Query gi|254780391|ref|YP_003064804.1| DNA polymerase III subunit chi [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 141
No_of_seqs 108 out of 530
Neff 7.4
Searched_HMMs 39220
Date Sun May 29 17:35:16 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780391.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05728 DNA polymerase III su 100.0 2E-41 0 270.2 16.9 135 1-140 1-139 (143)
2 pfam04364 DNA_pol3_chi DNA pol 100.0 1.7E-41 0 270.6 15.9 135 1-140 1-136 (136)
3 COG2927 HolC DNA polymerase II 100.0 1.8E-35 4.5E-40 234.4 15.2 136 1-140 1-138 (144)
4 PRK06646 DNA polymerase III su 100.0 6.3E-34 1.6E-38 225.0 15.3 133 1-138 1-139 (154)
5 TIGR00963 secA preprotein tran 91.7 0.82 2.1E-05 25.5 6.5 83 6-95 413-505 (904)
6 cd00079 HELICc Helicase superf 91.4 1.2 3E-05 24.6 7.1 40 11-50 11-50 (131)
7 PRK12904 preprotein translocas 78.2 4.7 0.00012 21.0 4.6 84 7-97 409-500 (833)
8 PRK13107 preprotein translocas 77.1 6.4 0.00016 20.2 8.2 107 8-130 429-543 (908)
9 PRK09200 preprotein translocas 75.5 6.6 0.00017 20.1 4.8 68 10-81 414-489 (799)
10 PRK12901 secA preprotein trans 75.3 7.2 0.00018 19.9 5.3 72 6-81 610-689 (1111)
11 PRK12906 secA preprotein trans 74.4 7.1 0.00018 19.9 4.7 84 7-97 419-510 (823)
12 PRK13103 secA preprotein trans 74.3 7.6 0.00019 19.7 5.8 111 6-132 427-545 (913)
13 PRK12326 preprotein translocas 73.2 8.1 0.00021 19.5 5.7 83 7-96 417-507 (775)
14 PRK12899 secA preprotein trans 73.1 8.1 0.00021 19.5 5.1 71 7-81 547-625 (969)
15 pfam07652 Flavi_DEAD Flaviviru 72.7 8.3 0.00021 19.5 5.0 115 4-136 7-124 (146)
16 KOG0331 consensus 72.5 8.4 0.00021 19.4 10.0 117 15-138 327-467 (519)
17 CHL00122 secA preprotein trans 71.5 8.8 0.00023 19.3 5.2 83 7-96 403-495 (891)
18 PRK13104 secA preprotein trans 71.0 9.1 0.00023 19.2 5.1 113 6-133 422-542 (896)
19 PRK12902 secA preprotein trans 70.7 9.2 0.00024 19.2 4.8 80 10-96 426-515 (946)
20 PRK12898 secA preprotein trans 69.8 9.6 0.00025 19.1 5.2 58 7-68 467-524 (673)
21 PRK04837 ATP-dependent RNA hel 68.1 10 0.00027 18.9 6.9 89 5-95 235-331 (423)
22 TIGR02743 TraW type-F conjugat 66.5 11 0.00029 18.7 4.9 30 103-132 130-159 (217)
23 PRK04537 ATP-dependent RNA hel 65.2 12 0.00031 18.5 6.0 82 12-95 243-332 (574)
24 PRK11776 ATP-dependent RNA hel 62.2 14 0.00035 18.2 6.6 111 5-120 220-352 (459)
25 PRK12900 secA preprotein trans 61.8 14 0.00035 18.1 4.8 77 10-93 536-620 (983)
26 PRK12903 secA preprotein trans 58.3 16 0.00041 17.8 4.5 67 11-81 409-483 (885)
27 TIGR00643 recG ATP-dependent D 53.8 12 0.0003 18.6 2.6 81 14-94 514-616 (721)
28 PTZ00110 helicase; Provisional 53.4 19 0.00049 17.3 11.0 122 11-138 412-554 (602)
29 pfam11513 TA0956 Thermoplasma 51.3 11 0.00027 18.8 2.0 28 113-140 81-108 (110)
30 COG4221 Short-chain alcohol de 48.2 23 0.00059 16.8 3.4 85 5-101 9-94 (246)
31 PRK01297 ATP-dependent RNA hel 45.0 26 0.00067 16.5 6.6 82 12-95 318-407 (472)
32 PRK10590 ATP-dependent RNA hel 43.5 28 0.0007 16.3 6.7 111 13-128 232-363 (457)
33 COG2256 MGS1 ATPase related to 42.2 29 0.00074 16.2 9.0 108 2-137 72-184 (436)
34 cd03364 TOPRIM_DnaG_primases T 42.1 28 0.00072 16.3 3.0 38 103-141 39-77 (79)
35 cd01458 vWA_ku Ku70/Ku80 N-ter 40.6 31 0.00078 16.1 3.6 25 117-141 144-168 (218)
36 pfam00782 DSPc Dual specificit 34.4 38 0.00098 15.5 3.3 22 16-37 59-80 (131)
37 TIGR00956 3a01205 Pleiotropic 32.0 42 0.0011 15.2 4.0 38 15-52 1004-1043(1466)
38 pfam08350 DUF1724 Domain of un 31.9 42 0.0011 15.2 2.9 29 105-135 33-61 (64)
39 PRK05580 primosome assembly pr 31.8 42 0.0011 15.2 5.1 50 13-62 199-249 (699)
40 KOG3350 consensus 31.3 43 0.0011 15.2 3.5 40 20-60 156-195 (217)
41 cd00127 DSPc Dual specificity 30.4 45 0.0011 15.1 3.4 21 17-37 70-90 (139)
42 COG1200 RecG RecG-like helicas 28.7 48 0.0012 14.9 4.2 131 4-138 449-612 (677)
43 PRK06196 oxidoreductase; Provi 27.2 51 0.0013 14.7 2.5 64 25-99 47-110 (316)
44 KOG0391 consensus 27.1 51 0.0013 14.7 4.2 36 13-48 1261-1296(1958)
45 PRK13738 conjugal transfer pil 26.9 52 0.0013 14.7 4.7 53 75-129 91-143 (210)
46 PRK11192 ATP-dependent RNA hel 26.3 53 0.0014 14.6 6.4 118 6-128 224-365 (417)
47 smart00195 DSPc Dual specifici 26.1 53 0.0014 14.6 3.7 22 16-37 66-87 (138)
48 KOG0327 consensus 25.9 54 0.0014 14.6 6.3 108 4-117 241-371 (397)
49 PRK10917 ATP-dependent DNA hel 25.5 55 0.0014 14.5 3.9 129 7-138 446-606 (677)
50 TIGR00750 lao LAO/AO transport 25.5 55 0.0014 14.5 4.4 40 17-57 55-109 (333)
51 COG0653 SecA Preprotein transl 25.0 56 0.0014 14.5 2.8 47 14-64 415-461 (822)
52 COG4742 Predicted transcriptio 23.1 61 0.0016 14.3 3.2 103 18-139 154-258 (260)
53 cd02429 PTH2_like Peptidyl-tRN 22.6 62 0.0016 14.2 4.2 48 25-80 52-99 (116)
54 COG1203 CRISPR-associated heli 22.1 64 0.0016 14.1 3.5 46 18-63 430-475 (733)
55 COG4063 MtrA Tetrahydromethano 21.8 41 0.001 15.3 1.0 89 21-135 58-154 (238)
56 KOG3661 consensus 21.0 23 0.00058 16.9 -0.4 96 27-140 420-519 (1019)
57 TIGR01689 EcbF-BcbF capsule bi 20.5 49 0.0013 14.8 1.2 15 123-137 28-42 (126)
No 1
