Query 008989
Match_columns 547
No_of_seqs 188 out of 1688
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 19:03:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008989.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008989hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0544 Tig FKBP-type peptidyl 100.0 1.3E-75 2.7E-80 625.0 48.2 415 90-538 1-419 (441)
2 PRK01490 tig trigger factor; P 100.0 1.3E-71 2.8E-76 600.6 50.4 413 90-538 1-417 (435)
3 TIGR00115 tig trigger factor. 100.0 1.8E-70 4E-75 587.1 49.7 400 102-535 1-404 (408)
4 PF05697 Trigger_N: Bacterial 100.0 3.5E-28 7.6E-33 224.8 16.5 135 90-235 1-139 (145)
5 PF05698 Trigger_C: Bacterial 99.8 2.5E-19 5.5E-24 167.4 12.2 160 372-538 1-160 (162)
6 PF00254 FKBP_C: FKBP-type pep 99.0 1.1E-09 2.3E-14 93.4 9.4 84 259-348 3-94 (94)
7 PRK15095 FKBP-type peptidyl-pr 98.8 2.9E-08 6.4E-13 93.0 9.4 86 260-351 4-144 (156)
8 COG1047 SlpA FKBP-type peptidy 98.8 4.2E-08 9E-13 92.5 10.3 87 260-352 2-142 (174)
9 PRK10737 FKBP-type peptidyl-pr 98.7 4.3E-08 9.2E-13 94.8 8.6 94 261-364 3-149 (196)
10 TIGR03516 ppisom_GldI peptidyl 98.4 1.8E-06 3.9E-11 82.6 9.6 86 260-351 85-176 (177)
11 PRK10902 FKBP-type peptidyl-pr 98.3 2.3E-06 5.1E-11 86.9 10.4 85 260-352 160-250 (269)
12 KOG0549 FKBP-type peptidyl-pro 98.3 3.5E-06 7.7E-11 79.5 9.7 90 258-353 82-178 (188)
13 COG0545 FkpA FKBP-type peptidy 98.3 3.5E-06 7.6E-11 81.1 9.7 85 259-351 114-205 (205)
14 KOG0544 FKBP-type peptidyl-pro 98.2 7.9E-06 1.7E-10 68.9 8.7 84 261-350 17-107 (108)
15 KOG0552 FKBP-type peptidyl-pro 98.0 2.7E-05 5.9E-10 76.6 8.7 87 260-351 134-226 (226)
16 PRK11570 peptidyl-prolyl cis-t 97.9 8E-05 1.7E-09 73.0 9.9 84 260-351 116-206 (206)
17 PRK10770 peptidyl-prolyl cis-t 95.9 0.067 1.5E-06 57.8 11.8 68 417-498 20-87 (413)
18 PRK04405 prsA peptidylprolyl i 94.7 0.63 1.4E-05 48.3 13.8 118 394-533 56-178 (298)
19 PRK00059 prsA peptidylprolyl i 94.7 0.86 1.9E-05 47.8 15.0 103 388-500 86-190 (336)
20 PRK00059 prsA peptidylprolyl i 93.7 1.5 3.2E-05 46.0 14.4 73 457-531 83-170 (336)
21 PF09312 SurA_N: SurA N-termin 93.6 1.5 3.3E-05 39.0 12.1 57 459-520 42-98 (118)
22 PRK12450 foldase protein PrsA; 92.4 0.84 1.8E-05 47.6 10.0 78 464-543 56-143 (309)
23 PRK01326 prsA foldase protein 91.4 1.5 3.2E-05 45.8 10.5 63 463-527 53-123 (310)
24 TIGR02933 nifM_nitrog nitrogen 91.4 4.5 9.7E-05 41.0 13.7 85 394-500 34-118 (256)
25 PRK03095 prsA peptidylprolyl i 91.2 1.5 3.3E-05 45.2 10.2 73 451-526 36-116 (287)
26 PRK12450 foldase protein PrsA; 90.4 5.1 0.00011 41.8 13.4 86 396-496 59-145 (309)
27 TIGR02933 nifM_nitrog nitrogen 90.3 2.5 5.3E-05 42.9 10.7 68 474-543 42-112 (256)
28 PRK01326 prsA foldase protein 90.2 5.7 0.00012 41.4 13.6 79 396-495 57-141 (310)
29 PRK10788 periplasmic folding c 90.1 4.3 9.3E-05 46.4 13.6 74 455-530 83-170 (623)
30 PRK04980 hypothetical protein; 88.9 1.9 4.2E-05 37.6 7.4 44 337-383 44-87 (102)
31 PRK03002 prsA peptidylprolyl i 88.7 7.8 0.00017 39.9 13.1 131 372-532 39-169 (285)
32 PRK03095 prsA peptidylprolyl i 88.2 7.9 0.00017 39.9 12.8 91 372-494 36-130 (287)
33 PRK02998 prsA peptidylprolyl i 88.1 3.9 8.4E-05 42.1 10.4 73 451-525 37-117 (283)
34 PRK03002 prsA peptidylprolyl i 87.9 3.4 7.5E-05 42.5 9.9 70 452-523 40-117 (285)
35 PRK04405 prsA peptidylprolyl i 87.6 3.8 8.1E-05 42.6 10.0 58 465-524 55-121 (298)
36 PF13624 SurA_N_3: SurA N-term 87.5 2.1 4.7E-05 39.2 7.4 65 461-527 77-141 (154)
37 cd06552 ASCH_yqfb_like ASC-1 h 86.1 3.3 7.1E-05 35.4 7.3 41 340-382 42-82 (100)
38 KOG0543 FKBP-type peptidyl-pro 85.8 56 0.0012 35.3 24.3 86 262-354 102-193 (397)
39 PRK02998 prsA peptidylprolyl i 85.0 17 0.00037 37.3 13.2 95 372-493 37-131 (283)
40 PRK10770 peptidyl-prolyl cis-t 80.2 49 0.0011 35.7 15.1 90 392-497 53-147 (413)
41 PF13623 SurA_N_2: SurA N-term 72.4 27 0.00057 32.4 8.9 36 458-493 80-115 (145)
42 PRK10788 periplasmic folding c 72.1 90 0.002 35.7 15.1 33 391-423 91-123 (623)
43 KOG0543 FKBP-type peptidyl-pro 71.6 4.7 0.0001 43.2 4.2 54 261-320 9-63 (397)
44 PF05698 Trigger_C: Bacterial 71.3 20 0.00044 32.8 8.1 67 466-532 23-106 (162)
45 PRK01490 tig trigger factor; P 69.2 45 0.00098 36.3 11.4 68 465-532 282-363 (435)
46 PRK05892 nucleoside diphosphat 68.5 43 0.00093 31.5 9.5 33 307-352 124-156 (158)
47 PF01272 GreA_GreB: Transcript 67.5 12 0.00025 30.6 4.9 32 307-351 45-76 (77)
48 TIGR00115 tig trigger factor. 66.4 61 0.0013 34.9 11.7 67 466-532 273-353 (408)
49 COG2411 Uncharacterized conser 65.0 23 0.00049 33.8 6.8 58 312-383 32-89 (188)
50 PRK01885 greB transcription el 64.4 71 0.0015 30.0 10.1 32 307-351 124-155 (157)
51 cd06541 ASCH ASC-1 homology or 63.6 28 0.0006 30.3 6.8 49 338-386 42-91 (105)
52 TIGR01462 greA transcription e 62.5 86 0.0019 29.1 10.3 19 307-325 120-138 (151)
53 cd06553 ASCH_Ef3133_like ASC-1 62.0 40 0.00087 30.6 7.7 49 340-388 57-105 (127)
54 TIGR01461 greB transcription e 55.4 72 0.0016 29.9 8.5 32 307-351 122-153 (156)
55 PRK14720 transcript cleavage f 55.2 66 0.0014 38.6 9.9 36 307-355 870-905 (906)
56 PF09312 SurA_N: SurA N-termin 53.9 1.2E+02 0.0026 26.7 9.3 58 395-460 50-109 (118)
57 PRK00226 greA transcription el 53.7 44 0.00095 31.2 6.8 19 307-325 125-143 (157)
58 TIGR02925 cis_trans_EpsD pepti 49.4 1.3E+02 0.0029 29.4 9.9 38 462-500 96-133 (232)
59 COG2511 GatE Archaeal Glu-tRNA 48.5 3.8E+02 0.0083 30.3 13.6 131 357-498 439-583 (631)
60 COG0544 Tig FKBP-type peptidyl 48.4 2E+02 0.0044 31.7 11.8 71 461-531 278-362 (441)
61 PRK06342 transcription elongat 42.9 1.7E+02 0.0036 27.7 8.8 17 307-323 133-149 (160)
62 PRK05753 nucleoside diphosphat 39.7 70 0.0015 29.3 5.6 33 307-351 94-126 (137)
63 PF06857 ACP: Malonate decarbo 36.2 1.2E+02 0.0027 25.6 6.1 53 82-134 8-61 (87)
64 PRK12907 secY preprotein trans 35.5 26 0.00056 38.5 2.5 37 106-148 330-366 (434)
65 PF11867 DUF3387: Domain of un 29.9 6.7E+02 0.015 26.3 15.3 88 356-443 154-248 (335)
66 PF10884 DUF2683: Protein of u 27.9 44 0.00094 27.8 2.0 26 355-380 45-78 (80)
67 PF13624 SurA_N_3: SurA N-term 27.9 3.8E+02 0.0082 24.1 8.6 34 391-424 79-112 (154)
68 TIGR00134 gatE_arch glutamyl-t 27.4 1E+03 0.022 27.6 17.4 27 473-499 549-576 (620)
69 TIGR02920 acc_sec_Y2 accessory 25.8 1E+02 0.0022 33.4 4.9 37 107-149 296-332 (395)
70 COG0201 SecY Preprotein transl 25.7 87 0.0019 34.5 4.4 22 127-148 348-369 (436)
71 TIGR00967 3a0501s007 preprotei 24.0 57 0.0012 35.5 2.7 37 107-149 315-351 (410)
72 PF00344 SecY: SecY translocas 24.0 91 0.002 33.0 4.1 46 123-169 273-319 (346)
73 PF11221 Med21: Subunit 21 of 22.9 5.9E+02 0.013 23.3 10.8 79 451-534 63-142 (144)
74 CHL00161 secY preprotein trans 22.5 59 0.0013 35.5 2.4 36 107-148 317-352 (417)
75 TIGR03595 Obg_CgtA_exten Obg f 22.2 84 0.0018 25.3 2.6 29 242-270 35-63 (69)
76 TIGR03342 dsrC_tusE_dsvC sulfu 21.7 3.5E+02 0.0075 23.9 6.6 43 473-518 27-71 (108)
77 PF13623 SurA_N_2: SurA N-term 20.7 1.7E+02 0.0036 27.2 4.7 18 499-516 98-115 (145)
78 PF09682 Holin_LLH: Phage holi 20.2 1.7E+02 0.0037 25.5 4.5 25 477-501 81-105 (108)
79 PF09269 DUF1967: Domain of un 20.1 75 0.0016 25.5 2.0 28 242-269 35-62 (69)
No 1
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-75 Score=625.04 Aligned_cols=415 Identities=26% Similarity=0.434 Sum_probs=366.1
Q ss_pred cEEEEeecCCceEEEEEEEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhChHHHHHHHHHHHHHhhHHHHH
Q 008989 90 IEVTESPEPNSTVRLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILKRTLPHAM 169 (547)
Q Consensus 90 m~vt~~~~~~~~~~l~V~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G~~~i~~e~~e~li~~~~~~al 169 (547)
|+|++++.+++.++++|+||++.+++++++++++++|+++||||||||||++||+++|| .++++++++++++++|.+++
T Consensus 1 M~v~~e~~~~~~~~l~v~vp~~~~~~~~~~~~~~~~k~v~IpGFRkGKvP~~ii~~ryg-~~v~~d~~~~ll~~~~~~a~ 79 (441)
T COG0544 1 MKVTVEKLEGLEVRLTVEVPAEEIKKALDKALKKLAKKVKIPGFRKGKVPRKVIEQRYG-EAVRQDVLNELLPEAFEEAI 79 (441)
T ss_pred CCeeeeecCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCcCCCCCCCCCCHHHHHHHHh-HHHHHHHHHHHHHHHHHHHH
Confidence 88999999999999999999999999999999999999999999999999999999999 58999999999999999999
Q ss_pred HhhhcccCCcccccccccchhhcccCCCCceEEEEEEEeecccccCCCCCCceeEEEEe----cchhhHHHHHHHHHHHH
Q 008989 170 TSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKNLKIVVE----IDNDTAAQQAAEEELRR 245 (547)
Q Consensus 170 ~e~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~f~v~vev~Pev~l~~~~dYk~l~v~~~----~de~vd~~~~~e~~l~~ 245 (547)
++.++.++++|. +. ...++++++|+|++.|+|+|+|+++ ||++|+|+++ ++++|++ .|..
T Consensus 80 ~e~~~~~~~~p~-~~------~~~~e~~~~~~f~~~~ev~Pev~l~---d~~~i~v~~~~~ev~d~dvd~------~L~~ 143 (441)
T COG0544 80 KEEGLKPAGQPE-IE------ITEFEKGEDFEFTAEVEVYPEVELG---DYKGIEVEKPVVEVTDEDVDE------ELEK 143 (441)
T ss_pred HHhCcCcCCCCC-cc------cccccCCCceEEEEEEEEeeceecC---ccccceeecCCcccCHHHHHH------HHHH
Confidence 999999998762 21 1356788899999999999999996 9999999987 3455554 6888
Q ss_pred HHHhcCccccccccCcccccEEEEEEEEeeeccCCCCCcccCCCCccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEE
Q 008989 246 RHKSLGSLKIVTDRGLQVGDIAIVDISATTIDEDESNVQNIPDAETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRL 325 (547)
Q Consensus 246 ~~~~~a~~~~v~dr~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~ 325 (547)
+++++++|.++.++ ++.||+|+|||.|+ .||++|+|++++||.|.+| +++|+|||+++|+|||+||+++|++
T Consensus 144 l~~~~a~~~~~e~~-a~~gD~v~IDf~g~------iDg~~fegg~ae~~~l~lG-s~~fipgFe~~LvG~k~Ge~k~i~v 215 (441)
T COG0544 144 LRKRFATLEPVEGA-AENGDRVTIDFEGS------VDGEEFEGGKAENFSLELG-SGRFIPGFEDQLVGMKAGEEKDIKV 215 (441)
T ss_pred HHHhcCcccccccc-cccCCEEEEEEEEE------EcCeeccCccccCeEEEEc-CCCchhhHHhhhccCcCCCeeEEEE
Confidence 89999999886545 99999999999998 7899999999999999999 5799999999999999999999999
Q ss_pred eCCCCCCCcCCCCCeeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008989 326 AFPESWRQEHLRGVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKCREVEQTAKDQATDNAILDQLY 405 (547)
Q Consensus 326 ~fPedy~~~~laGk~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~ 405 (547)
+||++||.++|+||.++|+|||++|+.+++|||||||||+++... |+++||++||++|+.+.+....+..+++++++|.
