Query gi|254780776|ref|YP_003065189.1| ribosome recycling factor [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 186
No_of_seqs 108 out of 1882
Neff 6.4
Searched_HMMs 39220
Date Sun May 29 18:48:27 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780776.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00496 frr ribosome recycli 100.0 0 0 433.9 13.6 176 11-186 1-177 (177)
2 COG0233 Frr Ribosome recycling 100.0 0 0 410.4 22.8 180 7-186 8-187 (187)
3 PRK00083 frr ribosome recyclin 100.0 0 0 409.2 23.5 184 1-186 2-185 (185)
4 cd00520 RRF Ribosome recycling 100.0 0 0 391.4 23.0 178 7-184 2-179 (179)
5 pfam01765 RRF Ribosome recycli 100.0 0 0 374.1 20.8 165 20-184 1-165 (165)
6 KOG4759 consensus 100.0 1.6E-42 0 312.4 21.6 181 3-185 81-262 (263)
7 CHL00118 atpG ATP synthase CF0 80.8 5.5 0.00014 21.3 8.7 82 102-183 43-127 (156)
8 PRK13454 F0F1 ATP synthase sub 79.7 5.9 0.00015 21.1 7.4 74 100-183 50-136 (181)
9 pfam04461 DUF520 Protein of un 58.0 11 0.00028 19.2 3.0 92 13-105 14-134 (160)
10 pfam10615 DUF2470 Protein of u 57.7 7 0.00018 20.6 2.0 41 61-118 39-82 (82)
11 PRK13461 F0F1 ATP synthase sub 57.5 17 0.00044 17.9 8.8 81 103-183 27-110 (159)
12 PRK05412 nucleotide-binding pr 55.2 13 0.00034 18.7 3.0 91 13-104 14-133 (161)
13 PTZ00248 eukaryotic translatio 54.1 19 0.0005 17.5 5.8 145 11-166 136-290 (324)
14 PRK01060 endonuclease IV; Prov 52.9 20 0.00052 17.4 4.7 71 56-126 29-99 (281)
15 PRK05759 F0F1 ATP synthase sub 52.8 20 0.00052 17.4 8.9 82 102-183 25-109 (156)
16 PRK09174 F0F1 ATP synthase sub 52.7 20 0.00052 17.4 8.0 74 100-183 72-158 (204)
17 TIGR01801 CM_A chorismate muta 52.6 8.3 0.00021 20.1 1.7 46 49-102 54-99 (104)
18 PRK13520 L-tyrosine decarboxyl 51.7 21 0.00054 17.3 5.5 54 68-121 318-372 (375)
19 PRK13453 F0F1 ATP synthase sub 51.6 21 0.00054 17.3 8.7 82 102-183 39-123 (173)
20 TIGR01462 greA transcription e 51.0 22 0.00055 17.2 6.8 68 105-179 1-68 (155)
21 PRK06569 F0F1 ATP synthase sub 50.7 22 0.00056 17.2 7.8 13 101-113 30-44 (157)
22 cd02643 R3H_NF-X1 R3H domain o 49.3 21 0.00053 17.3 3.3 47 71-118 6-52 (74)
23 cd07022 S49_Sppa_36K_type Sign 48.6 24 0.0006 16.9 4.1 55 88-142 125-183 (214)
24 PRK07353 F0F1 ATP synthase sub 46.1 26 0.00066 16.7 8.8 60 119-178 56-116 (140)
25 PRK13460 F0F1 ATP synthase sub 45.5 26 0.00067 16.6 8.8 72 103-174 38-123 (173)
26 TIGR02400 trehalose_OtsA alpha 45.1 12 0.00031 18.9 1.6 34 36-70 349-382 (476)
27 PRK05892 nucleoside diphosphat 45.1 27 0.00068 16.6 8.7 71 101-179 5-76 (161)
28 TIGR00422 valS valyl-tRNA synt 40.9 31 0.00078 16.2 5.2 121 10-139 714-852 (970)
29 pfam03786 UxuA D-mannonate deh 39.9 32 0.00081 16.1 4.1 81 46-135 8-97 (350)
30 pfam00244 14-3-3 14-3-3 protei 38.3 34 0.00086 15.9 6.6 30 104-133 32-61 (236)
31 COG1666 Uncharacterized protei 38.2 33 0.00085 15.9 2.9 95 5-103 13-136 (165)
32 PRK03906 mannonate dehydratase 37.7 34 0.00087 15.8 5.4 81 46-135 8-95 (389)
33 cd06061 PurM-like1 AIR synthas 37.2 23 0.00059 17.0 2.0 53 73-127 56-112 (298)
34 PRK04457 spermidine synthase; 37.0 35 0.0009 15.8 6.0 96 34-130 133-243 (262)
35 TIGR03562 osmo_induc_OsmC pero 36.2 36 0.00092 15.7 3.3 29 98-126 97-125 (135)
36 pfam00430 ATP-synt_B ATP synth 35.7 37 0.00094 15.6 8.8 79 102-180 20-112 (132)
37 PRK13022 secF preprotein trans 34.2 39 0.00099 15.5 6.8 64 61-124 41-107 (294)
38 COG3696 Putative silver efflux 34.1 17 0.00044 17.9 0.9 18 40-57 671-689 (1027)
39 COG1867 TRM1 N2,N2-dimethylgua 32.6 41 0.0011 15.3 2.7 39 36-74 120-158 (380)
40 cd00952 CHBPH_aldolase Trans-o 32.1 22 0.00056 17.1 1.2 22 98-119 283-304 (309)
41 pfam02825 WWE WWE domain. The 32.1 42 0.0011 15.2 2.8 43 68-110 19-61 (72)
42 KOG2916 consensus 32.0 42 0.0011 15.2 4.7 112 10-129 134-254 (304)
43 TIGR02637 RhaS rhamnose ABC tr 31.6 43 0.0011 15.2 3.4 45 36-89 77-121 (307)
44 PRK08476 F0F1 ATP synthase sub 31.1 44 0.0011 15.1 8.8 57 123-179 62-119 (141)
45 cd01232 PH_TRIO Trio pleckstri 29.8 46 0.0012 15.0 3.1 44 80-123 56-113 (114)
46 pfam10835 DUF2573 Protein of u 29.5 29 0.00073 16.4 1.4 32 12-43 2-33 (82)
47 pfam00922 Phosphoprotein Vesic 29.4 46 0.0012 14.9 5.0 44 84-127 98-147 (283)
48 PRK00943 selenophosphate synth 28.7 48 0.0012 14.9 3.7 74 54-127 51-134 (347)
49 pfam03982 DAGAT Diacylglycerol 28.6 48 0.0012 14.9 3.5 23 158-180 261-283 (297)
50 TIGR02394 rpoS_proteo RNA poly 27.9 49 0.0013 14.8 2.9 107 48-155 165-292 (292)
51 TIGR01136 cysKM cysteine synth 27.7 47 0.0012 14.9 2.3 67 49-115 7-105 (315)
52 cd07023 S49_Sppa_N_C Signal pe 27.4 50 0.0013 14.7 4.7 46 99-144 133-178 (208)
53 TIGR01818 ntrC nitrogen regula 26.2 53 0.0013 14.6 3.2 60 97-162 299-362 (471)
54 cd02046 hsp47 Heat shock prote 25.7 12 0.00031 18.9 -1.0 59 64-122 226-285 (366)
55 pfam03480 SBP_bac_7 Bacterial 24.9 56 0.0014 14.4 8.2 69 104-172 216-285 (285)
56 cd00954 NAL N-Acetylneuraminic 24.1 57 0.0015 14.3 2.5 22 47-69 141-162 (288)
57 cd03788 GT1_TPS Trehalose-6-Ph 24.0 32 0.0008 16.1 0.8 31 39-70 338-368 (460)
58 cd02054 angiotensinogen Angiot 23.7 17 0.00044 17.9 -0.6 60 63-122 231-291 (372)
59 cd02049 bacterial_SERPIN SERin 23.6 18 0.00047 17.7 -0.4 59 64-122 220-279 (364)
60 smart00518 AP2Ec AP endonuclea 23.4 59 0.0015 14.2 4.5 69 55-126 26-94 (273)
61 TIGR00308 TRM1 N2,N2-dimethylg 23.3 45 0.0011 15.0 1.5 65 21-85 152-222 (462)
62 cd00172 SERPIN SERine Proteina 23.2 15 0.00038 18.3 -1.0 59 64-122 222-281 (364)
63 KOG3813 consensus 22.8 61 0.0015 14.1 2.4 36 99-134 266-303 (640)
64 cd02047 HCII Heparin cofactor 22.7 24 0.0006 16.9 -0.1 11 64-74 88-98 (436)
65 PRK10117 trehalose-6-phosphate 22.3 38 0.00097 15.5 0.9 32 38-70 328-359 (474)
66 PRK06007 fliF flagellar MS-rin 22.0 63 0.0016 14.0 4.1 34 69-103 385-420 (540)
67 pfam02005 TRM N2,N2-dimethylgu 21.5 64 0.0016 14.0 3.5 69 36-104 119-221 (375)
68 PRK05657 RNA polymerase sigma 21.2 65 0.0017 13.9 3.3 30 125-154 298-327 (328)
69 cd02056 alpha-1-antitrypsin_li 20.9 23 0.00058 17.1 -0.4 58 64-122 221-279 (361)
70 TIGR01139 cysK cysteine syntha 20.9 66 0.0017 13.9 2.4 67 49-115 7-102 (312)
71 pfam08952 DUF1866 Domain of un 20.7 67 0.0017 13.9 4.7 54 39-93 70-125 (145)
72 pfam08112 ATP-synt_E_2 ATP syn 20.5 67 0.0017 13.8 3.3 14 160-173 34-47 (56)
73 cd00716 creatine_kinase_like P 20.3 68 0.0017 13.8 2.3 55 75-135 240-309 (357)
No 1
>TIGR00496 frr ribosome recycling factor; InterPro: IPR002661 The ribosome recycling factor or ribosome release factor (RRF) dissociates ribosomes from mRNA after termination of translation, and is essential for bacterial growth . Thus ribosomes are 'recycled' and ready for another round of protein synthesis.; GO: 0006412 translation.
Probab=100.00 E-value=0 Score=433.94 Aligned_cols=176 Identities=47% Similarity=0.751 Sum_probs=174.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECC-HHHHHHHHHHHHCCCCC
Q ss_conf 99999999999999753138888967824507885586423998765120578389899659-67899999996317889
Q gi|254780776|r 11 KDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWD-KEMVASVERGIHESNLG 89 (186)
Q Consensus 11 ~~~m~~~i~~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D-~~~ik~I~kAI~~s~l~ 89 (186)
+.+|+|+++||+.+|++|||||+||+|||+|.|+|||..|||+|||+|.+++||+|+|+||| .+++++|++||+.||||
T Consensus 1 k~~M~K~~~al~~~~~tiRTGR~~p~llD~i~VeYYG~~TPL~qLa~i~~~dar~l~I~PfD~k~~~~~IE~aI~~adLG 80 (177)
T TIGR00496 1 KEKMDKSIQALKRELSTIRTGRANPSLLDRILVEYYGARTPLNQLASITVPDARTLVIKPFDVKSLINAIEKAILRADLG 80 (177)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCHHHCCEEEEECCCCCHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCC
T ss_conf 91567999998645644202467800017104651588203452140101898567763022225306899999860688
Q ss_pred CCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 98454773478861555689999999999998889999999999999999998753589997899888999999999999
Q gi|254780776|r 90 LNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTI 169 (186)
Q Consensus 90 l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~~~~ 169 (186)
|||++||+.|||+|||||+|+|++++|.||+++|++|+++||||||+++.+|+++|++++|||+.++++++|||+||.|+
T Consensus 81 l~P~~DG~~IR~~~PplT~ErRke~~K~aKk~~E~~kvavRNvRrDand~vKkleKd~eisED~~~~~~e~iQK~TD~yi 160 (177)
T TIGR00496 81 LNPNNDGEVIRINFPPLTEERRKELVKVAKKIAEQAKVAVRNVRRDANDKVKKLEKDKEISEDEERKLQEEIQKITDEYI 160 (177)
T ss_pred CCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHEEEEEEEHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 77778876210258898746678778887643210133552002647889998524788880045655778742648888
Q ss_pred HHHHHHHHHHHHHHHCC
Q ss_conf 99999999999887449
Q gi|254780776|r 170 KNIDSFFEEKKKEIMHF 186 (186)
Q Consensus 170 ~~id~~~~~Kekell~~ 186 (186)
++||++++.||+|||.|
T Consensus 161 kkid~~~~~KE~ei~~v 177 (177)
T TIGR00496 161 KKIDEILKDKEKEILEV 177 (177)
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 99999999889987229
No 2
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=410.38 Aligned_cols=180 Identities=49% Similarity=0.781 Sum_probs=178.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHCC
Q ss_conf 89999999999999999975313888896782450788558642399876512057838989965967899999996317
Q gi|254780776|r 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHES 86 (186)
Q Consensus 7 l~~~~~~m~~~i~~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s 86 (186)
+.+++++|++++++|+++|+++|||||||++||+|.|+|||+.+||+|||+||+|++|+|+|+|||++.+++|++||..|
T Consensus 8 ~~~~e~kM~k~~e~l~~~l~~iRTGRanp~lld~i~VeyYG~~tPl~qvAsIsvpe~r~l~I~p~Dks~~~~IekaI~~s 87 (187)
T COG0233 8 LKDAEEKMEKALEALKNELSKIRTGRANPSLLDRITVEYYGSPTPLNQLASISVPEARTLVIKPFDKSMVKAIEKAILAS 87 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCEEEEECCCCCCHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHC
T ss_conf 99999999999999998887631478986785654432337988688875436788655776137600299999999975
Q ss_pred CCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 88998454773478861555689999999999998889999999999999999998753589997899888999999999
Q gi|254780776|r 87 NLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 (186)
Q Consensus 87 ~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~ 166 (186)
||||||.++|++|||+||+||+|||++|+|.|++++|++|++|||+||++++++|+++|+++||||+.++++++||++||
T Consensus 88 nLglnP~~dG~~IRv~~P~lTeErRkelvK~~k~~~EeakvaiRniRrda~d~iKK~~K~~~isEDe~k~~e~~iQKlTd 167 (187)
T COG0233 88 NLGLNPNNDGNVIRVPLPPLTEERRKELVKVAKKYAEEAKVAVRNIRRDANDKIKKLEKDKEISEDEVKKAEEEIQKLTD 167 (187)
T ss_pred CCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 79998676887677549998879999999999998899999999999999999998752587656788889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999999999887449
Q gi|254780776|r 167 STIKNIDSFFEEKKKEIMHF 186 (186)
Q Consensus 167 ~~~~~id~~~~~Kekell~~ 186 (186)
+|+++||++++.||+|||.|
T Consensus 168 ~yi~~iD~~~~~KEkEim~v 187 (187)
T COG0233 168 EYIKKIDELLKDKEKEIMEV 187 (187)
T ss_pred HHHHHHHHHHHHHHHHHHCC
T ss_conf 99999999999999887449
No 3
>PRK00083 frr ribosome recycling factor; Reviewed
Probab=100.00 E-value=0 Score=409.19 Aligned_cols=184 Identities=48% Similarity=0.786 Sum_probs=180.0
Q ss_pred CCHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHHHHHHHH
Q ss_conf 94200789999999999999999975313888896782450788558642399876512057838989965967899999
Q gi|254780776|r 1 MNQVIDLQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVE 80 (186)
Q Consensus 1 ~~e~~dl~~~~~~m~~~i~~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~~ik~I~ 80 (186)
|++++ ++++.+|++++++|+.+|+++|||||||+|||+|+|+|||+++||++||+|++++|++|+|+|||++++++|+
T Consensus 2 ~~~il--~~~~~kM~k~i~~~~~el~~irtGRasp~lld~i~V~~yg~~~pL~qlA~Isv~~~~~l~I~~~D~~~v~~I~ 79 (185)
T PRK00083 2 INEIL--KDAEERMEKSVEALKRELAKIRTGRANPSLLDGIKVDYYGSPTPLNQVASISVPEARTLLIQPWDKSMLKAIE 79 (185)
T ss_pred HHHHH--HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCEEEEECCCCCCHHHHHHCCCCCCCEEEEEECCHHHHHHHH
T ss_conf 68999--9999999999999999997633589997884784784579978689885223789887988607264489999
Q ss_pred HHHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99631788998454773478861555689999999999998889999999999999999998753589997899888999
Q gi|254780776|r 81 RGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLEND 160 (186)
Q Consensus 81 kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~ 160 (186)
+||++||||+||++||++|+||||+||+|+|++++|.+++.+|+||++||++||++++++|+++|.+++|||+.++++++
T Consensus 80 kAI~~s~LglnP~~dg~~Iri~iP~lT~E~R~elvK~~k~~~E~aKv~iRniR~~~~~~iKk~~k~~~iseD~~k~~~~~ 159 (185)
T PRK00083 80 KAIRASDLGLNPSNDGTVIRLPIPPLTEERRKELVKVAKKEAEEAKVAIRNIRRDANDKLKKLEKDKEISEDEERRAEDE 159 (185)
T ss_pred HHHHHCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 99984799988654786688758988899999999999999999999999999999999987650478877889889999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999999999999999887449
Q gi|254780776|r 161 IQKITDSTIKNIDSFFEEKKKEIMHF 186 (186)
Q Consensus 161 iq~lt~~~~~~id~~~~~Kekell~~ 186 (186)
||++||+|++++|++++.||+|||+.