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=100.00 E-value=2e-41 Score=270.15 Aligned_cols=135 Identities=30% Similarity=0.479 Sum_probs=120.4
Q ss_pred CCEEEEEECCCC----HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf 982799631674----8999999999999779849998299899999999852188233313322477765444220699
Q gi|254780391|r 1 MRTLLFYRFKND----WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVL 76 (141)
Q Consensus 1 Mt~v~FY~l~~~----~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~ 76 (141)
||+|+||+|.++ .+.++|+|++|++++|+|++|+|+|+++++.||++||+|+++|||||++.+++ ..+.+||+
T Consensus 1 Mt~i~FY~L~~~~~~~~~~~~c~L~~k~~~~g~~i~I~~~d~~~~~~lD~~LWt~~~~sFiPH~~~~~~---~~~~~PI~ 77 (143)
T PRK05728 1 MTRADFYHLTRDTLSALEQLLCRLAEKALRAGWRVLVQCEDEEQAEALDEALWTFDDESFVPHGLAGEG---PAAGQPVL 77 (143)
T ss_pred CCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCC---CCCCCCEE
T ss_conf 987899975798666899999999999998699189993999999999999848997321344446888---76789989
Q ss_pred EECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 8328667899819999816877821131175799997598989999999999999988998603
Q gi|254780391|r 77 LTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV 140 (141)
Q Consensus 77 i~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~ 140 (141)
|+++.. ++..+.++||||++..|+++++|+||+||| ++|++.++.||+|||+||++||+++.
T Consensus 78 i~~~~~-~~~~~~~vLinl~~~~p~~~~~f~Rvie~v-~~d~~~~~~aR~r~k~yk~~G~~l~y 139 (143)
T PRK05728 78 LAWPGN-RNGAHRDLLINLAAAVPAFAAAFERVVDFV-GYDEAALQAARERWKAYRAAGYNLTY 139 (143)
T ss_pred EECCCC-CCCCCCEEEEECCCCCCCHHHHCCEEEEEE-CCCHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf 965888-887774699989988864101017899994-89989999999999999988997635
No 2
>pfam04364 DNA_pol3_chi DNA polymerase III chi subunit, HolC. The DNA polymerase III holoenzyme (EC:2.7.7.7) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either either the tau or gamma product of gene dnax, complexed to delta.delta' and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi.
Probab=100.00 E-value=1.7e-41 Score=270.59 Aligned_cols=135 Identities=27% Similarity=0.475 Sum_probs=121.4
Q ss_pred CCEEEEEECCC-CHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf 98279963167-48999999999999779849998299899999999852188233313322477765444220699832
Q gi|254780391|r 1 MRTLLFYRFKN-DWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTI 79 (141)
Q Consensus 1 Mt~v~FY~l~~-~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~ 79 (141)
||+|+||++++ +.++++|+|++|++++|+|++|+|+|+++++.||++||+|+++|||||++.+++ ....+||+|++
T Consensus 1 M~~i~FY~l~~~~~~~~~c~L~~k~~~~~~ri~I~~~d~~~~~~lD~~LWt~~~~sFiPH~~~~~~---~~~~~PI~i~~ 77 (136)
T pfam04364 1 MTRVDFYHLTRDPLEALACRLAEKALRQGWRVLVRCEDEEQAEALDELLWTFRPDSFLPHGLAGEG---PAAGQPVLLGW 77 (136)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCC---CCCCCCEEEEC
T ss_conf 987899956887199999999999998699189993999999999999857997331444446888---72449918563
Q ss_pred CCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 8667899819999816877821131175799997598989999999999999988998603
Q gi|254780391|r 80 SSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV 140 (141)
Q Consensus 80 ~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~ 140 (141)
..+.++.. .++||||++..|+++++|+|++|||+ +||+.|+.||+|||+||++||+++.
T Consensus 78 ~~~~~~~~-~~vLiNL~~~~~~~~~~f~rvieiv~-~~e~~~~~aR~r~k~Yk~~G~~~~~ 136 (136)
T pfam04364 78 DGENPNGH-ADVLINLDGAVPEFASRFERVIEFVD-GDDAAKQAARERWKAYRAAGYELTY 136 (136)
T ss_pred CCCCCCCC-CCEEEECCCCCCCHHHHHHEEEEEEC-CCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 77667772-79999899988633431207888848-9989999999999999986998859
No 3
>COG2927 HolC DNA polymerase III, chi subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.8e-35 Score=234.35 Aligned_cols=136 Identities=23% Similarity=0.462 Sum_probs=123.8
Q ss_pred CCEEEEEECCCC-HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf 982799631674-8999999999999779849998299899999999852188233313322477765444220699832
Q gi|254780391|r 1 MRTLLFYRFKND-WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTI 79 (141)
Q Consensus 1 Mt~v~FY~l~~~-~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~ 79 (141)
|++++||++..+ .+.++|+|++|+|..|+|++|.|.|+++++.||+.||+|+++|||||++.+ ++.+..+||+|++
T Consensus 1 M~~~~FY~l~~~~~~~~~c~L~~k~~~~G~rvlI~~~d~~q~e~LD~~LWt~~~~sFiPH~~~~---e~~~~~qPIli~~ 77 (144)
T COG2927 1 MKEATFYLLSESTLLAAACRLAEKAWRSGWRVLIQCEDEAQAEALDEHLWTFSAESFIPHNLAG---EPPPAGQPILIAW 77 (144)
T ss_pred CCEEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCHHCCCCCCCCC---CCCCCCCCEEEEC
T ss_conf 9636899716303999999999999976996999948999999998763236611106776577---8888889899876
Q ss_pred CCCCCCCCCEEEEEECCCCCCCHHHCC-CEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 866789981999981687782113117-5799997598989999999999999988998603
Q gi|254780391|r 80 SSLNANTSTIRFLVDEASMHIGDVDYY-EKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV 140 (141)
Q Consensus 80 ~~~~~~~~~~~~linl~~~~p~~~~~f-~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~ 140 (141)
...++|.+.+++||||+...+.....| -+|+++| +++++.++.||+|||.||+.||+...