T Consensus 216 tFP~dy~a~~LaGK~a~F~V~vkeVk~~elpEldDEfAk~~~~~~-tL~~Lk~~~r~~le~~~~~~~~~~~~~~~~~~L~ 294 (441)
T COG0544 216 TFPEDYHAEELAGKEATFKVKVKEVKKRELPELDDEFAKKLGEED-TLEELKEKLRKNLERELKEATLEKRKEQLLDALV 294 (441)
T ss_pred EcccccchhHhCCCceEEEEEEEEEeecCCCCCCHHHHHhcCccc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999996434 9999999999999999999999999999999999
Q ss_pred hhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC
Q 008989 406 KMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQNLAVGDIFKRENLQFS 485 (547)
Q Consensus 406 e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~Vt 485 (547)
+.++|++|++||+++++.++++...++ +++|++. + .. ++.+.+++++++++.|+++||.+|+|++||+.++|+||
T Consensus 295 e~~~~dlP~sli~~E~~~l~~~~~~~l-~~~~~~~--~-~~-~~~~~~~~~e~~~~~A~krVk~~Lil~~ia~~~~i~v~ 369 (441)
T COG0544 295 EANDFDLPESLVEAEIDNLLKQALQQL-QQQGIDS--L-EA-SGESEEELREEFKEEAEKRVKLGLLLEEIAKEEKLEVT 369 (441)
T ss_pred hhcCCCCCHHHHHHHHHHHHHHHHHHH-Hhcccch--h-hh-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcCC
Confidence 999999999999999999999999999 4678775 2 11 23467899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhhhhcccch
Q 008989 486 TEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQSQNSSHI 538 (547)
Q Consensus 486 eeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~~~~~~~~ 538 (547)
+++|++++..+++ +||.....+.++.+..+...+..+-..++....--++
T Consensus 370 ~eei~~~i~~~a~---~y~~~~~~e~~~~~~~~~~~~~~~k~~~~~~k~v~~~ 419 (441)
T COG0544 370 EEEIKAEIEELAR---QYGGEQPEEVIKLYYNNQELLDALKADILEEKAVDLL 419 (441)
T ss_pred HHHHHHHHHHHHH---HhCCCcHHHHHHHHhcChHHHHHHHHHHHHHHHHHHH
Confidence 9999999999987 6665443343343444445555444444444443333
No 2
>PRK01490 tig trigger factor; Provisional
Probab=100.00 E-value=1.3e-71 Score=600.65 Aligned_cols=413 Identities=25% Similarity=0.416 Sum_probs=363.7
Q ss_pred cEEEEeecCCceEEEEEEEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhChHHHHHHHHHHHHHhhHHHHH
Q 008989 90 IEVTESPEPNSTVRLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILKRTLPHAM 169 (547)
Q Consensus 90 m~vt~~~~~~~~~~l~V~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G~~~i~~e~~e~li~~~~~~al 169 (547)
|+++++.+++|++.++|+||+++|+.++++++++++++++||||||||||++||+++||+ .|+.++++++++.+|.+|+
T Consensus 1 M~v~~~~~~~~~~~l~v~v~~~~~~~~~~~~~~~~~k~~~ipGFRkGkvP~~ii~k~~g~-~i~~e~~~~li~~~~~~~i 79 (435)
T PRK01490 1 MQVTVEKLEGLERRLTITVPAEEIEKAVDKALKKLAKTVRIPGFRKGKVPRKIVEQRYGE-SVRQEALNDLLPEAYEEAI 79 (435)
T ss_pred CcceEEEcCCcEEEEEEEEcHHHHHHHHHHHHHHHHhhCcCCCccCCCCCHHHHHHHHhH-HHHHHHHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999999999999999998 5999999999999999999
Q ss_pred HhhhcccCCcccccccccchhhcccCCCCceEEEEEEEeecccccCCCCCCceeEEEEe----cchhhHHHHHHHHHHHH
Q 008989 170 TSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKNLKIVVE----IDNDTAAQQAAEEELRR 245 (547)
Q Consensus 170 ~e~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~f~v~vev~Pev~l~~~~dYk~l~v~~~----~de~vd~~~~~e~~l~~ 245 (547)
++.++.|+++|. +. . .++.++++|+|+++|+++|+|+|+ +|++++|+++ ++++|+. .|++
T Consensus 80 ~~~~~~~~~~p~-i~----~--~~~~~~~~~~~~~~~~v~Pev~l~---~y~~i~v~~~~~~vtde~vd~------~i~~ 143 (435)
T PRK01490 80 KEEGIRPAGQPE-IE----P--TEEEKGKDLEFTAEVEVYPEVELG---DYKGLEVEKPVVEVTDEDVDE------ELER 143 (435)
T ss_pred HHcCCCcCCCCc-cc----c--cccCCCCcEEEEEEeeecCCcccC---CCCceEEEeccCCCCHHHHHH------HHHH
Confidence 999999998652 21 1 346678899999999999999996 8999999976 3556654 5888
Q ss_pred HHHhcCccccccccCcccccEEEEEEEEeeeccCCCCCcccCCCCccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEE
Q 008989 246 RHKSLGSLKIVTDRGLQVGDIAIVDISATTIDEDESNVQNIPDAETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRL 325 (547)
Q Consensus 246 ~~~~~a~~~~v~dr~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~ 325 (547)
+++++++|.++ +++++.||+|+|||+++ .+|++++++..+++.|.+|. +.++|||+++|+||++|++++|++
T Consensus 144 l~~~~a~~~~~-~~~~~~gD~V~vd~~~~------~~g~~~~~~~~~~~~~~lg~-~~~~~~fee~L~G~k~Ge~~~~~~ 215 (435)
T PRK01490 144 LRKQFATLVPV-ERPAENGDRVTIDFVGS------IDGEEFEGGKAEDFSLELGS-GRFIPGFEEQLVGMKAGEEKTIDV 215 (435)
T ss_pred HHHhCCccccc-cccCCCCCEEEEEEEEE------ECCEECcCCCCCceEEEEcC-CCcchhHHHHhCCCCCCCeeEEEe
Confidence 89999999876 58999999999999998 58999999999999999995 689999999999999999999999
Q ss_pred eCCCCCCCcCCCCCeeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008989 326 AFPESWRQEHLRGVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKCREVEQTAKDQATDNAILDQLY 405 (547)
Q Consensus 326 ~fPedy~~~~laGk~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~ 405 (547)
+||++|+.++++|++++|+|+|++|+++++|+||||||++++ .++|+++||++||++|+.+.+...++.++++|+++|+
T Consensus 216 ~~p~~~~~~~lagk~~~f~v~v~~V~~~~~pel~Defak~~~-~~~tleelk~~ik~~l~~~~~~~~~~~~~~~i~~~L~ 294 (435)
T PRK01490 216 TFPEDYHAEDLAGKEATFKVTVKEVKEKELPELDDEFAKKLG-EFETLEELKADIRKNLEREKKEAQRAKVKEAVLDALV 294 (435)
T ss_pred cCccccccccCCCCeEEEEEEEEEeccCCCCCCCHHHHHhcC-CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999885 3499999999999999999999999999999999999
Q ss_pred hhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC
Q 008989 406 KMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQNLAVGDIFKRENLQFS 485 (547)
Q Consensus 406 e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~Vt 485 (547)
++++|++|+++|+++++.+++++..++. .++ .+|... .+.+.++|.++++..|++++|+.|||++||+++||+||
T Consensus 295 ~~~~~~lPe~lv~~e~~~~~~~~~~~~~-~~~---~~~~~~-~~~~~e~~~~~~~~~A~~~vk~~lil~~Ia~~e~i~vs 369 (435)
T PRK01490 295 ENAEIDLPEALVEQEIDRLLRQALQQGL-DLE---GQFLED-TGTTEEEPREEFREQAERRVKLGLLLDEIAKAEEIEVS 369 (435)
T ss_pred HhCCCCCCHHHHHHHHHHHHHHHHHHhh-hhh---hhhhhh-cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence 9999999999999999999988765442 111 233332 22356789999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhhhhcccch
Q 008989 486 TEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQSQNSSHI 538 (547)
Q Consensus 486 eeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~~~~~~~~ 538 (547)
++||++++++++. +||. +.+.+++++.+......+...|+.+.....|
T Consensus 370 ~eei~~~~~~~a~---~~~~--~~~~~~~~~~~~~~~~~i~~~l~~~Kv~~~l 417 (435)
T PRK01490 370 DEEVKAEIEEMAS---QYGQ--PPEVIEFYLKNPQLLAALRADVLEEKVVDFL 417 (435)
T ss_pred HHHHHHHHHHHHH---HcCC--CHHHHHHHHhChhhHHHHHHHHHHHHHHHHH
Confidence 9999999999885 6776 6777887776555555555555555544444
No 3
>TIGR00115 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.
Probab=100.00 E-value=1.8e-70 Score=587.12 Aligned_cols=400 Identities=25% Similarity=0.430 Sum_probs=363.7
Q ss_pred EEEEEEEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhChHHHHHHHHHHHHHhhHHHHHHhhhcccCCccc
Q 008989 102 VRLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILKRTLPHAMTSVTGRALRDSV 181 (547)
Q Consensus 102 ~~l~V~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G~~~i~~e~~e~li~~~~~~al~e~~~~~l~~~~ 181 (547)
+.++|+||+++|++++++++++++++++||||||||||++||+++||+ .|+.++++++++.+|.+++++.++.+++.|.
T Consensus 1 ~~l~v~v~~~~~~~~~~k~~~~~~k~~~ipGFRkGKvP~~~i~k~~g~-~i~~e~~~~li~~~~~~~~~~~~~~~~~~p~ 79 (408)
T TIGR00115 1 RKLTVEVPAEEVEEEVDKALKELAKKVKIPGFRKGKVPRSVVEKRYGK-EVRQEALNELLQEAFSEAVKEEKIRPIGQPE 79 (408)
T ss_pred CeEEEEECHHHHHHHHHHHHHHHHhhCCCCCccCCCCCHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHhCCCCcCCCCc
Confidence 468999999999999999999999999999999999999999999998 5999999999999999999999999998753
Q ss_pred ccccccchhhcccCCCCceEEEEEEEeecccccCCCCCCceeEEEEe----cchhhHHHHHHHHHHHHHHHhcCcccccc
Q 008989 182 RIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKNLKIVVE----IDNDTAAQQAAEEELRRRHKSLGSLKIVT 257 (547)
Q Consensus 182 ~i~~~~~~~~~~~~~~~~~~f~v~vev~Pev~l~~~~dYk~l~v~~~----~de~vd~~~~~e~~l~~~~~~~a~~~~v~ 257 (547)
+. ..++.++++|+|+++|+++|+|+++ +|++++|+++ ++++|+. .|+++++++++|.++.
T Consensus 80 -~~------~~~~~~~~~~~~~~~~~v~Pev~l~---~y~~i~v~~~~~~vtde~vd~------~i~~l~~~~a~~~~~~ 143 (408)
T TIGR00115 80 -IE------VKEIEDGKDLEFTAEFEVYPEVELG---DYKGIEVEKPEVEVTDEDVDE------ELEKLREQNATLVPVE 143 (408)
T ss_pred -cc------cccccCCCCEEEEEEEEecCceecC---CCCceEEEeccCCCCHHHHHH------HHHHHHHhCCcccccc
Confidence 21 1356678999999999999999996 8999999986 2455554 5888899999998876
Q ss_pred ccCcccccEEEEEEEEeeeccCCCCCcccCCCCccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCCC
Q 008989 258 DRGLQVGDIAIVDISATTIDEDESNVQNIPDAETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHLR 337 (547)
Q Consensus 258 dr~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~la 337 (547)
+++++.||+|++||+++ .+|++++++..+++.+.+|. +.++|||+++|+||++|++++|+++||++|+.++++
T Consensus 144 ~~~~~~gD~V~v~~~~~------~dg~~~~~~~~~~~~~~lg~-~~~~~~~ee~L~G~k~Gd~~~~~v~~p~~~~~~~~~ 216 (408)
T TIGR00115 144 RRAAEKGDRVTIDFEGF------IDGEAFEGGKAENFSLELGS-GQFIPGFEEQLVGMKAGEEKEIKVTFPEDYHAEELA 216 (408)
T ss_pred ccccCCCCEEEEEEEEE------ECCEECcCCCCCCeEEEECC-CCcchhHHHHhCCCCCCCeeEEEecCccccCcccCC
Confidence 67999999999999998 57999999888999999994 689999999999999999999999999999999999
Q ss_pred CCeeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHH
Q 008989 338 GVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLF 417 (547)
Q Consensus 338 Gk~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~e~~~~dlPeslv 417 (547)
|+++.|+|+|++|+++.+|+|||+||++++++++|+++||++|+++|+.+.+...++.++++|+++|++.++|++|+++|
T Consensus 217 gk~~~f~v~i~~I~~~~~peldDefak~~~~~~~t~~elr~~ik~~l~~~~~~~~~~~~~~~i~~~l~~~~~~~lPe~~v 296 (408)
T TIGR00115 217 GKEATFKVTVKEVKEKELPELDDEFAKELGEEFETLEELKADIRKNLEREKKERAKNKLKEQLLDKLVENNEFELPESLV 296 (408)
T ss_pred CCeEEEEEEEEEeccCCCCCCCHHHHHhcCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHH
Confidence 99999999999999999999999999999544899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 008989 418 EEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSI 497 (547)
Q Consensus 418 e~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~ 497 (547)
+++++.+++++..++ +++|++.++|.+. +.++|.+++++.|++++|++||+++||+++||+||++|+++++++++
T Consensus 297 ~~~~~~~~~~~~~~~-~~~g~~~~~~~~~----~~e~~~~~~~~~a~~~~k~~lil~~ia~~e~I~vt~eei~~~~~~~a 371 (408)
T TIGR00115 297 EQEIDRLLEQALQQL-QQQGIDLEEYLKD----TEEELREEFREEAERRVKLGLILEEIAKKEKIEVSEEEVEAEIEELA 371 (408)
T ss_pred HHHHHHHHHHHHHHH-HHcCCCHHHhhcc----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 999999999999998 4689999888753 35789999999999999999999999999999999999999999988
Q ss_pred HHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhhhhcc
Q 008989 498 AELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQSQNS 535 (547)
Q Consensus 498 ~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~~~~~ 535 (547)
. +||. +++.+++.+..+.....+...++.+...
T Consensus 372 ~---~~g~--~~~~~~~~~~~~~~~~~i~~~i~~~Kv~ 404 (408)
T TIGR00115 372 Q---QYGE--DPEEVKKYYKKNELLEQLRNDLLEEKVV 404 (408)
T ss_pred H---HcCC--CHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 6 6776 7889999998876666777777766543
No 4
>PF05697 Trigger_N: Bacterial trigger factor protein (TF); InterPro: IPR008881 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This group of sequences contain the ribosomal subunit association domain.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 2D3O_1 1W26_A 1P9Y_A 1OMS_C 1T11_A 3GU0_A 2NSB_A 2NSC_A 3GTY_X.
Probab=99.96 E-value=3.5e-28 Score=224.75 Aligned_cols=135 Identities=32% Similarity=0.570 Sum_probs=115.2
Q ss_pred cEEEEeecCCceEEEEEEEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhChHHHHHHHHHHHHHhhHHHHH
Q 008989 90 IEVTESPEPNSTVRLSVEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILKRTLPHAM 169 (547)
Q Consensus 90 m~vt~~~~~~~~~~l~V~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G~~~i~~e~~e~li~~~~~~al 169 (547)
|+|++++.++|.+.++|+||+++|++++++++++++++++||||||||||+++|+++||.. |+.++++++++.++.+|+
T Consensus 1 M~v~~~~~~~~~~~~~v~v~~~~~~~~~~~~l~~~~k~~~ipGFRkGK~P~~vi~~~~g~~-i~~~~~~~~~~~~~~~~~ 79 (145)
T PF05697_consen 1 MKVTVEKIEDSKVKLEVEVPAEEVEKAYEKALKELAKKVKIPGFRKGKAPRNVIEKRYGKE-IREEAIEELLQEAYEEAI 79 (145)
T ss_dssp -EEEEEEESTTEEEEEEEE-HHHHHHHHHHHHHHHHTTTTBTTS-TTSS-HHHHHHHHCHH-HHHHHHHHHHHHHHHHHH
T ss_pred CccEEEECCCcEEEEEEEECHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999986 999999999999999999
Q ss_pred HhhhcccCCcccccccccchhhcccCCCCceEEEEEEEeecccccCCCCCCceeEEEEe----cchhhHH
Q 008989 170 TSVTGRALRDSVRIVTKFSEMEKNYSSLNSLSYDVLVDVAPEVKWNPGNGYKNLKIVVE----IDNDTAA 235 (547)
Q Consensus 170 ~e~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~f~v~vev~Pev~l~~~~dYk~l~v~~~----~de~vd~ 235 (547)
++.++.++++|. + . ...+.++++|+|++.|+++|+|+++ +|++++++++ ++++|++
T Consensus 80 ~~~~~~~i~~p~-i----~--~~~~~~~~~~~~~~~~~~~Pev~l~---~~~~i~v~~~~~~vtd~~V~~ 139 (145)
T PF05697_consen 80 KEEKIKPIGDPE-I----E--EKDFKEGEDFEFEVEFEVFPEVELK---DYKGIKVEKPEVEVTDEDVDE 139 (145)
T ss_dssp HHTTS-ESSEEE-E----E--EEEEETTS-EEEEEEEEE--ECEET---TCTTSEEEEEEHHHHHHHHHH
T ss_pred HHcCCCcccccc-c----c--ccccccCCCEEEEEEEEecCCcccC---CCCCceeeecccCcCHHHHHH
Confidence 999999997652 2 1 1457789999999999999999996 8999999986 2455554
No 5
>PF05698 Trigger_C: Bacterial trigger factor protein (TF) C-terminus; InterPro: IPR008880 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This entry represents the C-terminal domain of bacterial trigger factor proteins, which has a multi-helical structure consisting of an irregular array of long and short helices. This domain is structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 1T11_A 3GU0_A 3GTY_X 2NSA_A 1ZXJ_A 1W26_A.