T Consensus 160 iqkltd~~~~~id~~~~~Kekeil~v 185 (185)
T PRK00083 160 IQKLTDKYIKKIDELLAEKEKEIMEV 185 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99999999999999999999986359
No 4
>cd00520 RRF Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.
Probab=100.00 E-value=0 Score=391.39 Aligned_cols=178 Identities=44% Similarity=0.734 Sum_probs=176.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHCC
Q ss_conf 89999999999999999975313888896782450788558642399876512057838989965967899999996317
Q gi|254780776|r 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHES 86 (186)
Q Consensus 7 l~~~~~~m~~~i~~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s 86 (186)
+++++.+|+++++||+.+|+++|+||+||++||+|+|++||+++||++||+|++++|++|+|+|||++++++|++||++|
T Consensus 2 l~~~~~~m~k~i~~l~~~~~~irtGrasp~lld~i~V~~yg~~~pL~~lA~Is~~~~~~l~I~~~D~~~v~~I~kAI~~s 81 (179)
T cd00520 2 LKEAKEKMEKSLEALKEELNKIRTGRANPALLDSITVEYYGAPTPLNQLASISVPEPRTIVINPFDKSAIKAIEKAILNS 81 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCEEEEECCCCCCHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHCC
T ss_conf 27899999999999999997643178997880875885489966699997610688776887507855599999998407
Q ss_pred CCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 88998454773478861555689999999999998889999999999999999998753589997899888999999999
Q gi|254780776|r 87 NLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 (186)
Q Consensus 87 ~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~ 166 (186)
|||+||++||++|+|+|||||+|+|++++|.||+.+|+||++||++|++++++++++++++++|||+.++++++||++||
T Consensus 82 ~l~l~P~~dg~~Iri~iP~lT~E~R~~l~K~ak~~~E~aK~~iR~iR~~~~~~ikk~~k~~~iseD~~k~~~~~iqkltd 161 (179)
T cd00520 82 DLGLNPNNDGAVIRVNLPPLTEERRKELVKDAKKIAEEAKVAIRNIRRDANDKIKKLEKEKEISEDEVKKAEEDLQKLTD 161 (179)
T ss_pred CCCCCCEECCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf 99976223687667369989999999999999999999999999999999999987663389987688899999999999
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999998874
Q gi|254780776|r 167 STIKNIDSFFEEKKKEIM 184 (186)
Q Consensus 167 ~~~~~id~~~~~Kekell 184 (186)
+|++++|++++.||+|||
T Consensus 162 ~~~~~id~~~~~Kekeil 179 (179)
T cd00520 162 EYIKKIDELLKSKEKELL 179 (179)
T ss_pred HHHHHHHHHHHHHHHHHC
T ss_conf 999999999999988539
No 5
>pfam01765 RRF Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis.
Probab=100.00 E-value=0 Score=374.15 Aligned_cols=165 Identities=50% Similarity=0.810 Sum_probs=163.5
Q ss_pred HHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCEE
Q ss_conf 99999753138888967824507885586423998765120578389899659678999999963178899845477347
Q gi|254780776|r 20 FLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVL 99 (186)
Q Consensus 20 ~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I 99 (186)
+|+.+|+++||||+||+|||+|+|+|||+++||++||+||+++|++|+|+|||++++++|++||++|||||||++||++|
T Consensus 1 ~l~~~l~~irtGrasp~lld~i~V~~yg~~~pL~~lA~Isv~~~~~l~I~~~D~~~v~~I~kAI~~s~LglnP~~dg~~I 80 (165)
T pfam01765 1 ALKKELSKIRTGRANPSLLDNIRVDYYGSPTPLNQLASISVPEARTLLITPWDKSLIKAIEKAILASDLGLNPQNDGQVI 80 (165)
T ss_pred CHHHHHHHCCCCCCCHHHHCCEEEEECCCCCCHHHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCEE
T ss_conf 94778632536889978848869856899765899853027898879987342443799999998579997877478778
Q ss_pred EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88615556899999999999988899999999999999999987535899978998889999999999999999999999
Q gi|254780776|r 100 RIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEK 179 (186)
Q Consensus 100 ~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~~~~~~id~~~~~K 179 (186)
+|+||+||+|+|++++|.||+.+|+||++||++|+++++++|++++.+++|||+.++++++||++||+|++++|++++.|
T Consensus 81 rv~iP~lT~E~R~~lvK~~k~~~E~aKv~iR~iR~~~~~~iKk~~~~~~iseD~~k~~~~~iq~ltd~~~~~id~~~~~K 160 (165)
T pfam01765 81 RIPIPPLTEERRKELVKQAKKLAEEAKVAIRNIRRDANDKLKKLEKDKEISEDEVKKAEKEIQKLTDKYIKKIDELLKKK 160 (165)
T ss_pred EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 98589888999999999999999999999999999999999876504999877888999999999999999999999999
Q ss_pred HHHHH
Q ss_conf 98874
Q gi|254780776|r 180 KKEIM 184 (186)
Q Consensus 180 ekell 184 (186)
|+|||
T Consensus 161 ekeil 165 (165)
T pfam01765 161 EKELM 165 (165)
T ss_pred HHHHC
T ss_conf 98639
No 6
>KOG4759 consensus
Probab=100.00 E-value=1.6e-42 Score=312.43 Aligned_cols=181 Identities=34% Similarity=0.564 Sum_probs=174.9
Q ss_pred HHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECC-HHHHHHHHH
Q ss_conf 2007899999999999999999753138888967824507885586423998765120578389899659-678999999
Q gi|254780776|r 3 QVIDLQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWD-KEMVASVER 81 (186)
Q Consensus 3 e~~dl~~~~~~m~~~i~~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D-~~~ik~I~k 81 (186)
+...+.++.+.|+++++.|+++|.++++||++|++||.|.|.+||.++||++||+||.++|++|+|+||| |..+++|.+
T Consensus 81 ~~~~~~~~~sqmek~ie~lke~~~k~~~gr~~~~~~d~I~vk~~g~~~~L~~IA~vS~K~p~~ilIn~~d~p~~ikai~k 160 (263)
T KOG4759 81 ENAVEAKANSQMEKTIEALKEDFNKIRQGRFNPGMLDKIVVKANGPKRPLNEIAQVSLKGPQTILINPFDFPVDIKAILK 160 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHEEEECCCCCCCHHHHHHHHCCCCCEEEEECCCCCHHHHHHHH
T ss_conf 77899999999999999999998876036778655641342159986357999988537976489844668167999999
Q ss_pred HHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 96317889984547734788615556899999999999988899999999999999999987535899978998889999
Q gi|254780776|r 82 GIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDI 161 (186)
Q Consensus 82 AI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~i 161 (186)
||++|+||+||++||++|+|++||+|.|+|++++|.++..+|++|.+||.+|+++++++++.++. +++|++++++.++
T Consensus 161 AI~~S~lnltP~~dg~~l~vsiP~~T~E~Re~laK~~~~~~ee~K~slr~ir~~~~kk~~k~~~~--~~~D~vkkae~~l 238 (263)
T KOG4759 161 AIEASGLNLTPNLDGTVLRVSIPPVTKESREKLAKVLKRYFEEYKQSLRKIRTKSIKKSKKNKKS--LSEDEVKKAEAEL 238 (263)
T ss_pred HHHHCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHH
T ss_conf 99967999885778717985499767599999999999998999999999999988888736344--7845899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999999999999999988744
Q gi|254780776|r 162 QKITDSTIKNIDSFFEEKKKEIMH 185 (186)
Q Consensus 162 q~lt~~~~~~id~~~~~Kekell~ 185 (186)
|+++|.|+.++|++++.||||||+
T Consensus 239 ~~l~k~~v~~ld~llkskeKellk 262 (263)
T KOG4759 239 QKLAKDAVNKLDDLLKSKEKELLK 262 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999999999999999998734
No 7
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=80.78 E-value=5.5 Score=21.30 Aligned_cols=82 Identities=17% Similarity=0.169 Sum_probs=42.0
Q ss_pred ECCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6155568--999999999999888999999999999999999875358-9997899888999999999999999999999
Q gi|254780776|r 102 PVPETTE--ERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSG-KASEDMVASLENDIQKITDSTIKNIDSFFEE 178 (186)
Q Consensus 102 ~iP~lT~--E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~-~iseD~~~~~~~~iq~lt~~~~~~id~~~~~ 178 (186)
-+||++. +-|++.+...-..++..+.....++.++...+...++.. .+-++-....++..+.+.++...+++.+.+.
T Consensus 43 ~~~Pi~~~ld~R~~~I~~~l~~Ae~~~~ea~~~~~eye~~L~~Ar~Ea~~ii~~A~~~a~~~~~~i~~~A~~ea~~~i~~ 122 (156)
T CHL00118 43 FYKPIGKILDEREEYIRSNLAKASSKLAKANELTAQYEEQLSKARKEAQLLIAQSQKEAQEIVQEELKQAQKNAESLVEE 122 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 89899999999999999889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q ss_conf 99887
Q gi|254780776|r 179 KKKEI 183 (186)
Q Consensus 179 Kekel 183 (186)
.+++|
T Consensus 123 A~~eI 127 (156)
T CHL00118 123 ATKQL 127 (156)
T ss_pred HHHHH
T ss_conf 99999
No 8
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=79.72 E-value=5.9 Score=21.07 Aligned_cols=74 Identities=18% Similarity=0.239 Sum_probs=34.1
Q ss_pred EEECCCCCH--HHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 886155568--999999999999888999-----------9999999999999998753589997899888999999999
Q gi|254780776|r 100 RIPVPETTE--ERRLALVKVAHAYAEKSK-----------ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 (186)
Q Consensus 100 ~i~iP~lT~--E~R~~lvK~~k~~~E~~K-----------~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~ 166 (186)
++.+|++.. |-|+..+..-=..++++| ..|.+.|.++..-+... ....+.+++....
T Consensus 50 k~~lPrI~~vLe~R~~~I~~dL~~Ae~~k~eAe~~~~~ye~~L~~Ar~eA~~ii~eA----------r~~a~~~~~~~~~ 119 (181)
T PRK13454 50 RVALPRIGAVLAERQGTITNDLAAAEELKQKAVEAEKAYNKALADARAEAQRIVAET----------RAEIQAELDVAIA 119 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHH
T ss_conf 999988898999999999988999999999999999999999999999999999999----------9999999999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999887
Q gi|254780776|r 167 STIKNIDSFFEEKKKEI 183 (186)
Q Consensus 167 ~~~~~id~~~~~Kekel 183 (186)
+...+++...+..|++|
T Consensus 120 ~a~~el~~~i~~AE~~I 136 (181)
T PRK13454 120 KADAEIAAKAAESEKRI 136 (181)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999
No 9
>pfam04461 DUF520 Protein of unknown function (DUF520). Family of uncharacterized proteins.
Probab=57.99 E-value=11 Score=19.21 Aligned_cols=92 Identities=14% Similarity=0.282 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHHH---CCCCCCCHHHHCC-EEEEECCCCCHHHHHHHHHC--------------------CCCCEEEE
Q ss_conf 999999999999753---1388889678245-07885586423998765120--------------------57838989
Q gi|254780776|r 13 RMGDTISFLKKDMMT---LRTGRVSPSMLDL-VKVEAYGSHVPLNQVANVTV--------------------LEPRMLVV 68 (186)
Q Consensus 13 ~m~~~i~~l~~el~~---irtGrasp~lld~-i~V~~~g~~~pL~~lA~Is~--------------------~~~~~l~I 68 (186)
.+..|++...+|+++ ++.-.++-.+=+. |.+. -.+.+.|.++-.|-. .++.++-.