T Consensus 78 ~~~~pn~~~~~~lInl~d~~~~~~~~~~~~v~d~V-~d~~~~~~~AR~r~k~yr~~G~~~~~ 138 (144)
T COG2927 78 PGGNPNSARVDLLINLADEFPDFAYEFVTRVFDFV-PDEEALLQLARERWKAYRGAGFQQNT 138 (144)
T ss_pred CCCCCCCCCEEEEEECCCCCCCCCCEEEEEEEECC-CCCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 88899987601898456467776315889986055-76789999999999999866586576
No 4
>PRK06646 DNA polymerase III subunit chi; Provisional
Probab=100.00 E-value=6.3e-34 Score=224.98 Aligned_cols=133 Identities=16% Similarity=0.321 Sum_probs=120.3
Q ss_pred CCEEEEEECC-CCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf 9827996316-748999999999999779849998299899999999852188233313322477765444220699832
Q gi|254780391|r 1 MRTLLFYRFK-NDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTI 79 (141)
Q Consensus 1 Mt~v~FY~l~-~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~ 79 (141)
||+|.||||. .+.+.++++|+||+++.|+|++|++.++++++.||+.||||+++||||||..+ ++.++.|||+||.
T Consensus 1 Mtei~FYHL~~~~Le~aLp~LLeKsl~~Gwr~vV~~~~~er~~~Ld~~LWTy~~~SFLPHG~~~---~~~~~~QPV~LT~ 77 (154)
T PRK06646 1 MQQFSIYQTSDELLLKSILLLIEKCYYSDLKSVILTTDADQQEMLNKNLWTYSRKQFIPHGSKL---DPQPEKQPIYITD 77 (154)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCC---CCCCCCCCEEEEC
T ss_conf 9716889737760999999999999975983999948999999998642226888766776667---9984659889767
Q ss_pred CCCCCCCCCEEEEEECCCC-----CCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 8667899819999816877-----8211311757999975989899999999999999889986
Q gi|254780391|r 80 SSLNANTSTIRFLVDEASM-----HIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAP 138 (141)
Q Consensus 80 ~~~~~~~~~~~~linl~~~-----~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~ 138 (141)
..++||++.+++||.+++. .+++.+.|+||+.+||+. +.++.||.|||.||..|+..
T Consensus 78 ~~eNPN~A~vlflvdgad~~~~~~~~~~~~~f~R~v~~fD~~--dd~~~ar~r~~~~k~~~~~l 139 (154)
T PRK06646 78 ELQNPNNASVLVIISPTDIGKILQAKEYIRVFKRIIIITDLP--EDLKELTVKINKFTEQENKI 139 (154)
T ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCHHHHEEEEEEECCCH--HHHHHHHHHHHHHHHCCCCC
T ss_conf 888998882899975887432222220220002799954877--78999999999986089973
No 5
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185 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 . SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=91.68 E-value=0.82 Score=25.54 Aligned_cols=83 Identities=14% Similarity=0.115 Sum_probs=60.8
Q ss_pred EEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC----------EE
Q ss_conf 96316748999999999999779849998299899999999852188233313322477765444220----------69
Q gi|254780391|r 6 FYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQ----------PV 75 (141)
Q Consensus 6 FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~----------PV 75 (141)
+|....-.-.|++.=|.+.+++|+.|+|=+-+-|.++.|+.+|=. .=|||.+....|..+...+ -|
T Consensus 413 vY~te~~Kw~Av~~e~~~~h~~GqPvLvGT~svE~SE~LS~lL~~----~~I~H~VLNAKPENh~rEAeIia~AG~kGAV 488 (904)
T TIGR00963 413 VYKTEEEKWKAVVDEIKEIHAKGQPVLVGTTSVEKSELLSKLLKE----RGIPHNVLNAKPENHEREAEIIAQAGRKGAV 488 (904)
T ss_pred EECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCE
T ss_conf 464768899999999999874689877752217778999999985----7898122478744677899999960888641
Q ss_pred EEECCCCCCCCCCEEEEEEC
Q ss_conf 98328667899819999816
Q gi|254780391|r 76 LLTISSLNANTSTIRFLVDE 95 (141)
Q Consensus 76 ~i~~~~~~~~~~~~~~linl 95 (141)
.|+|+. .+.+.|+.+.|
T Consensus 489 TIATNM---AGRGTDI~LGG 505 (904)
T TIGR00963 489 TIATNM---AGRGTDIKLGG 505 (904)
T ss_pred EEEECC---CCCCCCEEECC
T ss_conf 676247---87764503178
No 6
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=91.42 E-value=1.2 Score=24.57 Aligned_cols=40 Identities=33% Similarity=0.491 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHC
Q ss_conf 7489999999999997798499982998999999998521
Q gi|254780391|r 11 NDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWT 50 (141)
Q Consensus 11 ~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~ 50 (141)
++....+..++.+....|.|++|+|...+.++.|-+.|=.
