 Identities=21% Similarity=0.456 Sum_probs=11.6
Q ss_pred hhcCCCCCCEEEEE
Q 026620 207 QYYGLERGQVVKVT 220 (236)
Q Consensus 207 ry~g~~~GdVvkI~ 220 (236)
+--|+++||.|+|-
T Consensus 50 ~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 50 RKAGAKDGDTVRIG 63 (69)
T ss_pred HHcCCCCCCEEEEc
Confidence 44599999999994
No 32
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=33.57 E-value=44 Score=26.17 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=17.7
Q ss_pred ccCCccccCCchhhhcCCCCCCEEEE--Eec
Q 026620 194 KQLPRMLKKDAIAQYYGLERGQVVKV--TYS 222 (236)
Q Consensus 194 ~qLP~I~~~DPvary~g~~~GdVvkI--~R~ 222 (236)
.+--++.+-||- .-++.||+|+| +||
T Consensus 42 ~r~kK~~aHde~---~~~k~GD~V~I~EtRP 69 (87)
T COG0186 42 RRSKKYHAHDEC---NEAKVGDIVRIAETRP 69 (87)
T ss_pred EEEeeeEeeccc---ccCCCCCEEEEEEccc
Confidence 334566677743 34899999999 555
No 33
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=33.32 E-value=67 Score=27.10 Aligned_cols=35 Identities=14% Similarity=0.110 Sum_probs=27.0
Q ss_pred CccccCCchhhhc-CCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 197 PRMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 197 P~I~~~DPvary~-g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
=+|+..-|+++.+ |.+.||.|.+.-++. ...|.++
T Consensus 115 ~~IS~~SPlG~ALlGk~~GD~v~v~~p~g----~~~~eI~ 150 (156)
T TIGR01461 115 NYISIDSPLARALLKKEVGDEVVVNTPAG----EASWYVN 150 (156)
T ss_pred CeECCCCHHHHHHcCCCCCCEEEEEcCCC----cEEEEEE
Confidence 3888999999875 999999999976663 2455543
No 34
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=33.01 E-value=60 Score=25.05 Aligned_cols=37 Identities=11% Similarity=0.051 Sum_probs=25.6
Q ss_pred cCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 195 QLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 195 qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
.--++.+-||-. .++.||+|.|. .+........|+++
T Consensus 38 r~kk~~aHDe~n---~~~~GD~V~I~-e~RPlSKtK~~~v~ 74 (84)
T CHL00142 38 KTKKYLVHDEEN---ECNIGDQVLIE-ETRPLSKTKRWILK 74 (84)
T ss_pred eeEEEEEeCCCC---CCCCCCEEEEE-EcCCCCCcEEEEEE
Confidence 344678888877 58999999996 33334466666664
No 35
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=31.65 E-value=1.4e+02 Score=24.67 Aligned_cols=79 Identities=19% Similarity=0.371 Sum_probs=38.5
Q ss_pred HHHHHHhcCCCcccC-----ccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHH
Q 026620 47 RTVLEMLKDRGYAVA-----LSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQI 121 (236)
Q Consensus 47 rTv~eMl~DRGY~v~-----~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~ 121 (236)
-++++++.+||.-++ =.+..++..|+.+.|.+ ||..++.+.|.+. ++.=+.|++.+
T Consensus 15 ~~~~~~~~~~g~g~s~~vs~Gn~~dv~~~d~l~~~~~---------------D~~t~~I~ly~E~----~~d~~~f~~~~ 75 (138)
T PF13607_consen 15 TAILDWAQDRGIGFSYVVSVGNEADVDFADLLEYLAE---------------DPDTRVIVLYLEG----IGDGRRFLEAA 75 (138)
T ss_dssp HHHHHHHHHTT-EESEEEE-TT-SSS-HHHHHHHHCT----------------SS--EEEEEES------S-HHHHHHHH
T ss_pred HHHHHHHHHcCCCeeEEEEeCccccCCHHHHHHHHhc---------------CCCCCEEEEEccC----CCCHHHHHHHH
Confidence 467888899988775 23456789999988744 5555566666652 22336666666
Q ss_pred hhcCCCcEEEEEEcCCCCHHHHHH
Q 026620 122 VNRDTLTGLILILQNQITSQATKA 145 (236)
Q Consensus 122 ~~~en~~~~IiV~q~~lt~~Ark~ 145 (236)
..-...+=|++++..-|+..+++
T Consensus 76 -~~a~~~KPVv~lk~Grt~~g~~a 98 (138)
T PF13607_consen 76 -RRAARRKPVVVLKAGRTEAGARA 98 (138)
T ss_dssp -HHHCCCS-EEEEE----------
T ss_pred -HHHhcCCCEEEEeCCCchhhhhh
Confidence 33332356777777766655443
No 36
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=31.30 E-value=57 Score=27.17 Aligned_cols=31 Identities=23% Similarity=0.363 Sum_probs=24.3
Q ss_pred ecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEec
Q 026620 176 VLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222 (236)
Q Consensus 176 ~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~ 222 (236)
.|+++|.+.+|+... + -.++++||.|+|+.-
T Consensus 76 ~l~~~Ei~~il~~~~-------------~---~~~~~~G~~V~I~~G 106 (153)
T PRK08559 76 EISFEEVEHFLKPKP-------------I---VEGIKEGDIVELIAG 106 (153)
T ss_pred CCCHHHHHHHHhccC-------------c---ccCCCCCCEEEEecc
Confidence 499999999995521 1 257999999999874
No 37
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=31.15 E-value=1.3e+02 Score=27.22 Aligned_cols=68 Identities=12% Similarity=0.154 Sum_probs=37.7
Q ss_pred cchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc-ceEeeeeeceeeeecccccccCceeecChH
Q 026620 109 VKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-FKVEMFQITDLLVNITKHVLKPKHQVLTDQ 180 (236)
Q Consensus 109 vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~-~~IEiF~e~eLl~nit~H~lVPkH~~Ls~e 180 (236)