T Consensus 14 E~~NAv~qa~rEi~~RyDFKgs~~~iel~~~~i~i~-a~~e~kl~~~~diL~~k~~KR~i~~k~ld~~~~e~asG~~~rq 92 (160)
T pfam04461 14 EVDNAVDQANREISTRFDFKGSKASIELKEKEITLT-AESDFQLKQVKDILRTKLIKRGVDLKALDFGKVEKASGKTVKQ 92 (160)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEECCCEEEEE-ECCHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCEEEE
T ss_conf 999999999887750004699961599659889999-5978999999999999998539981101358742467987999
Q ss_pred E-----ECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCC
Q ss_conf 9-----659678999999963178899845477347886155
Q gi|254780776|r 69 S-----VWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPE 105 (186)
Q Consensus 69 ~-----~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~ 105 (186)
+ --|....+.|.+.|.++.+-++++..|..|||+=++
T Consensus 93 ~i~lk~GI~~e~AKkI~K~IK~~klKVqa~IQGd~vRVsgKk 134 (160)
T pfam04461 93 EVKLKQGIDQELAKKIVKLIKDSKLKVQAAIQGDQVRVTGKK 134 (160)
T ss_pred EEEHHCCCCHHHHHHHHHHHHHCCCCEEEEECCCEEEEECCC
T ss_conf 988220438899999999998448803688648578861598
No 10
>pfam10615 DUF2470 Protein of unknown function (DUF2470). This family is a putative haem-iron utilisation family, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however this could not be confirmed.
Probab=57.72 E-value=7 Score=20.58 Aligned_cols=41 Identities=34% Similarity=0.498 Sum_probs=27.8
Q ss_pred CCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCC---CHHHHHHHHHHH
Q ss_conf 5783898996596789999999631788998454773478861555---689999999999
Q gi|254780776|r 61 LEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPET---TEERRLALVKVA 118 (186)
Q Consensus 61 ~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~l---T~E~R~~lvK~~ 118 (186)
.+++++.|.++ |+.-..+|..+|||||++ ..|.|..||+.+
T Consensus 39 ~~a~m~~id~~-----------------G~~l~~~~~~~ri~F~~pl~~~~~~R~~LV~ma 82 (82)
T pfam10615 39 ESARMTGIDPE-----------------GMDLRVDGATLRIPFDHPLTDSEDARQTLVAMA 82 (82)
T ss_pred CCEEEEEEECC-----------------CCEEEECCEEEEEECCCCCCCHHHHHHHHHHCC
T ss_conf 84489998217-----------------368998999999858885889999999998619
No 11
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=57.47 E-value=17 Score=17.88 Aligned_cols=81 Identities=20% Similarity=0.271 Sum_probs=39.1
Q ss_pred CCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 155568--999999999999888999999999999999999875358-99978998889999999999999999999999
Q gi|254780776|r 103 VPETTE--ERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSG-KASEDMVASLENDIQKITDSTIKNIDSFFEEK 179 (186)
Q Consensus 103 iP~lT~--E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~-~iseD~~~~~~~~iq~lt~~~~~~id~~~~~K 179 (186)
+||++. +.|++.+...-.-+++++......+.++...+...+... .+-++-...++...+.+..+...+++.+.+..
T Consensus 27 ~~pi~~~l~~R~~~I~~~l~~Ae~~~~ea~~~~~e~e~~L~~a~~ea~~Ii~~A~~~A~~~~~~i~~~A~~ea~~i~~~A 106 (159)
T PRK13461 27 FDKIKAVIDSRQSEIDEKIEKADEDAEKARELKLKNERILKSAKEEGKKIVEEYKSKAENVYEEIVKEAHEEAESIIERA 106 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHH
Q ss_conf 9887
Q gi|254780776|r 180 KKEI 183 (186)
Q Consensus 180 ekel 183 (186)
+.+|
T Consensus 107 ~~~I 110 (159)
T PRK13461 107 KLEI 110 (159)
T ss_pred HHHH
T ss_conf 9999
No 12
>PRK05412 nucleotide-binding protein; Reviewed
Probab=55.21 E-value=13 Score=18.68 Aligned_cols=91 Identities=14% Similarity=0.294 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHH---CCCCCCCHHHHCC-EEEEECCCCCHHHHHHHHH--------------------CCCCCEE--
Q ss_conf 999999999999753---1388889678245-0788558642399876512--------------------0578389--
Q gi|254780776|r 13 RMGDTISFLKKDMMT---LRTGRVSPSMLDL-VKVEAYGSHVPLNQVANVT--------------------VLEPRML-- 66 (186)
Q Consensus 13 ~m~~~i~~l~~el~~---irtGrasp~lld~-i~V~~~g~~~pL~~lA~Is--------------------~~~~~~l-- 66 (186)
.+..|++...+|+++ ++.-.++-.+=+. |.+.+ .+.+.|.++-.|- ..++.++
T Consensus 14 Ev~NAvdqa~rEI~~RyDFKgs~~~iel~~~~i~i~a-~~e~kl~qv~diL~~kl~KR~i~~k~ld~~~~e~asG~~vrq 92 (161)
T PRK05412 14 EVDNAVDQANREISTRFDFKGSKASIELKEEEITLTA-ESDFQLKQVLDILRSKLIKRGIDLKALDYGKVEKASGKTVKQ 92 (161)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCEEEEEE-CCHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCEEEE
T ss_conf 9999999998877500046999516996487899996-978999999999999998539981101468843467987999
Q ss_pred --EEE-ECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECC
Q ss_conf --899-65967899999996317889984547734788615
Q gi|254780776|r 67 --VVS-VWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVP 104 (186)
Q Consensus 67 --~I~-~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP 104 (186)
.+. --|....+.|.+.|.++.|-++++..|..+||+=.
T Consensus 93 ~i~lk~GI~~e~AKkI~k~IK~~klKVqa~IQGd~vRVtgK 133 (161)
T PRK05412 93 EVKLKQGIEQELAKKIVKLIKDSKLKVQAQIQGDQVRVTGK 133 (161)
T ss_pred EEEHHCCCCHHHHHHHHHHHHHCCCCEEEEECCCEEEEECC
T ss_conf 98812043889999999999844881368864857886159
No 13
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=54.14 E-value=19 Score=17.52 Aligned_cols=145 Identities=12% Similarity=0.109 Sum_probs=81.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCH-HHHCCEEEEECCCCCHHHHHHHHHCCCCC----EEEEEECCHHHHHHHHHHHHC
Q ss_conf 9999999999999975313888896-78245078855864239987651205783----898996596789999999631
Q gi|254780776|r 11 KDRMGDTISFLKKDMMTLRTGRVSP-SMLDLVKVEAYGSHVPLNQVANVTVLEPR----MLVVSVWDKEMVASVERGIHE 85 (186)
Q Consensus 11 ~~~m~~~i~~l~~el~~irtGrasp-~lld~i~V~~~g~~~pL~~lA~Is~~~~~----~l~I~~~D~~~ik~I~kAI~~ 85 (186)
..+...++++|+.. -.+| ++|+.+.+.-.-...=+.+|..--.|.|- -+-|+||...-|.+|..|+.+
T Consensus 136 ~kkyghaydaFk~a-------v~dp~~vl~~~~i~~ev~~~L~~~I~rrltPq~vKIRADiEvtCf~yeGIdAIK~AL~a 208 (324)
T PTZ00248 136 YKKYGHALDALKEA-------ASNPENVFKGLDISEEVKDSLMEDIQLRLKPQALKLRARIDVWCFGYEGIDAVKEALIA 208 (324)
T ss_pred HHCCCCHHHHHHHH-------HCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCHHHHHHHHHHH
T ss_conf 30236199999998-------52937533578999999999999999646887537887799995785529999999999
Q ss_pred CCCCCCCCCCCCEEEEECCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 788998454773478861555-----689999999999998889999999999999999998753589997899888999
Q gi|254780776|r 86 SNLGLNPIVEGQVLRIPVPET-----TEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLEND 160 (186)
Q Consensus 86 s~l~l~p~~dg~~I~i~iP~l-----T~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~ 160 (186)
+- ..++..-+-.|++.-||+ |.--|+.=+..+.+.++..+..|...+.- .++-...-+.+|+.+...+...
T Consensus 209 g~-~~s~e~~~IkIkLiApPlYvitt~t~dk~~Gi~~l~~ai~~I~~~I~~~~gG---~~~vk~~Pk~V~~~de~~l~~~ 284 (324)
T PTZ00248 209 GK-KKSNDEVKISIKLIAPPQYVIVTTCIDKDAGVKIMKQALEVISNKIKKYKGG---DFKQKGEPKVVGGDDEKHLEDL 284 (324)
T ss_pred HH-HCCCCCCCEEEEEECCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCC---EEEEEECCEECCHHHHHHHHHH
T ss_conf 98-6498765279999759817999741578888999999999999998644498---1799648752371548999999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780776|r 161 IQKITD 166 (186)
Q Consensus 161 iq~lt~ 166 (186)
++++-.
T Consensus 285 me~~e~ 290 (324)
T PTZ00248 285 LEKDES 290 (324)
T ss_pred HHHHHH
T ss_conf 999876
No 14
>PRK01060 endonuclease IV; Provisional
Probab=52.94 E-value=20 Score=17.40 Aligned_cols=71 Identities=7% Similarity=-0.002 Sum_probs=52.8
Q ss_pred HHHHCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 65120578389899659678999999963178899845477347886155568999999999999888999
Q gi|254780776|r 56 ANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126 (186)
Q Consensus 56 A~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K 126 (186)
-||-+++||++.-.|.++..+...-.+...++++..+..-=..-.|.+-.+..|.|+..++.+..-.+.+.
T Consensus 29 ~QiF~~npr~w~~~~~~~~~~~~f~~~~~~~~~~~~~iv~Ha~YlINLasp~~~~~~kS~~~l~~el~r~~ 99 (281)
T PRK01060 29 FMIFTGNPQQWKRKPLEELNIEAFKAACEKYGISPEDILVHAPYLINLGNPNPEKLEKSRDALIDEIERCE 99 (281)
T ss_pred EEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCEECCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99878998889999999899999999999819997545752453232689987899999999999999999
No 15
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=52.77 E-value=20 Score=17.38 Aligned_cols=82 Identities=16% Similarity=0.163 Sum_probs=36.8
Q ss_pred ECCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6155568--999999999999888999999999999999999875358-9997899888999999999999999999999
Q gi|254780776|r 102 PVPETTE--ERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSG-KASEDMVASLENDIQKITDSTIKNIDSFFEE 178 (186)
Q Consensus 102 ~iP~lT~--E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~-~iseD~~~~~~~~iq~lt~~~~~~id~~~~~ 178 (186)
-+||++. +.|++.+...-..++..+...-....++...+...+... .+-++-...++...+.+..+....++.+...
T Consensus 25 ~~~pi~~~l~~R~~~I~~~l~~Ae~~~~~a~~~~~e~~~~l~~a~~ea~~ii~~a~~~a~~~~~~~~~~a~~e~~~~~~~ 104 (156)
T PRK05759 25 VWPPIMKALEERQKKIADGLAAAERAKKELEAAQAKAEEQLAEARAEAAEIIEQAKKRAAQIIEEAKAEAEAEAARIKAQ 104 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 78789999999999999899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q ss_conf 99887
Q gi|254780776|r 179 KKKEI 183 (186)
Q Consensus 179 Kekel 183 (186)
.+++|
T Consensus 105 a~~~I 109 (156)
T PRK05759 105 AQAEI 109 (156)
T ss_pred HHHHH
T ss_conf 99999
No 16
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=52.72 E-value=20 Score=17.37 Aligned_cols=74 Identities=12% Similarity=0.145 Sum_probs=32.3
Q ss_pred EEECCCCCH--HHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 886155568--99999999-----------99998889999999999999999998753589997899888999999999
Q gi|254780776|r 100 RIPVPETTE--ERRLALVK-----------VAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 (186)
Q Consensus 100 ~i~iP~lT~--E~R~~lvK-----------~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~ 166 (186)
++.+|++.. |.|..-+. .+....+.+...+...|.++..-+... ...+..+++.-..
T Consensus 72 k~~lPrI~~vLe~R~~~I~~DLe~Ae~lk~EAe~~~a~Ye~~LaeAR~eA~~Ii~~A----------r~~a~~~~e~~~a 141 (204)
T PRK09174 72 RVILPRIGGIIETRRDRIAQDLDQAARLKQEADAAVAAYEQELAQARSKAASIAQAA----------REAAKAKAEAERA 141 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHH
T ss_conf 997603777999999999879999999999999999999999999999999999999----------9999999999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999887
Q gi|254780776|r 167 STIKNIDSFFEEKKKEI 183 (186)
Q Consensus 167 ~~~~~id~~~~~Kekel 183 (186)
+...++...+...|++|
T Consensus 142 ~~ea~L~~kia~AE~~I 158 (204)
T PRK09174 142 EIEASLEKKLKEAEERI 158 (204)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999
No 17
>TIGR01801 CM_A chorismate mutase; InterPro: IPR010954 This entry represents chorismate mutase (CM) domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some Gram-positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44 0dentity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the Gram-positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role..
Probab=52.57 E-value=8.3 Score=20.06 Aligned_cols=46 Identities=13% Similarity=0.193 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEE
Q ss_conf 423998765120578389899659678999999963178899845477347886
Q gi|254780776|r 49 HVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIP 102 (186)
Q Consensus 49 ~~pL~~lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~ 102 (186)
..-|++|-.+ -+| ||..++|+.|-|-|..|+|.|+-..+...+.|.
T Consensus 54 ~~~L~~li~~-N~G-------PF~~~Tik~iFKEIFkAsl~L~es~~~K~LlVS 99 (104)
T TIGR01801 54 KEMLNELIES-NDG-------PFEDATIKQIFKEIFKASLELQESDDKKALLVS 99 (104)
T ss_pred HHHHHHHHHC-CCC-------CCCCHHHHHHHHHHHHHHHHHHHCCCCCCEECC
T ss_conf 9999999860-787-------688404778889998750454301477642114
No 18
>PRK13520 L-tyrosine decarboxylase; Provisional
Probab=51.73 E-value=21 Score=17.27 Aligned_cols=54 Identities=20% Similarity=0.243 Sum_probs=27.4
Q ss_pred EEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEC-CCCCHHHHHHHHHHHHHH
Q ss_conf 996596789999999631788998454773478861-555689999999999998
Q gi|254780776|r 68 VSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPV-PETTEERRLALVKVAHAY 121 (186)
Q Consensus 68 I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~i-P~lT~E~R~~lvK~~k~~ 121 (186)
|-+|....+..+...+...+-.++....+..++|.+ |-+|.+.-++++..+++.
T Consensus 318 iV~Fr~~~~~~l~d~l~~~GW~v~~~~~P~~lhivv~~~~~~~~id~fl~DL~e~ 372 (375)
T PRK13520 318 IVAFDDPNPHEVRKKLRERGWRVSVTRCPEALRIVVMPHVTREHIEAFLEDLDEV 372 (375)
T ss_pred EEEEECCCHHHHHHHHHHCCCEECCCCCCCEEEEEEECCCCHHHHHHHHHHHHHH
T ss_conf 9999579999999999976987457889984899995999989999999999999
No 19
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=51.63 E-value=21 Score=17.26 Aligned_cols=82 Identities=16% Similarity=0.229 Sum_probs=37.4
Q ss_pred ECCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6155568--999999999999888999999999999999999875358-9997899888999999999999999999999
Q gi|254780776|r 102 PVPETTE--ERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSG-KASEDMVASLENDIQKITDSTIKNIDSFFEE 178 (186)
Q Consensus 102 ~iP~lT~--E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~-~iseD~~~~~~~~iq~lt~~~~~~id~~~~~ 178 (186)
-+||++. +-|++-+..-=.-+++++...-..+.++...+....... .+-++-....+...+.+..+...+++.+.+.