T Consensus 11 ~~K~~~l~~~i~~~~~~~~kviIF~~~~~~~~~l~~~L~~ 50 (131)
T cd00079 11 DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRK 50 (131)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf 6999999999999997899099997889999999999955
No 7
>PRK12904 preprotein translocase subunit SecA; Reviewed
Probab=78.15 E-value=4.7 Score=20.97 Aligned_cols=84 Identities=14% Similarity=0.110 Sum_probs=58.1
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--------CEEEEE
Q ss_conf 631674899999999999977984999829989999999985218823331332247776544422--------069983
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF--------QPVLLT 78 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~--------~PV~i~ 78 (141)
|........++..-+.+..++|+.|+|-+.+.+.++.|+.+|=.. =|||.+.........+. --|.|+
T Consensus 409 y~t~~~K~~ai~~ei~~~~~~gqPvLvGT~sve~SE~ls~~L~~~----~i~h~vLNAk~~~~EA~Iia~AG~~gaVTiA 484 (833)
T PRK12904 409 YKTEKEKFDAVVEDIKERHKKGQPVLVGTTSIEKSELLSKLLKKA----GIPHNVLNAKNHEREAEIIAQAGRPGAVTIA 484 (833)
T ss_pred ECCHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHC----CCCHHHCCCCHHHHHHHHHHHCCCCCCEEEE
T ss_conf 079999999999999999976997899427479899999999873----7827761773666688999955999976874
Q ss_pred CCCCCCCCCCEEEEEECCC
Q ss_conf 2866789981999981687
Q gi|254780391|r 79 ISSLNANTSTIRFLVDEAS 97 (141)
Q Consensus 79 ~~~~~~~~~~~~~linl~~ 97 (141)
++. .+.+.|+.+.+.+
T Consensus 485 TNM---AGRGTDI~LGGn~ 500 (833)
T PRK12904 485 TNM---AGRGTDIKLGGNP 500 (833)
T ss_pred ECC---CCCCCCEECCCCH
T ss_conf 025---6788682168863
No 8
>PRK13107 preprotein translocase subunit SecA; Reviewed
Probab=77.07 E-value=6.4 Score=20.15 Aligned_cols=107 Identities=12% Similarity=0.068 Sum_probs=66.8
Q ss_pred ECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--------CCEEEEEC
Q ss_conf 3167489999999999997798499982998999999998521882333133224777654442--------20699832
Q gi|254780391|r 8 RFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSS--------FQPVLLTI 79 (141)
Q Consensus 8 ~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~--------~~PV~i~~ 79 (141)
........++..-+.+..+.|+.|+|-+.+.+.++.|+.+|=. .=|||.+.........+ .--|.|++
T Consensus 429 ~t~~~K~~Av~~ei~~~~~~gqPVLvGT~sve~SE~ls~~L~~----~gi~h~VLNAk~h~~EA~Iia~AG~~gaVTIAT 504 (908)
T PRK13107 429 LTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVK----EKIPHEVLNAKFHEREAEIVAQAGRTGAVTIAT 504 (908)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCCCEECCCCHHHHHHHHHHCCCCCCEEEEC
T ss_conf 5899999999999999997599889950528999999999974----678530104887688999999549999879833
Q ss_pred CCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf 866789981999981687782113117579999759898999999999999
Q gi|254780391|r 80 SSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRS 130 (141)
Q Consensus 80 ~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~ 130 (141)
+. .+.+.++.+-|.... -++-.....++.+..-+.-|+.
T Consensus 505 NM---AGRGTDI~LGGn~~~---------~~~~~~~~~~~~~~~~~~~~~~ 543 (908)
T PRK13107 505 NM---AGRGTDIVLGGNWNM---------EIEALENPTAEQKAKIKADWQI 543 (908)
T ss_pred CC---CCCCCCEECCCCCHH---------HHHHCCCCCHHHHHHHHHHHHH
T ss_conf 36---789868425886202---------1332028648789999999988
No 9
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=75.52 E-value=6.6 Score=20.09 Aligned_cols=68 Identities=13% Similarity=0.196 Sum_probs=50.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--------CEEEEECCC
Q ss_conf 674899999999999977984999829989999999985218823331332247776544422--------069983286
Q gi|254780391|r 10 KNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF--------QPVLLTISS 81 (141)
Q Consensus 10 ~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~--------~PV~i~~~~ 81 (141)
......+++.-+.+..++|+.|+|-|.+-+.++.|+++|=. .=|||.+.........+. --|.|+++.
T Consensus 414 ~~~k~~av~~~v~~~~~~g~pvLvgt~sv~~Se~~s~~L~~----~~i~h~vLnAk~~~~Ea~Iia~AG~~g~vTiaTnM 489 (799)
T PRK09200 414 VDEKYKAVIEEVKERHETGRPVLIGTGSIEQSEYFSKLLFE----AGIPHNLLNAKNAAQEAQIIAEAGQKGAVTVATNM 489 (799)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCHHHCCCCCHHHHHHHHHHCCCCCEEEEECCC
T ss_conf 99999999999999985799889983857999999999986----57643320532177899999827899948984545
No 10
>PRK12901 secA preprotein translocase subunit SecA; Reviewed
Probab=75.26 E-value=7.2 Score=19.86 Aligned_cols=72 Identities=18% Similarity=0.165 Sum_probs=51.8
Q ss_pred EEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--------CCEEEE
Q ss_conf 963167489999999999997798499982998999999998521882333133224777654442--------206998
Q gi|254780391|r 6 FYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSS--------FQPVLL 77 (141)
Q Consensus 6 FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~--------~~PV~i 77 (141)
.|........+++.-+....++|+.|+|-+.+.+.++.|+.+|=. .=|||.+.........+ .--|.|
T Consensus 610 iy~t~~~K~~Aii~ei~~~~~~GqPVLVGT~SVe~SE~lS~~L~~----~gi~h~VLNAk~h~~EAeIIA~AG~~GaVTI 685 (1111)
T PRK12901 610 VYKTKREKYNAVIEEIVELVEAGRPVLVGTTSVEISELLSRMLKM----RKIPHNVLNAKLHQKEAEIVAEAGQKGTVTI 685 (1111)
T ss_pred EECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCHHHHHCCCCHHHHHHHHHHCCCCCCEEE
T ss_conf 866999999999999999996499789971718889999999987----7873877377877999999984689996797
Q ss_pred ECCC
Q ss_conf 3286
Q gi|254780391|r 78 TISS 81 (141)
Q Consensus 78 ~~~~ 81 (141)
+++.