Probab=99.80 E-value=2.5e-19 Score=167.42 Aligned_cols=160 Identities=23% Similarity=0.343 Sum_probs=134.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhH
Q 008989 372 TIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKA 451 (547)
Q Consensus 372 Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~ 451 (547)
|+++||++|+++|..+.+....+.++++|+++|++.++|++|+++|+++++.++.++..++ ..+|++.++|++..+. +
T Consensus 1 Tleelk~~i~~~l~~~~~~~~~~~~~~~v~~~L~~~~~~~lP~~lv~~~~~~~~~~~~~~~-~~~g~~~e~~~~~~~~-~ 78 (162)
T PF05698_consen 1 TLEELKEKIREELEKQKKQQIEQQKREAVLDALIENSEVELPESLVEEEIERLIEQMEQQL-KQQGMSLEQYLQMSGK-T 78 (162)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEE-HHHHHHHHHHHHHHHHHTT----TSSCCCHHHHHCT-C
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHh-hhhhhHHHHHHHhcCC-C
Confidence 7999999999999999999999999999999999999999999999999999999999888 6789999888765443 4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhh
Q 008989 452 VKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQ 531 (547)
Q Consensus 452 ~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~ 531 (547)
.++|.+.+++.|++.+|+.||+++||+.+||+||++|+++++..++. .||. +++.+++.+.+...+..+.+.|+.
T Consensus 79 ~~~~~~~~~~~a~~~lk~~lil~~Ia~~e~I~v~~eev~~~~~~~a~---~~~~--~~~~~~~~~~~~~~~~~~~~~l~~ 153 (162)
T PF05698_consen 79 EEEFREEFREEAEKRLKQQLILDAIAKKEKIEVSDEEVEEEIEKLAQ---QYGM--NPEELKEQYEKNKQLEQLRDDLLE 153 (162)
T ss_dssp CCSHCHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHH---CSTS---HHHHHHHHHCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH---HcCC--CHHHHHHHHHhChhHHHHHHHHHH
Confidence 57788999999999999999999999999999999999999999876 6775 899999999888877777777777
Q ss_pred hhcccch
Q 008989 532 SQNSSHI 538 (547)
Q Consensus 532 ~~~~~~~ 538 (547)
+....+|
T Consensus 154 ~Kv~~~l 160 (162)
T PF05698_consen 154 DKVIDFL 160 (162)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 7655443
No 6
>PF00254 FKBP_C: FKBP-type peptidyl-prolyl cis-trans isomerase; InterPro: IPR001179 Synonym(s): Peptidylprolyl cis-trans isomerase FKBP-type peptidylprolyl isomerases (5.2.1.8 from EC) in vertebrates, are receptors for the two immunosuppressants, FK506 and rapamycin. The drugs inhibit T cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. Peptidylprolyl isomerases accelerate protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides. These proteins are found in a variety of organisms.; GO: 0006457 protein folding; PDB: 1IX5_A 3JXV_A 3JYM_A 1T11_A 1PBK_A 1FD9_A 2VCD_A 3B7X_A 1Q6H_B 1Q6I_B ....
Probab=99.04 E-value=1.1e-09 Score=93.41 Aligned_cols=84 Identities=19% Similarity=0.374 Sum_probs=73.3
Q ss_pred cCcccccEEEEEEEEeeeccCCCCCcccCCC--CccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCC
Q 008989 259 RGLQVGDIAIVDISATTIDEDESNVQNIPDA--ETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHL 336 (547)
Q Consensus 259 r~~~~GD~V~id~~~~~~d~d~~~G~~~~~~--~~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~l 336 (547)
+.++.||.|+++|++.. .+|+.+++. ...++.|.+|. +.++|+|+++|.||++||++.|.++.+..|.....
T Consensus 3 ~~~~~gd~V~i~y~~~~-----~~g~~~~~~~~~~~~~~~~~g~-~~~i~g~e~al~~m~~Ge~~~~~vp~~~ayg~~~~ 76 (94)
T PF00254_consen 3 RTPKEGDTVTIHYTGRL-----EDGKVFDSSYQEGEPFEFRLGS-GQVIPGLEEALIGMKVGEKREFYVPPELAYGEKGL 76 (94)
T ss_dssp SSBSTTSEEEEEEEEEE-----TTSEEEEETTTTTSEEEEETTS-SSSSHHHHHHHTTSBTTEEEEEEEEGGGTTTTTTB
T ss_pred ccCCCCCEEEEEEEEEE-----CCCcEEEEeeecCcceeeeecc-CccccchhhhcccccCCCEeeeEeCChhhcCcccc
Confidence 56899999999999983 478898887 56789999995 67999999999999999999999999999987766
Q ss_pred C------CCeeEEEEEEe
Q 008989 337 R------GVQAQFTVECR 348 (547)
Q Consensus 337 a------Gk~~~F~VtVk 348 (547)
. ++++.|+|++.
T Consensus 77 ~~~~ip~~~~l~f~Iell 94 (94)
T PF00254_consen 77 EPPKIPPNSTLVFEIELL 94 (94)
T ss_dssp CTTTBTTTSEEEEEEEEE
T ss_pred CCCCcCCCCeEEEEEEEC
Confidence 4 48999999874
No 7
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=98.77 E-value=2.9e-08 Score=93.02 Aligned_cols=86 Identities=20% Similarity=0.315 Sum_probs=72.1
Q ss_pred CcccccEEEEEEEEeeeccCCCCCcccCCCC--ccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEe-----------
Q 008989 260 GLQVGDIAIVDISATTIDEDESNVQNIPDAE--TKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLA----------- 326 (547)
Q Consensus 260 ~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~--~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~----------- 326 (547)
.++.||.|.++|+++. .+|+.++.+. ..++.|.+|. +.++|||+++|.||++|++++|.++
T Consensus 4 ~i~~~~~V~v~Y~~~~-----~dG~v~dst~~~~~P~~f~~G~-g~vi~gle~aL~gm~~Ge~~~v~ipp~~ayG~~d~~ 77 (156)
T PRK15095 4 SVQSNSAVLVHFTLKL-----DDGSTAESTRNNGKPALFRLGD-GSLSEGLEQQLLGLKVGDKKTFSLEPEAAFGVPSPD 77 (156)
T ss_pred ccCCCCEEEEEEEEEe-----CCCCEEEECCCCCCCEEEEeCC-CCccHHHHHHHcCCCCCCEEEEEEChHHhcCCCChH
Confidence 4789999999999983 4688888765 3789999994 6899999999999999999999887
Q ss_pred ---------CCCC--C-------------------------------CCcCCCCCeeEEEEEEeEee
Q 008989 327 ---------FPES--W-------------------------------RQEHLRGVQAQFTVECRELF 351 (547)
Q Consensus 327 ---------fPed--y-------------------------------~~~~laGk~~~F~VtVk~Ik 351 (547)
||.+ . .+..||||++.|+|+|.+|.
T Consensus 78 ~v~~vp~~~f~~~~~~~~G~~~~~~~~~G~~~~~~V~~i~~~~v~vD~NHPLAGk~L~f~v~i~~v~ 144 (156)
T PRK15095 78 LIQYFSRRDFMDAGEPEIGAIMLFTAMDGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEVLEID 144 (156)
T ss_pred HEEEecHHHCCcccCCCCCCEEEEECCCCCEEEEEEEEEcCCEEEEECCCcCCCCEEEEEEEEEEec
Confidence 3321 0 16789999999999999996
No 8
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=98.77 E-value=4.2e-08 Score=92.45 Aligned_cols=87 Identities=16% Similarity=0.316 Sum_probs=72.2
Q ss_pred CcccccEEEEEEEEeeeccCCCCCcccCCCCc--cCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCC------
Q 008989 260 GLQVGDIAIVDISATTIDEDESNVQNIPDAET--KGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESW------ 331 (547)
Q Consensus 260 ~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~~--~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy------ 331 (547)
++++||+|.|+|+... .+|+.++.+.. .++.+.+| .++++|+|+++|+||.+|+++++.++--+.|
T Consensus 2 ~i~k~~~V~i~Y~~~~-----~dg~v~Dtt~e~~~P~~~i~G-~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~ 75 (174)
T COG1047 2 KIEKGDVVSLHYTLKV-----EDGEVVDTTDENYGPLTFIVG-AGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPD 75 (174)
T ss_pred cccCCCEEEEEEEEEe-----cCCcEEEcccccCCCeEEEec-CCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChH
Confidence 4789999999999983 45888876543 58999999 5789999999999999999999999722222
Q ss_pred ----------------------------------------------CCcCCCCCeeEEEEEEeEeee
Q 008989 332 ----------------------------------------------RQEHLRGVQAQFTVECRELFY 352 (547)
Q Consensus 332 ----------------------------------------------~~~~laGk~~~F~VtVk~Ik~ 352 (547)
.+..||||++.|+|+|.+|..
T Consensus 76 lvq~vp~~~F~~~~~~~vGm~~~~~~~~~~~~~~V~~V~~~~V~VDfNHpLAGktL~feveVv~v~~ 142 (174)
T COG1047 76 LVQRVPRDEFQGVGELEVGMEVEAEGGDGEIPGVVTEVSGDRVTVDFNHPLAGKTLHFEVEVVEVRE 142 (174)
T ss_pred HeEEecHHHhCcCCCCCCCcEEEEcCCCceeeEEEEEEcCCEEEEeCCCcCCCCeEEEEEEEEEEec
Confidence 167899999999999999964
No 9
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=98.71 E-value=4.3e-08 Score=94.82 Aligned_cols=94 Identities=13% Similarity=0.221 Sum_probs=75.9
Q ss_pred cccccEEEEEEEEeeeccCCCCCcccCCCC-ccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEe-------------
Q 008989 261 LQVGDIAIVDISATTIDEDESNVQNIPDAE-TKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLA------------- 326 (547)
Q Consensus 261 ~~~GD~V~id~~~~~~d~d~~~G~~~~~~~-~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~------------- 326 (547)
+++|++|+|+|+.+. .+|+.++.+. ..++.|.+|. ++++|+|+++|+||++|++++|+++
T Consensus 3 I~~~~vV~l~Y~l~~-----~dG~v~dst~~~~Pl~~~~G~-g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV 76 (196)
T PRK10737 3 VAKDLVVSLAYQVRT-----EDGVLVDESPVSAPLDYLHGH-GSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLV 76 (196)
T ss_pred cCCCCEEEEEEEEEe-----CCCCEEEecCCCCCeEEEeCC-CcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHE
Confidence 678999999999982 4788888765 4899999994 7899999999999999999999987
Q ss_pred -------CCCC--C------------------------------CCcCCCCCeeEEEEEEeEeeecCCCCCCHHHHh
Q 008989 327 -------FPES--W------------------------------RQEHLRGVQAQFTVECRELFYRDLPKLDDSLAG 364 (547)
Q Consensus 327 -------fPed--y------------------------------~~~~laGk~~~F~VtVk~Ik~~~lPELdDEfak 364 (547)
||.. . .+..|||+++.|+|+|.+|. +.-.+|++.
T Consensus 77 ~~vpr~~F~~~~~l~~G~~~~~~~~~G~~~~~V~ev~~d~V~vD~NHPLAG~~L~F~veV~~vr----~at~eEi~~ 149 (196)
T PRK10737 77 QRVPKDVFMGVDELQVGMRFLAETDQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIR----EATEEELAH 149 (196)
T ss_pred EEecHHHCCCccCCCCCCEEEEeCCCCcEEEEEEEEcCCEEEEECCCcCCCCEEEEEEEEEEec----cCCHHHHhc
Confidence 3321 0 15679999999999999996 333456654
No 10
>TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype.
Probab=98.37 E-value=1.8e-06 Score=82.62 Aligned_cols=86 Identities=14% Similarity=0.187 Sum_probs=69.8
Q ss_pred CcccccEEEEEEEEeeeccCCCCCcccCCCC-ccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCC--
Q 008989 260 GLQVGDIAIVDISATTIDEDESNVQNIPDAE-TKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHL-- 336 (547)
Q Consensus 260 ~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~-~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~l-- 336 (547)
.++.||.|+++|++.. .+|+.+++.. ..++.+.+|. +.++|||+++|.||++||+.+|.++....|+....
T Consensus 85 ~p~~gd~V~v~Y~~~~-----~dG~v~~ss~~~~P~~f~vg~-~~vi~Gl~e~L~~Mk~Ge~~~~~iP~~~AYG~~g~~~ 158 (177)
T TIGR03516 85 TPEFGDLVTFEYDIRA-----LDGDVIYSEEELGPQTYKVDQ-QDLFSGLRDGLKLMKEGETATFLFPSHKAYGYYGDQN 158 (177)
T ss_pred cCCCCCEEEEEEEEEe-----CCCCEEEeCCCCCCEEEEeCC-cchhHHHHHHHcCCCCCCEEEEEECHHHcCCCCCCCC
Confidence 4588999999999983 5788887654 3578899984 67999999999999999999999886556655433
Q ss_pred ---CCCeeEEEEEEeEee
Q 008989 337 ---RGVQAQFTVECRELF 351 (547)
Q Consensus 337 ---aGk~~~F~VtVk~Ik 351 (547)
.+.++.|+|++.+|+
T Consensus 159 ~Ippns~L~f~IeL~~i~ 176 (177)
T TIGR03516 159 KIGPNLPIISTVTLLNIK 176 (177)
T ss_pred CcCcCCcEEEEEEEEEec
Confidence 456789999999985
No 11
>PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=98.35 E-value=2.3e-06 Score=86.95 Aligned_cols=85 Identities=16% Similarity=0.316 Sum_probs=68.9
Q ss_pred CcccccEEEEEEEEeeeccCCCCCcccCCCCc--cCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCCC
Q 008989 260 GLQVGDIAIVDISATTIDEDESNVQNIPDAET--KGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHLR 337 (547)
Q Consensus 260 ~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~~--~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~la 337 (547)
.++.||.|+|+|.++. .+|+.|++... .++.|.++ .++|||+++|.||++|++..|.++.+..|+.....
T Consensus 160 ~p~~gD~V~V~Y~g~l-----~dG~vfdss~~~g~p~~f~l~---~vipG~~EaL~~Mk~Gek~~l~IP~~laYG~~g~~ 231 (269)
T PRK10902 160 APKDSDTVVVNYKGTL-----IDGKEFDNSYTRGEPLSFRLD---GVIPGWTEGLKNIKKGGKIKLVIPPELAYGKAGVP 231 (269)
T ss_pred CCCCCCEEEEEEEEEe-----CCCCEeeccccCCCceEEecC---CcchHHHHHHhcCCCCcEEEEEECchhhCCCCCCC
Confidence 3578999999999983 57888877543 45666654 59999999999999999999998877788877765
Q ss_pred CCe----eEEEEEEeEeee
Q 008989 338 GVQ----AQFTVECRELFY 352 (547)
Q Consensus 338 Gk~----~~F~VtVk~Ik~ 352 (547)
|.. +.|+|+|.+|+.
T Consensus 232 gIppns~LvfeVeLl~V~~ 250 (269)
T PRK10902 232 GIPANSTLVFDVELLDVKP 250 (269)
T ss_pred CCCCCCcEEEEEEEEEecc
Confidence 554 499999999964
No 12
>KOG0549 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.30 E-value=3.5e-06 Score=79.47 Aligned_cols=90 Identities=13% Similarity=0.180 Sum_probs=72.9
Q ss_pred ccCcccccEEEEEEEEeeeccCCCCCcccCCCC--ccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcC
Q 008989 258 DRGLQVGDIAIVDISATTIDEDESNVQNIPDAE--TKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEH 335 (547)
Q Consensus 258 dr~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~--~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~ 335 (547)
...++.||.|.++|++.. .||..|+.+- +.+|+|.+| .++.|+|++.+|.||.+||++.+.++.-=.|....
T Consensus 82 ~~kak~GD~l~~HY~g~l-----eDGt~fdSS~~rg~P~~f~LG-~gqVIkG~Dqgl~gMCvGEkRkl~IPp~LgYG~~G 155 (188)
T KOG0549|consen 82 PEKAKKGDTLHVHYTGSL-----EDGTKFDSSYSRGAPFTFTLG-TGQVIKGWDQGLLGMCVGEKRKLIIPPHLGYGERG 155 (188)
T ss_pred cccccCCCEEEEEEEEEe-----cCCCEEeeeccCCCCEEEEeC-CCceeccHhHHhhhhCcccceEEecCccccCccCC
Confidence 467889999999999974 6899998754 368999999 57999999999999999999999887444565444
Q ss_pred CCC-----CeeEEEEEEeEeeec
Q 008989 336 LRG-----VQAQFTVECRELFYR 353 (547)
Q Consensus 336 laG-----k~~~F~VtVk~Ik~~ 353 (547)
..+ ....|.|++.+|.+.
T Consensus 156 ~~~~IP~~A~LiFdiELv~i~~~ 178 (188)
T KOG0549|consen 156 APPKIPGDAVLIFDIELVKIERG 178 (188)
T ss_pred CCCCCCCCeeEEEEEEEEEeecC
Confidence 322 367999999999764
No 13
>COG0545 FkpA FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]
Probab=98.30 E-value=3.5e-06 Score=81.07 Aligned_cols=85 Identities=16% Similarity=0.286 Sum_probs=72.4
Q ss_pred cCcccccEEEEEEEEeeeccCCCCCcccCCC--CccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCC
Q 008989 259 RGLQVGDIAIVDISATTIDEDESNVQNIPDA--ETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHL 336 (547)
Q Consensus 259 r~~~~GD~V~id~~~~~~d~d~~~G~~~~~~--~~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~l 336 (547)
..+..||.|.++|+|+. .||+.|+.+ ..+++.|.+| .+|||+.++|.||++|+++.+.++-+-.|+....