T Consensus 39 ~~~pi~~~L~~R~~~I~~~l~~Ae~~k~eA~~~~~e~e~~L~~a~~ea~~Ii~~A~~~Ae~~~~~~~~~A~~ea~~i~~~ 118 (173)
T PRK13453 39 AWGPLKDVMDKRERDINRDIDDAEQAKLNAQKLEEENKQKLKETQEEVQKILEDAKVQARQQQEQIIHEANVRANGMIET 118 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 89899999999999999889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q ss_conf 99887
Q gi|254780776|r 179 KKKEI 183 (186)
Q Consensus 179 Kekel 183 (186)
.+++|
T Consensus 119 A~~~I 123 (173)
T PRK13453 119 AQSEI 123 (173)
T ss_pred HHHHH
T ss_conf 99999
No 20
>TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359 Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes. The 2.2 Å resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein. ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=51.04 E-value=22 Score=17.20 Aligned_cols=68 Identities=16% Similarity=0.180 Sum_probs=52.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 556899999999999988899999999999999999987535899978998889999999999999999999999
Q gi|254780776|r 105 ETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEK 179 (186)
Q Consensus 105 ~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq~lt~~~~~~id~~~~~K 179 (186)
+||.|.-+.|.+-++. -...-|.+....|+...-.|.+||.-...+-++=|.-....|.+|+.+++..
T Consensus 1 ~~T~~g~~kL~~EL~~-------Lk~v~RpeI~~~I~~AR~~GDLsENAEY~AAKe~Q~~~E~RI~~le~~l~~A 68 (155)
T TIGR01462 1 PLTQEGYEKLKEELEY-------LKTVKRPEISEEIKEAREHGDLSENAEYHAAKEEQGFIEGRIAELEDLLANA 68 (155)
T ss_pred CCCHHHHHHHHHHHHH-------HHCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCE
T ss_conf 9788899999999988-------5026118999999999851886556003899999999988999999887620
No 21
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=50.72 E-value=22 Score=17.16 Aligned_cols=13 Identities=23% Similarity=0.417 Sum_probs=5.7
Q ss_pred EECCCCCH--HHHHH
Q ss_conf 86155568--99999
Q gi|254780776|r 101 IPVPETTE--ERRLA 113 (186)
Q Consensus 101 i~iP~lT~--E~R~~ 113 (186)
+.+|.+.. |.|+.
T Consensus 30 ~~lPri~~~le~R~~ 44 (157)
T PRK06569 30 FITPKAEEIFNNRQT 44 (157)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 986048779998999
No 22
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=49.31 E-value=21 Score=17.30 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHH
Q ss_conf 596789999999631788998454773478861555689999999999
Q gi|254780776|r 71 WDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVA 118 (186)
Q Consensus 71 ~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~ 118 (186)
-||..++.|++.+.+-=.+.+-. .-..-...||||+.|.|.-+--.|
T Consensus 6 kdp~fv~~VE~~l~~LV~~~~~~-~q~~rsh~FppM~~~~R~~iHela 52 (74)
T cd02643 6 KDPKFVKDVEKDLIELVESVNKG-KQTSRSHSFPPMNREKRRIVHELA 52 (74)
T ss_pred HCCHHHHHHHHHHHHHHHHHHCC-CCCCCEEECCCCCHHHHHHHHHHH
T ss_conf 09499999999999999986517-887651557999989999999999
No 23
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=48.58 E-value=24 Score=16.94 Aligned_cols=55 Identities=20% Similarity=0.126 Sum_probs=40.0
Q ss_pred CCCCCC--CCCC--EEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899845--4773--478861555689999999999998889999999999999999998
Q gi|254780776|r 88 LGLNPI--VEGQ--VLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKK 142 (186)
Q Consensus 88 l~l~p~--~dg~--~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk 142 (186)
+|+++. ..|. ..--|+.++|.|.|+.+...+....+.....|..-|....+.++.
T Consensus 125 ~Gi~~~~~~sg~~K~~~~p~~~~s~e~~~~~q~~ld~~~~~F~~~Va~~R~~~~~~~~~ 183 (214)
T cd07022 125 AGLKVTLIFAGAHKVDGNPDEPLSDEARARLQAEVDALYAMFVAAVARNRGLSAAAVRA 183 (214)
T ss_pred CCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 79547874057633236875656889999999999999999999999857999778887
No 24
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=46.10 E-value=26 Score=16.69 Aligned_cols=60 Identities=7% Similarity=0.149 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 998889999999999999999998753589-997899888999999999999999999999
Q gi|254780776|r 119 HAYAEKSKISVRNIRRDGMDHLKKSRKSGK-ASEDMVASLENDIQKITDSTIKNIDSFFEE 178 (186)
Q Consensus 119 k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~-iseD~~~~~~~~iq~lt~~~~~~id~~~~~ 178 (186)
....+++...+...|.++..-+...+.... ..++-...+..+.+.+.++....|+.--..
T Consensus 56 ~~~~~e~e~~l~~Ar~ea~~ii~~A~~~a~~~~~~~~~~A~~e~~~~~~~A~~~Ie~ek~~ 116 (140)
T PRK07353 56 EKLEAQYEQQLASARKQAQQVIAEAEAEADKLYAEALAEAQAEAQASKEKARREIEQQKQS 116 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999999999999999999999999999999999999999999999
No 25
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=45.47 E-value=26 Score=16.63 Aligned_cols=72 Identities=13% Similarity=0.228 Sum_probs=28.6
Q ss_pred CCCCCH--HHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 155568--999999999-----------999888999999999999999999875358-999789988899999999999
Q gi|254780776|r 103 VPETTE--ERRLALVKV-----------AHAYAEKSKISVRNIRRDGMDHLKKSRKSG-KASEDMVASLENDIQKITDST 168 (186)
Q Consensus 103 iP~lT~--E~R~~lvK~-----------~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~-~iseD~~~~~~~~iq~lt~~~ 168 (186)
.||++. +.|++.++. +....+++...++.+|.++..-+...+... ...++-...+..+++.+.++.
T Consensus 38 ~~pi~~~Ld~R~~~I~~~l~~Ae~~k~eA~~~~~e~e~~L~~A~~ea~~Ii~~A~~~Ae~~~~~~~~~A~~ea~~i~~~A 117 (173)
T PRK13460 38 WDVILKALDERASGVQNDINKASELRLEAEALLKDYEARLNSAKDEANAIVAEAKSDALKLKNKLLEETNNEVKAQKDQA 117 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88899999999999998899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780776|r 169 IKNIDS 174 (186)
Q Consensus 169 ~~~id~ 174 (186)
...|+.
T Consensus 118 ~~~Ie~ 123 (173)
T PRK13460 118 VKEIEL 123 (173)
T ss_pred HHHHHH
T ss_conf 999999
No 26
>TIGR02400 trehalose_OtsA alpha,alpha-trehalose-phosphate synthase [UDP-forming]; InterPro: IPR012766 This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This entry excludes glucosylglycerol-phosphate synthase, an enzyme of an analogous osmoprotectant system in many cyanobacterial strains. This entry does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. Sequences that score in the gray zone between the trusted and noise cut offs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. The gray zone also includes the OtsA of Cornyebacterium glutamicum (and related species), shown to be responsible for synthesis of only trace amounts of trehalose while the majority is synthesized by the TreYZ pathway; the significance of OtsA in this species is unclear (see ).; GO: 0003825 alphaalpha-trehalose-phosphate synthase (UDP-forming) activity, 0005992 trehalose biosynthetic process.
Probab=45.14 E-value=12 Score=18.92 Aligned_cols=34 Identities=12% Similarity=0.149 Sum_probs=15.9
Q ss_pred HHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEE
Q ss_conf 78245078855864239987651205783898996
Q gi|254780776|r 36 SMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSV 70 (186)
Q Consensus 36 ~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~ 70 (186)
+-+|-++|-|-...+|-..|++.=.- +..-.|||
T Consensus 349 g~~~WtPi~Y~~~~~~~~~L~aLYr~-adV~LVTp 382 (476)
T TIGR02400 349 GTLDWTPIRYLNRSYPREELMALYRA-ADVGLVTP 382 (476)
T ss_pred CCCCCEEEEEECCCCCHHHHHHHHHH-CCEEEECC
T ss_conf 78885367872388886899999741-03266545
No 27
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=45.14 E-value=27 Score=16.59 Aligned_cols=71 Identities=18% Similarity=0.164 Sum_probs=50.0
Q ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 86155568999999999999888999999999999999999875-35899978998889999999999999999999999
Q gi|254780776|r 101 IPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSR-KSGKASEDMVASLENDIQKITDSTIKNIDSFFEEK 179 (186)
Q Consensus 101 i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~-k~~~iseD~~~~~~~~iq~lt~~~~~~id~~~~~K 179 (186)
+.=|.||.|-++.|..-+... |..|+.....+.... ..|.+||.-....-++-|...+..|..++..+...
T Consensus 5 ~~~p~lTpeG~~~L~~EL~~L--------k~~rr~~v~~~~~~a~~~GDlSENaEY~~aK~eq~~ie~RI~~Le~~L~~a 76 (161)
T PRK05892 5 VESPGLADAARDHLAAELARL--------RQRRDRLEVEVKNDRGMIGDHGDAAEAIQRADELAILGDRINELDRRLRTG 76 (161)
T ss_pred CCCCCCCHHHHHHHHHHHHHH--------HHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 579997999999999999999--------882639999999999977994566739999999999999999999999728
No 28
>TIGR00422 valS valyl-tRNA synthetase; InterPro: IPR002303 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=40.93 E-value=31 Score=16.16 Aligned_cols=121 Identities=15% Similarity=0.230 Sum_probs=87.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHH------------HCCEEEEECCCC-C----HHHHHHHHHCCCCCEEEEEECC
Q ss_conf 9999999999999997531388889678------------245078855864-2----3998765120578389899659
Q gi|254780776|r 10 IKDRMGDTISFLKKDMMTLRTGRVSPSM------------LDLVKVEAYGSH-V----PLNQVANVTVLEPRMLVVSVWD 72 (186)
Q Consensus 10 ~~~~m~~~i~~l~~el~~irtGrasp~l------------ld~i~V~~~g~~-~----pL~~lA~Is~~~~~~l~I~~~D 72 (186)
.-++++.+|....+.|.+.+=+-|+-.+ +|-++...||+. . ...+... ++.+.-+.++.||=
T Consensus 714 ILs~L~~~i~~v~~~ld~Y~F~~a~~~ly~F~W~dFCD~YIE~~K~~~~~~~~~~~k~~A~~~L~-~vLd~~l~LLhPf~ 792 (970)
T TIGR00422 714 ILSKLNRTIKEVREALDKYRFNEAAKALYEFIWNDFCDWYIELVKYRLYNGNDEAEKKAARDTLA-YVLDKALRLLHPFM 792 (970)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHCCCC
T ss_conf 99999999999999884036778875765210134512354421431478973899999999999-99999999852455
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCEEEEE-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 678999999963178899845477347886-1555689999999999998889999999999999999
Q gi|254780776|r 73 KEMVASVERGIHESNLGLNPIVEGQVLRIP-VPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDH 139 (186)
Q Consensus 73 ~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~-iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ 139 (186)
|-..-.|...+...- +.+|.+. .|....+.-.+-+-..-+..-++=++||++|.+.+=.
T Consensus 793 PF~tE~iwq~~~~~~--------~~si~~~~yP~~~~~~~D~~~~~~~~~~~~~i~~~R~~k~~~~~~ 852 (970)
T TIGR00422 793 PFITEEIWQHLKEGE--------ADSIMLQSYPEVDAEFVDEEAEKAFELLKEIIVSIRNLKAESNIP 852 (970)
T ss_pred CHHHHHHHHHHCCCC--------CEEEEECCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 225789998843610--------104221357652334157756888999999999998889870678
No 29
>pfam03786 UxuA D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.
Probab=39.92 E-value=32 Score=16.06 Aligned_cols=81 Identities=28% Similarity=0.371 Sum_probs=48.5
Q ss_pred CC---CCCHHHHHHHH-HCCCCCEE-----EEEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHH
Q ss_conf 58---64239987651-20578389-----89965967899999996317889984547734788615556899999999
Q gi|254780776|r 46 YG---SHVPLNQVANV-TVLEPRML-----VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVK 116 (186)
Q Consensus 46 ~g---~~~pL~~lA~I-s~~~~~~l-----~I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK 116 (186)
|| .+.+|.+|.|+ .+.+--+- .=.+|+...+....+-|.+++|.|.... .+|. . |.-+-=.-
T Consensus 8 ~Gp~~Dpv~L~~irQ~pG~~giV~aLh~~p~GevW~~~~I~~~k~~ie~~GL~~~vVE-------SvPv-h-e~Ik~g~~ 78 (350)
T pfam03786 8 YGPGNDPVTLWRIRQIPGVTGVVGALHDIPVGEVWPKEEIMALKEIIEDAGLTLSVIE-------SVPV-H-EDIKLGTP 78 (350)
T ss_pred ECCCCCCCCHHHHHCCCCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEE-------CCCC-H-HHHHCCCC
T ss_conf 0799985259998454798645430568999894899999999999997499699994-------7786-6-88874998
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 9999888999999999999
Q gi|254780776|r 117 VAHAYAEKSKISVRNIRRD 135 (186)
Q Consensus 117 ~~k~~~E~~K~~iR~iR~~ 135 (186)
...+..|.++.+|||+=+-
T Consensus 79 ~rd~~Ieny~~tirNLa~~ 97 (350)
T pfam03786 79 TRDRYIENYKQTIRNLARA 97 (350)
T ss_pred CHHHHHHHHHHHHHHHHHC
T ss_conf 7899999999999999977
No 30
>pfam00244 14-3-3 14-3-3 protein.
Probab=38.27 E-value=34 Score=15.89 Aligned_cols=30 Identities=23% Similarity=0.106 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 555689999999999998889999999999
Q gi|254780776|r 104 PETTEERRLALVKVAHAYAEKSKISVRNIR 133 (186)
Q Consensus 104 P~lT~E~R~~lvK~~k~~~E~~K~~iR~iR 133 (186)
|.||.|-|.-|.-.-|...-.-|.+.|.+.