T Consensus 686 ATNM 689 (1111)
T PRK12901 686 ATNM 689 (1111)
T ss_pred ECCC
T ss_conf 2434
No 11
>PRK12906 secA preprotein translocase subunit SecA; Reviewed
Probab=74.43 E-value=7.1 Score=19.90 Aligned_cols=84 Identities=14% Similarity=0.081 Sum_probs=58.1
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--------CCEEEEE
Q ss_conf 63167489999999999997798499982998999999998521882333133224777654442--------2069983
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSS--------FQPVLLT 78 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~--------~~PV~i~ 78 (141)
|........++..-+.+..++|+.|+|-+.+.+.++.|+++|=. .=|||.+.........+ .--|.|+
T Consensus 419 y~t~~~K~~Ai~~ei~~~~~~gqPvLvGT~SVe~SE~ls~~L~~----~gi~h~vLNAk~~~~EA~IIa~AG~~GaVTIA 494 (823)
T PRK12906 419 YPTLDSKFNAVVDDIKERHAKGQPVLVGTVSIESSERLSQLLDK----AGIPHAVLNAKNHAKEAEIIAQAGQRGAVTIA 494 (823)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCHHHHCCCCHHHHHHHHHHCCCCCEEEEE
T ss_conf 47999999999999999986799889971758999999999997----68703530687757899999834899938970
Q ss_pred CCCCCCCCCCEEEEEECCC
Q ss_conf 2866789981999981687
Q gi|254780391|r 79 ISSLNANTSTIRFLVDEAS 97 (141)
Q Consensus 79 ~~~~~~~~~~~~~linl~~ 97 (141)
++. .+.+.|+.+.+.+
T Consensus 495 TNM---AGRGTDI~LGg~~ 510 (823)
T PRK12906 495 TNM---AGRGTDIKLGGNP 510 (823)
T ss_pred CCC---CCCCCCEEECCCC
T ss_conf 655---6898796308973
No 12
>PRK13103 secA preprotein translocase subunit SecA; Reviewed
Probab=74.26 E-value=7.6 Score=19.70 Aligned_cols=111 Identities=10% Similarity=0.070 Sum_probs=70.7
Q ss_pred EEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--------CCEEEE
Q ss_conf 963167489999999999997798499982998999999998521882333133224777654442--------206998
Q gi|254780391|r 6 FYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSS--------FQPVLL 77 (141)
Q Consensus 6 FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~--------~~PV~i 77 (141)
.|........++..-+....++|+.|+|-+.+.+.++.|+.+|=.. =|||.+.........+ .--|.|
T Consensus 427 iy~t~~~K~~Av~~ei~~~~~~gqPVLvGT~Sve~SE~ls~~L~~~----gi~h~VLNAk~~~~EA~Iia~AG~~gaVTI 502 (913)
T PRK13103 427 VYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKE----GIEHKVLNAKYHEKEAEIIAQAGAPGALTI 502 (913)
T ss_pred EECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHC----CCCCEEECCCCHHHHHHHHHHCCCCCCEEE
T ss_conf 9838999999999999999974998899627468899999999976----997512048873799999983378997897
Q ss_pred ECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf 3286678998199998168778211311757999975989899999999999999
Q gi|254780391|r 78 TISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLK 132 (141)
Q Consensus 78 ~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk 132 (141)
+++. .+.+.|+.+-+.+.. .+..+- ..+++.....+..|...+
T Consensus 503 ATNM---AGRGTDI~LGgn~e~--------~~~~~~-~~~~e~~~~~~~~~~~~~ 545 (913)
T PRK13103 503 ATNM---AGRGTDILLGGNWEV--------EVAALE-NPTPEQIAQIKADWQKRH 545 (913)
T ss_pred ECCC---CCCCCCEECCCCHHH--------HHHHCC-CCCHHHHHHHHHHHHHHH
T ss_conf 1645---689869526886034--------443103-676778999999999887
No 13
>PRK12326 preprotein translocase subunit SecA; Reviewed
Probab=73.16 E-value=8.1 Score=19.54 Aligned_cols=83 Identities=13% Similarity=0.064 Sum_probs=56.9
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--------CEEEEE
Q ss_conf 631674899999999999977984999829989999999985218823331332247776544422--------069983
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF--------QPVLLT 78 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~--------~PV~i~ 78 (141)
|........++..-+.+..++|+.|+|-+.+-+.++.|+++|=. .=|||.+.........+. --|.|+
T Consensus 417 y~t~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~ls~~L~~----~gi~h~VLNAk~~~~EA~IIA~AG~~GaVTIA 492 (775)
T PRK12326 417 YATAAEKNDAIVEHIAEVHETGQPVLVGTRDVAESEELAERLVR----RGVPAVVLNAKNDAEEAAVIAEAGKYGAVTVS 492 (775)
T ss_pred ECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCCEECCCCCHHHHHHHHHHCCCCCCEEEE
T ss_conf 46999999999999999997599889970718989999999987----69983023689727699999945999987982
Q ss_pred CCCCCCCCCCEEEEEECC
Q ss_conf 286678998199998168
Q gi|254780391|r 79 ISSLNANTSTIRFLVDEA 96 (141)
Q Consensus 79 ~~~~~~~~~~~~~linl~ 96 (141)
++. .+.+.++.+-++
T Consensus 493 TNM---AGRGTDIkLGg~ 507 (775)
T PRK12326 493 TQM---AGRGTDIRLGGS 507 (775)
T ss_pred CCC---CCCCCCEECCCC
T ss_conf 336---789868414897
No 14
>PRK12899 secA preprotein translocase subunit SecA; Reviewed
Probab=73.08 E-value=8.1 Score=19.53 Aligned_cols=71 Identities=13% Similarity=0.119 Sum_probs=50.9
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--------CCEEEEE
Q ss_conf 63167489999999999997798499982998999999998521882333133224777654442--------2069983
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSS--------FQPVLLT 78 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~--------~~PV~i~ 78 (141)
|........++..-+..+.+.|+.|+|-+.+-+.++.|+.+|=. .=|||.+.........+ .--|.|+
T Consensus 547 y~T~~~K~~Avi~eI~~~h~~GqPVLVGT~SVe~SE~lS~~L~~----~gI~H~VLNAK~h~~EAeIIA~AG~~GaVTIA 622 (969)
T PRK12899 547 YMTEREKYHAIVNEIASIHRSGNPILIGTESVEVSEKLSRILRQ----NRIEHTVLNAKNHAQEAEIIAGAGKLGAVTVA 622 (969)
T ss_pred ECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCHHHCCCHHHHHHHHHHHHCCCCCCEEEE
T ss_conf 52899999999999999995799889983857999999999998----69964541511178999999955999977971
Q ss_pred CCC
Q ss_conf 286
Q gi|254780391|r 79 ISS 81 (141)
Q Consensus 79 ~~~ 81 (141)
++.
T Consensus 623 TNM 625 (969)
T PRK12899 623 TNM 625 (969)
T ss_pred CCC
T ss_conf 326
No 15
>pfam07652 Flavi_DEAD Flavivirus DEAD domain.