T Consensus 114 ~~~~~~~~V~vhY~G~l-----~~G~vFDsS~~rg~p~~f~l~---~vI~Gw~egl~~M~vG~k~~l~IP~~laYG~~g~ 185 (205)
T COG0545 114 AAPKKGDTVTVHYTGTL-----IDGTVFDSSYDRGQPAEFPLG---GVIPGWDEGLQGMKVGGKRKLTIPPELAYGERGV 185 (205)
T ss_pred CCCCCCCEEEEEEEEec-----CCCCccccccccCCCceeecC---CeeehHHHHHhhCCCCceEEEEeCchhccCcCCC
Confidence 34677999999999985 689999986 3578899887 5999999999999999999999987778887776
Q ss_pred CC-----CeeEEEEEEeEee
Q 008989 337 RG-----VQAQFTVECRELF 351 (547)
Q Consensus 337 aG-----k~~~F~VtVk~Ik 351 (547)
.| -+..|+|++.+|+
T Consensus 186 ~g~Ippns~LvFeVeLl~v~ 205 (205)
T COG0545 186 PGVIPPNSTLVFEVELLDVK 205 (205)
T ss_pred CCCCCCCCeEEEEEEEEecC
Confidence 66 6789999998874
No 14
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=7.9e-06 Score=68.89 Aligned_cols=84 Identities=15% Similarity=0.273 Sum_probs=69.0
Q ss_pred cccccEEEEEEEEeeeccCCCCCcccCCCC--ccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCCC-
Q 008989 261 LQVGDIAIVDISATTIDEDESNVQNIPDAE--TKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHLR- 337 (547)
Q Consensus 261 ~~~GD~V~id~~~~~~d~d~~~G~~~~~~~--~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~la- 337 (547)
.+.||.|+++|+++. .||+.|+.+. .++|.|.+|- +.+|.|+++++..|.+||.-.+++.-+=.|......
T Consensus 17 pK~Gqtvt~hYtg~L-----~dG~kfDSs~dr~kPfkf~IGk-geVIkGwdegv~qmsvGekakLti~pd~aYG~~G~p~ 90 (108)
T KOG0544|consen 17 PKKGQTVTVHYTGTL-----QDGKKFDSSRDRGKPFKFKIGK-GEVIKGWDEGVAQMSVGEKAKLTISPDYAYGPRGHPG 90 (108)
T ss_pred CCCCCEEEEEEEeEe-----cCCcEeecccccCCCeeEEecC-cceeechhhcchhccccccceeeeccccccCCCCCCC
Confidence 678999999999984 6899999865 4789999995 789999999999999999999888754455444333
Q ss_pred ----CCeeEEEEEEeEe
Q 008989 338 ----GVQAQFTVECREL 350 (547)
Q Consensus 338 ----Gk~~~F~VtVk~I 350 (547)
+.+..|+|++.+|
T Consensus 91 ~IppNatL~FdVEll~v 107 (108)
T KOG0544|consen 91 GIPPNATLVFDVELLKV 107 (108)
T ss_pred ccCCCcEEEEEEEEEec
Confidence 3578999999876
No 15
>KOG0552 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=97.97 E-value=2.7e-05 Score=76.59 Aligned_cols=87 Identities=15% Similarity=0.177 Sum_probs=72.7
Q ss_pred CcccccEEEEEEEEeeeccCCCCCcccCCCC-ccCEE-EEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcCC-
Q 008989 260 GLQVGDIAIVDISATTIDEDESNVQNIPDAE-TKGFH-FDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEHL- 336 (547)
Q Consensus 260 ~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~-~~~~~-l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~l- 336 (547)
.+..|+.|.++|.|... .+|+.|+..- .++|. |.+| ++.+|||++-.+.||++|.++.+.|+-|-.|+...+
T Consensus 134 ~a~~G~rV~v~Y~Gkl~----~~GkvFd~~~~~kp~~~f~lg-~g~VIkG~d~gv~GMkvGGkRrviIPp~lgYg~~g~~ 208 (226)
T KOG0552|consen 134 SAKKGKRVSVRYIGKLK----GNGKVFDSNFGGKPFKLFRLG-SGEVIKGWDVGVEGMKVGGKRRVIIPPELGYGKKGVP 208 (226)
T ss_pred CCCCCCEEEEEEEEEec----CCCeEeecccCCCCccccccC-CCCCCchHHHhhhhhccCCeeEEEeCccccccccCcC
Confidence 47789999999999842 2788888754 47788 9999 478999999999999999999999998778877654
Q ss_pred ---CCCeeEEEEEEeEee
Q 008989 337 ---RGVQAQFTVECRELF 351 (547)
Q Consensus 337 ---aGk~~~F~VtVk~Ik 351 (547)
.+.+..|.|++..|+
T Consensus 209 ~IppnstL~fdVEL~~v~ 226 (226)
T KOG0552|consen 209 EIPPNSTLVFDVELLSVK 226 (226)
T ss_pred cCCCCCcEEEEEEEEecC
Confidence 457889999998773
No 16
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=97.86 E-value=8e-05 Score=73.03 Aligned_cols=84 Identities=13% Similarity=0.156 Sum_probs=66.5
Q ss_pred CcccccEEEEEEEEeeeccCCCCCcccCCCC--ccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCcC--
Q 008989 260 GLQVGDIAIVDISATTIDEDESNVQNIPDAE--TKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQEH-- 335 (547)
Q Consensus 260 ~~~~GD~V~id~~~~~~d~d~~~G~~~~~~~--~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~~-- 335 (547)
.+..||.|+|+|.++. .+|+.|+++. ..++.|.++ .++|||+++|.||++|++..|.++.-..|+...
T Consensus 116 ~p~~~d~V~v~Y~g~l-----~dG~vfdss~~~g~P~~f~l~---~vipG~~eaL~~M~~G~k~~~~IP~~lAYG~~g~~ 187 (206)
T PRK11570 116 IPARTDRVRVHYTGKL-----IDGTVFDSSVARGEPAEFPVN---GVIPGWIEALTLMPVGSKWELTIPHELAYGERGAG 187 (206)
T ss_pred CCCCCCEEEEEEEEEE-----CCCCEEEeccCCCCCeEEEee---chhhHHHHHHcCCCCCCEEEEEECHHHcCCCCCCC
Confidence 3578999999999984 5788888754 367888876 489999999999999999999887544555432
Q ss_pred ---CCCCeeEEEEEEeEee
Q 008989 336 ---LRGVQAQFTVECRELF 351 (547)
Q Consensus 336 ---laGk~~~F~VtVk~Ik 351 (547)
-.+-++.|+|+|.+|+
T Consensus 188 ~~Ipp~s~Lif~veLl~i~ 206 (206)
T PRK11570 188 ASIPPFSTLVFEVELLEIL 206 (206)
T ss_pred CCcCCCCeEEEEEEEEEEC
Confidence 2456889999999883
No 17
>PRK10770 peptidyl-prolyl cis-trans isomerase SurA; Provisional
Probab=95.93 E-value=0.067 Score=57.78 Aligned_cols=68 Identities=16% Similarity=0.135 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 008989 417 FEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENS 496 (547)
Q Consensus 417 ve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~ 496 (547)
++.+++++++....+++ ++|.+.. . . +.++.++.++|....++.++|+++||+||+++|++++.++
T Consensus 20 ~~~ev~~~~~~~~~~~~-~~g~~~~------~---~----~~l~~~~l~~Li~~~Ll~q~A~~~gi~vsd~ev~~~i~~~ 85 (413)
T PRK10770 20 LESDVDGLMQSVKLNAQ-QAGQQLP------D---D----ATLRHQILERLIMDNIILQMAQKMGVKISDEQLDQAIANI 85 (413)
T ss_pred cHHHHHHHHHHHHHHHH-HcCCCCC------c---H----HHHHHHHHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHH
Confidence 45566666666555552 3443211 1 1 2357788999999999999999999999999999999887
Q ss_pred HH
Q 008989 497 IA 498 (547)
Q Consensus 497 ~~ 498 (547)
+.
T Consensus 86 ~~ 87 (413)
T PRK10770 86 AA 87 (413)
T ss_pred HH
Confidence 65
No 18
>PRK04405 prsA peptidylprolyl isomerase; Provisional
Probab=94.72 E-value=0.63 Score=48.34 Aligned_cols=118 Identities=12% Similarity=0.069 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHHh-hcCCCCCHHHHHHHHHHHHHHHHHH----HHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHH
Q 008989 394 QATDNAILDQLYK-MVEIDIPQSLFEEQGRQLYGAQLLQ----MQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIK 468 (547)
Q Consensus 394 ~~~~~~il~~L~e-~~~~dlPeslve~e~~~~~~~~~~~----l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK 468 (547)
+.+.+.|++.++. +..+.+.+.-|+++++++.+++-.+ | .++|++. +.|+ .++|
T Consensus 56 ~~L~~li~~k~l~~~~~~~v~~~evd~~i~~i~~~~g~~f~~~L-~~~G~t~------------~~~r--------~~ir 114 (298)
T PRK04405 56 TVLANMIIYRALEKQYGKKVSTKKVDKQYNSYKKQYGSSFDSVL-SQNGMTT------------SSFK--------QNLR 114 (298)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHH-HHcCCCH------------HHHH--------HHHH
Confidence 3455555555443 5667888888887776655432211 2 3344443 2333 2344
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhhhh
Q 008989 469 QNLAVGDIFKRENLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQSQ 533 (547)
Q Consensus 469 ~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~~~ 533 (547)
.+++++.+.. ..+.||++||++.+++...++.-.-.-++.+...+.+.+.+..+.-|..|-.+.
T Consensus 115 ~~~l~~~~v~-~~i~Vtd~ei~~~y~~~~~~~~v~hIlv~~~~~A~~v~~~l~~G~~F~~lA~~~ 178 (298)
T PRK04405 115 TNLLSEAALK-KLKKVTNSQLKKAWKSYQPKVTVQHILVSKKSTAETVIKKLKDGKDFAKLAKKY 178 (298)
T ss_pred HHHHHHHHHh-ccCCCCHHHHHHHHHHhhhhEEEEEEEecChHHHHHHHHHHHCCCCHHHHHHHh
Confidence 5566665544 579999999999887532221100000223333334444444455677766653
No 19
>PRK00059 prsA peptidylprolyl isomerase; Provisional
Probab=94.69 E-value=0.86 Score=47.77 Aligned_cols=103 Identities=14% Similarity=0.162 Sum_probs=65.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhc--CChhHHHHHHHHHHHHHHH
Q 008989 388 EQTAKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAAL--SSPKAVKEFLENQRENITN 465 (547)
Q Consensus 388 ~~~~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~--~~~~~~ee~~e~~~~~A~k 465 (547)
.....++.+.+.++.+-+++..+.+++..|+++++..+..+..+ .+++.+.|.+. ..+-+.++|++. .++
T Consensus 86 ~~~vL~~LI~~~ll~q~a~~~gi~vsd~ei~~~i~~~~~~~~~~----~~~~~~~~~~~L~~~g~t~~~~~~~----~~~ 157 (336)
T PRK00059 86 KEQILDSLITEKVLLQKAKELKLIPSEEELNKEVDKKINEIKKQ----FNNDEEQFEEALKATGFTEETFKEY----LKN 157 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHh----cCCCHHHHHHHHHHcCCCHHHHHHH----HHH
Confidence 44455667778888888888999999999988887665544321 24455544321 112233445433 334
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 008989 466 VIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL 500 (547)
Q Consensus 466 ~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~ 500 (547)
.+....+++.|.. ++.||++|+.+.++.....|
T Consensus 158 ~ll~~~l~~~i~~--~~~vsd~ei~~~y~~~~~~~ 190 (336)
T PRK00059 158 QIIIEKVINEVVK--DVKVTDKDAQKYYNENKSKF 190 (336)
T ss_pred HHHHHHHHHHHhc--cCCCCHHHHHHHHHHhhhhh
Confidence 4555556666653 79999999999988766544
No 20
>PRK00059 prsA peptidylprolyl isomerase; Provisional
Probab=93.71 E-value=1.5 Score=45.97 Aligned_cols=73 Identities=22% Similarity=0.268 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH---------------hccCCCCHHHHHHHHHHhhh
Q 008989 457 ENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELK---------------QQKQEYDEDRVREQVSTFSY 521 (547)
Q Consensus 457 e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~---------------~~g~~~~~~~l~e~~~e~~~ 521 (547)
...+.++..++-...++..-|++.||+||+++|.+++...+..|+ ++|. +++.++++++..+.
T Consensus 83 ~~~~~~vL~~LI~~~ll~q~a~~~gi~vsd~ei~~~i~~~~~~~~~~~~~~~~~~~~~L~~~g~--t~~~~~~~~~~~ll 160 (336)
T PRK00059 83 KQQKEQILDSLITEKVLLQKAKELKLIPSEEELNKEVDKKINEIKKQFNNDEEQFEEALKATGF--TEETFKEYLKNQII 160 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHcCC--CHHHHHHHHHHHHH
Confidence 345777777888888888899999999999999888776543332 3333 66667777777766
Q ss_pred hHHHHHHHhh
Q 008989 522 VGLIFCGIMQ 531 (547)
Q Consensus 522 ~~~~~~~lm~ 531 (547)
.+.+...+..
T Consensus 161 ~~~l~~~i~~ 170 (336)
T PRK00059 161 IEKVINEVVK 170 (336)
T ss_pred HHHHHHHHhc
Confidence 6666665554
No 21
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=93.56 E-value=1.5 Score=38.98 Aligned_cols=57 Identities=16% Similarity=0.208 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhh
Q 008989 459 QRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFS 520 (547)
Q Consensus 459 ~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~ 520 (547)
++.++...+=..-++..-|++.||.||+++|++.+.++++ ++|. +.+.++.++...+
T Consensus 42 l~~qvLd~LI~e~L~~q~ak~~gI~vsd~evd~~i~~ia~---~n~l--s~~ql~~~L~~~G 98 (118)
T PF09312_consen 42 LRKQVLDQLIDEKLQLQEAKRLGIKVSDEEVDEAIANIAK---QNNL--SVEQLRQQLEQQG 98 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCT----HHHHHHHHHHHHH---HTT----HHHHHHHCHHCT
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH---HcCC--CHHHHHHHHHHcC
Confidence 3455555555556667789999999999999999999875 3444 4555555555443
No 22
>PRK12450 foldase protein PrsA; Reviewed
Probab=92.39 E-value=0.84 Score=47.62 Aligned_cols=78 Identities=6% Similarity=0.026 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH--------hccCCCCHHHHHHHHHHhhhhHHHHHHHhhh--h
Q 008989 464 TNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELK--------QQKQEYDEDRVREQVSTFSYVGLIFCGIMQS--Q 533 (547)
Q Consensus 464 ~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~--------~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~~--~ 533 (547)
.+.+...||-+.|..++++.|+++||++.+.+...+++ ++|. +.+.++++++..++++.++..++.+ +
T Consensus 56 ~~~~l~~li~~~L~~q~~~kvsd~eVd~~i~~~~~q~g~~f~~~L~~~G~--T~~~~ke~Ir~~ll~~~~~~~~~~~~~V 133 (309)
T PRK12450 56 QKAMLSLVISRVFETQYANKVSDKEVEKAYKQTADQYGTSFKTVLAQSGL--TPETYKKQIRLTKLVEYAVKEQAKNETI 133 (309)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 56677788888888999999999999999998876542 4555 7888999998888877777776654 3
Q ss_pred cccchhhhhh
Q 008989 534 NSSHISCFWN 543 (547)
Q Consensus 534 ~~~~~~~~~~ 543 (547)
+..-|--||+
T Consensus 134 td~evk~~y~ 143 (309)
T PRK12450 134 SKKDYRQAYD 143 (309)
T ss_pred CHHHHHHHHH
Confidence 5555656664
No 23
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=91.43 E-value=1.5 Score=45.84 Aligned_cols=63 Identities=11% Similarity=0.037 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH--------HhccCCCCHHHHHHHHHHhhhhHHHHH
Q 008989 463 ITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL--------KQQKQEYDEDRVREQVSTFSYVGLIFC 527 (547)
Q Consensus 463 A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~--------~~~g~~~~~~~l~e~~~e~~~~~~~~~ 527 (547)
..+.+...++-..+.++.+|.|+++||++++.++.+++ +++|. +.+.+|++++....++.++.