T Consensus 32 ~~Ls~eERnLLsvayKn~i~~rR~s~R~l~ 61 (236)
T pfam00244 32 EELSVEERNLLSVAYKNVIGARRASWRIIS 61 (236)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 989999999999999987410099999998
No 31
>COG1666 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.16 E-value=33 Score=15.92 Aligned_cols=95 Identities=16% Similarity=0.305 Sum_probs=62.0
Q ss_pred HCHHHHHHHHHHHHHHHHHHHHH---CCCCCCCHHHHCCEEEEEC-CCCCHHHHHHHH--------------------HC
Q ss_conf 07899999999999999999753---1388889678245078855-864239987651--------------------20
Q gi|254780776|r 5 IDLQNIKDRMGDTISFLKKDMMT---LRTGRVSPSMLDLVKVEAY-GSHVPLNQVANV--------------------TV 60 (186)
Q Consensus 5 ~dl~~~~~~m~~~i~~l~~el~~---irtGrasp~lld~i~V~~~-g~~~pL~~lA~I--------------------s~ 60 (186)
+|+.++.+ |++.-.+++++ +|.-.++-++-|+-.|..- .+.+.|.++--| ..
T Consensus 13 vd~qEv~N----Ave~A~kel~sR~Dfkg~~~~iel~e~e~i~l~s~sdf~l~ql~DIl~~kliKRgi~~k~~d~~~~~~ 88 (165)
T COG1666 13 VDLQEVRN----AVENANKELASRFDFKGVKASIELKENETIKLTSESDFQLEQLKDILRSKLIKRGISGKALDIPKEEV 88 (165)
T ss_pred CCHHHHHH----HHHHHHHHHHHHHCCCCCCCEEECCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCHHHCCCCCHHH
T ss_conf 13999999----99999998765505578842175078715998506366699999999999987399755414530012
Q ss_pred CCCCEEEEEE-----CCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEC
Q ss_conf 5783898996-----596789999999631788998454773478861
Q gi|254780776|r 61 LEPRMLVVSV-----WDKEMVASVERGIHESNLGLNPIVEGQVLRIPV 103 (186)
Q Consensus 61 ~~~~~l~I~~-----~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~i 103 (186)
.+|.++.... -+..+.|-|.+-|.+|.|-++.+..|..+||+=
T Consensus 89 ~sG~~~~~~~klkqGI~~e~AKKI~KlIkDsklKVqaqIQGdqVRVtg 136 (165)
T COG1666 89 ASGKTVRQEAKLKQGIESENAKKIVKLIKDSKLKVQAQIQGDQVRVTG 136 (165)
T ss_pred HCCCEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEEEEC
T ss_conf 038746775408642417889999999882241000043064678705
No 32
>PRK03906 mannonate dehydratase; Provisional
Probab=37.74 E-value=34 Score=15.84 Aligned_cols=81 Identities=21% Similarity=0.338 Sum_probs=50.3
Q ss_pred CC--CCCHHHHHHHHHCCCCCEEE--E---EECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHH
Q ss_conf 58--64239987651205783898--9---96596789999999631788998454773478861555689999999999
Q gi|254780776|r 46 YG--SHVPLNQVANVTVLEPRMLV--V---SVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVA 118 (186)
Q Consensus 46 ~g--~~~pL~~lA~Is~~~~~~l~--I---~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~ 118 (186)
|| .+++|.+|.|+.+.+-=+-. | .+|....|..-...|.+++|.|...- ++| +.+..+ -=....
T Consensus 8 fGp~D~V~L~~irQ~G~~giVtaLh~ip~GevW~~eeI~~~k~~Ie~~GL~w~VVE-------SvP-Vhe~IK-~g~~~~ 78 (389)
T PRK03906 8 YGPNDPVTLEDIRQAGATGIVTALHHIPNGEVWPVEEILKRKAEIEAAGLEWSVVE-------SVP-VHEDIK-TGTPNR 78 (389)
T ss_pred CCCCCCCCHHHHHHHCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEE-------CCC-CHHHHH-CCCCCH
T ss_conf 59989616899986388706500236899886799999999999997498189984-------678-568887-499878
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99888999999999999
Q gi|254780776|r 119 HAYAEKSKISVRNIRRD 135 (186)
Q Consensus 119 k~~~E~~K~~iR~iR~~ 135 (186)
.+..|.+|.+|||+-+-
T Consensus 79 d~~Ienyk~sirNLa~~ 95 (389)
T PRK03906 79 DQYIENYKQTLRNLAAA 95 (389)
T ss_pred HHHHHHHHHHHHHHHHC
T ss_conf 99999999999999976
No 33
>cd06061 PurM-like1 AIR synthase (PurM) related protein, subgroup 1 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.
Probab=37.22 E-value=23 Score=16.99 Aligned_cols=53 Identities=17% Similarity=0.199 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHCCC---CCCCCCCCCCEEEEECCC-CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 678999999963178---899845477347886155-5689999999999998889999
Q gi|254780776|r 73 KEMVASVERGIHESN---LGLNPIVEGQVLRIPVPE-TTEERRLALVKVAHAYAEKSKI 127 (186)
Q Consensus 73 ~~~ik~I~kAI~~s~---l~l~p~~dg~~I~i~iP~-lT~E~R~~lvK~~k~~~E~~K~ 127 (186)
|..+..+.-|..-|| +|-.|. .-++.+.+|+ .+.+.=+++++-..+.|+++.+
T Consensus 56 ~~~~G~~ava~~~sDI~amGa~P~--~~l~~l~~p~~~~~~~l~~i~~Gi~~~~~~~g~ 112 (298)
T cd06061 56 GKDAGWLAVHIAANDIATSGARPR--WLLVTLLLPPGTDEEELKAIMREINEAAKELGV 112 (298)
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEH--HHHHHEECCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 136999999987999998599828--876121188999999999999999999998399
No 34
>PRK04457 spermidine synthase; Provisional
Probab=36.96 E-value=35 Score=15.76 Aligned_cols=96 Identities=15% Similarity=0.230 Sum_probs=63.5
Q ss_pred CHHHHCCEEEEECCCCCH---------HHHHHHHHCCCCCEEEEEECCH-----HHHHHHHHHHHCCCCCCCCCCCCCEE
Q ss_conf 967824507885586423---------9987651205783898996596-----78999999963178899845477347
Q gi|254780776|r 34 SPSMLDLVKVEAYGSHVP---------LNQVANVTVLEPRMLVVSVWDK-----EMVASVERGIHESNLGLNPIVEGQVL 99 (186)
Q Consensus 34 sp~lld~i~V~~~g~~~p---------L~~lA~Is~~~~~~l~I~~~D~-----~~ik~I~kAI~~s~l~l~p~~dg~~I 99 (186)
.++-.|-|.|+.|+...+ +.+.... ..++-.++++.|.. ..+..+..+..+.-+-+-+..+||.|
T Consensus 133 ~~~~~DvI~vD~fd~~g~~~~L~t~~Fy~~c~~~-L~~~Gvlv~Nl~~~~~~~~~~l~~i~~~F~~~~~~~~~~~~GN~I 211 (262)
T PRK04457 133 FPASTDVILVDGFDGEQIVDALVTQPFFRDCRNA-LSSDGVFVTNLWSGDKRYQRYIERLLSVFEGRVLELPAESHGNVA 211 (262)
T ss_pred CCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHHH-CCCCCEEEEECCCCCCCHHHHHHHHHHHHCCEEEEEECCCCCEEE
T ss_conf 8677788999688988886000829999999986-498939999868899865999999999728739997258998089
Q ss_pred EEECCCCCHHH-HHHHHHHHHHHHHHHHHHHH
Q ss_conf 88615556899-99999999998889999999
Q gi|254780776|r 100 RIPVPETTEER-RLALVKVAHAYAEKSKISVR 130 (186)
Q Consensus 100 ~i~iP~lT~E~-R~~lvK~~k~~~E~~K~~iR 130 (186)
-+.+-....+. ..+|...|+..-.+....++
T Consensus 212 v~A~k~~~~~~~~~~L~~rA~~L~~~~gl~~~ 243 (262)
T PRK04457 212 VFAFQSAPKEQRWDKLKKRADKLSNAYGLDFH 243 (262)
T ss_pred EEEECCCCCCCCHHHHHHHHHHHHHHHCCCHH
T ss_conf 99978999986899999999999997797999
No 35
>TIGR03562 osmo_induc_OsmC peroxiredoxin, OsmC subfamily. pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress.
Probab=36.22 E-value=36 Score=15.68 Aligned_cols=29 Identities=24% Similarity=0.247 Sum_probs=24.4
Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 47886155568999999999999888999
Q gi|254780776|r 98 VLRIPVPETTEERRLALVKVAHAYAEKSK 126 (186)
Q Consensus 98 ~I~i~iP~lT~E~R~~lvK~~k~~~E~~K 126 (186)
.+++.+|.+.+|.-++++..|++.|==+|
T Consensus 97 ~v~~~vpg~d~e~a~~l~~~Ah~~CPySk 125 (135)
T TIGR03562 97 TVRAKVPGIDEAKFQEIAEKAKEGCPVSK 125 (135)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHCCHHH
T ss_conf 99997489899999999999975496524
No 36
>pfam00430 ATP-synt_B ATP synthase B/B' CF(0). Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006
Probab=35.70 E-value=37 Score=15.62 Aligned_cols=79 Identities=14% Similarity=0.220 Sum_probs=29.6
Q ss_pred ECCCCCH--HHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHH
Q ss_conf 6155568--9999999999998889-----------999999999999999998753589-9978998889999999999
Q gi|254780776|r 102 PVPETTE--ERRLALVKVAHAYAEK-----------SKISVRNIRRDGMDHLKKSRKSGK-ASEDMVASLENDIQKITDS 167 (186)
Q Consensus 102 ~iP~lT~--E~R~~lvK~~k~~~E~-----------~K~~iR~iR~~~~~~ikk~~k~~~-iseD~~~~~~~~iq~lt~~ 167 (186)
.+||++. +.|++.+..--..+++ +...+...|.++..-+........ ..++....+.++++.+..+
T Consensus 20 ~~~pi~~~l~~R~~~I~~~l~~a~~~~~ea~~~~~~~e~~l~~a~~ea~~i~~~a~~~a~~~~~~~~~~a~~e~~~~~~~ 99 (132)
T pfam00430 20 GYKPLGKILDERKEKIANNIKEAEERLKQAAALLAEAEQQLAQARAEASEIINNAKKEAQKLKEEILAEAQKDAERLLES 99 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 79889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999999
Q gi|254780776|r 168 TIKNIDSFFEEKK 180 (186)
Q Consensus 168 ~~~~id~~~~~Ke 180 (186)
....++..-....
T Consensus 100 a~~~i~~e~~~a~ 112 (132)
T pfam00430 100 ARAEIEQEKEQAL 112 (132)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999999
No 37
>PRK13022 secF preprotein translocase subunit SecF; Reviewed
Probab=34.23 E-value=39 Score=15.47 Aligned_cols=64 Identities=13% Similarity=0.123 Sum_probs=42.2
Q ss_pred CCCCEEEEEECCHHHHHHHHHHHHCCCCCCC-CC--CCCCEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 5783898996596789999999631788998-45--4773478861555689999999999998889
Q gi|254780776|r 61 LEPRMLVVSVWDKEMVASVERGIHESNLGLN-PI--VEGQVLRIPVPETTEERRLALVKVAHAYAEK 124 (186)
Q Consensus 61 ~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~-p~--~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~ 124 (186)
.+|..+.+..-.+-....+..++.+++++-. .| .+++.+.|..|.++.|.++++...+.+....
T Consensus 41 tGGt~i~v~~~~~~~~~~vr~~l~~~~~~~~~vq~~g~~~~~~Ir~~~~~~~~~~~v~~~l~~~~~~ 107 (294)
T PRK13022 41 TGGTVIEVEFEQPADLDQVREALAKAGFEDASVQNFGSGRDVLIRLPTLSEEQSNKVIKALNKALGD 107 (294)
T ss_pred CCCEEEEEEECCCCCHHHHHHHHHHCCCCCCCEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf 7975999981898988999999986599886079816997799994688857999999999986389
No 38
>COG3696 Putative silver efflux pump [Inorganic ion transport and metabolism]
Probab=34.07 E-value=17 Score=17.87 Aligned_cols=18 Identities=22% Similarity=0.562 Sum_probs=9.1
Q ss_pred CEEEEECCCCC-HHHHHHH
Q ss_conf 50788558642-3998765
Q gi|254780776|r 40 LVKVEAYGSHV-PLNQVAN 57 (186)
Q Consensus 40 ~i~V~~~g~~~-pL~~lA~ 57 (186)
.+-|..||.-. .|+++|.
T Consensus 671 dvaIKvfG~Dl~~L~~la~ 689 (1027)
T COG3696 671 DLAIKVFGDDLAELNELAE 689 (1027)
T ss_pred CEEEEEECCCHHHHHHHHH
T ss_conf 4489984787999999999
No 39
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=32.58 E-value=41 Score=15.29 Aligned_cols=39 Identities=23% Similarity=0.418 Sum_probs=34.8
Q ss_pred HHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHH
Q ss_conf 782450788558642399876512057838989965967
Q gi|254780776|r 36 SMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKE 74 (186)
Q Consensus 36 ~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~ 74 (186)
.-||-|-|+-||++.|.-+-|--+++.+-.|.||.-|.+
T Consensus 120 ~~fd~IDiDPFGSPaPFlDaA~~s~~~~G~l~vTATD~a 158 (380)
T COG1867 120 RAFDVIDIDPFGSPAPFLDAALRSVRRGGLLCVTATDTA 158 (380)
T ss_pred CCCCEEECCCCCCCCHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf 876378138999972679999997222988999851552
No 40
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=32.09 E-value=22 Score=17.14 Aligned_cols=22 Identities=14% Similarity=0.013 Sum_probs=8.9
Q ss_pred EEEEECCCCCHHHHHHHHHHHH
Q ss_conf 4788615556899999999999
Q gi|254780776|r 98 VLRIPVPETTEERRLALVKVAH 119 (186)
Q Consensus 98 ~I~i~iP~lT~E~R~~lvK~~k 119 (186)
.+|.|+++++++.++.+.+.++
T Consensus 283 ~vR~Pl~~~~ea~~E~lre~~r 304 (309)
T cd00952 283 PARPPYNTAPEAYLEGARESGR 304 (309)
T ss_pred CCCCCCCCCCHHHHHHHHHHHH
T ss_conf 9899999899999999999999
No 41
>pfam02825 WWE WWE domain. The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Probab=32.08 E-value=42 Score=15.24 Aligned_cols=43 Identities=14% Similarity=0.162 Sum_probs=33.9
Q ss_pred EEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCHHH
Q ss_conf 9965967899999996317889984547734788615556899
Q gi|254780776|r 68 VSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEER 110 (186)
Q Consensus 68 I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~ 110 (186)
=.|||+..-..||.|.....-.+....-|..-.|-|+.||+-.