+.+..+.++-..+ .+..++-+||-++..-.-.+...+.+.+ ..| ..-+-.-.++++|+-| +|+-|+.+
T Consensus 130 v~V~~~d~le~~v-~~~dv~iaiLtVPa~~AQ~vad~Lv~aGVkGI--lNFtPv~l~~pe~V~V-~~iDLt~e 198 (211)
T COG2344 130 VPVYDLDDLEKFV-KKNDVEIAILTVPAEHAQEVADRLVKAGVKGI--LNFTPVRLQVPEGVIV-ENIDLTAE 198 (211)
T ss_pred eeeechHHHHHHH-HhcCccEEEEEccHHHHHHHHHHHHHcCCceE--EeccceEecCCCCcEE-EEeehHHH
Confidence 4455667777777 7788999998886543222223333333 233 3333444456666544 55555553
No 38
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=31.08 E-value=1.9e+02 Score=23.30 Aligned_cols=56 Identities=18% Similarity=0.280 Sum_probs=35.4
Q ss_pred HHHHHHHhCC----CCCCCceEEEeecCCCCCCcEEEEecCC-CccchhhHHHHHHHHhhcCCCc
Q 026620 69 VQDFRAIYGQ----DPDVDRLRISISHQSDPSKRILVVFCGP-GIVKVNVIRSIISQIVNRDTLT 128 (236)
Q Consensus 69 l~eF~~~y~~----~~~r~~L~~~~~~~~~p~~~I~VfF~~~-~~vgvk~Ir~~~~~~~~~en~~ 128 (236)
+.+|.++|.- .|.-...-|++ -+...+-+-|-|++. +.+ .+.|+++++.. ...+++
T Consensus 45 lmdFIsryARTDEImPEDKTvGFvv--iN~dKK~mSvsFsdideNm-K~~i~ei~kky-kd~Gyk 105 (110)
T PF11513_consen 45 LMDFISRYARTDEIMPEDKTVGFVV--INKDKKMMSVSFSDIDENM-KNSIEEIVKKY-KDSGYK 105 (110)
T ss_dssp HHHHHHHH---S---TTSEEEEEEE--EETTTTEEEEEE-S--CCH-HHHHHHHHHHH-HCCS-E
T ss_pred HHHHHHHhhcccccCCCCceeEEEE--EecCCeEEEEEecchhHHH-HHHHHHHHHHh-hcCCce
Confidence 8999999953 24444555555 344556688999874 444 68899998888 666654
No 39
>KOG1232 consensus Proteins containing the FAD binding domain [Energy production and conversion]
Probab=31.00 E-value=33 Score=34.05 Aligned_cols=62 Identities=21% Similarity=0.366 Sum_probs=45.4
Q ss_pred cccccCCCCCCCC-----cccccccc------CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHH
Q 026620 11 MEMEGGNGYNGEP-----TESCLSGF------VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFR 73 (236)
Q Consensus 11 ~~~~~~~~~~~~~-----~~~c~~~~------m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~ 73 (236)
+|-.|.|+-+-++ +.+|+.+. +.++..+..++|+.|..+=+-|..-||. -..|+.+.+++|-
T Consensus 332 iETsGSn~dhD~eKl~afl~d~lek~lIsDGv~a~d~~~~~~lW~~Re~ip~a~~~~g~v-yKyDvSLpL~d~Y 404 (511)
T KOG1232|consen 332 IETSGSNKDHDEEKLTAFLEDCLEKGLISDGVLAQDEAEAQKLWKIRESIPEALQKAGGV-YKYDVSLPLEDLY 404 (511)
T ss_pred EEecCCCccccHHHHHHHHHHhhhhcccccceecCCHHHHHHHHHHHhccHHHHHhcCCE-EEeeccccHHHHH
Confidence 4555666655443 45676654 6677889999999999999999999954 4556777777764
No 40
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=30.21 E-value=30 Score=25.31 Aligned_cols=12 Identities=25% Similarity=0.540 Sum_probs=7.6
Q ss_pred hcCCCCCCEEEE
Q 026620 208 YYGLERGQVVKV 219 (236)
Q Consensus 208 y~g~~~GdVvkI 219 (236)
-.|++.||.|+|
T Consensus 51 ~~G~~~GD~V~I 62 (69)
T PF09269_consen 51 KAGAKEGDTVRI 62 (69)
T ss_dssp TTT--TT-EEEE
T ss_pred HcCCCCCCEEEE
Confidence 449999999998
No 41
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=30.17 E-value=21 Score=23.65 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=17.6
Q ss_pred ceeecChHHHHHHHhhhcCCcccC
Q 026620 173 KHQVLTDQEKEKLLKKYSIEEKQL 196 (236)
Q Consensus 173 kH~~Ls~eEk~~ll~~y~i~~~qL 196 (236)
.|+--|++||++|.+.-+++..|+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi 30 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQI 30 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHH
Confidence 466779999999999999887764
No 42
>KOG0975 consensus Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism]
Probab=29.69 E-value=29 Score=33.77 Aligned_cols=67 Identities=16% Similarity=0.359 Sum_probs=44.4
Q ss_pred CCCCcccccccCCCCCCCCccccccccCCCCchhhHH--HH------HHHHHHHHHhcCCC-cccCccccccCHHHHHH
Q 026620 5 NGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLR--YY------LSRRTVLEMLKDRG-YAVALSEINLSVQDFRA 74 (236)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~c~~~~m~~~~~e~~r--l~------r~rrTv~eMl~DRG-Y~v~~~el~~sl~eF~~ 74 (236)
.||..-+-.-|-++ +..++..|---|+-....|+.- += -.|++++|+.+|+| |.|.+.. +|.+||.+
T Consensus 241 ~G~~dvLwL~~d~~-~ItEv~tmNiF~v~~n~~elvTPp~dg~ILpGvTR~sileLa~~~g~~~V~Er~--vtv~e~~~ 316 (379)
T KOG0975|consen 241 KGASDVLWLDGDGG-YITEVGTMNIFMVKKNEDELVTPPLDGTILPGVTRKSILELARDLGEFKVEERD--VTVDELKT 316 (379)
T ss_pred cCcceeEEEecCCC-ceeeccceeEEEEEcCceeEecCCCCCcccCCccHHHHHHHHHHhCceEEEEEE--EeHHHhhh
Confidence 46666666666677 7788877766554433222211 11 25899999999999 9998754 56778864
No 43
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=29.47 E-value=34 Score=27.38 Aligned_cols=16 Identities=31% Similarity=0.370 Sum_probs=14.3
Q ss_pred hcCCCCCCEEEEEecC
Q 026620 208 YYGLERGQVVKVTYSG 223 (236)
Q Consensus 208 y~g~~~GdVvkI~R~s 223 (236)
..|.++|+.|||-|+.