T Consensus 53 ~~~~l~~~~i~~~l~~q~~i~Vsd~EVd~~i~~i~~q~g~~f~~~L~~~G~--t~~~~k~~ir~~ll~~~~~~ 123 (310)
T PRK01326 53 AQQAMLNLTISRVFEKQYGDKVSDKEVEKAYAKTAKQYGASFSRALAQAGL--TPETYKAQIRTSKLVEYAVK 123 (310)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHHHH
Confidence 34556667777778899999999999999998887643 34565 77888888887766555443
No 24
>TIGR02933 nifM_nitrog nitrogen fixation protein NifM. Members of this protein family, found in a subset of nitrogen-fixing bacteria, are the nitrogen fixation protein NifM. NifM, homologous to peptidyl-prolyl cis-trans isomerases, appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase.
Probab=91.39 E-value=4.5 Score=40.99 Aligned_cols=85 Identities=14% Similarity=0.144 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 008989 394 QATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQNLAV 473 (547)
Q Consensus 394 ~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~Lil 473 (547)
+.+.+.++-+..+...+.+++.-|++..+ ++...| ...|++.+.| ++..++.+.+..++
T Consensus 34 ~lI~e~l~lq~A~~~gi~v~~~ev~~~~e----~~~~~L-~~~G~~~~~~----------------r~~ir~~i~~~~~~ 92 (256)
T TIGR02933 34 QRHIEQAVVRAADEIGVVIPPSLLEEAPQ----ALAQAL-DEQALDAAER----------------RAMLAHHLRLEAQL 92 (256)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHH----HHHHHH-HHcCCCHHHH----------------HHHHHHHHHHHHHH
Confidence 55667777888899999999999987643 344455 4568775332 33444455555555
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 008989 474 GDIFKRENLQFSTEDLVKEVENSIAEL 500 (547)
Q Consensus 474 ~~Iak~E~I~VteeEi~~ei~~~~~~~ 500 (547)
..+.+ ..+.||++||+..+.....+|
T Consensus 93 ~~~~~-~~i~ise~ei~~yy~~~~~~~ 118 (256)
T TIGR02933 93 ACVCA-QAPQPDDADVEAWYRRHAEQF 118 (256)
T ss_pred HHHhc-CCCCCCHHHHHHHHHHHHHhc
Confidence 55553 358999999999988766544
No 25
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=91.18 E-value=1.5 Score=45.19 Aligned_cols=73 Identities=15% Similarity=0.234 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH--------HhccCCCCHHHHHHHHHHhhhh
Q 008989 451 AVKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL--------KQQKQEYDEDRVREQVSTFSYV 522 (547)
Q Consensus 451 ~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~--------~~~g~~~~~~~l~e~~~e~~~~ 522 (547)
+.++|...++....+.+-.+||++.+..+ +|.||+++|++++.++.+++ .++|. +.+.+|++++..+..
T Consensus 36 T~~e~~~~~k~~~~~~~L~~~I~~~l~~~-~i~vs~~evd~~i~~i~~~~~~~f~~~L~~~g~--s~~~~r~~lr~~l~~ 112 (287)
T PRK03095 36 TKDEFYEQMKTQAGKQVLNNMVMEKVLIK-NYKVEDKEVDKKYDEMKKQYGDQFDTLLKQQGI--KEETLKTGVRAQLAQ 112 (287)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHHhhHHHHHHHHHcCC--CHHHHHHHHHHHHHH
Confidence 34556666666667778888998888754 89999999999999887643 23454 677788888887765
Q ss_pred HHHH
Q 008989 523 GLIF 526 (547)
Q Consensus 523 ~~~~ 526 (547)
+.++
T Consensus 113 ~kl~ 116 (287)
T PRK03095 113 EKAI 116 (287)
T ss_pred HHHh
Confidence 5443
No 26
>PRK12450 foldase protein PrsA; Reviewed
Probab=90.38 E-value=5.1 Score=41.79 Aligned_cols=86 Identities=12% Similarity=0.087 Sum_probs=45.3
Q ss_pred HHHHHHHHHH-hhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 008989 396 TDNAILDQLY-KMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQNLAVG 474 (547)
Q Consensus 396 ~~~~il~~L~-e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~Lil~ 474 (547)
+.+.+++.++ .+....++..-|+++++.+..++ |.+.+.++...+- +.+.|++ +.+..+.+..++.
T Consensus 59 ~l~~li~~~L~~q~~~kvsd~eVd~~i~~~~~q~--------g~~f~~~L~~~G~-T~~~~ke----~Ir~~ll~~~~~~ 125 (309)
T PRK12450 59 MLSLVISRVFETQYANKVSDKEVEKAYKQTADQY--------GTSFKTVLAQSGL-TPETYKK----QIRLTKLVEYAVK 125 (309)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH--------hHHHHHHHHHcCC-CHHHHHH----HHHHHHHHHHHHH
Confidence 4455555544 66666788888887776654432 2222222222211 2233432 2222333444444
Q ss_pred HHHHHcCCCCCHHHHHHHHHHH
Q 008989 475 DIFKRENLQFSTEDLVKEVENS 496 (547)
Q Consensus 475 ~Iak~E~I~VteeEi~~ei~~~ 496 (547)
.+ ...+.||++|+++.++..
T Consensus 126 ~~--~~~~~Vtd~evk~~y~~~ 145 (309)
T PRK12450 126 EQ--AKNETISKKDYRQAYDAY 145 (309)
T ss_pred HH--hccCCCCHHHHHHHHHHh
Confidence 43 256789999999988764
No 27
>TIGR02933 nifM_nitrog nitrogen fixation protein NifM. Members of this protein family, found in a subset of nitrogen-fixing bacteria, are the nitrogen fixation protein NifM. NifM, homologous to peptidyl-prolyl cis-trans isomerases, appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase.
Probab=90.34 E-value=2.5 Score=42.87 Aligned_cols=68 Identities=7% Similarity=0.091 Sum_probs=52.1
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhhhh---cccchhhhhh
Q 008989 474 GDIFKRENLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQSQ---NSSHISCFWN 543 (547)
Q Consensus 474 ~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~~~---~~~~~~~~~~ 543 (547)
-..|++.||.|++++|++..+.+.+.+++.|. +.+.++++++..+....++..++.++ .+.-|--|++
T Consensus 42 lq~A~~~gi~v~~~ev~~~~e~~~~~L~~~G~--~~~~~r~~ir~~i~~~~~~~~~~~~~i~ise~ei~~yy~ 112 (256)
T TIGR02933 42 VRAADEIGVVIPPSLLEEAPQALAQALDEQAL--DAAERRAMLAHHLRLEAQLACVCAQAPQPDDADVEAWYR 112 (256)
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Confidence 55689999999999999988777777778887 78889999998888887777776533 3444444443
No 28
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=90.22 E-value=5.7 Score=41.43 Aligned_cols=79 Identities=13% Similarity=0.053 Sum_probs=42.9
Q ss_pred HHHHHHHH-HHhhcCCCCCHHHHHHHHHHHHHHHH----HHHHhcCCCCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHH
Q 008989 396 TDNAILDQ-LYKMVEIDIPQSLFEEQGRQLYGAQL----LQMQAGMKLNEQQLAALSSPKAVKEFLENQRENITNVIKQN 470 (547)
Q Consensus 396 ~~~~il~~-L~e~~~~dlPeslve~e~~~~~~~~~----~~l~~~~~~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~ 470 (547)
+.+.+++. |.++..+.+.+.-|+++++.+.+++. ..| .++|++. +.|++.+ |.+
T Consensus 57 l~~~~i~~~l~~q~~i~Vsd~EVd~~i~~i~~q~g~~f~~~L-~~~G~t~------------~~~k~~i--------r~~ 115 (310)
T PRK01326 57 MLNLTISRVFEKQYGDKVSDKEVEKAYAKTAKQYGASFSRAL-AQAGLTP------------ETYKAQI--------RTS 115 (310)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhHHHHHHH-HHcCCCH------------HHHHHHH--------HHH
Confidence 33444444 44667788888888887776654322 111 2334332 3343333 233
Q ss_pred HHHHHHHH-HcCCCCCHHHHHHHHHH
Q 008989 471 LAVGDIFK-RENLQFSTEDLVKEVEN 495 (547)
Q Consensus 471 Lil~~Iak-~E~I~VteeEi~~ei~~ 495 (547)
+++..+.+ .-++.||++|+++.+..
T Consensus 116 ll~~~~~~~~~~~~Vtd~ei~~~y~~ 141 (310)
T PRK01326 116 KLVEYAVKEAAKKELTDEAYKKAYEE 141 (310)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence 44443332 23368999999987654
No 29
>PRK10788 periplasmic folding chaperone; Provisional
Probab=90.08 E-value=4.3 Score=46.41 Aligned_cols=74 Identities=14% Similarity=0.196 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH--------------HHHhccCCCCHHHHHHHHHHhh
Q 008989 455 FLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIA--------------ELKQQKQEYDEDRVREQVSTFS 520 (547)
Q Consensus 455 ~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~--------------~~~~~g~~~~~~~l~e~~~e~~ 520 (547)
+...++.++-+++=..-++..-|++.||.||+++|...|.++-. .+.+.|. +++.+++++++.+
T Consensus 83 ~~~~l~~qvl~~LI~~~Ll~q~A~~lgi~vsd~ev~~~I~~~p~Fq~~G~Fd~~~y~~~L~~~g~--t~~~f~~~ir~~l 160 (623)
T PRK10788 83 YMKQLRQQVLNRLIDEALLDQYARELGLGISDEQVKQAIFATPAFQTDGKFDNNKYLAILNQMGM--TADQYAQALRQQL 160 (623)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhCcccccCCCcCHHHHHHHHHHcCC--CHHHHHHHHHHHH
Confidence 34456788888888888899999999999999999999877421 0122332 5666666666666
Q ss_pred hhHHHHHHHh
Q 008989 521 YVGLIFCGIM 530 (547)
Q Consensus 521 ~~~~~~~~lm 530 (547)
..+.++..|+
T Consensus 161 ~~~~l~~~i~ 170 (623)
T PRK10788 161 TTQQLINGVA 170 (623)
T ss_pred HHHHHHHHHh
Confidence 6555555554
No 30
>PRK04980 hypothetical protein; Provisional
Probab=88.91 E-value=1.9 Score=37.56 Aligned_cols=44 Identities=14% Similarity=0.141 Sum_probs=38.1
Q ss_pred CCCeeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHHH
Q 008989 337 RGVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQK 383 (547)
Q Consensus 337 aGk~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~~ 383 (547)
.+-...+.+.|.+|....+-+|||+.|++= |+ |+++||+.|++.
T Consensus 44 e~g~~~c~ieI~sV~~i~f~eLte~hA~qE--g~-sL~elk~~i~~i 87 (102)
T PRK04980 44 EDDRYFCTIEVLSVSPVTFDELNEKHAEQE--NM-TLPELKQVIAEI 87 (102)
T ss_pred CCCcEEEEEEEEEEEEEehhhCCHHHHHHh--CC-CHHHHHHHHHHH
Confidence 345678899999999999999999999875 56 899999999874
No 31
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=88.66 E-value=7.8 Score=39.88 Aligned_cols=131 Identities=11% Similarity=0.132 Sum_probs=66.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhH
Q 008989 372 TIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKA 451 (547)
Q Consensus 372 Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~ 451 (547)
|.++|.+.++.+... +.+.+.|.+.+++. .+.+++.-|+++++.+..++-.+ +..++...+-.+
T Consensus 39 t~~~~~~~l~~~~g~-------~~l~~li~~~~~~~-~i~vsd~evd~~i~~i~~~~g~~--------f~~~L~~~G~~~ 102 (285)
T PRK03002 39 TKSDFEKQLKDRYGK-------DMLYEMMAQDVITK-KYKVSDDDVDKEVQKAKSQYGDQ--------FKNVLKNNGLKD 102 (285)
T ss_pred CHHHHHHHHHHHHHH-------HHHHHHHHHHHHHc-CCCcCHHHHHHHHHHHHHHhhHH--------HHHHHHHcCCCC
Confidence 667777766653322 23455556666653 67899999988877665432111 111221111112
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHHhh
Q 008989 452 VKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGIMQ 531 (547)
Q Consensus 452 ~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~lm~ 531 (547)
.++|+ ..+|..+++..+.+. .||++||++.+..... .... -++.+...+.+.+.+..+.-|..|..
T Consensus 103 ~~~~r--------~~ir~~l~~~~~~~~---~vtd~ei~~~Y~~~~~-~~~I--lv~~~~~A~~i~~~l~~G~~F~~lA~ 168 (285)
T PRK03002 103 EADFK--------NQIKFKLAMNEAIKK---SVTEKDVKDHYKPEIK-ASHI--LVSDENEAKEIKKKLDAGASFEELAK 168 (285)
T ss_pred HHHHH--------HHHHHHHHHHHHHhC---CCCHHHHHHhhccceE-EEEE--EECCHHHHHHHHHHHHCCCCHHHHHH
Confidence 23443 334556666666654 7999999987542110 0000 01222222344444445566777665
Q ss_pred h
Q 008989 532 S 532 (547)
Q Consensus 532 ~ 532 (547)
+
T Consensus 169 ~ 169 (285)
T PRK03002 169 Q 169 (285)
T ss_pred H
Confidence 4
No 32
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=88.23 E-value=7.9 Score=39.92 Aligned_cols=91 Identities=9% Similarity=0.160 Sum_probs=52.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHH----HHHHhcCCCCHHHHHhcC
Q 008989 372 TIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQL----LQMQAGMKLNEQQLAALS 447 (547)
Q Consensus 372 Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~----~~l~~~~~~~~e~~~~~~ 447 (547)
|.++|.+.++.... .+.+.+.|++.|+.. .+.+++.-|+++++++.+++- ..| .++|++.
T Consensus 36 T~~e~~~~~k~~~~-------~~~L~~~I~~~l~~~-~i~vs~~evd~~i~~i~~~~~~~f~~~L-~~~g~s~------- 99 (287)
T PRK03095 36 TKDEFYEQMKTQAG-------KQVLNNMVMEKVLIK-NYKVEDKEVDKKYDEMKKQYGDQFDTLL-KQQGIKE------- 99 (287)
T ss_pred cHHHHHHHHHHHHH-------HHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHHhhHHHHHHH-HHcCCCH-------
Confidence 67888777766442 334556666666554 578888888887776654321 111 2334332
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 008989 448 SPKAVKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVE 494 (547)
Q Consensus 448 ~~~~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~ 494 (547)
++|++ .+|..|+.+++.. ..||++|+++.+.
T Consensus 100 -----~~~r~--------~lr~~l~~~kl~~---~~vtd~ei~~~y~ 130 (287)
T PRK03095 100 -----ETLKT--------GVRAQLAQEKAIE---KTITDKELKDNYK 130 (287)
T ss_pred -----HHHHH--------HHHHHHHHHHHhc---ccCCHHHHHhhhc
Confidence 33332 3334444555544 3789999987654
No 33
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=88.09 E-value=3.9 Score=42.08 Aligned_cols=73 Identities=16% Similarity=0.231 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH--------HhccCCCCHHHHHHHHHHhhhh
Q 008989 451 AVKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL--------KQQKQEYDEDRVREQVSTFSYV 522 (547)
Q Consensus 451 ~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~--------~~~g~~~~~~~l~e~~~e~~~~ 522 (547)
+.++|..+++...-+.+-..||+.++.. .+|.||++||++++.++.+++ .++|.. +.+.++++++..+..
T Consensus 37 t~~e~~~~~~~~~g~~~l~~li~~k~~~-~~i~vsd~ev~~~i~~~~~~~~~~f~~~L~~~G~~-~~~~~r~~i~~~l~~ 114 (283)
T PRK02998 37 TEKELSKELRQKYGESTLYQMVLSKALL-DKYKVSDEEAKKQVEEAKDKMGDNFKSTLEQVGLK-NEDELKEKMKPEIAF 114 (283)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHH
Confidence 3456666666666677777888888775 479999999999999887643 234442 356677777777665
Q ss_pred HHH
Q 008989 523 GLI 525 (547)
Q Consensus 523 ~~~ 525 (547)
+.+
T Consensus 115 ~~~ 117 (283)
T PRK02998 115 EKA 117 (283)
T ss_pred HHH
Confidence 543
No 34
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=87.92 E-value=3.4 Score=42.51 Aligned_cols=70 Identities=16% Similarity=0.270 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH--------HhccCCCCHHHHHHHHHHhhhhH
Q 008989 452 VKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL--------KQQKQEYDEDRVREQVSTFSYVG 523 (547)
Q Consensus 452 ~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~--------~~~g~~~~~~~l~e~~~e~~~~~ 523 (547)
..+|..+++.+....+-..||..++.+ .+|.||+++|++++.+++.++ ++.|.. +.+.+|++++..+...