T Consensus 19 W~~Y~~~~~~~IE~a~~~~~~~~~~~~~g~~Y~IDf~~M~Q~n 61 (72)
T pfam02825 19 WTPYSPHVSKHIENAYAAKKPTLEVSICGRPYTIDFNSMTQLR 61 (72)
T ss_pred EEECCHHHHHHHHHHHHCCCCEEEEEECCCEEEEECCCCEEEC
T ss_conf 4718879999999999859988999838927999878438984
No 42
>KOG2916 consensus
Probab=31.97 E-value=42 Score=15.22 Aligned_cols=112 Identities=14% Similarity=0.167 Sum_probs=64.6
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEECCCCCHHHHHHHHHCCCC----CEEEEEECCHHHHHHHHHHHHC
Q ss_conf 999999999999999753138888967824507885586423998765120578----3898996596789999999631
Q gi|254780776|r 10 IKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEP----RMLVVSVWDKEMVASVERGIHE 85 (186)
Q Consensus 10 ~~~~m~~~i~~l~~el~~irtGrasp~lld~i~V~~~g~~~pL~~lA~Is~~~~----~~l~I~~~D~~~ik~I~kAI~~ 85 (186)
+..++..+++.|+.- -.+|.+||.+.++-.-...-|++|.-=-+|.+ --+-+.||.-.-|-+|..|+.+
T Consensus 134 ~~rk~g~aYdaFK~~-------vtd~tV~d~l~~~~~vk~~Llk~Irrrltpq~vKIRADIEv~Cf~yeGI~aIK~alk~ 206 (304)
T KOG2916 134 LERKYGHAYDAFKIA-------VTDPTVLDELDLSEEVKEVLLKNIRRRLTPQTVKIRADIEVSCFGYEGIDAIKAALKA 206 (304)
T ss_pred HHHHHCHHHHHHHHH-------CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCHHHHHHHHHH
T ss_conf 366636099999886-------2684302666777789999999998754886557873258986065679999999998
Q ss_pred CCCCCCCCCCCCEEEEECCCC---CH--HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 788998454773478861555---68--999999999999888999999
Q gi|254780776|r 86 SNLGLNPIVEGQVLRIPVPET---TE--ERRLALVKVAHAYAEKSKISV 129 (186)
Q Consensus 86 s~l~l~p~~dg~~I~i~iP~l---T~--E~R~~lvK~~k~~~E~~K~~i 129 (186)
.+++.|..-+-.|.+.-||+ |. --|..-.+.+...++..+..|
T Consensus 207 -a~~~~te~~piki~LIApPlYVlTT~tldK~~g~e~l~~Ai~~i~~~I 254 (304)
T KOG2916 207 -ALNLSTEECPIKIKLIAPPLYVLTTQTLDKTKGLEVLEEAIEVIISKI 254 (304)
T ss_pred -HHHCCCCCCCEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHHHHHH
T ss_conf -872796657458998558648998863020111999999999999988
No 43
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein; InterPro: IPR013459 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of the gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source..
Probab=31.64 E-value=43 Score=15.19 Aligned_cols=45 Identities=24% Similarity=0.291 Sum_probs=26.5
Q ss_pred HHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHCCCCC
Q ss_conf 782450788558642399876512057838989965967899999996317889
Q gi|254780776|r 36 SMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLG 89 (186)
Q Consensus 36 ~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s~l~ 89 (186)
++..+|+|-+|++-+ .|++|.|.|+|-|...|..+.=-+.+..|+
T Consensus 77 A~~rgI~Vv~~DS~v---------~pegR~l~~n~a~~~~IG~~~vql~A~~~~ 121 (307)
T TIGR02637 77 AMKRGIKVVTWDSGV---------APEGRKLFLNQADAELIGRTQVQLAAEQLE 121 (307)
T ss_pred HHHCCCEEEEECCCC---------CCCCCEEEECCCCHHHHHHHHHHHHHHHHC
T ss_conf 985698299852788---------813454422646831288999999999717
No 44
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=31.07 E-value=44 Score=15.12 Aligned_cols=57 Identities=7% Similarity=0.150 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999999999999987535-899978998889999999999999999999999
Q gi|254780776|r 123 EKSKISVRNIRRDGMDHLKKSRKS-GKASEDMVASLENDIQKITDSTIKNIDSFFEEK 179 (186)
Q Consensus 123 E~~K~~iR~iR~~~~~~ikk~~k~-~~iseD~~~~~~~~iq~lt~~~~~~id~~~~~K 179 (186)
+++...++..|.++..-+....+. ....+.....+..+++.....+..+++.--...
T Consensus 62 ~e~e~~L~~Ar~ea~~ii~~A~~~A~~~~~~~~~~Ar~eae~~~~~a~~~ie~ek~~a 119 (141)
T PRK08476 62 AEIEAILKNAREEANKIRQEAIAAAKEEAEQKIEAKKEELESKYEAFAQQLANQKQEL 119 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999999999999999999999999999999999999999999999
No 45
>cd01232 PH_TRIO Trio pleckstrin homology (PH) domain. Trio is a multidomain signaling protein that contains two RhoGEF(DH)-PH domains in tandem. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=29.81 E-value=46 Score=14.98 Aligned_cols=44 Identities=25% Similarity=0.355 Sum_probs=32.5
Q ss_pred HHHHHCCCCCCCCCCCCCEE--------------EEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99963178899845477347--------------886155568999999999999888
Q gi|254780776|r 80 ERGIHESNLGLNPIVEGQVL--------------RIPVPETTEERRLALVKVAHAYAE 123 (186)
Q Consensus 80 ~kAI~~s~l~l~p~~dg~~I--------------~i~iP~lT~E~R~~lvK~~k~~~E 123 (186)
...|.-|+||++..++|+.. +..+-..|.|.+++.++..+.+.+
T Consensus 56 K~~ik~s~lgltE~v~gd~~kF~iw~~~~~~~~~~~ilQA~s~e~K~~Wv~~I~~iL~ 113 (114)
T cd01232 56 KSKLQVSKMGLTEHVEGDPCRFALWSGDPPISDNRIILKANSQETKQEWVKKIREILQ 113 (114)
T ss_pred ECCEECCCCCCEECCCCCCCEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf 2000337514767369998789999468999860899988998999999999999971
No 46
>pfam10835 DUF2573 Protein of unknown function (DUF2573). Some members in this bacterial family of proteins are annotated as YusU however no function is currently known. This family of proteins appears to be restricted to Bacillus spp.
Probab=29.49 E-value=29 Score=16.37 Aligned_cols=32 Identities=16% Similarity=0.261 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEE
Q ss_conf 99999999999997531388889678245078
Q gi|254780776|r 12 DRMGDTISFLKKDMMTLRTGRVSPSMLDLVKV 43 (186)
Q Consensus 12 ~~m~~~i~~l~~el~~irtGrasp~lld~i~V 43 (186)
++++.-++.|-+.|+.+.+|-+|+.+-+.|++
T Consensus 2 ~kl~eqldgL~eKytELLlGet~ee~ke~Vk~ 33 (82)
T pfam10835 2 EKLKEQLDGLLEKYTELLLGETNEELKEKVKK 33 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 47789999999999999836898999999999
No 47
>pfam00922 Phosphoprotein Vesiculovirus phosphoprotein.
Probab=29.44 E-value=46 Score=14.94 Aligned_cols=44 Identities=25% Similarity=0.264 Sum_probs=35.2
Q ss_pred HCCCCCCCCC-----CCCCEEEEECCC-CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3178899845-----477347886155-5689999999999998889999
Q gi|254780776|r 84 HESNLGLNPI-----VEGQVLRIPVPE-TTEERRLALVKVAHAYAEKSKI 127 (186)
Q Consensus 84 ~~s~l~l~p~-----~dg~~I~i~iP~-lT~E~R~~lvK~~k~~~E~~K~ 127 (186)
..++.+|.+- ..|.++++..|. ||.+.+.+..+.++.+++.+|.
T Consensus 98 F~~~~~W~~p~~k~~~g~~~l~L~~P~gLt~~Q~~QW~~tI~Al~~ssk~ 147 (283)
T pfam00922 98 FEEDRPWKPPVQKSDNGRKTLELSAPEGLTGEQLSQWLSTIKAVMESSKY 147 (283)
T ss_pred CCCCCCCCCCEEECCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 15788655643760698548997378888989999999999999987457
No 48
>PRK00943 selenophosphate synthetase; Provisional
Probab=28.69 E-value=48 Score=14.86 Aligned_cols=74 Identities=15% Similarity=0.123 Sum_probs=44.0
Q ss_pred HHHHHHCCCCCEEEEE-----E--CCHHHHHHHHHHHHCCC---CCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 8765120578389899-----6--59678999999963178---899845477347886155568999999999999888
Q gi|254780776|r 54 QVANVTVLEPRMLVVS-----V--WDKEMVASVERGIHESN---LGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAE 123 (186)
Q Consensus 54 ~lA~Is~~~~~~l~I~-----~--~D~~~ik~I~kAI~~s~---l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E 123 (186)
+-|-+...+++.|+-+ | .||.....|..+-.-|| +|-.|..-=..+-+|.+.+..|.-.++.+.+...+.
T Consensus 51 Daavi~~~~~~~lv~T~D~f~piv~Dp~~~G~IAa~~alsDi~AmGa~P~~aL~~~~~p~~~l~~e~l~~il~g~~~~~~ 130 (347)
T PRK00943 51 DAAVYDLNNGQAIVSTTDFFMPIVDDPFDFGRIAATNAISDVYAMGGKPIMALAILGWPINVLPPEVAREVLEGGRDVCR 130 (347)
T ss_pred CEEEEEECCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 55899728980899980466677568788899999985768988389488999884302021679999999999999999
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254780776|r 124 KSKI 127 (186)
Q Consensus 124 ~~K~ 127 (186)
++.+
T Consensus 131 e~gv 134 (347)
T PRK00943 131 EAGI 134 (347)
T ss_pred HCCC
T ss_conf 8599
No 49
>pfam03982 DAGAT Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT).
Probab=28.65 E-value=48 Score=14.85 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999
Q gi|254780776|r 158 ENDIQKITDSTIKNIDSFFEEKK 180 (186)
Q Consensus 158 ~~~iq~lt~~~~~~id~~~~~Ke 180 (186)
+++|+++++.|++.+.++|++-.
T Consensus 261 ~e~Vd~~H~~Yi~~L~~LFe~~K 283 (297)
T pfam03982 261 QEQIDELHGQYMEALRELFEEHK 283 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999978
No 50
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=27.87 E-value=49 Score=14.76 Aligned_cols=107 Identities=18% Similarity=0.286 Sum_probs=72.8
Q ss_pred CCCHHHHHHHHHCCCCCEEEEE-ECCHHH-HHHHHHHHHCCCCCCCCC--CCC----CEEEEECCCCCHHHHHHHHH---
Q ss_conf 6423998765120578389899-659678-999999963178899845--477----34788615556899999999---
Q gi|254780776|r 48 SHVPLNQVANVTVLEPRMLVVS-VWDKEM-VASVERGIHESNLGLNPI--VEG----QVLRIPVPETTEERRLALVK--- 116 (186)
Q Consensus 48 ~~~pL~~lA~Is~~~~~~l~I~-~~D~~~-ik~I~kAI~~s~l~l~p~--~dg----~~I~i~iP~lT~E~R~~lvK--- 116 (186)
-.-|..+|+.|=.-++++-++. |-|... .+.+.-.|-+-+ .-.|. ... ..|.--+-+|++-.|+=++.
T Consensus 165 ~~kpvedv~~~L~Lne~~~S~D~Pl~~D~n~~Sl~d~~ADe~-~~~P~~~~~~~~l~~~~~~~L~~Lne~~R~V~~rRFG 243 (292)
T TIGR02394 165 LDKPVEDVSKVLALNERIASLDAPLDEDSNSKSLLDTIADEQ-SIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFG 243 (292)
T ss_pred HCCCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHCHHHHEEHHHHCC
T ss_conf 389888999998417995253057787743012100047888-7780764218999999999886106321121010037
Q ss_pred ----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf ----------999988899999999999999999987535899978998
Q gi|254780776|r 117 ----------VAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVA 155 (186)
Q Consensus 117 ----------~~k~~~E~~K~~iR~iR~~~~~~ikk~~k~~~iseD~~~ 155 (186)
.+.+...-.|..||.|..++..+||......+++.|.++
T Consensus 244 L~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~~G~~~e~Lf 292 (292)
T TIGR02394 244 LRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILERKGVDREALF 292 (292)
T ss_pred CCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHCC
T ss_conf 6654266699999872881047899889999999999986488455229
No 51
>TIGR01136 cysKM cysteine synthases; InterPro: IPR005856 This model discriminates cysteine synthases (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblance to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded. Cysteine synthase (O-acetylserine (thiol)-lyase) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM). CysM differs from CysK in that it can also use thiosulphate instead of sulphide, to produce cysteine thiosulphonate instead of cysteine. ; GO: 0004124 cysteine synthase activity, 0006535 cysteine biosynthetic process from serine.
Probab=27.72 E-value=47 Score=14.89 Aligned_cols=67 Identities=18% Similarity=0.252 Sum_probs=34.3
Q ss_pred CCHHHHHH---HHHCCCC-CEEEEEE--CCHH-------HHHHHHHHHHCCCCCCCCC-C---CCC--------------
Q ss_conf 42399876---5120578-3898996--5967-------8999999963178899845-4---773--------------
Q gi|254780776|r 49 HVPLNQVA---NVTVLEP-RMLVVSV--WDKE-------MVASVERGIHESNLGLNPI-V---EGQ-------------- 97 (186)
Q Consensus 49 ~~pL~~lA---~Is~~~~-~~l~I~~--~D~~-------~ik~I~kAI~~s~l~l~p~-~---dg~-------------- 97 (186)
.+||-.|= .++.... -.+.+.+ +.|+ .+.-|..|-..-.|+-.-. + .||
T Consensus 7 nTPLV~L~RCirl~~~~~~~~v~~KLE~~NP~gSVKDR~A~~MI~~AE~~G~lk~G~~iiEaTSGNTGIaLAMvAAarGY 86 (315)
T TIGR01136 7 NTPLVRLNRCIRLSEGCDEAEVLVKLEGFNPGGSVKDRIALNMILDAEKRGLLKPGTTIIEATSGNTGIALAMVAAARGY 86 (315)
T ss_pred CCCEEEEEEEEECCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHHHCCC
T ss_conf 88714410035427898851799997066989766568889999999865887888889842778448999999986199
Q ss_pred EEEEECCC-CCHHHHHHHH
Q ss_conf 47886155-5689999999
Q gi|254780776|r 98 VLRIPVPE-TTEERRLALV 115 (186)
Q Consensus 98 ~I~i~iP~-lT~E~R~~lv 115 (186)
.+.+++|. ||.|||+-|.