T Consensus 37 ~ig~~RGskVrIlR~E 52 (101)
T PLN00045 37 PIGPKRGSKVKILRPE 52 (101)
T ss_pred CcccCCCCEEEEcccc
Confidence 4699999999999985
No 44
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=29.03 E-value=86 Score=26.05 Aligned_cols=35 Identities=26% Similarity=0.387 Sum_probs=27.2
Q ss_pred CccccCCchhhh-cCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 197 PRMLKKDAIAQY-YGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 197 P~I~~~DPvary-~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
=+|+..-|+.+. +|.+.||.|.+..++. ...|+++
T Consensus 118 ~~IS~~SPlG~aLlGk~~Gd~v~~~~p~g----~~~~~I~ 153 (157)
T PRK00226 118 GKISIESPIARALIGKKVGDTVEVTTPGG----EYEYEIL 153 (157)
T ss_pred CeeccCChHHHHHhCCCCCCEEEEEcCCC----cEEEEEE
Confidence 378999999986 4999999999987763 3455543
No 45
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=28.95 E-value=3.1e+02 Score=23.43 Aligned_cols=77 Identities=12% Similarity=0.198 Sum_probs=47.5
Q ss_pred HHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCC
Q 026620 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDT 126 (236)
Q Consensus 47 rTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~en 126 (236)
+-+-.+|+..||.|..--.+.+.++|.+.-... +| +-|.+.+.. .-....++.+++.+ .+.+
T Consensus 100 ~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~--------------~~-d~v~lS~~~--~~~~~~~~~~i~~l-r~~~ 161 (201)
T cd02070 100 NLVATMLEANGFEVIDLGRDVPPEEFVEAVKEH--------------KP-DILGLSALM--TTTMGGMKEVIEAL-KEAG 161 (201)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc--------------CC-CEEEEeccc--cccHHHHHHHHHHH-HHCC
Confidence 334568899999998766778899998764211 11 112222222 23456789999998 6666
Q ss_pred C--cEEEEEEcCCCCHH
Q 026620 127 L--TGLILILQNQITSQ 141 (236)
Q Consensus 127 ~--~~~IiV~q~~lt~~ 141 (236)
. +-.|+|-...+++.
T Consensus 162 ~~~~~~i~vGG~~~~~~ 178 (201)
T cd02070 162 LRDKVKVMVGGAPVNQE 178 (201)
T ss_pred CCcCCeEEEECCcCCHH
Confidence 5 44466655556654
No 46
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=28.55 E-value=2.9e+02 Score=22.89 Aligned_cols=53 Identities=19% Similarity=0.117 Sum_probs=29.9
Q ss_pred HHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHH
Q 026620 51 EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQI 121 (236)
Q Consensus 51 eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~ 121 (236)
.=|++|||.|... . .|. .+ +... ..+...-+.........+....|-.+....
T Consensus 42 kDLR~RGyvVk~G-~-----kfg----------~~-~~~~-~~~~s~ylV~Vl~E~~~is~~eL~~~vr~a 94 (124)
T PRK09539 42 VDLKQRGRKTIDG-I-----DEI----------SL-IIKD-KENKYTAMVLIVDENEKVSFKKILDKLHFS 94 (124)
T ss_pred hhHHhCCCeeccC-C-----cee----------EE-EEec-CCCCceEEEEEecCCCccCHHHHHHHHHHH
Confidence 3489999999774 1 221 11 1111 123333333334556889988898877665
No 47
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=28.47 E-value=76 Score=27.49 Aligned_cols=56 Identities=23% Similarity=0.163 Sum_probs=36.0
Q ss_pred eceeeeeccccc--ccCce----eecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEec
Q 026620 158 ITDLLVNITKHV--LKPKH----QVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222 (236)
Q Consensus 158 e~eLl~nit~H~--lVPkH----~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~ 222 (236)
+.-.++.=|.|+ +|.-+ ..++++|...+|....-. .+|..--.++++||.|+|+..
T Consensus 74 ~~w~~Vr~tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~---------~~~~~~~~~~e~Gd~VrI~~G 135 (178)
T COG0250 74 EAWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEE---------VAPKKPKVDFEPGDVVRIIDG 135 (178)
T ss_pred ceEEEEecCCCcEEEeccCCCCCcccCHHHHHHHHhhcccc---------ccCCcccccCCCCCEEEEecc
Confidence 334445545554 34433 789999999877765433 333344458999999999853
No 48
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.32 E-value=38 Score=24.26 Aligned_cols=36 Identities=25% Similarity=0.463 Sum_probs=26.5
Q ss_pred ecChHHHHHHHhhhcCCc--ccCCccccCCchhhhcCCCCCC
Q 026620 176 VLTDQEKEKLLKKYSIEE--KQLPRMLKKDAIAQYYGLERGQ 215 (236)
Q Consensus 176 ~Ls~eEk~~ll~~y~i~~--~qLP~I~~~DPvary~g~~~Gd 215 (236)
.||+|-|+.|-+-+++.. .+-=. =|.+-|+|++.|-
T Consensus 2 klS~esKerl~k~~~is~~vih~G~----IP~VlyLG~a~~a 39 (53)
T KOG4449|consen 2 KLSEESKERLVKVFNISKFVIHYGW----IPLVLYLGFAFGA 39 (53)
T ss_pred ccCHHHHHHHHHHeechheeeeech----hhHHHHhhhhhcC
Confidence 589999998888777642 23333 3899999998873
No 49
>PRK03298 hypothetical protein; Provisional
Probab=27.97 E-value=97 Score=28.22 Aligned_cols=51 Identities=14% Similarity=0.032 Sum_probs=35.8
Q ss_pred EEEEecCC-CccchhhHHHHHHHHhhcC--CCcEEEEEEcCCCCHHHHHHhhhcc
Q 026620 99 ILVVFCGP-GIVKVNVIRSIISQIVNRD--TLTGLILILQNQITSQATKAVGLFQ 150 (236)
Q Consensus 99 I~VfF~~~-~~vgvk~Ir~~~~~~~~~e--n~~~~IiV~q~~lt~~Ark~l~~~~ 150 (236)
++|...-. ..=++.++..|++.++.+. .--|||+|.| .+|++|+..+.+-+
T Consensus 149 V~vEvKRr~~idaV~QL~RYve~l~rd~~~~~VRGIlvAp-~It~~Ar~Ll~drG 202 (224)
T PRK03298 149 VAVEIKRRGEIDGVEQLTRYLELLNRDPLLAPVRGVFAAQ-EIKPQARTLAEDRG 202 (224)
T ss_pred EEEEEEecCCccHHHHHHHHHHHHhhCcCcCCceEEEECC-cCCHHHHHHHHHcC
Confidence 55555332 2237789999999984331 2368999986 59999999988766
No 50
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=27.92 E-value=90 Score=24.92 Aligned_cols=28 Identities=29% Similarity=0.440 Sum_probs=20.0
Q ss_pred hcCCCCCCEEEEEecCC--------CCcceeEEEEe
Q 026620 208 YYGLERGQVVKVTYSGE--------ITESHVTYRCV 235 (236)
Q Consensus 208 y~g~~~GdVvkI~R~s~--------tag~~v~YR~V 235 (236)
.+|+-.||+|++..... .+|...|+|++
T Consensus 23 a~glA~gDvV~~~~~~g~~~~~~~v~~sGnsTiRv~ 58 (117)
T PF14085_consen 23 AYGLALGDVVRAEPDDGELWFQKVVESSGNSTIRVI 58 (117)
T ss_pred cCCCCCCCEEEEEeCCCeEEEEEEEecCCCEEEEEE
Confidence 35999999999999872 22445566665
No 51
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=27.37 E-value=2.4e+02 Score=24.78 Aligned_cols=78 Identities=15% Similarity=0.153 Sum_probs=51.6
Q ss_pred HHHHHHhcCCCcccCccccccCHHHHHHHhCC-CCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 026620 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ-DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (236)
Q Consensus 47 rTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~-~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~e 125 (236)
+-+--||+.+||.|..--.+.+.++|.+...+ +|+ - +.+.+. ..-.+..++++++++ .+.