Probab=72.66 E-value=8.3 Score=19.47 Aligned_cols=115 Identities=17% Similarity=0.125 Sum_probs=65.0
Q ss_pred EEEEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf 79963167489999999999997798499982998999999998521882333133224777654442206998328667
Q gi|254780391|r 4 LLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLN 83 (141)
Q Consensus 4 v~FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~~~~ 83 (141)
+++|=.....-+.+++++..+++++.|++|+++.--.+.++-++|=..+ -+|--....++.... .-|-+.+...-
T Consensus 7 ld~HPGaGKTr~vLP~~v~~~i~~~lRtlVLaPTRVV~~Em~eAL~g~~-vr~~t~a~~~~~~~~----~ivdvmCHAT~ 81 (146)
T pfam07652 7 LDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLP-IRYHTPAVSSEHTGR----EIVDVMCHATF 81 (146)
T ss_pred EECCCCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHCCCC-CEEECHHHHCCCCCC----CEEEEECHHHH
T ss_conf 8538999970224899999999728618997727999999999975899-467523431366888----41889715988
Q ss_pred CCCCCEEEEEECCCCCCCHHHCCCEEEEEEC---CCCHHHHHHHHHHHHHHHHCCC
Q ss_conf 8998199998168778211311757999975---9898999999999999998899
Q gi|254780391|r 84 ANTSTIRFLVDEASMHIGDVDYYEKVVFIIN---TDDQGSLEWGRAHWRSLKNSGY 136 (141)
Q Consensus 84 ~~~~~~~~linl~~~~p~~~~~f~rvieiv~---~~d~~~~~~aR~rwk~yk~~G~ 136 (141)
.. .+ +.+. ...+|+-+| .| -.|+... +||-....+...|-
T Consensus 82 t~-----r~--l~~~---~~~ny~viI--MDE~H~~DP~SI-AarG~~~~~~~~g~ 124 (146)
T pfam07652 82 TQ-----RL--LSPV---RVPNYEVII--MDEAHFTDPASI-AARGYISTLVELGE 124 (146)
T ss_pred HH-----HH--HCCC---CCCCEEEEE--EECCCCCCHHHH-HHHHHHHHHHHCCC
T ss_conf 88-----97--3688---856447999--851223898999-98899998854386
No 16
>KOG0331 consensus
Probab=72.51 E-value=8.4 Score=19.45 Aligned_cols=117 Identities=19% Similarity=0.317 Sum_probs=74.4
Q ss_pred HHHHHHHHHHH-HCCCEEEEEECCHHHHHHHHHHHHC--CCCCCCCCCCCCCCC------CCCCCCCCEEEEECCC--CC
Q ss_conf 99999999999-7798499982998999999998521--882333133224777------6544422069983286--67
Q gi|254780391|r 15 YNLLVLLQDEY-EKGKRVSVQCGSERVRDSLNEYLWT--WKKDGFLPHGVDVGD------EGDFSSFQPVLLTISS--LN 83 (141)
Q Consensus 15 ~~~~~L~~K~~-~~~~ri~I~~~d~~~~~~lD~~LW~--~~~~sFiPH~~~~~~------~~~~~~~~PV~i~~~~--~~ 83 (141)
+-+..|+++.. ..+.|++|+|.....+..|...|=. ++..++ |+=.... .+-..-..||+++++- ..
T Consensus 327 ~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~i--HGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRG 404 (519)
T KOG0331 327 RKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAI--HGDKSQSERDWVLKGFREGKSPVLVATDVAARG 404 (519)
T ss_pred HHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEE--CCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCC
T ss_conf 879999999735689868999643364999998877517661550--066648899999975026885469881531256
Q ss_pred CCCCCEEEEEECCCCCCCHHHCC-------CE------EEEEECCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 89981999981687782113117-------57------999975989899999999999999889986
Q gi|254780391|r 84 ANTSTIRFLVDEASMHIGDVDYY-------EK------VVFIINTDDQGSLEWGRAHWRSLKNSGYAP 138 (141)
Q Consensus 84 ~~~~~~~~linl~~~~p~~~~~f-------~r------vieiv~~~d~~~~~~aR~rwk~yk~~G~~~ 138 (141)
..-.+++..||- ..|.+.+.| .| .+-+|. ......||+-|+..+.+|-.+
T Consensus 405 LDi~dV~lVIny--dfP~~vEdYVHRiGRTGRa~~~G~A~tfft---~~~~~~a~~l~~~l~e~~q~v 467 (519)
T KOG0331 405 LDVPDVDLVINY--DFPNNVEDYVHRIGRTGRAGKKGTAITFFT---SDNAKLARELIKVLREAGQTV 467 (519)
T ss_pred CCCCCCCEEEEC--CCCCCHHHHHHHCCCCCCCCCCCEEEEEEE---HHHHHHHHHHHHHHHHCCCCC
T ss_conf 887666479967--899998998865376545788824899972---788777899999999706878
No 17
>CHL00122 secA preprotein translocase subunit SecA; Validated
Probab=71.54 E-value=8.8 Score=19.31 Aligned_cols=83 Identities=13% Similarity=0.088 Sum_probs=57.9
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCC--------CCEEE
Q ss_conf 6316748999999999999779849998299899999999852188233313322477765--4442--------20699
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEG--DFSS--------FQPVL 76 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~--~~~~--------~~PV~ 76 (141)
|........++..-+....+.|+.|+|-+.+-+.++.|+.+|=.. =|||.+...... ...+ .--|.
T Consensus 403 y~t~~~K~~Av~~ei~~~h~~GqPVLvGT~SVe~SE~ls~~L~~~----gi~h~vLNAk~~n~~~EA~IiA~AG~~gaVT 478 (891)
T CHL00122 403 YKTEYSKWKAIADECFDMHKIGRPILVGTTSVEKSELLSQLLEEY----QLPHNLLNAKPENVKRESEIIAQAGRKGAIT 478 (891)
T ss_pred ECCHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHC----CCCCHHHCCCCCCHHHHHHHHHHCCCCCCEE
T ss_conf 788999999999999999967999898346558899999999974----7862202388430789999999569999389
Q ss_pred EECCCCCCCCCCEEEEEECC
Q ss_conf 83286678998199998168
Q gi|254780391|r 77 LTISSLNANTSTIRFLVDEA 96 (141)
Q Consensus 77 i~~~~~~~~~~~~~~linl~ 96 (141)
|+++. .+.+.|+.+-+.