T Consensus 40 ~~~~~~~l~~~~g~~~l~~li~~~~~~-~~i~vsd~evd~~i~~i~~~~g~~f~~~L~~~G~~-~~~~~r~~ir~~l~~~ 117 (285)
T PRK03002 40 KSDFEKQLKDRYGKDMLYEMMAQDVIT-KKYKVSDDDVDKEVQKAKSQYGDQFKNVLKNNGLK-DEADFKNQIKFKLAMN 117 (285)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCcCHHHHHHHHHHHHHHhhHHHHHHHHHcCCC-CHHHHHHHHHHHHHHH
Confidence 345555555556667777888888876 589999999999999887653 233331 4677777777766543
No 35
>PRK04405 prsA peptidylprolyl isomerase; Provisional
Probab=87.62 E-value=3.8 Score=42.59 Aligned_cols=58 Identities=14% Similarity=0.128 Sum_probs=41.8
Q ss_pred HHHHHHHHHH-HHHHHcCCCCCHHHHHHHHHHHHHH--------HHhccCCCCHHHHHHHHHHhhhhHH
Q 008989 465 NVIKQNLAVG-DIFKRENLQFSTEDLVKEVENSIAE--------LKQQKQEYDEDRVREQVSTFSYVGL 524 (547)
Q Consensus 465 k~vK~~Lil~-~Iak~E~I~VteeEi~~ei~~~~~~--------~~~~g~~~~~~~l~e~~~e~~~~~~ 524 (547)
+.+-..||++ .++++.++.|++++|++++.++.++ ++++|. +.+.++++++...+...
T Consensus 55 ~~~L~~li~~k~l~~~~~~~v~~~evd~~i~~i~~~~g~~f~~~L~~~G~--t~~~~r~~ir~~~l~~~ 121 (298)
T PRK04405 55 KTVLANMIIYRALEKQYGKKVSTKKVDKQYNSYKKQYGSSFDSVLSQNGM--TTSSFKQNLRTNLLSEA 121 (298)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHcCC--CHHHHHHHHHHHHHHHH
Confidence 4455555554 5566889999999999999888765 445666 67778888887765543
No 36
>PF13624 SurA_N_3: SurA N-terminal domain; PDB: 3NRK_A.
Probab=87.45 E-value=2.1 Score=39.25 Aligned_cols=65 Identities=9% Similarity=0.153 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHH
Q 008989 461 ENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFC 527 (547)
Q Consensus 461 ~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~ 527 (547)
..+.+.+=..-++..-|++.||.||+++++.++.+.-. |...|. ++++.+.+.++..+....-+.
T Consensus 77 ~~~l~~lI~~~ll~q~A~~~gi~vsd~ev~~~i~~~~~-f~~~g~-~~~~~f~~~L~~~g~t~~~~~ 141 (154)
T PF13624_consen 77 QQVLDQLIDQKLLLQEAKKLGISVSDAEVDDAIKQIPA-FQENGK-FDKEAFEEFLKQQGMTEEEFK 141 (154)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHH--H-HHHH-----HHHHHHHHH----------
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-HHHCCC-CCHHHHHHHHHHhhccccccc
Confidence 44455555566677889999999999999999988532 433333 577778777777665444333
No 37
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=86.08 E-value=3.3 Score=35.42 Aligned_cols=41 Identities=24% Similarity=0.247 Sum_probs=37.2
Q ss_pred eeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHH
Q 008989 340 QAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQ 382 (547)
Q Consensus 340 ~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~ 382 (547)
+....++|.+|....+.+|++++|..- |+.|+++|++.+++
T Consensus 42 ~~~~~~~v~~V~~~~~~~l~~~~A~~e--G~~s~~~~~~~l~~ 82 (100)
T cd06552 42 RIFGEAEITSVEEKTLGELTDEDARQE--GFPSLEELKEALKE 82 (100)
T ss_pred EEEEEEEEEEEEEEEhhhCCHHHHHhc--CCccHHHHHHHHHH
Confidence 788889999999999999999999876 78899999999985
No 38
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=85.80 E-value=56 Score=35.28 Aligned_cols=86 Identities=13% Similarity=0.205 Sum_probs=61.2
Q ss_pred ccccEEEEEEEEeeeccCCCCCcccCCCCccCEEEEecCCCCCcccHHHhhcCCCCCceEEEEEeCCCCCCCc--C----
Q 008989 262 QVGDIAIVDISATTIDEDESNVQNIPDAETKGFHFDTEDGDKVLPGFLDSISGIQRGETKSFRLAFPESWRQE--H---- 335 (547)
Q Consensus 262 ~~GD~V~id~~~~~~d~d~~~G~~~~~~~~~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~~~~~~~fPedy~~~--~---- 335 (547)
-.|-+|.++|.|.. .+| .|.. ..-+|.|.+|++..++.|++-+|-.|++||...|.+..-=-|+.. .
T Consensus 102 ~~g~~V~v~~~G~~-----~~~-~f~~-~~~~fe~~~Ge~~~vi~Gle~al~~M~~GE~a~v~i~~~YayG~~~~~~p~I 174 (397)
T KOG0543|consen 102 NKGAVVKVHLEGEL-----EDG-VFDQ-RELRFEFGEGEDIDVIEGLEIALRMMKVGEVALVTIDPKYAYGEEGGEPPLI 174 (397)
T ss_pred CCCcEEEEEEEEEE-----CCc-ceec-cccceEEecCCccchhHHHHHHHHhcCccceEEEEeCcccccCCCCCCCCCC
Confidence 34788999999983 233 5543 334588888865578889999999999999999988732223211 0
Q ss_pred CCCCeeEEEEEEeEeeecC
Q 008989 336 LRGVQAQFTVECRELFYRD 354 (547)
Q Consensus 336 laGk~~~F~VtVk~Ik~~~ 354 (547)
=-+-++.|+|++++...+.
T Consensus 175 PPnA~l~yEVeL~~f~~~~ 193 (397)
T KOG0543|consen 175 PPNATLLYEVELLDFELKE 193 (397)
T ss_pred CCCceEEEEEEEEeeecCc
Confidence 1245799999999986433
No 39
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=85.02 E-value=17 Score=37.34 Aligned_cols=95 Identities=12% Similarity=0.100 Sum_probs=52.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcCChhH
Q 008989 372 TIEQVKETLLQKCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALSSPKA 451 (547)
Q Consensus 372 Tleelr~~Ik~~l~~~~~~~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~~~~~ 451 (547)
|.++|.+.++.+.. .+.+.+.|+.+++.. .+.+.+.-|+++++.+.+++-.++ .+.+...+..+
T Consensus 37 t~~e~~~~~~~~~g-------~~~l~~li~~k~~~~-~i~vsd~ev~~~i~~~~~~~~~~f--------~~~L~~~G~~~ 100 (283)
T PRK02998 37 TEKELSKELRQKYG-------ESTLYQMVLSKALLD-KYKVSDEEAKKQVEEAKDKMGDNF--------KSTLEQVGLKN 100 (283)
T ss_pred cHHHHHHHHHHHHH-------HHHHHHHHHHHHHHh-CCCCCHHHHHHHHHHHHHHHHHHH--------HHHHHHcCCCc
Confidence 67777777766422 223445555555543 468888888887776654322111 11111111111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 008989 452 VKEFLENQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEV 493 (547)
Q Consensus 452 ~ee~~e~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei 493 (547)
.+.| ++.++..++++.+. .+.||++||.+.+
T Consensus 101 ~~~~--------r~~i~~~l~~~~~~---~~~Vtd~ei~~~y 131 (283)
T PRK02998 101 EDEL--------KEKMKPEIAFEKAI---KATVTEKDVKDNY 131 (283)
T ss_pred HHHH--------HHHHHHHHHHHHHh---cCCCCHHHHHHhc
Confidence 2233 33466667777776 4689999998764
No 40
>PRK10770 peptidyl-prolyl cis-trans isomerase SurA; Provisional
Probab=80.25 E-value=49 Score=35.66 Aligned_cols=90 Identities=8% Similarity=0.149 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcC--ChhHHHHHHHHHHHHHHHHHHH
Q 008989 392 KDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALS--SPKAVKEFLENQRENITNVIKQ 469 (547)
Q Consensus 392 ~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~--~~~~~ee~~e~~~~~A~k~vK~ 469 (547)
.++...+.++.+..++..+.+++.-|++++..+. .++|++.++|.+.. .+.+.+.| +..++.
T Consensus 53 l~~Li~~~Ll~q~A~~~gi~vsd~ev~~~i~~~~--------~~~~~~~~~~~~~L~~~g~~~~~~--------~~~ir~ 116 (413)
T PRK10770 53 LERLIMDNIILQMAQKMGVKISDEQLDQAIANIA--------AQNNMTLDQMRSRLAYDGLNYNTY--------RNQIRK 116 (413)
T ss_pred HHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH--------HHCCCCHHHHHHHHHHcCCCHHHH--------HHHHHH
Confidence 4555667888888999999999999998776533 23567776653221 11222333 334445
Q ss_pred HHHHHHHHHH---cCCCCCHHHHHHHHHHHH
Q 008989 470 NLAVGDIFKR---ENLQFSTEDLVKEVENSI 497 (547)
Q Consensus 470 ~Lil~~Iak~---E~I~VteeEi~~ei~~~~ 497 (547)
.++++.+... .+|.||+.|++..+....
T Consensus 117 ~l~~~~l~~~~~~~~i~vs~~ei~~~~~~~~ 147 (413)
T PRK10770 117 EMIISEVRNNEVRRRITILPQEVDSLAKQIG 147 (413)
T ss_pred HHHHHHHHHHHHhccCCCCHHHHHHHHHHHH
Confidence 5555555433 579999999998776544
No 41
>PF13623 SurA_N_2: SurA N-terminal domain
Probab=72.41 E-value=27 Score=32.45 Aligned_cols=36 Identities=19% Similarity=0.343 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 008989 458 NQRENITNVIKQNLAVGDIFKRENLQFSTEDLVKEV 493 (547)
Q Consensus 458 ~~~~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei 493 (547)
++++++=..+-...+|++=+++.||+||++|+...+
T Consensus 80 q~~~qvW~~~V~~~ll~~e~eklGi~Vs~~El~d~l 115 (145)
T PF13623_consen 80 QIRNQVWNQMVQNILLEQEFEKLGITVSDDELQDML 115 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCccCHHHHHHHH
Confidence 456666677778889999999999999999998877
No 42
>PRK10788 periplasmic folding chaperone; Provisional
Probab=72.11 E-value=90 Score=35.71 Aligned_cols=33 Identities=18% Similarity=0.237 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 008989 391 AKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQ 423 (547)
Q Consensus 391 ~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~ 423 (547)
..++.+.+.++.+-.++..+.+++..|...+..
T Consensus 91 vl~~LI~~~Ll~q~A~~lgi~vsd~ev~~~I~~ 123 (623)
T PRK10788 91 VLNRLIDEALLDQYARELGLGISDEQVKQAIFA 123 (623)
T ss_pred HHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHh
Confidence 345556677777888888899999999887765
No 43
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=71.61 E-value=4.7 Score=43.20 Aligned_cols=54 Identities=20% Similarity=0.342 Sum_probs=44.0
Q ss_pred cccccEEEEEEEEeeeccCCCCCcccCCCCc-cCEEEEecCCCCCcccHHHhhcCCCCCce
Q 008989 261 LQVGDIAIVDISATTIDEDESNVQNIPDAET-KGFHFDTEDGDKVLPGFLDSISGIQRGET 320 (547)
Q Consensus 261 ~~~GD~V~id~~~~~~d~d~~~G~~~~~~~~-~~~~l~lg~~~~~ip~fe~~LiG~k~Ge~ 320 (547)
...||.|.++|+++. .||..|+.+.. .+|.+.+|. +.++.++..++.-|+.|+.
T Consensus 9 p~~g~~v~~hytg~l-----~dgt~fdss~d~~~~~~~lg~-g~vi~~~~~gv~tm~~g~~ 63 (397)
T KOG0543|consen 9 PMTGDKVEVHYTGTL-----LDGTKFDSSRDGDPFKFDLGK-GSVIKGWDLGVATMKKGEA 63 (397)
T ss_pred CCCCceeEEEEeEEe-----cCCeecccccCCCceeeecCC-Ccccccccccccccccccc
Confidence 457999999999985 67888887543 689999995 6799998888888886554
No 44
>PF05698 Trigger_C: Bacterial trigger factor protein (TF) C-terminus; InterPro: IPR008880 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This entry represents the C-terminal domain of bacterial trigger factor proteins, which has a multi-helical structure consisting of an irregular array of long and short helices. This domain is structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 1T11_A 3GU0_A 3GTY_X 2NSA_A 1ZXJ_A 1W26_A.
Probab=71.33 E-value=20 Score=32.76 Aligned_cols=67 Identities=18% Similarity=0.281 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH----HhccCCCCH-------------HHHHHHHHHhhhhHHHHHH
Q 008989 466 VIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL----KQQKQEYDE-------------DRVREQVSTFSYVGLIFCG 528 (547)
Q Consensus 466 ~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~----~~~g~~~~~-------------~~l~e~~~e~~~~~~~~~~ 528 (547)
.-...=|+++|++...+.+.+.-|+++++.+..++ +++|.+++. +.++..+...+....+++.
T Consensus 23 ~~~~~~v~~~L~~~~~~~lP~~lv~~~~~~~~~~~~~~~~~~g~~~e~~~~~~~~~~~~~~~~~~~~a~~~lk~~lil~~ 102 (162)
T PF05698_consen 23 QQKREAVLDALIENSEVELPESLVEEEIERLIEQMEQQLKQQGMSLEQYLQMSGKTEEEFREEFREEAEKRLKQQLILDA 102 (162)
T ss_dssp HHHHHHHHHHHGGGEEEEE-HHHHHHHHHHHHHHHHHTT---TSSCCCHHHHHCTCCCSHCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556689999999999999999999999887665 345665443 5577777777887788877
Q ss_pred Hhhh
Q 008989 529 IMQS 532 (547)
Q Consensus 529 lm~~ 532 (547)
|...
T Consensus 103 Ia~~ 106 (162)
T PF05698_consen 103 IAKK 106 (162)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 7754
No 45
>PRK01490 tig trigger factor; Provisional
Probab=69.19 E-value=45 Score=36.32 Aligned_cols=68 Identities=15% Similarity=0.241 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHhccCC----------CCHHHHHH----HHHHhhhhHHHHHHHh
Q 008989 465 NVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAELKQQKQE----------YDEDRVRE----QVSTFSYVGLIFCGIM 530 (547)
Q Consensus 465 k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~~~~g~~----------~~~~~l~e----~~~e~~~~~~~~~~lm 530 (547)
++....-|+++|.+...+.+.+.-|++++..+..++.+.|.. .+.+.+++ .....++...+++.|.
T Consensus 282 ~~~~~~~i~~~L~~~~~~~lPe~lv~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~A~~~vk~~lil~~Ia 361 (435)
T PRK01490 282 RAKVKEAVLDALVENAEIDLPEALVEQEIDRLLRQALQQGLDLEGQFLEDTGTTEEEPREEFREQAERRVKLGLLLDEIA 361 (435)
T ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566789999999999999999999988887666322211 24444444 4444566666666665
Q ss_pred hh
Q 008989 531 QS 532 (547)
Q Consensus 531 ~~ 532 (547)
+.
T Consensus 362 ~~ 363 (435)
T PRK01490 362 KA 363 (435)
T ss_pred HH
Confidence 54
No 46
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=68.51 E-value=43 Score=31.53 Aligned_cols=33 Identities=24% Similarity=0.377 Sum_probs=24.5
Q ss_pred cHHHhhcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEeee
Q 008989 307 GFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELFY 352 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik~ 352 (547)
.+-.+|+|+++||++++.+ |. |+ .+++|.+|..
T Consensus 124 PlG~ALlGk~vGD~v~v~~--p~--------g~---~~~eI~~I~~ 156 (158)
T PRK05892 124 PLGQALAGHQAGDTVTYST--PQ--------GP---AQVELLAVKL 156 (158)
T ss_pred HHHHHHhCCCCCCEEEEEc--CC--------Cc---EEEEEEEEEc
Confidence 4789999999999999765 42 32 4566777754
No 47
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=67.55 E-value=12 Score=30.61 Aligned_cols=32 Identities=19% Similarity=0.217 Sum_probs=22.9
Q ss_pred cHHHhhcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEee
Q 008989 307 GFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELF 351 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik 351 (547)
.+-.+|+|+++||++++.+. .| ..+++|.+|.
T Consensus 45 PLG~ALlG~~~Gd~v~~~~~----------~g---~~~~~I~~I~ 76 (77)
T PF01272_consen 45 PLGKALLGKKVGDEVEVELP----------GG---ERKYEILEIE 76 (77)
T ss_dssp HHHHHHTT-BTT-EEEEEET----------TB---EEEEEEEEEE
T ss_pred HHHHHhcCCCCCCEEEEEeC----------Cc---eEEEEEEEEE
Confidence 47899999999999999773 12 5567777775
No 48
>TIGR00115 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.