T Consensus 106 ~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~~~~--~--------------V~lS~~--~~~~~~~~~~~i~~L-~~~ 166 (213)
T cd02069 106 NLVGVILSNNGYEVIDLGVMVPIEKILEAAKEHKAD--I--------------IGLSGL--LVPSLDEMVEVAEEM-NRR 166 (213)
T ss_pred HHHHHHHHhCCCEEEECCCCCCHHHHHHHHHHcCCC--E--------------EEEccc--hhccHHHHHHHHHHH-Hhc
Confidence 44567899999999998888999999877522 122 1 222222 234567789999999 667
Q ss_pred CCcEEEEEEcCCCCHHHH
Q 026620 126 TLTGLILILQNQITSQAT 143 (236)
Q Consensus 126 n~~~~IiV~q~~lt~~Ar 143 (236)
+.+--|+|-...+|....
T Consensus 167 ~~~~~i~vGG~~~~~~~~ 184 (213)
T cd02069 167 GIKIPLLIGGAATSRKHT 184 (213)
T ss_pred CCCCeEEEEChhcCHHHH
Confidence 775556666556665443
No 52
>cd06573 PASTA PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=27.20 E-value=1.1e+02 Score=19.30 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=16.5
Q ss_pred cCceeecChHHHHHHHhhhcCC
Q 026620 171 KPKHQVLTDQEKEKLLKKYSIE 192 (236)
Q Consensus 171 VPkH~~Ls~eEk~~ll~~y~i~ 192 (236)
+|.-.-++.+|.++.|+. .+.
T Consensus 2 ~p~~~g~~~~~a~~~l~~-g~~ 22 (53)
T cd06573 2 VPDLVGISKKDLEEQLYD-LLK 22 (53)
T ss_pred CCcccCCcHHHHHHHHHc-CCc
Confidence 566677899999999987 554
No 53
>TIGR01118 lacA galactose-6-phosphate isomerase, LacA subunit. This family contains members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway.
Probab=27.04 E-value=1.6e+02 Score=24.76 Aligned_cols=20 Identities=20% Similarity=0.287 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhcCCCcccCc
Q 026620 43 YLSRRTVLEMLKDRGYAVAL 62 (236)
Q Consensus 43 ~r~rrTv~eMl~DRGY~v~~ 62 (236)
|..+..+.+.|.++||.|.+
T Consensus 12 ~~lK~~i~~~L~~~G~eV~D 31 (141)
T TIGR01118 12 KRLKDVIKNFLVDNGFEVID 31 (141)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 56678899999999999976
No 54
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=26.80 E-value=3e+02 Score=23.65 Aligned_cols=77 Identities=13% Similarity=0.120 Sum_probs=49.2
Q ss_pred HHHHHHhcCCCcccCccccccCHHHHHHHhCC-CCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 026620 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ-DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (236)
Q Consensus 47 rTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~-~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~Ir~~~~~~~~~e 125 (236)
+-+..|++..||.|..--.+.+.++|.+.-.. .|+ -+.+++ .. .-.+..++++++.+ .+.
T Consensus 102 ~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~~pd--~v~lS~--------------~~--~~~~~~~~~~i~~l-~~~ 162 (197)
T TIGR02370 102 NIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKPL--MLTGSA--------------LM--TTTMYGQKDINDKL-KEE 162 (197)
T ss_pred HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCC--EEEEcc--------------cc--ccCHHHHHHHHHHH-HHc
Confidence 45567999999999988888999999876522 222 122222 11 22345678888888 666
Q ss_pred CCc--EEEEEEcCCCCHHH
Q 026620 126 TLT--GLILILQNQITSQA 142 (236)
Q Consensus 126 n~~--~~IiV~q~~lt~~A 142 (236)
+.. -.|+|-...+++..
T Consensus 163 ~~~~~v~i~vGG~~~~~~~ 181 (197)
T TIGR02370 163 GYRDSVKFMVGGAPVTQDW 181 (197)
T ss_pred CCCCCCEEEEEChhcCHHH
Confidence 554 34666655666643
No 55
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=26.63 E-value=91 Score=23.35 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=19.1
Q ss_pred CccccCCchhhhcCCCCCCEEEEEecC
Q 026620 197 PRMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 197 P~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
|.|...-=-|+-+|++-||.|+|.-+.
T Consensus 30 ~~v~inp~dA~~~Gi~~Gd~V~v~s~~ 56 (110)
T PF01568_consen 30 PFVEINPEDAAKLGIKDGDWVRVSSPR 56 (110)
T ss_dssp EEEEEEHHHHHHCT--TTCEEEEEETT
T ss_pred CEEEEcHHHHHHhcCcCCCEEEEEecc
Confidence 455555556788899999999998765
No 56
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=26.43 E-value=85 Score=26.97 Aligned_cols=28 Identities=18% Similarity=0.321 Sum_probs=20.8
Q ss_pred hhhhcCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 205 IAQYYGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 205 vary~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
....-.+++||.|.+++.+ |.+..||+.
T Consensus 103 F~~L~~L~~GD~I~v~~~~---g~~~~Y~V~ 130 (174)
T TIGR03784 103 FAFLQELRPGDVIRLQTPD---GQWQSYQVT 130 (174)
T ss_pred CCChhhCCCCCEEEEEECC---CeEEEEEEe
Confidence 4444578999999999876 556778763
No 57
>PRK06437 hypothetical protein; Provisional
Probab=25.78 E-value=60 Score=23.43 Aligned_cols=41 Identities=7% Similarity=0.195 Sum_probs=32.0
Q ss_pred HHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEec
Q 026620 182 KEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222 (236)
Q Consensus 182 k~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~ 222 (236)
..+||+++++++..+--.....++..-.-++.||-|.|.+.