T Consensus 479 IATNM---AGRGTDI~LGGn 495 (891)
T CHL00122 479 IATNM---AGRGTDIILGGN 495 (891)
T ss_pred EECCC---CCCCCCEECCCC
T ss_conf 71555---689878425886
No 18
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=70.98 E-value=9.1 Score=19.24 Aligned_cols=113 Identities=12% Similarity=0.066 Sum_probs=70.0
Q ss_pred EEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--------CCEEEE
Q ss_conf 963167489999999999997798499982998999999998521882333133224777654442--------206998
Q gi|254780391|r 6 FYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSS--------FQPVLL 77 (141)
Q Consensus 6 FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~--------~~PV~i 77 (141)
.|........++..-+....+.|+.|+|-+.+.+.++.|+.+|=. .=|||.+.........+ .--|.|
T Consensus 422 vy~t~~~K~~Av~~ei~~~~~~gqPVLvGT~sve~SE~ls~~L~~----~gi~h~VLNAk~~~~EA~Iia~AG~~gaVTI 497 (896)
T PRK13104 422 VYLTQADKFQAIIEDVRECGVRRQPVLVGTVSIEASEFLSQLLKK----ENIKHQVLNAKFHEKEAQIIAEAGRPGAVTI 497 (896)
T ss_pred EECCHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHH----CCCCHHHHCCCCHHHHHHHHHHCCCCCCEEE
T ss_conf 972899999999999999997599789934857989999999998----6992465267874789999983389996897
Q ss_pred ECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf 32866789981999981687782113117579999759898999999999999998
Q gi|254780391|r 78 TISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKN 133 (141)
Q Consensus 78 ~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~ 133 (141)
+++. .+.+.|+.+-+. ....+.. +-....+..++..++.|..-++
T Consensus 498 ATNM---AGRGTDI~LGg~--~~~~~~~------~~~~~~~~~~e~~~~~~~~~~~ 542 (896)
T PRK13104 498 ATNM---AGRGTDIVLGGS--LAADLAN------LPADASEQEKEAVKKEWQKRHD 542 (896)
T ss_pred CCCC---CCCCCCCCCCCC--CHHHHHC------CCCCCHHHHHHHHHHHHHHHHH
T ss_conf 1655---688858217875--1244430------5655116679999999998533
No 19
>PRK12902 secA preprotein translocase subunit SecA; Reviewed
Probab=70.74 E-value=9.2 Score=19.20 Aligned_cols=80 Identities=11% Similarity=0.030 Sum_probs=56.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCC--------CCEEEEEC
Q ss_conf 6748999999999999779849998299899999999852188233313322477765--4442--------20699832
Q gi|254780391|r 10 KNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEG--DFSS--------FQPVLLTI 79 (141)
Q Consensus 10 ~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~--~~~~--------~~PV~i~~ 79 (141)
......++..-+....+.|+.|+|-+.+-+.++.|+.+|=. .=|||.+...... ...+ .--|.|++
T Consensus 426 ~~~K~~Av~~ei~~~~~~gqPVLVGT~SVe~SE~ls~lL~~----~gi~h~VLNAk~~n~~~EAeIIA~AG~~gaVTIAT 501 (946)
T PRK12902 426 EIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLAE----QGIPHNLLNAKPENVEREAEIVAQAGRKGAVTIAT 501 (946)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCCCEEECCCCCCHHHHHHHHHCCCCCCEEEEC
T ss_conf 99999999999999975899889972757989999999985----58862032578644278999999469999689745
Q ss_pred CCCCCCCCCEEEEEECC
Q ss_conf 86678998199998168
Q gi|254780391|r 80 SSLNANTSTIRFLVDEA 96 (141)
Q Consensus 80 ~~~~~~~~~~~~linl~ 96 (141)
+. .+.+.|+.+-|.
T Consensus 502 NM---AGRGTDI~LGGn 515 (946)
T PRK12902 502 NM---AGRGTDIILGGN 515 (946)
T ss_pred CC---CCCCCCEECCCC
T ss_conf 44---689869507887
No 20
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=69.85 E-value=9.6 Score=19.09 Aligned_cols=58 Identities=17% Similarity=0.110 Sum_probs=46.4
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf 63167489999999999997798499982998999999998521882333133224777654
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGD 68 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~ 68 (141)
|........++..-+.+..++|+.|+|-+.+.+.++.|+++|=. .=|||.+.......
T Consensus 467 y~t~~~K~~Aii~ei~~~~~~GqPVLVGT~SVe~SE~lS~~L~~----~gi~h~VLNAk~~~ 524 (673)
T PRK12898 467 FLTLAAKWAAVAARVRELHASGRPVLVGTRSVAASERLSALLRE----AGLPHQVLNAKQDA 524 (673)
T ss_pred ECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCHHHCCCCCHH
T ss_conf 56999999999999999986799889983758999999999998----69975664786668
No 21
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=68.12 E-value=10 Score=18.87 Aligned_cols=89 Identities=12% Similarity=0.062 Sum_probs=45.8
Q ss_pred EEEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC------CCCCCCEEEEE
Q ss_conf 996316748999999999999779849998299899999999852188233313322477765------44422069983
Q gi|254780391|r 5 LFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEG------DFSSFQPVLLT 78 (141)
Q Consensus 5 ~FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~------~~~~~~PV~i~ 78 (141)
.||-...+....+..|+++.+ ..+++|+|...+.++.+-..|=...-....=|+-.....- -......|+++
T Consensus 235 ~~~~~~~~K~~~L~~ll~~~~--~~k~iIF~nt~~~~~~l~~~L~~~g~~~~~lhg~~~q~~R~~~l~~F~~g~~~vLVa 312 (423)
T PRK04837 235 LFYPSNEEKMRLLQTLIEEEW--PDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVPQKKRLRILEQFTRGDLDILVA 312 (423)
T ss_pred EEEECHHHHHHHHHHHHHHHC--CCCEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf 999172779999999998408--874688616288899999999765981787225457999999999997699989987
Q ss_pred CCC--CCCCCCCEEEEEEC
Q ss_conf 286--67899819999816
Q gi|254780391|r 79 ISS--LNANTSTIRFLVDE 95 (141)
Q Consensus 79 ~~~--~~~~~~~~~~linl 95 (141)
++- ....-.++...||-
T Consensus 313 TDvaaRGLDi~~V~~VIny 331 (423)
T PRK04837 313 TDVAARGLHIPDVTHVFNY 331 (423)
T ss_pred HHHHHCCCCCCCCCEEEEE
T ss_conf 0043277772679889996
No 22
>TIGR02743 TraW type-F conjugative transfer system protein TraW; InterPro: IPR014114 This entry represents TraW, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm , ..
Probab=66.51 E-value=11 Score=18.67 Aligned_cols=30 Identities=20% Similarity=0.378 Sum_probs=27.1
Q ss_pred HHCCCEEEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf 311757999975989899999999999999
Q gi|254780391|r 103 VDYYEKVVFIINTDDQGSLEWGRAHWRSLK 132 (141)
Q Consensus 103 ~~~f~rvieiv~~~d~~~~~~aR~rwk~yk 132 (141)
.=.|.+...+||++||+.++.|+..+..+.
T Consensus 130 ~v~ls~~LlFfDAdD~~Q~~wA~~~~~~~~ 159 (217)
T TIGR02743 130 RVSLSKTLLFFDADDPKQLAWAQQLLAQLP 159 (217)
T ss_pred CCCCCCCEEEEECCCHHHHHHHHHHHHCCC
T ss_conf 843276178881888899999998732038
No 23
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=65.15 E-value=12 Score=18.51 Aligned_cols=82 Identities=12% Similarity=0.057 Sum_probs=43.1
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC------CCCCCCCEEEEECCC--CC
Q ss_conf 4899999999999977984999829989999999985218823331332247776------544422069983286--67
Q gi|254780391|r 12 DWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDE------GDFSSFQPVLLTISS--LN 83 (141)
Q Consensus 12 ~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~------~~~~~~~PV~i~~~~--~~ 83 (141)
.....++.|+.+ ....+++|+|.+...++.+...|=...-....=|+-..... .-......|+++++- ..