Probab=66.41 E-value=61 Score=34.92 Aligned_cols=67 Identities=16% Similarity=0.300 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH----HHhccCCC------CHHHHH----HHHHHhhhhHHHHHHHhh
Q 008989 466 VIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAE----LKQQKQEY------DEDRVR----EQVSTFSYVGLIFCGIMQ 531 (547)
Q Consensus 466 ~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~----~~~~g~~~------~~~~l~----e~~~e~~~~~~~~~~lm~ 531 (547)
.....-|+++|++...+.+.+.-|++++..+..+ ++++|.++ +.+.+. ..+...++...+++.|.+
T Consensus 273 ~~~~~~i~~~l~~~~~~~lPe~~v~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~e~~~~~~~~~a~~~~k~~lil~~ia~ 352 (408)
T TIGR00115 273 NKLKEQLLDKLVENNEFELPESLVEQEIDRLLEQALQQLQQQGIDLEEYLKDTEEELREEFREEAERRVKLGLILEEIAK 352 (408)
T ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHhhccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455668999999999999999999888777654 44556531 233333 444445555566666554
Q ss_pred h
Q 008989 532 S 532 (547)
Q Consensus 532 ~ 532 (547)
.
T Consensus 353 ~ 353 (408)
T TIGR00115 353 K 353 (408)
T ss_pred H
Confidence 3
No 49
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=65.03 E-value=23 Score=33.81 Aligned_cols=58 Identities=14% Similarity=0.047 Sum_probs=46.8
Q ss_pred hcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHHH
Q 008989 312 ISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQK 383 (547)
Q Consensus 312 LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~~ 383 (547)
.++.++|+.+-+... -.+-=+..|+.|..+.+-||+||=|..= ||.|.+||-+.++..
T Consensus 32 ~~~~k~g~eVyIh~~------------g~i~gkAkIk~V~~KrV~ELTdEDAr~D--GF~sreELi~~Lkri 89 (188)
T COG2411 32 KIVLKPGSEVYIHSG------------GYIIGKAKIKKVKTKRVSELTDEDARLD--GFRSREELIEELKRI 89 (188)
T ss_pred cccCCCCCEEEEEEC------------CEEEEEEEEEEEEEeeHhhhhHHHHHhc--ccccHHHHHHHHHHH
Confidence 345788888887663 2677789999999999999999998643 899999998877754
No 50
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=64.37 E-value=71 Score=30.01 Aligned_cols=32 Identities=13% Similarity=0.168 Sum_probs=23.8
Q ss_pred cHHHhhcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEee
Q 008989 307 GFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELF 351 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik 351 (547)
.+-.+|+|+++||++++.+ |. | .++++|.+|.
T Consensus 124 PlG~ALlGk~vGd~v~v~~--p~--------g---~~~~eI~~I~ 155 (157)
T PRK01885 124 PMARALLKKEVGDEVTVNT--PA--------G---EAEWYVNEIE 155 (157)
T ss_pred HHHHHHhCCCCCCEEEEEc--CC--------C---cEEEEEEEEE
Confidence 4789999999999999765 32 3 2456667775
No 51
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=63.60 E-value=28 Score=30.25 Aligned_cols=49 Identities=14% Similarity=0.003 Sum_probs=39.2
Q ss_pred CCeeEEEEEEeEeeecCC-CCCCHHHHhhhCCCCCCHHHHHHHHHHHHHH
Q 008989 338 GVQAQFTVECRELFYRDL-PKLDDSLAGKLLPGCTTIEQVKETLLQKCRE 386 (547)
Q Consensus 338 Gk~~~F~VtVk~Ik~~~l-PELdDEfak~l~~~~~Tleelr~~Ik~~l~~ 386 (547)
|.+..+.++|.+|..... -+++++++...+.|..|++..++...+-...
T Consensus 42 ~~~~~~~i~v~~V~~~~~f~~~~~e~a~~eGegd~sl~~~~~~~~~~~~~ 91 (105)
T cd06541 42 GQQPLAIAEVVKVEIMPMVNELSEEQEQAEGEGDLTLLYELKEHAAFFKE 91 (105)
T ss_pred CCCcEEEEEEEEEEEEECHHHccHHHHHHcCCCchhHHHHHHHHHHHhhH
Confidence 336788999999999988 7999999998776777888888777655544
No 52
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=62.45 E-value=86 Score=29.07 Aligned_cols=19 Identities=11% Similarity=0.190 Sum_probs=17.0
Q ss_pred cHHHhhcCCCCCceEEEEE
Q 008989 307 GFLDSISGIQRGETKSFRL 325 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~ 325 (547)
.+-.+|+|+++||++++..
T Consensus 120 PlG~ALlG~~~Gd~v~v~~ 138 (151)
T TIGR01462 120 PLGKALIGKKVGDVVEVQT 138 (151)
T ss_pred HHHHHHcCCCCCCEEEEEe
Confidence 5789999999999999865
No 53
>cd06553 ASCH_Ef3133_like ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=62.00 E-value=40 Score=30.59 Aligned_cols=49 Identities=10% Similarity=-0.004 Sum_probs=40.4
Q ss_pred eeEEEEEEeEeeecCCCCCCHHHHhhhCCCCCCHHHHHHHHHHHHHHHH
Q 008989 340 QAQFTVECRELFYRDLPKLDDSLAGKLLPGCTTIEQVKETLLQKCREVE 388 (547)
Q Consensus 340 ~~~F~VtVk~Ik~~~lPELdDEfak~l~~~~~Tleelr~~Ik~~l~~~~ 388 (547)
+..+.+++.+|....+-++|++||..=+.|..|++.+|+..+.-.....
T Consensus 57 ~p~cvi~~~~V~~~~f~~vt~~~A~~EGegd~sl~~Wr~~h~~ff~~~~ 105 (127)
T cd06553 57 KPVCIIETTEVEVVPFNDVTEEFAYAEGEGDRSLEYWRKAHEAFFTREL 105 (127)
T ss_pred CEEEEEEEEEEEEEEcccCCHHHHHHhCCCccCHHHHHHHHHHHHHHHH
Confidence 4667789999999999999999998765567789999998887665543
No 54
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=55.41 E-value=72 Score=29.92 Aligned_cols=32 Identities=9% Similarity=0.125 Sum_probs=24.3
Q ss_pred cHHHhhcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEee
Q 008989 307 GFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELF 351 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik 351 (547)
.+-.+|+|+++||++++.+ |. | .+.++|.+|.
T Consensus 122 PlG~ALlGk~~GD~v~v~~--p~--------g---~~~~eI~~I~ 153 (156)
T TIGR01461 122 PLARALLKKEVGDEVVVNT--PA--------G---EASWYVNAIE 153 (156)
T ss_pred HHHHHHcCCCCCCEEEEEc--CC--------C---cEEEEEEEEE
Confidence 5789999999999999865 42 3 2566677775
No 55
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=55.16 E-value=66 Score=38.57 Aligned_cols=36 Identities=14% Similarity=0.215 Sum_probs=27.7
Q ss_pred cHHHhhcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEeeecCC
Q 008989 307 GFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELFYRDL 355 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik~~~l 355 (547)
.+..+|+|+++||++++.+ |. -..+++|.+|....+
T Consensus 870 PLGkALLGkkvGD~V~v~~--P~-----------g~~~yeIl~I~~~~~ 905 (906)
T PRK14720 870 PLGKSLLGKKEGDSLEFVI--ND-----------TETRYTVLKIERASL 905 (906)
T ss_pred HHHHHHcCCCCCCEEEEEE--CC-----------ceEEEEEEEEEeecC
Confidence 5789999999999999876 42 235677888876554
No 56
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=53.92 E-value=1.2e+02 Score=26.73 Aligned_cols=58 Identities=19% Similarity=0.145 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhcC--ChhHHHHHHHHHH
Q 008989 395 ATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQAGMKLNEQQLAALS--SPKAVKEFLENQR 460 (547)
Q Consensus 395 ~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~~~~~~~~e~~~~~~--~~~~~ee~~e~~~ 460 (547)
...+.++.+-++...+.+.+.-|++.+..+. ++.+++.+++.... .+-+.++|++.++
T Consensus 50 LI~e~L~~q~ak~~gI~vsd~evd~~i~~ia--------~~n~ls~~ql~~~L~~~G~s~~~~r~~ir 109 (118)
T PF09312_consen 50 LIDEKLQLQEAKRLGIKVSDEEVDEAIANIA--------KQNNLSVEQLRQQLEQQGISYEEYREQIR 109 (118)
T ss_dssp HHHHHHHHHHHHHCT----HHHHHHHHHHHH--------HHTT--HHHHHHHCHHCT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH--------HHcCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3344455555568889999988887766543 34577877765432 3345566654444
No 57
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=53.73 E-value=44 Score=31.19 Aligned_cols=19 Identities=16% Similarity=0.228 Sum_probs=17.0
Q ss_pred cHHHhhcCCCCCceEEEEE
Q 008989 307 GFLDSISGIQRGETKSFRL 325 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~ 325 (547)
.+-.+|+|+++||++++.+
T Consensus 125 PlG~aLlGk~~Gd~v~~~~ 143 (157)
T PRK00226 125 PIARALIGKKVGDTVEVTT 143 (157)
T ss_pred hHHHHHhCCCCCCEEEEEc
Confidence 5789999999999999866
No 58
>TIGR02925 cis_trans_EpsD peptidyl-prolyl cis-trans isomerase, EpsD family. Members of this family belong to the peptidyl-prolyl cis-trans isomerase family and are found in loci associated with exopolysaccharide biosynthesis. All members are encoded near a homolog of EpsH, as detected by TIGR02602.
Probab=49.42 E-value=1.3e+02 Score=29.38 Aligned_cols=38 Identities=8% Similarity=-0.038 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 008989 462 NITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAEL 500 (547)
Q Consensus 462 ~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~~ 500 (547)
.+++.+.....+....+ ..+.||++|+++++++....|
T Consensus 96 ~~r~~ll~~~~~~~~v~-~~~~vse~ev~~~Y~~~~~~f 133 (232)
T TIGR02925 96 AAKREILARAYLRQLAG-AQSKPSPEEAKSYFQEHPQLF 133 (232)
T ss_pred HHHHHHHHHHHHHHhhc-cCCCCCHHHHHHHHHhCHHhc
Confidence 34444444455555443 348999999999988765544
No 59
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=48.54 E-value=3.8e+02 Score=30.28 Aligned_cols=131 Identities=14% Similarity=0.193 Sum_probs=67.9
Q ss_pred CCCHHHHhhhCC-CCCCHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHH
Q 008989 357 KLDDSLAGKLLP-GCTTIEQVKETLLQ--KCREVEQTAKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQLYGAQLLQMQ 433 (547)
Q Consensus 357 ELdDEfak~l~~-~~~Tleelr~~Ik~--~l~~~~~~~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~~~~~~~~l~ 433 (547)
.+++++.++... --+..++..+.+.. -|.++...+.-...+-++++.|+++ -+|++++..-+-..+. .+
T Consensus 439 ~i~~~~l~~~~~~~Pe~~~ek~~r~~~eygLs~~LA~~~~~~~~~~~FEel~e~---~v~p~~~A~~L~~~~~----~L- 510 (631)
T COG2511 439 RIDEELLEKIKENLPELPEEKVERYVKEYGLSKELAEQLASDPRVDLFEELVEK---GVDPTLIASTLVNTLP----EL- 510 (631)
T ss_pred ccCHHHHHHHhhhCCCCHHHHHHHHHHHhCCCHHHHHHHHhhhhHHHHHHHHHc---CCCHHHHHHHHHHHHH----HH-
Confidence 456777765421 12455555555544 2344444444445556677777776 7888888765554444 33
Q ss_pred hcCC-----CCHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHcCC-CCCHHHHHHHHHHHHH
Q 008989 434 AGMK-----LNEQQLAALSSPKAVKEFLENQRENITNVIKQNL-----AVGDIFKRENL-QFSTEDLVKEVENSIA 498 (547)
Q Consensus 434 ~~~~-----~~~e~~~~~~~~~~~ee~~e~~~~~A~k~vK~~L-----il~~Iak~E~I-~VteeEi~~ei~~~~~ 498 (547)
.+.| ++.+.+..+...-..-.+ .++.++..++.-. -.+.++++.|+ ..+.|||++-|+++..
T Consensus 511 ~reg~~i~~l~~~~i~~~~~~~~~g~i---ake~iee~l~~l~~~p~~~~~e~~~~~gL~~ls~eEve~iI~eii~ 583 (631)
T COG2511 511 RREGVEIDNLDDEHIEELLRLVSEGKI---AKEAIEEILKALAENPGKDAAEIAEKLGLKELSEEEVEKIIDEIIE 583 (631)
T ss_pred HhcCCccccCCHHHHHHHHHHHhcccc---hHHHHHHHHHHHHhCCCCCHHHHHHHhccccCCHHHHHHHHHHHHH
Confidence 2233 343333211000000011 1223333222222 26788899985 6799999988888764
No 60
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=48.43 E-value=2e+02 Score=31.67 Aligned_cols=71 Identities=17% Similarity=0.295 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH----HHhccCCC------CHHHHHHHHHHh----hhhHHHH
Q 008989 461 ENITNVIKQNLAVGDIFKRENLQFSTEDLVKEVENSIAE----LKQQKQEY------DEDRVREQVSTF----SYVGLIF 526 (547)
Q Consensus 461 ~~A~k~vK~~Lil~~Iak~E~I~VteeEi~~ei~~~~~~----~~~~g~~~------~~~~l~e~~~e~----~~~~~~~ 526 (547)
..+....+..-+++++++...+.+.+.-|++++.++.++ +.++|..+ +.+.+++++++. +..+-++
T Consensus 278 ~~~~~~~~~~~~~~~L~e~~~~dlP~sli~~E~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~e~~~~~A~krVk~~Lil 357 (441)
T COG0544 278 KEATLEKRKEQLLDALVEANDFDLPESLVEAEIDNLLKQALQQLQQQGIDSLEASGESEEELREEFKEEAEKRVKLGLLL 357 (441)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHhcccchhhhccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456777889999999999999999999998888765 44566542 455566555554 4444555
Q ss_pred HHHhh
Q 008989 527 CGIMQ 531 (547)
Q Consensus 527 ~~lm~ 531 (547)
+.|-+
T Consensus 358 ~~ia~ 362 (441)
T COG0544 358 EEIAK 362 (441)
T ss_pred HHHHH
Confidence 55443
No 61
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=42.92 E-value=1.7e+02 Score=27.69 Aligned_cols=17 Identities=18% Similarity=0.231 Sum_probs=15.3
Q ss_pred cHHHhhcCCCCCceEEE
Q 008989 307 GFLDSISGIQRGETKSF 323 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~ 323 (547)
.+-.+|+|+++||++++
T Consensus 133 PlG~ALlGk~vGD~V~v 149 (160)
T PRK06342 133 PVARALMGKAVGDVVSV 149 (160)
T ss_pred HHHHHHcCCCCCCEEEE
Confidence 47899999999999986
No 62
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=39.69 E-value=70 Score=29.31 Aligned_cols=33 Identities=21% Similarity=0.342 Sum_probs=25.3
Q ss_pred cHHHhhcCCCCCceEEEEEeCCCCCCCcCCCCCeeEEEEEEeEee
Q 008989 307 GFLDSISGIQRGETKSFRLAFPESWRQEHLRGVQAQFTVECRELF 351 (547)
Q Consensus 307 ~fe~~LiG~k~Ge~~~~~~~fPedy~~~~laGk~~~F~VtVk~Ik 351 (547)
.+-.+|+|+++||++++.. |. |. .++++|.+|.
T Consensus 94 PlG~ALlG~~~Gd~v~v~~--p~--------G~--~~~~~I~~I~ 126 (137)
T PRK05753 94 PVGAALLGLSVGQSIDWPL--PG--------GK--ETHLEVLEVE 126 (137)
T ss_pred HHHHHHcCCCCCCEEEEEC--CC--------CC--EEEEEEEEEE
Confidence 5789999999999998764 43 43 3567788886
No 63
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=36.23 E-value=1.2e+02 Score=25.62 Aligned_cols=53 Identities=19% Similarity=0.310 Sum_probs=43.6
Q ss_pred cccCCCCccEEEEeecCCceEEEEEEEc-hhhHHHHHHHHHHHHHhhCCcCCCC
Q 008989 82 EKDRLPADIEVTESPEPNSTVRLSVEVP-EAVCKDSYKRVLNELMKQVKIPGFR 134 (547)
Q Consensus 82 ~~~~~~~~m~vt~~~~~~~~~~l~V~Vp-~~~v~~~~~k~l~~~~k~~~IPGFR 134 (547)
++.-...++.|++++.++..+.+.++=+ ...+.+.+++.+.+.-+..+|++-+
T Consensus 8 aGtleSsD~~V~v~p~~~~gi~i~l~S~v~~~fg~~i~~vi~~~l~~~~i~~~~ 61 (87)
T PF06857_consen 8 AGTLESSDLEVTVEPAESGGIEIELESSVVKQFGDQIRAVIRETLEELGIEDAK 61 (87)
T ss_pred EcccccCcEEEEEEeCCCCcEEEEEEchHHhhhHHHHHHHHHHHHHhcCCCceE
Confidence 3444457799999999778888888888 8888999999999999999998744
No 64
>PRK12907 secY preprotein translocase subunit SecY; Reviewed
Probab=35.47 E-value=26 Score=38.45 Aligned_cols=37 Identities=24% Similarity=0.435 Sum_probs=26.0
Q ss_pred EEEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhC
Q 008989 106 VEVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVG 148 (547)
Q Consensus 106 V~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G 148 (547)
|.++++++.+.+.|. -.-|||+||||.-...+++...