T Consensus 23 v~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Veiv~~ 63 (67)
T PRK06437 23 VNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLILEV 63 (67)
T ss_pred HHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEEEec
Confidence 56689999988777755566666667778899999999875
No 58
>PRK08621 galactose-6-phosphate isomerase subunit LacA; Reviewed
Probab=25.73 E-value=1.8e+02 Score=24.53 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhcCCCcccCc
Q 026620 43 YLSRRTVLEMLKDRGYAVAL 62 (236)
Q Consensus 43 ~r~rrTv~eMl~DRGY~v~~ 62 (236)
|-.+..+.+.|++.||.|.+
T Consensus 12 ~~lK~~l~~~L~~~G~eV~D 31 (142)
T PRK08621 12 FELKEVVKDYLEDNKYEVVD 31 (142)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55678899999999999975
No 59
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=25.54 E-value=53 Score=23.19 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=15.8
Q ss_pred hcCCCCCCEEEEEecCCCCcc
Q 026620 208 YYGLERGQVVKVTYSGEITES 228 (236)
Q Consensus 208 y~g~~~GdVvkI~R~s~tag~ 228 (236)
-+|+.||.-|+|.+..+..|.
T Consensus 30 ~lGl~~G~~i~v~~~~~~~~~ 50 (74)
T PF04023_consen 30 DLGLTPGSEITVIRKNPFGGP 50 (74)
T ss_dssp HCT-STTEEEEEEEEETTSSE
T ss_pred HCCCCCCCEEEEEEeCCCCCC
Confidence 469999999999987655444
No 60
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=25.44 E-value=1.1e+02 Score=25.76 Aligned_cols=35 Identities=11% Similarity=0.156 Sum_probs=26.7
Q ss_pred CCccccCCchhhhc-CCCCCCEEEEEecCCCCcceeEEEE
Q 026620 196 LPRMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRC 234 (236)
Q Consensus 196 LP~I~~~DPvary~-g~~~GdVvkI~R~s~tag~~v~YR~ 234 (236)
-=+|+..-|+++.| |.+.||.|.+.=+ |....|.+
T Consensus 110 ~~~IS~~SPig~aLlGk~vGd~v~v~~p----~g~~~~~I 145 (151)
T COG0782 110 KGKISVDSPLGRALLGKKVGDTVEVNTP----GGEKEVEI 145 (151)
T ss_pred cCceeccCHHHHHHhCCCCCCEEEEecC----CceEEEEE
Confidence 45899999999975 9999999999755 34444544
No 61
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=25.29 E-value=72 Score=21.16 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=16.6
Q ss_pred chhhhcCCCCCCEEEEEecC
Q 026620 204 AIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 204 Pvary~g~~~GdVvkI~R~s 223 (236)
.+++.+|+++||.|.|.-..
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEET
T ss_pred HHHHHcCCCCCCEEEEEEeC
Confidence 46677899999999998765
No 62
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=25.25 E-value=52 Score=23.38 Aligned_cols=19 Identities=21% Similarity=0.485 Sum_probs=14.0
Q ss_pred cccCCchhhhcCCCCCCEEE
Q 026620 199 MLKKDAIAQYYGLERGQVVK 218 (236)
Q Consensus 199 I~~~DPvary~g~~~GdVvk 218 (236)
|....|.++. |+++||+|-
T Consensus 20 v~~~s~a~~~-gl~~GD~I~ 38 (85)
T cd00988 20 VLPGSPAAKA-GIKAGDIIV 38 (85)
T ss_pred ecCCCCHHHc-CCCCCCEEE
Confidence 4455676665 999999984
No 63
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=25.05 E-value=32 Score=29.75 Aligned_cols=15 Identities=40% Similarity=0.840 Sum_probs=12.3
Q ss_pred HHHHHhcCCCcccCc
Q 026620 48 TVLEMLKDRGYAVAL 62 (236)
Q Consensus 48 Tv~eMl~DRGY~v~~ 62 (236)
-++++|++|||.|..
T Consensus 244 gvl~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 244 GVLDLLRKKGYTVEP 258 (259)
T ss_pred hHHHHHHhCCceeec
Confidence 478999999998863
No 64
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=24.66 E-value=95 Score=22.62 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=23.0
Q ss_pred CccccCCchhhhcCCCCCCEEEEEecC
Q 026620 197 PRMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 197 P~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
|.+..+..-|+.+|++.||.|.|...-
T Consensus 23 ~~v~~~~~da~~lgl~~Gd~v~v~~~~ 49 (101)
T cd02775 23 PVVEINPEDAAALGIKDGDLVRVESRR 49 (101)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 677778888999999999999988665
No 65
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=24.64 E-value=1.9e+02 Score=26.83 Aligned_cols=94 Identities=15% Similarity=0.169 Sum_probs=53.0
Q ss_pred EEEEecCCCccchhhHHHHHHHHhh---cCCCcEEEEEEc-CCCCHHHHHHhhh-c---cceEeeeeece----eeeecc
Q 026620 99 ILVVFCGPGIVKVNVIRSIISQIVN---RDTLTGLILILQ-NQITSQATKAVGL-F---QFKVEMFQITD----LLVNIT 166 (236)
Q Consensus 99 I~VfF~~~~~vgvk~Ir~~~~~~~~---~en~~~~IiV~q-~~lt~~Ark~l~~-~---~~~IEiF~e~e----Ll~nit 166 (236)
+..+.++...+++..||++++.+ . ..+-.+.+||-. +.+|..|..++.. + +..+-++..++ |+-=|-
T Consensus 80 ~~~i~~~~~~i~id~ir~l~~~~-~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIr 158 (329)
T PRK08058 80 VHLVAPDGQSIKKDQIRYLKEEF-SKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTIL 158 (329)
T ss_pred EEEeccccccCCHHHHHHHHHHH-hhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHH
Confidence 33344556779999999999887 4 344456777755 4678766554432 2 22222222221 111122
Q ss_pred cccccCceeecChHHHHHHHhhhcCCc
Q 026620 167 KHVLKPKHQVLTDQEKEKLLKKYSIEE 193 (236)
Q Consensus 167 ~H~lVPkH~~Ls~eEk~~ll~~y~i~~ 193 (236)
+--.+=....+++++..+.|++.++.+
T Consensus 159 SRc~~i~~~~~~~~~~~~~L~~~gi~~ 185 (329)
T PRK08058 159 SRCQVVEFRPLPPESLIQRLQEEGISE 185 (329)
T ss_pred hhceeeeCCCCCHHHHHHHHHHcCCCh
Confidence 333333445678888888887765543
No 66
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=24.53 E-value=41 Score=24.90 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=17.2
Q ss_pred ccCCchhhhcCCCCCCEEEE-Eec
Q 026620 200 LKKDAIAQYYGLERGQVVKV-TYS 222 (236)
Q Consensus 200 ~~~DPvary~g~~~GdVvkI-~R~ 222 (236)
..+=...|-|||++||+|.= +|+
T Consensus 30 yVs~~~Irr~~LR~GD~V~G~vr~ 53 (68)
T cd04459 30 YVSPSQIRRFNLRTGDTVVGQIRP 53 (68)
T ss_pred EECHHHHHHhCCCCCCEEEEEEeC
Confidence 33445788999999999986 454
No 67
>PRK05571 ribose-5-phosphate isomerase B; Provisional
Probab=23.32 E-value=2.1e+02 Score=24.15 Aligned_cols=20 Identities=20% Similarity=0.336 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhcCCCcccCc
Q 026620 43 YLSRRTVLEMLKDRGYAVAL 62 (236)
Q Consensus 43 ~r~rrTv~eMl~DRGY~v~~ 62 (236)
|-.+..+.++|++.||.|.+
T Consensus 12 ~~lK~~l~~~L~~~g~eV~D 31 (148)
T PRK05571 12 FELKEEIIEHLEELGHEVID 31 (148)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55677889999999999975
No 68
>PRK06033 hypothetical protein; Validated
Probab=23.14 E-value=57 Score=24.82 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=16.3
Q ss_pred chhhhcCCCCCCEEEEEec
Q 026620 204 AIAQYYGLERGQVVKVTYS 222 (236)
Q Consensus 204 Pvary~g~~~GdVvkI~R~ 222 (236)
|+...++|++||||.+.++
T Consensus 21 ~l~dlL~L~~GDVI~L~~~ 39 (83)
T PRK06033 21 PIHQVLRMGRGAVIPLDAT 39 (83)
T ss_pred cHHHHhCCCCCCEEEeCCC
Confidence 5778899999999999664
No 69
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=23.14 E-value=59 Score=23.95 Aligned_cols=19 Identities=16% Similarity=0.342 Sum_probs=16.3
Q ss_pred chhhhcCCCCCCEEEEEec
Q 026620 204 AIAQYYGLERGQVVKVTYS 222 (236)
Q Consensus 204 Pvary~g~~~GdVvkI~R~ 222 (236)
|+...++|++|||+.+.++
T Consensus 22 tl~ell~L~~Gdvi~L~~~ 40 (77)
T TIGR02480 22 TLGDLLKLGEGSVIELDKL 40 (77)
T ss_pred EHHHHhcCCCCCEEEcCCC
Confidence 6778899999999999754
No 70
>PF01939 DUF91: Protein of unknown function DUF91; InterPro: IPR002793 The function of these prokaryotic proteins is unknown. Computational analysis suggests that they may form a restriction endonuclease-like fold, similar to that found in a variety of endonucleases and DNA repair enzymes [].; PDB: 2VLD_A.
Probab=22.88 E-value=1.3e+02 Score=27.33 Aligned_cols=58 Identities=14% Similarity=0.107 Sum_probs=33.5
Q ss_pred cEEEEecCC--CccchhhHHHHHHHHhhcCC--CcEEEEEEcCCCCHHHHHHhhhccceEeeeee
Q 026620 98 RILVVFCGP--GIVKVNVIRSIISQIVNRDT--LTGLILILQNQITSQATKAVGLFQFKVEMFQI 158 (236)
Q Consensus 98 ~I~VfF~~~--~~vgvk~Ir~~~~~~~~~en--~~~~IiV~q~~lt~~Ark~l~~~~~~IEiF~e 158 (236)
-+.|...-. ..=.+.++..|.+.+..+.+ --|+|||.++ +|+.|+..+.+.+ +|+...
T Consensus 149 ~VVIElKR~~a~~~aV~QL~rY~~~l~~~~~~~~VRGilvA~~-i~~~a~~ll~~~g--lef~~l 210 (228)
T PF01939_consen 149 LVVIELKRRRADRDAVEQLLRYVELLKRDPGLEPVRGILVAPS-ITPQARELLEDRG--LEFVEL 210 (228)
T ss_dssp EEEEEE-SS-B-HHHHHHHHHHHHHHHHHH--S-EEEEEEES--B-HHHHHHHHHHT---EEEE-
T ss_pred EEEEEEEeccCCHHHHHHHHHHHHHHhhccCCCceeEEEECCC-CCHHHHHHHHHcC--CEEEEe
Confidence 466666543 22334667777777732222 3489999976 9999999988766 555443
No 71
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=22.42 E-value=1.3e+02 Score=23.20 Aligned_cols=37 Identities=16% Similarity=0.196 Sum_probs=24.3
Q ss_pred cCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEe
Q 026620 195 QLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCV 235 (236)
Q Consensus 195 qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V 235 (236)
.--++.+-||-. -++.||+|+|.-- ........|+++
T Consensus 41 r~kk~~aHD~~n---~~k~GD~V~I~e~-rPlSK~K~~~v~ 77 (84)
T PRK05610 41 RSKKYHAHDENN---EAKIGDVVRIMET-RPLSKTKRWRLV 77 (84)
T ss_pred cceEEEEECCCC---CCCCCCEEEEEEc-ccCCCCEEEEEE
Confidence 345788999965 5999999999532 222255555543
No 72
>COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]
Probab=22.23 E-value=84 Score=32.93 Aligned_cols=65 Identities=25% Similarity=0.244 Sum_probs=42.3
Q ss_pred cccccCCCCCCCCccccccccCCCC--chhhHHHHHHHHHHHHHhcCCCccc-C--ccccccCHHHHHHHhCCC
Q 026620 11 MEMEGGNGYNGEPTESCLSGFVDNG--SRDSLRYYLSRRTVLEMLKDRGYAV-A--LSEINLSVQDFRAIYGQD 79 (236)
Q Consensus 11 ~~~~~~~~~~~~~~~~c~~~~m~~~--~~e~~rl~r~rrTv~eMl~DRGY~v-~--~~el~~sl~eF~~~y~~~ 79 (236)
.|+||++ .+++.|.+.-.|-- ..++..++..|+.++|||-...=.. . +.-=+=.|+++.-.||-.