T Consensus 87 kliL~MPetmS~ERr~~l~ 105 (315)
T TIGR01136 87 KLILTMPETMSLERRKLLK 105 (315)
T ss_pred CEEEECCCCHHHHHHHHHH
T ss_conf 1899858871789999998
No 52
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=27.45 E-value=50 Score=14.71 Aligned_cols=46 Identities=22% Similarity=0.083 Sum_probs=36.6
Q ss_pred EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7886155568999999999999888999999999999999999875
Q gi|254780776|r 99 LRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSR 144 (186)
Q Consensus 99 I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~ 144 (186)
.--|++++|.|.|+.+...+....+.....|..-|......++.+.
T Consensus 133 ~~~~~~~~s~e~~~~~~~~ld~~~~~F~~~Va~~R~~~~~~v~~~~ 178 (208)
T cd07023 133 KGSPDRPLTEEERAILQALVDDIYDQFVDVVAEGRGMSGERLDKLA 178 (208)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 4577778999999999999999999999999986699989999985
No 53
>TIGR01818 ntrC nitrogen regulation protein NR(I); InterPro: IPR010114 This entry represents Nitrogen regulatory protein C (NtrC), which is a bacterial enhancer-binding protein that activates the transcription of genes encoding enzymes required for nitrogen metabolism. It is phosphorylated by NtrB and interacts with sigma-54. One of the best studied examples is its activation of the gene glnA, which encodes the enzyme glutamine synthetase.. NtrC is composed of three domains , . The 124 residue N-terminal domain is homologous to receiver domains of other response regulator proteins in two-component signal transduction systems , . The 240 residue central domain of NtrC is homologous to a domain found in all activators of the sigma-54 RNA polymerase holoenzyme , . The C-terminal domain has been indicated to contain the determinants necessary for both DNA-binding and dimerization of full-length NtrC.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0009399 nitrogen fixation, 0050906 detection of stimulus during sensory perception.
Probab=26.15 E-value=53 Score=14.56 Aligned_cols=60 Identities=23% Similarity=0.365 Sum_probs=42.9
Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 347886155568999999999999888999999----999999999999875358999789988899999
Q gi|254780776|r 97 QVLRIPVPETTEERRLALVKVAHAYAEKSKISV----RNIRRDGMDHLKKSRKSGKASEDMVASLENDIQ 162 (186)
Q Consensus 97 ~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~i----R~iR~~~~~~ikk~~k~~~iseD~~~~~~~~iq 162 (186)
++|+|.+||+- |||+.+-+.++..+..|-..+ +.+...+.+.++++. +. -.++.+|+-.-
T Consensus 299 ~Vi~i~lPpLr-ER~eDi~~L~rhFL~~a~~~l~~~~k~L~~~~~~~L~~~~----WP-GNVR~LEN~cR 362 (471)
T TIGR01818 299 NVIRIHLPPLR-ERREDIPRLARHFLALAAKELDVEPKLLSPEALEALKRYD----WP-GNVRELENVCR 362 (471)
T ss_pred CEEEECCCCCC-CHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCC----CC-CCHHHHHHHHH
T ss_conf 33462168721-2266899999999999887428651134889999997258----89-85245778999
No 54
>cd02046 hsp47 Heat shock protein 47 (Hsp47), also called colligin, because of its collagen binding ability, is a chaperone specific for procollagen. It has been shown to be essential for collagen biosynthesis, but its exact function is still unclear. Hsp47 is a non-inhibitory member of the SERPIN superfamily and corresponds to clade H.
Probab=25.72 E-value=12 Score=18.92 Aligned_cols=59 Identities=15% Similarity=0.207 Sum_probs=32.8
Q ss_pred CEEEEEECCHHHHHHHHHHHHCCCCC-CCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 38989965967899999996317889-984547734788615556899999999999988
Q gi|254780776|r 64 RMLVVSVWDKEMVASVERGIHESNLG-LNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122 (186)
Q Consensus 64 ~~l~I~~~D~~~ik~I~kAI~~s~l~-l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~ 122 (186)
.+++|-|.+...+..+++.+....+. +.-.-.-..+.|.+|+.+-|..-+|...++.++
T Consensus 226 sm~iiLP~~~~~l~~l~~~l~~~~l~~~~~~~~~~~v~v~lPKF~i~~~~~L~~~L~~lG 285 (366)
T cd02046 226 SMIFIMPYHVEPLERLEKLLTREQLKTWISKMKKRAVAISLPKVSLEVSHDLQKHLGDLG 285 (366)
T ss_pred EEEEECCCCCCCHHHHHHHCCHHHHHHHHHHCCEEEEEEEECCEEEEEECCHHHHHHHCC
T ss_conf 899984787886668887429999999997472567999705678863056699998769
No 55
>pfam03480 SBP_bac_7 Bacterial extracellular solute-binding protein, family 7. This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component.
Probab=24.89 E-value=56 Score=14.40 Aligned_cols=69 Identities=7% Similarity=0.025 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 555689999999999998889999999999999999998753-589997899888999999999999999
Q gi|254780776|r 104 PETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRK-SGKASEDMVASLENDIQKITDSTIKNI 172 (186)
Q Consensus 104 P~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~~~~~ikk~~k-~~~iseD~~~~~~~~iq~lt~~~~~~i 172 (186)
-.|+.|.|+.+.+.+.+..+................++.... -.++|+++.....+-.+.+.++|.+++
T Consensus 216 ~~L~~~~q~~i~~a~~~a~~~~~~~~~~~~~~~~~~~~~~g~~v~~~s~~e~~~~~~a~~pv~~~~~~~v 285 (285)
T pfam03480 216 DSLPPDLQAILEEAAKEATELQRKLAEELLKEKELLKAAGKTEVIVLTPEDREAFREALKPVYKEFEKEI 285 (285)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 6499999999999999999999999999889999999978996999999999999999699999998559
No 56
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=24.09 E-value=57 Score=14.30 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=8.1
Q ss_pred CCCCHHHHHHHHHCCCCCEEEEE
Q ss_conf 86423998765120578389899
Q gi|254780776|r 47 GSHVPLNQVANVTVLEPRMLVVS 69 (186)
Q Consensus 47 g~~~pL~~lA~Is~~~~~~l~I~ 69 (186)
|..++...+..++ ..++..-|.
T Consensus 141 g~~l~~~~l~~L~-~~~~vvgiK 162 (288)
T cd00954 141 GVNLTLEQFLELF-EIPNVIGVK 162 (288)
T ss_pred CCCCCHHHHHHHH-CCCCEEEEE
T ss_conf 7689999999996-368978999
No 57
>cd03788 GT1_TPS Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a nonreducing disaccharide present in a wide variety of organisms and may serve as a source of energy and carbon. It is characterized most notably in insect, plant, and microbial cells. Its production is often associated with a variety of stress conditions, including desiccation, dehydration, heat, cold, and oxidation. This family represents the catalytic domain of the TPS. Some members of this domain family coexist with a C-terminal trehalose phosphatase domain.
Probab=24.03 E-value=32 Score=16.09 Aligned_cols=31 Identities=16% Similarity=0.177 Sum_probs=12.2
Q ss_pred CCEEEEECCCCCHHHHHHHHHCCCCCEEEEEE
Q ss_conf 45078855864239987651205783898996
Q gi|254780776|r 39 DLVKVEAYGSHVPLNQVANVTVLEPRMLVVSV 70 (186)
Q Consensus 39 d~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~ 70 (186)
+-.+|.|....+|..+++..=.- +..+.|||
T Consensus 338 ~w~PI~y~~~~~~~~el~aly~~-ADv~lVT~ 368 (460)
T cd03788 338 DWTPVRYLYRSLPREELAALYRA-ADVALVTP 368 (460)
T ss_pred CCEEEEEEECCCCHHHHHHHHHH-HHEEEECC
T ss_conf 97029999179999999999986-10578553
No 58
>cd02054 angiotensinogen Angiotensinogen is part of the renin-angiotensin system (RAS), which plays an important role in blood pressure regulation, renal haemodynamics, fluid and electrolyte homeostasis. It is also involved in normal and abnormal growth processes. The growth promoting actions of angiotensin have been shown in a variety of cells and tissues. This subgroup represents clade A8 of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones.
Probab=23.75 E-value=17 Score=17.85 Aligned_cols=60 Identities=12% Similarity=0.165 Sum_probs=31.7
Q ss_pred CCEEEEEECCHHHHHHHHHHHHCCCC-CCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 83898996596789999999631788-9984547734788615556899999999999988
Q gi|254780776|r 63 PRMLVVSVWDKEMVASVERGIHESNL-GLNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122 (186)
Q Consensus 63 ~~~l~I~~~D~~~ik~I~kAI~~s~l-~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~ 122 (186)
..+++|-|.+...+..+++++....+ .+.-.-....+.|.+|+.+-|.+..|.+.++.++
T Consensus 231 ~sm~iiLP~~~~~l~~l~~~l~~~~~~~~~~~~~~~~v~v~lPKF~i~~~~~L~~~L~~lG 291 (372)
T cd02054 231 ACLLLVQPHEGSDLDKVEGKLPQQNSSNWLKNLSPRTIELTLPKFSLQGSYDLQDLLAQME 291 (372)
T ss_pred EEEEEEECCCCCCHHHHHHHCCHHHHHHHHHHCCEEEEEEECCCEEEEEEECHHHHHHHCC
T ss_conf 2899995699998999997517989999998587226899757489862535899998719
No 59
>cd02049 bacterial_SERPIN SERine Proteinase INhibitors (serpins), prokaryotic subgroup. Little information about specific functions is available for this subgroup, most likely they are inhibitory members of the serpin superfamily. In general, serpins exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors.
Probab=23.60 E-value=18 Score=17.68 Aligned_cols=59 Identities=10% Similarity=0.044 Sum_probs=36.2
Q ss_pred CEEEEEECCHHHHHHHHHHHHCCCC-CCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 3898996596789999999631788-9984547734788615556899999999999988
Q gi|254780776|r 64 RMLVVSVWDKEMVASVERGIHESNL-GLNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122 (186)
Q Consensus 64 ~~l~I~~~D~~~ik~I~kAI~~s~l-~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~ 122 (186)
.+++|-|-+...+..+++.+...++ .+...-....+.|.+|+.+-+..-++...+++++
T Consensus 220 sm~iiLP~~~~~L~~l~~~l~~~~~~~~~~~~~~~~v~l~lPKF~i~~~~~l~~~L~~lG 279 (364)
T cd02049 220 SMYVFLPKENVSLREFVKTLTAEKWRKWIEQFRMREGSLSLPRFQLEYEIELRDALKALG 279 (364)
T ss_pred EEEEEECCCCCCHHHHHHHCCHHHHHHHHHHCCEEEEEEEEEEEEEECCCCHHHHHHHCC
T ss_conf 999996799999999998639999999997585778999610288730446699998769
No 60
>smart00518 AP2Ec AP endonuclease family 2. These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites
Probab=23.45 E-value=59 Score=14.22 Aligned_cols=69 Identities=12% Similarity=0.122 Sum_probs=51.9
Q ss_pred HHHHHCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 765120578389899659678999999963178899845477347886155568999999999999888999
Q gi|254780776|r 55 VANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126 (186)
Q Consensus 55 lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~E~~K 126 (186)
..||-..+||.+...++++..+.....+....++.+ ..-+ .-.|.+-.+..|.|+..++.+..-++.+.
T Consensus 26 ~~QiF~~~pr~w~~~~~~~~~~~~f~~~~~~~~i~~--~~Ha-~YlINLas~~~e~~~kS~~~l~~el~~~~ 94 (273)
T smart00518 26 SFQLFLGNPRSWKGVRLSEETAEKFKEALKENNIDV--SVHA-PYLINLASPDKEKVEKSIERLIDEIKRCE 94 (273)
T ss_pred EEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCE--EEEC-CCEECCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 999978898889999999999999999999839966--8644-21004579988999999999999999999
No 61
>TIGR00308 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs . The enzyme is found in both eukaryotes and archaea .; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing.
Probab=23.26 E-value=45 Score=15.02 Aligned_cols=65 Identities=15% Similarity=0.347 Sum_probs=47.2
Q ss_pred HHHHHHH-CCC-CCCCHHHHCCEEEEECCCCCHHHHHHH-HHCCCCCEEEEEECCHHHH-H--HHHHHHHC
Q ss_conf 9999753-138-888967824507885586423998765-1205783898996596789-9--99999631
Q gi|254780776|r 21 LKKDMMT-LRT-GRVSPSMLDLVKVEAYGSHVPLNQVAN-VTVLEPRMLVVSVWDKEMV-A--SVERGIHE 85 (186)
Q Consensus 21 l~~el~~-irt-Grasp~lld~i~V~~~g~~~pL~~lA~-Is~~~~~~l~I~~~D~~~i-k--~I~kAI~~ 85 (186)
+..|-+. ++. .+|+-.-|+.|=+|=||++.|.-+=|- -+..+...|.||.-|-+.+ + ...+.+..
T Consensus 152 ~n~Da~~~L~~~nkat~~~F~viDiDPFGspAPFvd~A~~~~~~~NglL~vTATDta~LcG~G~~~~CL~k 222 (462)
T TIGR00308 152 INEDAAAVLRKRNKATFRKFEVIDIDPFGSPAPFVDSAIRASAKRNGLLLVTATDTAALCGSGYKKSCLRK 222 (462)
T ss_pred CCCHHHHHHHHHCHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCCCCHHHHH
T ss_conf 55037999875121123676437647877974158999999974686044066789986278886212454
No 62
>cd00172 SERPIN SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia.