T Consensus 330 i~~nP~~iAenL~k~------G~~IPGiRPGk~T~~yL~~~i~ 366 (434)
T PRK12907 330 IQVNPEQMAENLKKQ------NGYVPGIRPGKSTEQYVTKILY 366 (434)
T ss_pred HccCHHHHHHHHHHC------CCcCCCcCCChhHHHHHHHHHH
Confidence 456666666555443 5689999999988887765543
No 65
>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.
Probab=29.92 E-value=6.7e+02 Score=26.29 Aligned_cols=88 Identities=14% Similarity=0.094 Sum_probs=49.0
Q ss_pred CCCCHHHHhhhCC-CCC--CHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCC-CCCHHHHHHHHHHHHHHHHH
Q 008989 356 PKLDDSLAGKLLP-GCT--TIEQVKETLLQKCREVEQTAKD-QATDNAILDQLYKMVEI-DIPQSLFEEQGRQLYGAQLL 430 (547)
Q Consensus 356 PELdDEfak~l~~-~~~--Tleelr~~Ik~~l~~~~~~~~~-~~~~~~il~~L~e~~~~-dlPeslve~e~~~~~~~~~~ 430 (547)
.=|||+|.+++.. +.. -++.|+..|+..|.......-- ..-...-++.+++++.- .+-..-+-+++-.+.++...
T Consensus 154 sild~eFl~~v~~~~~k~~~~e~L~~~l~~~I~~~~~~N~~~~~~fsErLe~iI~~Y~~~~i~~~e~~~eLi~la~el~~ 233 (335)
T PF11867_consen 154 SILDDEFLEEVKKMKSKNLKAELLEKLLRDEIKVRMKENPVRYKKFSERLEEIIEKYNNRSISSEEVIEELIKLAKELRE 233 (335)
T ss_pred hhcCHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHH
Confidence 4478999888742 222 2678999999998887766543 23444555677766543 23222222233333333332
Q ss_pred HHH--hcCCCCHHHH
Q 008989 431 QMQ--AGMKLNEQQL 443 (547)
Q Consensus 431 ~l~--~~~~~~~e~~ 443 (547)
.-+ ...|++.+++
T Consensus 234 ~~~r~~~~gLseeE~ 248 (335)
T PF11867_consen 234 EEERAEELGLSEEEL 248 (335)
T ss_pred HHhcccccCCCHHHH
Confidence 211 3457887764
No 66
>PF10884 DUF2683: Protein of unknown function (DUF2683); InterPro: IPR020271 This entry contains proteins with no known function.
Probab=27.87 E-value=44 Score=27.80 Aligned_cols=26 Identities=12% Similarity=0.300 Sum_probs=21.0
Q ss_pred CCCCCHHHHhhhC--------CCCCCHHHHHHHH
Q 008989 355 LPKLDDSLAGKLL--------PGCTTIEQVKETL 380 (547)
Q Consensus 355 lPELdDEfak~l~--------~~~~Tleelr~~I 380 (547)
-|||+.||++++. +.++|+++||+.+
T Consensus 45 EpElkPEfVeki~~i~k~~~~i~i~svd~LRk~~ 78 (80)
T PF10884_consen 45 EPELKPEFVEKIKKIMKGKKFIPIGSVDELRKRY 78 (80)
T ss_pred ccccCHHHHHHHHHHHhcccCcCcCcHHHHHHHh
Confidence 3899999998752 2488999999876
No 67
>PF13624 SurA_N_3: SurA N-terminal domain; PDB: 3NRK_A.
Probab=27.86 E-value=3.8e+02 Score=24.12 Aligned_cols=34 Identities=24% Similarity=0.277 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHH
Q 008989 391 AKDQATDNAILDQLYKMVEIDIPQSLFEEQGRQL 424 (547)
Q Consensus 391 ~~~~~~~~~il~~L~e~~~~dlPeslve~e~~~~ 424 (547)
..++.+.+.++.+-.++..+.+++..|+.++..+
T Consensus 79 ~l~~lI~~~ll~q~A~~~gi~vsd~ev~~~i~~~ 112 (154)
T PF13624_consen 79 VLDQLIDQKLLLQEAKKLGISVSDAEVDDAIKQI 112 (154)
T ss_dssp HHHHHHHHHHHHHHHHHTT----HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 4555677788888888889999999999887764
No 68
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA.
Probab=27.36 E-value=1e+03 Score=27.57 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=21.2
Q ss_pred HHHHHHHcCC-CCCHHHHHHHHHHHHHH
Q 008989 473 VGDIFKRENL-QFSTEDLVKEVENSIAE 499 (547)
Q Consensus 473 l~~Iak~E~I-~VteeEi~~ei~~~~~~ 499 (547)
..+|+++.|+ ++|+++|.+.+++.+++
T Consensus 549 ~~~iiee~gL~qlsdeel~~iV~evI~e 576 (620)
T TIGR00134 549 AEDAARKLKLKLLAEEEIESIIQEIIEE 576 (620)
T ss_pred HHHHHHHcCCcCCCHHHHHHHHHHHHHh
Confidence 3568888886 77999999888887753
No 69
>TIGR02920 acc_sec_Y2 accessory Sec system translocase SecY2. Members of this family are restricted to the Firmicutes lineage (low-GC Gram-positive bacteria) and appear to be paralogous to, and much more divergent than, the preprotein translocase SecY. Members include the SecY2 protein of the accessory Sec system in Streptococcus gordonii, involved in export of the highly glycosylated platelet-binding protein GspB.
Probab=25.84 E-value=1e+02 Score=33.44 Aligned_cols=37 Identities=22% Similarity=0.345 Sum_probs=25.2
Q ss_pred EEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhCh
Q 008989 107 EVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGE 149 (547)
Q Consensus 107 ~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G~ 149 (547)
.++++++.+.+. ....-|||+||||.=...+++...+
T Consensus 296 ~~nP~diA~~Lk------k~g~~IpGiRpG~~T~~yL~~~i~~ 332 (395)
T TIGR02920 296 NINPKEISKSFR------KSGNYIPGIAPGKDTQRYLNRLARR 332 (395)
T ss_pred eECHHHHHHHHH------HCCCCccCcCCCchHHHHHHHHHHH
Confidence 344666644443 2367999999999888888766544
No 70
>COG0201 SecY Preprotein translocase subunit SecY [Intracellular trafficking and secretion]
Probab=25.68 E-value=87 Score=34.45 Aligned_cols=22 Identities=41% Similarity=0.531 Sum_probs=17.5
Q ss_pred hCCcCCCCCCCCcHHHHHHhhC
Q 008989 127 QVKIPGFRPGKIPESVLVGFVG 148 (547)
Q Consensus 127 ~~~IPGFRkGKvP~~vv~k~~G 148 (547)
-.-|||+||||.=.+.+.+...
T Consensus 348 G~~IPGiRpg~~te~yL~rvi~ 369 (436)
T COG0201 348 GGFIPGIRPGKDTEKYLNRVIP 369 (436)
T ss_pred CCcCCCcCCChhHHHHHHHHHH
Confidence 4689999999988888865544
No 71
>TIGR00967 3a0501s007 preprotein translocase, SecY subunit.
Probab=24.04 E-value=57 Score=35.50 Aligned_cols=37 Identities=27% Similarity=0.485 Sum_probs=24.5
Q ss_pred EEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhCh
Q 008989 107 EVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVGE 149 (547)
Q Consensus 107 ~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G~ 149 (547)
.++++++.+.+.| ...-|||+||||.-...+++..-+
T Consensus 315 ~~~p~~iA~~lkk------~g~~IpGiRpG~~T~~yL~~~i~~ 351 (410)
T TIGR00967 315 QLNPEDMAKNLKK------QGMFIPGIRPGKMTEKYLKRVIPR 351 (410)
T ss_pred ccCHHHHHHHHHH------CCCcCCCcCCChhHHHHHHHHHHH
Confidence 3455555444432 356899999998878887766543
No 72
>PF00344 SecY: SecY translocase; InterPro: IPR002208 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The eubacterial secY protein [] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions. Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export []. Homologs of secY are found in archaebacteria []. SecY is also encoded in the chloroplast genome of some algae [] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0015031 protein transport, 0016020 membrane; PDB: 3J01_A 2ZJS_Y 2ZQP_Y 2WWA_A 2WW9_A 2YXR_A 1RHZ_A 3KCR_A 3DKN_A 2YXQ_A ....
Probab=24.03 E-value=91 Score=33.00 Aligned_cols=46 Identities=30% Similarity=0.407 Sum_probs=28.7
Q ss_pred HHHh-hCCcCCCCCCCCcHHHHHHhhChHHHHHHHHHHHHHhhHHHHH
Q 008989 123 ELMK-QVKIPGFRPGKIPESVLVGFVGEQNVKKATVESILKRTLPHAM 169 (547)
Q Consensus 123 ~~~k-~~~IPGFRkGKvP~~vv~k~~G~~~i~~e~~e~li~~~~~~al 169 (547)
+++| ..-|||+||||.-+..+++..-+-.+.....--++ ..++..+
T Consensus 273 ~lkk~g~~I~GirpG~~T~~yL~~~i~~~~~~G~~~l~~i-a~~p~~~ 319 (346)
T PF00344_consen 273 NLKKSGDYIPGIRPGKPTEKYLNKVIPRLSFLGALFLALI-AVLPLIF 319 (346)
T ss_dssp HCHCTTSSSSTCTTSCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
T ss_pred HHHHhCCEeCCCCCChhHHHHHHHHHHHHhhhhHHHHHHH-HHHHHHH
Confidence 4444 57899999999999998877655444444333332 2344444
No 73
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=22.89 E-value=5.9e+02 Score=23.31 Aligned_cols=79 Identities=16% Similarity=0.235 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHhhhhHHHHHHH
Q 008989 451 AVKEFLENQRENITNVIKQNLAVGDIFKRE-NLQFSTEDLVKEVENSIAELKQQKQEYDEDRVREQVSTFSYVGLIFCGI 529 (547)
Q Consensus 451 ~~ee~~e~~~~~A~k~vK~~Lil~~Iak~E-~I~VteeEi~~ei~~~~~~~~~~g~~~~~~~l~e~~~e~~~~~~~~~~l 529 (547)
..+.|.+...+-|..-++..--++.++... |+.+|+++-.+.|.++-.+.+..+ ..+++.+++.-.+-..++++
T Consensus 63 ~~~~~~~~~~elA~dIi~kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~-----~el~~~v~e~e~ll~~v~~~ 137 (144)
T PF11221_consen 63 PPEEFEENIKELATDIIRKAKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAE-----EELQEAVKEAEELLKQVQEL 137 (144)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
T ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
Confidence 346777778888888888888888888777 889999998888888876554422 23445555544444555555
Q ss_pred hhhhc
Q 008989 530 MQSQN 534 (547)
Q Consensus 530 m~~~~ 534 (547)
+...+
T Consensus 138 i~~ia 142 (144)
T PF11221_consen 138 IREIA 142 (144)
T ss_dssp HHTT-
T ss_pred HHHHh
Confidence 55444
No 74
>CHL00161 secY preprotein translocase subunit SecY; Validated
Probab=22.47 E-value=59 Score=35.49 Aligned_cols=36 Identities=25% Similarity=0.376 Sum_probs=24.3
Q ss_pred EEchhhHHHHHHHHHHHHHhhCCcCCCCCCCCcHHHHHHhhC
Q 008989 107 EVPEAVCKDSYKRVLNELMKQVKIPGFRPGKIPESVLVGFVG 148 (547)
Q Consensus 107 ~Vp~~~v~~~~~k~l~~~~k~~~IPGFRkGKvP~~vv~k~~G 148 (547)
.++++++.+.+. ....-|||+||||--.+.+++..-
T Consensus 317 ~~~p~~iA~~Lk------k~g~~IpGvRpG~~T~~yL~~~i~ 352 (417)
T CHL00161 317 VLNPKDISENLQ------KMAVSIPGIRPGKATTKYLKKTLN 352 (417)
T ss_pred hcCHHHHHHHHH------HCCCcCCCcCCChhHHHHHHHHHH
Confidence 355666544443 346799999999877877765543
No 75
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=22.15 E-value=84 Score=25.29 Aligned_cols=29 Identities=24% Similarity=0.394 Sum_probs=22.2
Q ss_pred HHHHHHHhcCccccccccCcccccEEEEE
Q 008989 242 ELRRRHKSLGSLKIVTDRGLQVGDIAIVD 270 (547)
Q Consensus 242 ~l~~~~~~~a~~~~v~dr~~~~GD~V~id 270 (547)
.+.+.++..+-.......+++.||.|.|-
T Consensus 35 ~f~~~L~~~Gv~~~L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 35 RFARKLKKLGVEDALRKAGAKDGDTVRIG 63 (69)
T ss_pred HHHHHHHHCCHHHHHHHcCCCCCCEEEEc
Confidence 57777777776555557899999999874
No 76
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=21.71 E-value=3.5e+02 Score=23.93 Aligned_cols=43 Identities=2% Similarity=0.030 Sum_probs=26.4
Q ss_pred HHHHHHHcCCCCCHHHHH--HHHHHHHHHHHhccCCCCHHHHHHHHHH
Q 008989 473 VGDIFKRENLQFSTEDLV--KEVENSIAELKQQKQEYDEDRVREQVST 518 (547)
Q Consensus 473 l~~Iak~E~I~VteeEi~--~ei~~~~~~~~~~g~~~~~~~l~e~~~e 518 (547)
-.+||+.|||++|++-.+ ..+++. |.+||....--.+-+.+..
T Consensus 27 A~~lA~~egieLT~~Hw~vI~~lR~~---y~e~~~~P~~R~l~K~~~~ 71 (108)
T TIGR03342 27 AEALAEEEGIELTEAHWEVINFLRDF---YAEYNISPAVRMLVKAMGK 71 (108)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHH---HHHHCCCCcHHHHHHHHHH
Confidence 357899999999999744 333332 4567775544444444443
No 77
>PF13623 SurA_N_2: SurA N-terminal domain
Probab=20.70 E-value=1.7e+02 Score=27.15 Aligned_cols=18 Identities=11% Similarity=0.327 Sum_probs=10.5
Q ss_pred HHHhccCCCCHHHHHHHH
Q 008989 499 ELKQQKQEYDEDRVREQV 516 (547)
Q Consensus 499 ~~~~~g~~~~~~~l~e~~ 516 (547)
++++.|...+++.+...+
T Consensus 98 e~eklGi~Vs~~El~d~l 115 (145)
T PF13623_consen 98 EFEKLGITVSDDELQDML 115 (145)
T ss_pred HHHHhCCccCHHHHHHHH
Confidence 455666666666665555
No 78
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=20.25 E-value=1.7e+02 Score=25.50 Aligned_cols=25 Identities=16% Similarity=0.496 Sum_probs=20.7
Q ss_pred HHHcCCCCCHHHHHHHHHHHHHHHH
Q 008989 477 FKRENLQFSTEDLVKEVENSIAELK 501 (547)
Q Consensus 477 ak~E~I~VteeEi~~ei~~~~~~~~ 501 (547)
....||.+|+++++..|+....++.
T Consensus 81 L~~~gi~~t~~~i~~~IEaAV~~m~ 105 (108)
T PF09682_consen 81 LKKKGIKVTDEQIEGAIEAAVKEMN 105 (108)
T ss_pred HHHcCCCCCHHHHHHHHHHHHHHHh
Confidence 4567999999999999998876554
No 79
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=20.12 E-value=75 Score=25.54 Aligned_cols=28 Identities=25% Similarity=0.462 Sum_probs=18.8
Q ss_pred HHHHHHHhcCccccccccCcccccEEEE
Q 008989 242 ELRRRHKSLGSLKIVTDRGLQVGDIAIV 269 (547)
Q Consensus 242 ~l~~~~~~~a~~~~v~dr~~~~GD~V~i 269 (547)
.+.+.++..+-.......+++.||.|.|
T Consensus 35 rf~~~L~~~Gv~~~L~~~G~~~GD~V~I 62 (69)
T PF09269_consen 35 RFQRKLKKMGVEKALRKAGAKEGDTVRI 62 (69)
T ss_dssp HHHHHHHHTTHHHHHHTTT--TT-EEEE
T ss_pred HHHHHHHHCCHHHHHHHcCCCCCCEEEE
Confidence 5777777777655555789999999976
Done!