T Consensus 50 VEveg~~----k~~~SC~tpv~dGM~I~T~s~~vk~~R~~vmE~LLiNHPlDCpiCD~gGeCeLQD~a~~~G~~ 119 (693)
T COG1034 50 VEVEGAP----KLVASCATPVTDGMVISTNSEEVKKAREGVMEFLLINHPLDCPVCDKGGECELQDLAVKYGVS 119 (693)
T ss_pred EEecCCC----ccccccccccCCCeEEecCCHHHHHHHHHHHHHHHhcCCCCCCccCCCCCchhHHHHHHhCCC
Confidence 5788876 89999999754411 3456789999999999985322111 1 111123478888888744
No 73
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=22.20 E-value=44 Score=22.63 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=9.7
Q ss_pred cCCCCCCEEEEE
Q 026620 209 YGLERGQVVKVT 220 (236)
Q Consensus 209 ~g~~~GdVvkI~ 220 (236)
|.+++||+|.|+
T Consensus 16 Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 16 LSFKKGDVIEVL 27 (55)
T ss_dssp -EB-TTEEEEEE
T ss_pred eEEecCCEEEEE
Confidence 889999999999
No 74
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.14 E-value=1.3e+02 Score=22.85 Aligned_cols=27 Identities=30% Similarity=0.350 Sum_probs=19.2
Q ss_pred CccccCCchhhhcCCCCCCEEEEEecC
Q 026620 197 PRMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 197 P~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
|-+..+-=-|.-+|++.||.|+|..+.
T Consensus 31 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 31 PTLLIHPADAAARGIADGDLVVVFNDR 57 (116)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 444444445777899999999997655
No 75
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.72 E-value=1.2e+02 Score=22.23 Aligned_cols=23 Identities=26% Similarity=0.293 Sum_probs=16.7
Q ss_pred CCCCCEEEEE--ecCCCCcceeEEEE
Q 026620 211 LERGQVVKVT--YSGEITESHVTYRC 234 (236)
Q Consensus 211 ~~~GdVvkI~--R~s~tag~~v~YR~ 234 (236)
..+||.|.+. -.+.+-| .+.||+
T Consensus 47 i~vGD~V~ve~~~~~~~~g-~Iv~r~ 71 (72)
T PRK00276 47 ILPGDKVTVELSPYDLTKG-RITYRH 71 (72)
T ss_pred cCCCCEEEEEEcccCCCeE-EEEEEe
Confidence 4789999998 4444444 788885
No 76
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=21.72 E-value=77 Score=22.80 Aligned_cols=52 Identities=12% Similarity=0.215 Sum_probs=30.8
Q ss_pred cccccCCCCCCCCccccccccCCCCchhhHHHHHHHHHHHHHhcCCCcccCcc
Q 026620 11 MEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALS 63 (236)
Q Consensus 11 ~~~~~~~~~~~~~~~~c~~~~m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~ 63 (236)
...+|..-+.-..+..-...... .......|..+.+.+-+.++++||..+.-
T Consensus 6 i~~~G~~~~~~~~l~~~~~~~~g-~~l~~~~l~~~~~~l~~~y~~~GY~~s~v 57 (76)
T PF08479_consen 6 IRFEGNTLLPEEELQAILAPYIG-RCLTLADLQQLADALTNYYREKGYITSRV 57 (76)
T ss_dssp EEEES-TSSSCCHHHHHHGGGTT-SBB-HHHHHHHHHHHHHHHHHTT-TT-EE
T ss_pred EEEECCCcCCHHHHHHHHHHhcC-CCcCHHHHHHHHHHHHHHHHHcCceEEEE
Confidence 44555554555444444343332 12335778899999999999999998753
No 77
>cd01900 YchF YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
Probab=21.58 E-value=42 Score=30.83 Aligned_cols=24 Identities=29% Similarity=0.616 Sum_probs=21.4
Q ss_pred cChHHHHHHHhhhcCCcccCCccc
Q 026620 177 LTDQEKEKLLKKYSIEEKQLPRML 200 (236)
Q Consensus 177 Ls~eEk~~ll~~y~i~~~qLP~I~ 200 (236)
|+++|++++|+.|++++..||||-
T Consensus 244 l~~ee~~~fl~~~gi~es~l~riI 267 (274)
T cd01900 244 LDEEEAAEFLEELGLEESGLDRLI 267 (274)
T ss_pred CCHHHHHHHHHHcCCccccHHHHH
Confidence 578999999999999998998874
No 78
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=21.58 E-value=56 Score=24.76 Aligned_cols=32 Identities=19% Similarity=0.337 Sum_probs=22.2
Q ss_pred hcCCcccCCccccCCchhhhcCCCCCCEEEEE
Q 026620 189 YSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220 (236)
Q Consensus 189 y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~ 220 (236)
|+++.++==.++.--.-.+-+||+|||-.+|.
T Consensus 31 yr~~Vq~NGnLLIG~AYT~~m~L~PGdEFeI~ 62 (71)
T PF14250_consen 31 YRVSVQGNGNLLIGSAYTKQMGLKPGDEFEIK 62 (71)
T ss_pred EEEEEecCCCEEEcHHHHHHhCCCCCCEEEEE
Confidence 34444444455555666788999999999985
No 79
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=21.52 E-value=53 Score=23.70 Aligned_cols=19 Identities=16% Similarity=0.399 Sum_probs=14.1
Q ss_pred chhhhcCCCCCCEEEEEec
Q 026620 204 AIAQYYGLERGQVVKVTYS 222 (236)
Q Consensus 204 Pvary~g~~~GdVvkI~R~ 222 (236)
|+...+.|++|||+.+..+
T Consensus 22 ~l~el~~L~~Gdvi~l~~~ 40 (77)
T PF01052_consen 22 TLGELLNLKVGDVIPLDKP 40 (77)
T ss_dssp EHHHHHC--TT-EEEECCE
T ss_pred EHHHHhcCCCCCEEEeCCC
Confidence 6778899999999999887
No 80
>PRK03972 ribosomal biogenesis protein; Validated
Probab=21.29 E-value=4.8e+02 Score=23.41 Aligned_cols=121 Identities=11% Similarity=0.041 Sum_probs=74.1
Q ss_pred chhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc----ceEeeeee------cee----eeecccccccCcee
Q 026620 110 KVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ----FKVEMFQI------TDL----LVNITKHVLKPKHQ 175 (236)
Q Consensus 110 gvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~----~~IEiF~e------~eL----l~nit~H~lVPkH~ 175 (236)
|...++++++.+ .+.++..+|+|...+=.|..- .+-.+. .-.-.|.. .|+ .-.+++| .| |.