Probab=23.20 E-value=15 Score=18.34 Aligned_cols=59 Identities=20% Similarity=0.281 Sum_probs=38.0
Q ss_pred CEEEEEECCHHHHHHHHHHHHCCCC-CCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 3898996596789999999631788-9984547734788615556899999999999988
Q gi|254780776|r 64 RMLVVSVWDKEMVASVERGIHESNL-GLNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122 (186)
Q Consensus 64 ~~l~I~~~D~~~ik~I~kAI~~s~l-~l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~ 122 (186)
.+++|-|-+...+..+++.+....+ .+...-....+.|.+|+.+-+..-+|...+++++
T Consensus 222 sm~iiLP~~~~~l~~l~~~l~~~~l~~~~~~~~~~~v~l~lPKF~i~~~~~l~~~L~~lG 281 (364)
T cd00172 222 SMLIILPKEVTGLAELEEKLSAEKLDDLLSNLKEREVEVTLPKFKIESSLDLKEVLQALG 281 (364)
T ss_pred EEEEEECCCCCCHHHHHHHCCHHHHHHHHHHCCEEEEEEEECCEEEEEECCHHHHHHHCC
T ss_conf 999997489999999998609999999997577689999831489987416799997669
No 63
>KOG3813 consensus
Probab=22.82 E-value=61 Score=14.14 Aligned_cols=36 Identities=22% Similarity=0.336 Sum_probs=26.2
Q ss_pred EEEECCCCCHHHHHHHHHHHHH-HHHHH-HHHHHHHHH
Q ss_conf 7886155568999999999999-88899-999999999
Q gi|254780776|r 99 LRIPVPETTEERRLALVKVAHA-YAEKS-KISVRNIRR 134 (186)
Q Consensus 99 I~i~iP~lT~E~R~~lvK~~k~-~~E~~-K~~iR~iR~ 134 (186)
+-+.+||++.-+|..|.|...- ..+.- |..+|.+|+
T Consensus 266 ~~v~Lqpip~rrRraLLkaSGVrkIDaeEK~elralRn 303 (640)
T KOG3813 266 SNVSLQPIPQRRRRALLKASGVRKIDAEEKDELRALRN 303 (640)
T ss_pred HCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 11355778878999998751650013346789999874
No 64
>cd02047 HCII Heparin cofactor II (HCII) inhibits thrombin, the final protease of the coagulation cascade. HCII is allosterically activated by binding to cell surface glycosaminoglycans (GAGs). The specificity of HCII for thrombin is conferred by a highly acidic hirudin-like N-terminal tail, which becomes available after GAG binding for interaction with the anion-binding exosite I of thrombin. This subgroup corresponds to clade D of the serpin superfamily.
Probab=22.65 E-value=24 Score=16.94 Aligned_cols=11 Identities=0% Similarity=-0.034 Sum_probs=6.2
Q ss_pred CEEEEEECCHH
Q ss_conf 38989965967
Q gi|254780776|r 64 RMLVVSVWDKE 74 (186)
Q Consensus 64 ~~l~I~~~D~~ 74 (186)
..+.+.|+.-+
T Consensus 88 eNI~fSPlSIs 98 (436)
T cd02047 88 DNILLAPVGIS 98 (436)
T ss_pred CCEEECHHHHH
T ss_conf 84998769999
No 65
>PRK10117 trehalose-6-phosphate synthase; Provisional
Probab=22.28 E-value=38 Score=15.52 Aligned_cols=32 Identities=9% Similarity=0.062 Sum_probs=20.0
Q ss_pred HCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEE
Q ss_conf 245078855864239987651205783898996
Q gi|254780776|r 38 LDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSV 70 (186)
Q Consensus 38 ld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~ 70 (186)
++-.+|.|....+|..+++..=.- +....|||
T Consensus 328 ~~w~Pi~y~~~~~~~~~l~alyr~-ADv~lVTp 359 (474)
T PRK10117 328 LGWTPLYYLNQHFDRKLLMKIFRY-SDVGLVTP 359 (474)
T ss_pred CCCCEEEEEECCCCHHHHHHHHHH-CCEEEECC
T ss_conf 997149998268999999999974-66899645
No 66
>PRK06007 fliF flagellar MS-ring protein; Reviewed
Probab=22.00 E-value=63 Score=14.03 Aligned_cols=34 Identities=18% Similarity=0.377 Sum_probs=19.7
Q ss_pred EECCHHHHHHHHHHHHCCCCCCCCCCCCC--EEEEEC
Q ss_conf 96596789999999631788998454773--478861
Q gi|254780776|r 69 SVWDKEMVASVERGIHESNLGLNPIVEGQ--VLRIPV 103 (186)
Q Consensus 69 ~~~D~~~ik~I~kAI~~s~l~l~p~~dg~--~I~i~i 103 (186)
.||++.-+..|...+.+ -.|+++..-+. ...++|
T Consensus 385 ~p~s~~el~~I~~lV~~-AvG~d~~RGD~VtV~~~~F 420 (540)
T PRK06007 385 QPLSAEELAQIEKLVRS-AVGFDAARGDSVNVVNVPF 420 (540)
T ss_pred CCCCHHHHHHHHHHHHH-HHCCCCCCCCEEEEEEECC
T ss_conf 87999999999999998-7276756798699997326
No 67
>pfam02005 TRM N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria
Probab=21.48 E-value=64 Score=13.96 Aligned_cols=69 Identities=19% Similarity=0.336 Sum_probs=50.8
Q ss_pred HHHCCEEEEECCCCCHHHHHHHHHCCCCCEEEEEECCHHHH-------------------------------HHHHHHHH
Q ss_conf 78245078855864239987651205783898996596789-------------------------------99999963
Q gi|254780776|r 36 SMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMV-------------------------------ASVERGIH 84 (186)
Q Consensus 36 ~lld~i~V~~~g~~~pL~~lA~Is~~~~~~l~I~~~D~~~i-------------------------------k~I~kAI~ 84 (186)
.-||-|=++-||++.|.-+-|--+++.+-.|-||.-|...+ ..|...-.
T Consensus 119 ~~fD~IDlDPfGSp~pfldsAi~av~~~GlL~vTaTD~a~L~G~~~~~~~r~Yga~~~~~~~~hE~glRiLl~~i~r~Aa 198 (375)
T pfam02005 119 RRFDVIDLDPFGSPAPFLDSAVQSVKRGGLLCVTATDTAVLCGAYPEACLRKYGAVPLRGEFCHEVGLRILLGFIARYAA 198 (375)
T ss_pred CCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCHHHCCCCCHHHHHHCCCEECCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 86756867899992177999999831598899994463353178825789871997336603467889999999999999
Q ss_pred CCCCCCCCC---CCCCEEEEECC
Q ss_conf 178899845---47734788615
Q gi|254780776|r 85 ESNLGLNPI---VEGQVLRIPVP 104 (186)
Q Consensus 85 ~s~l~l~p~---~dg~~I~i~iP 104 (186)
.-+.++.|. ..+..+||-+=
T Consensus 199 ~~~~~i~PllS~~~~hy~RV~vr 221 (375)
T pfam02005 199 KYDKAIEPLLSYSIDHYVRVFVK 221 (375)
T ss_pred HHCCCEEEEEEEEECCEEEEEEE
T ss_conf 85896289999760758999999
No 68
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.16 E-value=65 Score=13.92 Aligned_cols=30 Identities=20% Similarity=0.365 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf 999999999999999998753589997899
Q gi|254780776|r 125 SKISVRNIRRDGMDHLKKSRKSGKASEDMV 154 (186)
Q Consensus 125 ~K~~iR~iR~~~~~~ikk~~k~~~iseD~~ 154 (186)
++..||.|...++.+++......+++.|..
T Consensus 298 SRERVRQIE~~AL~KLR~~l~~~~l~~~~~ 327 (328)
T PRK05657 298 TRERVRQIQVEALRRLREILQTQGLSKDAL 327 (328)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCHHHC
T ss_conf 999999999999999879999869973424
No 69
>cd02056 alpha-1-antitrypsin_like alpha-1-antitrypsin_like. This family contains a variety of different members of clade A of the serpin superfamily. They include the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and noninhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia.
Probab=20.94 E-value=23 Score=17.06 Aligned_cols=58 Identities=12% Similarity=0.197 Sum_probs=23.6
Q ss_pred CEEEEEECCHHHHHHHHHHHHCCCCC-CCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 38989965967899999996317889-984547734788615556899999999999988
Q gi|254780776|r 64 RMLVVSVWDKEMVASVERGIHESNLG-LNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122 (186)
Q Consensus 64 ~~l~I~~~D~~~ik~I~kAI~~s~l~-l~p~~dg~~I~i~iP~lT~E~R~~lvK~~k~~~ 122 (186)
.+++|-| +...+..++..+....+. +...-....+.|.+|+.+-|.+-++...+++++
T Consensus 221 sm~iiLP-~~~~l~~l~~~l~~~~l~~~~~~~~~~~v~v~lPKF~i~~~~dl~~~L~~lG 279 (361)
T cd02056 221 TAFFVLP-DEGKMKQVEAALSRDTLKKWSKLLSKRSVDLYLPKFSISGTYNLKDILPKMG 279 (361)
T ss_pred EEEEEEC-CCCCHHHHHHHHCHHHHHHHHHHCCCCEEEEECCCEEEEEEECHHHHHHHCC
T ss_conf 8999975-9998999998649999999998565432599756788861233799998669
No 70
>TIGR01139 cysK cysteine synthase A; InterPro: IPR005859 This model discriminates cysteine synthase A (CysK) and cysteine synthase B (CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblance to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded. Cysteine synthase (O-acetylserine (thiol)-lyase, 2.5.1.47 from EC) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM). CysK differs from CysM in that it can also use sulphide instead of thiosulphate, to produce cysteine instead of cysteine thiosulphonate. ; GO: 0004124 cysteine synthase activity, 0006535 cysteine biosynthetic process from serine.
Probab=20.88 E-value=66 Score=13.88 Aligned_cols=67 Identities=21% Similarity=0.276 Sum_probs=39.7
Q ss_pred CCHHHHHH-HHHCCCCCEEEEEE--CCHH-------HHHHHHHHHHCCCCCCCCC-C---CC--------------CEEE
Q ss_conf 42399876-51205783898996--5967-------8999999963178899845-4---77--------------3478
Q gi|254780776|r 49 HVPLNQVA-NVTVLEPRMLVVSV--WDKE-------MVASVERGIHESNLGLNPI-V---EG--------------QVLR 100 (186)
Q Consensus 49 ~~pL~~lA-~Is~~~~~~l~I~~--~D~~-------~ik~I~kAI~~s~l~l~p~-~---dg--------------~~I~ 100 (186)
.+||-.|= .+..+..-.+.|.+ +.|+ ...-|..|=..-.|+-.-. + .| -.+-
T Consensus 7 ~TPlVrLnRrl~~~~~~~v~~KlE~~NPs~SVKDRia~~MI~~AEk~G~lk~G~~IvEpTSGNTGIaLAmvAAArGYkli 86 (312)
T TIGR01139 7 NTPLVRLNRRLAEGNNADVFVKLEFFNPSGSVKDRIALNMIEDAEKRGLLKPGKTIVEPTSGNTGIALAMVAAARGYKLI 86 (312)
T ss_pred CCCEEECCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHHHHCCEEE
T ss_conf 98706616544688763389996045989867778899999999865886888889823777326999999987189499
Q ss_pred EECCC-CCHHHHHHHH
Q ss_conf 86155-5689999999
Q gi|254780776|r 101 IPVPE-TTEERRLALV 115 (186)
Q Consensus 101 i~iP~-lT~E~R~~lv 115 (186)
+++|. ||.|||.-|.
T Consensus 87 ltMPetMS~ERr~lL~ 102 (312)
T TIGR01139 87 LTMPETMSIERRKLLK 102 (312)
T ss_pred EECCCCHHHHHHHHHH
T ss_conf 9867432689999998
No 71
>pfam08952 DUF1866 Domain of unknown function (DUF1866). This domain, found in Synaptojanin, has no known function.
Probab=20.71 E-value=67 Score=13.86 Aligned_cols=54 Identities=20% Similarity=0.262 Sum_probs=38.6
Q ss_pred CCEEEEECCCCCHHH--HHHHHHCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 450788558642399--8765120578389899659678999999963178899845
Q gi|254780776|r 39 DLVKVEAYGSHVPLN--QVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPI 93 (186)
Q Consensus 39 d~i~V~~~g~~~pL~--~lA~Is~~~~~~l~I~~~D~~~ik~I~kAI~~s~l~l~p~ 93 (186)
|.+-|.+..+..-|+ ++.++.+. +++|.|++=.|.+++.++..|.....+..|.
T Consensus 70 d~mwVTF~dG~SAL~al~~~g~~v~-g~~l~i~LKspdW~~~le~Ei~l~~~n~vpl 125 (145)
T pfam08952 70 DDMWVTFRDGESALAALSKDGIKVL-GRQLNIRLKSPDWIKALEEEISLCTLEMIPV 125 (145)
T ss_pred CEEEEEECCCHHHHHHHCCCCCEEC-CEEEEEEECCHHHHHHHHHHHHHCCCCCCCC
T ss_conf 8389998677879997545771863-6389998689249999999997435672026
No 72
>pfam08112 ATP-synt_E_2 ATP synthase epsilon subunit. This family consists of epsilon subunits of the ATP synthase. The ATP synthase complex is composed of an oligomeric transmembrane sector (CF0), and a catalytic core (CF1). CF1 is composed of 5 subunits, of which the epsilon subunit functions as a potent inhibitor of ATPase activity in both soluble and bound CF1. Only when the epsilon inhibition is disabled is high ATPase activity detected in ATPase.
Probab=20.52 E-value=67 Score=13.83 Aligned_cols=14 Identities=14% Similarity=0.508 Sum_probs=5.0
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999999
Q gi|254780776|r 160 DIQKITDSTIKNID 173 (186)
Q Consensus 160 ~iq~lt~~~~~~id 173 (186)
+-+++.+....++|
T Consensus 34 eyek~lk~rl~eld 47 (56)
T pfam08112 34 EYEKLLKNRLDELD 47 (56)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999888999
No 73
>cd00716 creatine_kinase_like Phosphagen (guanidino) kinases such as creatine kinase and similar enzymes. Eukaryotic creatine kinase-like phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK), which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CKs are found as tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial, cytosolic, and flagellar) isoforms. Mitochondrial and cytoplasmic CKs are dimeric or octameric, while the flagellar isoforms are trimers with three CD domains fused as a single protein chain. CKs are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK, one
Probab=20.29 E-value=68 Score=13.80 Aligned_cols=55 Identities=15% Similarity=0.227 Sum_probs=34.9
Q ss_pred HHHHHHHHHHCCCCCC-----------CCCCCCCE----EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8999999963178899-----------84547734----7886155568999999999999888999999999999
Q gi|254780776|r 75 MVASVERGIHESNLGL-----------NPIVEGQV----LRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRD 135 (186)
Q Consensus 75 ~ik~I~kAI~~s~l~l-----------~p~~dg~~----I~i~iP~lT~E~R~~lvK~~k~~~E~~K~~iR~iR~~ 135 (186)
.++.+++.|...+..+ -|.+=|+. +.|.+|.|+...| .++++++-+.++|.+-.+
T Consensus 240 ~l~~lE~~lk~~g~~Fa~~~~lGyltsCPtNlGTglRaSv~v~LP~L~~~~~------~~~i~~~l~lq~RG~~Ge 309 (357)
T cd00716 240 GLTEVEKLMKKKGYEFMWNEHLGYVLTCPSNLGTGLRASVHVKLPNLSKDPR------FDEILRKLRLQKRGTGGV 309 (357)
T ss_pred HHHHHHHHHHHCCCCEEECCCCEEEEECCCCCCCCEEEEEEEECCCCCCCHH------HHHHHHHCCCEEEECCCC
T ss_conf 9999999998638540334773257436776766327999997755445462------999999839714355876
Done!