T Consensus 34 Gk~~lkel~~~A-~~~g~TdLIVV~E~rg~P~~L-~i~hLP~gP~GPTa~FkLsnV~l~~ei~~~~~~~~s~~--~p-~i 108 (208)
T PRK03972 34 GKKTIQDLLMEA-YDRGYERLLIINVWKGNPLKM-TFIKVGPEDWGYLGYLYLHGIKLQREMGFRNLRPIRED--MP-LV 108 (208)
T ss_pred CCccHHHHHHHH-HHCCCCeEEEEecCCCcCCeE-EEEcCCCCCCCceEEEEEccEEEHHHcccCCCCCcccc--cc-EE
Confidence 345688888888 888999999888765444321 111111 00112332 232 1223333 22 23
Q ss_pred ecC--------hHHHHHHHhhhcC-----CcccCCcc---ccCCchhhhcCCCCCCEEEEEe----cCCCCcceeEEEEe
Q 026620 176 VLT--------DQEKEKLLKKYSI-----EEKQLPRM---LKKDAIAQYYGLERGQVVKVTY----SGEITESHVTYRCV 235 (236)
Q Consensus 176 ~Ls--------~eEk~~ll~~y~i-----~~~qLP~I---~~~DPvary~g~~~GdVvkI~R----~s~tag~~v~YR~V 235 (236)
+.| .+.++++-+.+++ +...+..| ...|.+....|-.+|--|-.-| +.+..|..++||+-
T Consensus 109 Itts~kt~~g~~~~Ak~lA~eLgi~yV~R~k~Sl~~L~~~~~~d~vLVV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (208)
T PRK03972 109 ITTAKRVGLDHMAFAQVFAELTGGKFVPRGGKSLQDIADKYNTDVLGVIERHPRGMAVNFYRLDVTKERPVGPLIFVKIW 188 (208)
T ss_pred EEcCCCCCHHHHHHHHHHHHHhCCceeCcCCcCHHHHHhhhcCceEEEEecCCCceEEEEEEeccccccccCCcEEEEEE
Confidence 321 2567788888887 23455666 3457887778888898888888 78889999999863
No 81
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.91 E-value=1.4e+02 Score=22.44 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=19.7
Q ss_pred CccccCCchhhhcCCCCCCEEEEEecC
Q 026620 197 PRMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 197 P~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
|.+..+---|+-+|++.||.|+|....
T Consensus 35 ~~v~in~~dA~~lgi~~Gd~V~v~~~~ 61 (116)
T cd02790 35 EYVEINPEDAKRLGIEDGEKVRVSSRR 61 (116)
T ss_pred cEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 444444445778899999999998664
No 82
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=20.89 E-value=72 Score=22.21 Aligned_cols=16 Identities=25% Similarity=0.262 Sum_probs=11.8
Q ss_pred hhhhcCCCCCCEEEEE
Q 026620 205 IAQYYGLERGQVVKVT 220 (236)
Q Consensus 205 vary~g~~~GdVvkI~ 220 (236)
.|...|+++||+|-=+
T Consensus 24 ~a~~~gl~~GD~I~~i 39 (79)
T cd00989 24 PAAKAGLKAGDRILAI 39 (79)
T ss_pred HHHHcCCCCCCEEEEE
Confidence 4556799999988533
No 83
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=20.51 E-value=1.4e+02 Score=23.35 Aligned_cols=53 Identities=13% Similarity=0.276 Sum_probs=35.2
Q ss_pred cchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhccceEeeeeeceeeeec
Q 026620 109 VKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNI 165 (236)
Q Consensus 109 vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~~~IEiF~e~eLl~ni 165 (236)
+|.-.+.++.+.+ ...+++ .+|+.+.+||.-.+.+.... .++++.-..|..+|
T Consensus 41 iG~GK~eei~~~~-~~~~~d--~vvfd~~Lsp~Q~rNLe~~~-~~~V~DRt~LIL~I 93 (95)
T PF13167_consen 41 IGSGKVEEIKELI-EELDAD--LVVFDNELSPSQQRNLEKAL-GVKVIDRTQLILEI 93 (95)
T ss_pred echhHHHHHHHHH-hhcCCC--EEEECCCCCHHHHHHHHHHH-CCeeeccccHHHHH
Confidence 4554566666655 555553 45667789998877776554 67778877776655
No 84
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.51 E-value=1.2e+02 Score=23.09 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=21.3
Q ss_pred CCccccCCchhhhcCCCCCCEEEEEecC
Q 026620 196 LPRMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 196 LP~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
-|.+..+---|+-+|++.||.|+|..+.
T Consensus 34 ~~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 61 (122)
T cd02792 34 EMFVEISPELAAERGIKNGDMVWVSSPR 61 (122)
T ss_pred CcEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 3555555556888999999999998655
No 85
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=20.44 E-value=86 Score=17.87 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=12.7
Q ss_pred CCCCCEEEEEecCCCCcc
Q 026620 211 LERGQVVKVTYSGEITES 228 (236)
Q Consensus 211 ~~~GdVvkI~R~s~tag~ 228 (236)
+++||.|+|+.-. -+|.
T Consensus 2 ~~~G~~V~I~~G~-~~g~ 18 (28)
T smart00739 2 FEVGDTVRVIAGP-FKGK 18 (28)
T ss_pred CCCCCEEEEeECC-CCCc
Confidence 5799999999854 4443
No 86
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=20.38 E-value=1.2e+02 Score=23.06 Aligned_cols=28 Identities=29% Similarity=0.318 Sum_probs=22.3
Q ss_pred CCccccCCchhhhcCCCCCCEEEEEecC
Q 026620 196 LPRMLKKDAIAQYYGLERGQVVKVTYSG 223 (236)
Q Consensus 196 LP~I~~~DPvary~g~~~GdVvkI~R~s 223 (236)
.|.+..+.--|+-+|++.||.|+|....
T Consensus 34 ~~~v~in~~dA~~lgi~~Gd~V~v~~~~ 61 (122)
T cd02791 34 EPYVEIHPEDAARLGLKEGDLVRVTSRR 61 (122)
T ss_pred CCEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 4556666667888999999999998776
No 87
>KOG2776 consensus Metallopeptidase [General function prediction only]
Probab=20.04 E-value=69 Score=31.33 Aligned_cols=14 Identities=43% Similarity=0.717 Sum_probs=12.0
Q ss_pred hcCCCCCCEEEEEe
Q 026620 208 YYGLERGQVVKVTY 221 (236)
Q Consensus 208 y~g~~~GdVvkI~R 221 (236)
-|-||.||||||.=
T Consensus 100 ~~~Lk~GDvVKIdL 113 (398)
T KOG2776|consen 100 DYTLKEGDVVKIDL 113 (398)
T ss_pred cccccCCCEEEEEe
Confidence 57899999999963
Done!