T Consensus 243 ~K~~~L~~LL~~--~~~~k~IIF~nT~~~ve~l~~~L~~~g~~v~~LHG~lsQ~eR~~~L~~Fk~G~~~VLVaTDVAARG 320 (574)
T PRK04537 243 EKQTLLLGLLSR--SEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARG 320 (574)
T ss_pred HHHHHHHHHHHH--CCCCCCEEECCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCCCCC
T ss_conf 999999999972--677651153341899999999999779968997099999999999999976999799773500233
Q ss_pred CCCCCEEEEEEC
Q ss_conf 899819999816
Q gi|254780391|r 84 ANTSTIRFLVDE 95 (141)
Q Consensus 84 ~~~~~~~~linl 95 (141)
.+-.++...||.
T Consensus 321 IDIp~V~~VINY 332 (574)
T PRK04537 321 LHIDGVKYVYNY 332 (574)
T ss_pred CCCCCCCEEEEE
T ss_conf 571469979995
No 24
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=62.24 E-value=14 Score=18.19 Aligned_cols=111 Identities=12% Similarity=0.102 Sum_probs=60.2
Q ss_pred EEEECC-CCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC------CCCCCCEEEE
Q ss_conf 996316-748999999999999779849998299899999999852188233313322477765------4442206998
Q gi|254780391|r 5 LFYRFK-NDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEG------DFSSFQPVLL 77 (141)
Q Consensus 5 ~FY~l~-~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~------~~~~~~PV~i 77 (141)
.||... .+...++++|+.+. ...+++|+|...+.++.+-+.|=...-..-.=|+-.....- --.....|++
T Consensus 220 ~~~~v~~~~K~~~L~~ll~~~--~~~~~IIFcntk~~v~~l~~~L~~~g~~~~~lHg~m~q~~R~~~l~~F~~g~~~iLV 297 (459)
T PRK11776 220 RFYEVDPDERLPALQRLLLHY--RPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLV 297 (459)
T ss_pred EEEEECHHHHHHHHHHHHHHC--CCCCEEEEECCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEE
T ss_conf 999977187899999999736--876603761748999999999986799689987999999999999999779997998
Q ss_pred ECCC--CCCCCCCEEEEEECCCCCCCHHH----C---------CCEEEEEECCCCHHH
Q ss_conf 3286--67899819999816877821131----1---------757999975989899
Q gi|254780391|r 78 TISS--LNANTSTIRFLVDEASMHIGDVD----Y---------YEKVVFIINTDDQGS 120 (141)
Q Consensus 78 ~~~~--~~~~~~~~~~linl~~~~p~~~~----~---------f~rvieiv~~~d~~~ 120 (141)
+++- ...+-.++...||- ..|.+.+ | -...+-+|.+ +|..
T Consensus 298 aTDvaaRGIDi~~V~~VIny--DlP~~~e~YvHRiGRTGRaG~~G~ait~vt~-~e~~ 352 (459)
T PRK11776 298 ATDVAARGLDIKSLEAVINY--ELARDPEVHVHRIGRTGRAGSKGLALSLVAP-EEMQ 352 (459)
T ss_pred EHHHHHCCCCCCCCCEEEEE--CCCCCHHHHHHCCCHHHCCCCCEEEEEEECH-HHHH
T ss_conf 81043476771359889997--8989745520205251378996579999868-9999
No 25
>PRK12900 secA preprotein translocase subunit SecA; Reviewed
Probab=61.80 E-value=14 Score=18.14 Aligned_cols=77 Identities=14% Similarity=0.165 Sum_probs=52.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--------CEEEEECCC
Q ss_conf 674899999999999977984999829989999999985218823331332247776544422--------069983286
Q gi|254780391|r 10 KNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF--------QPVLLTISS 81 (141)
Q Consensus 10 ~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~--------~PV~i~~~~ 81 (141)
......++..-+....++|+.|+|-+.+.+.++.|+++|=. .=|||.+.........+. --|.|+++.
T Consensus 536 ~~~K~~Aii~ei~~~~~~gqPVLVGT~SVe~SE~lS~~L~~----~gI~h~VLNAk~h~~EA~IIa~AG~~GaVTIATNM 611 (983)
T PRK12900 536 RREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRA----KRIEHNVLNAKQNEREAEIVAEAGQKGAVTIATNM 611 (983)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHH----CCCCHHHHCCCCHHHHHHHHHHCCCCCCEEEECCC
T ss_conf 99999999999999974799889983878999999999998----59955651678478899999936999977982436
Q ss_pred CCCCCCCEEEEE
Q ss_conf 678998199998
Q gi|254780391|r 82 LNANTSTIRFLV 93 (141)
Q Consensus 82 ~~~~~~~~~~li 93 (141)
.+.+.|+.+
T Consensus 612 ---AGRGTDIkL 620 (983)
T PRK12900 612 ---AGRGTDIKL 620 (983)
T ss_pred ---CCCCCCCCC
T ss_conf ---789858254
No 26
>PRK12903 secA preprotein translocase subunit SecA; Reviewed
Probab=58.33 E-value=16 Score=17.77 Aligned_cols=67 Identities=15% Similarity=0.164 Sum_probs=49.2
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--------CEEEEECCC
Q ss_conf 74899999999999977984999829989999999985218823331332247776544422--------069983286
Q gi|254780391|r 11 NDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSF--------QPVLLTISS 81 (141)
Q Consensus 11 ~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~--------~PV~i~~~~ 81 (141)
.....+++.-+.+..+.|+.|+|-+.+.+.++.|+.+|=. .=|||.+.........+. --|.|+++.
T Consensus 409 ~~k~~av~~ei~~~~~~gqPvLvgt~sve~Se~ls~~L~~----~~i~h~vLNAk~~~~EA~Iia~AG~~g~VTiATNM 483 (885)
T PRK12903 409 HAKWKAVVKEVKRVHEKGQPILIGTAQVEDSEQLHEYLLE----ANIPHTVLNAKQHAREAEIIAKAGQKGAITIATNM 483 (885)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHH----CCCCCEEEECCCHHHHHHHHHHCCCCCCEEEECCC
T ss_conf 9999999999999985799889956847999999999985----68770355468658899999954899918983766
No 27
>TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=53.84 E-value=12 Score=18.56 Aligned_cols=81 Identities=22% Similarity=0.319 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH-----HHHHCCCCCCCCC-------CCCCCCCCCC------CCCCCEE
Q ss_conf 99999999999977984999829989999999-----9852188233313-------3224777654------4422069
Q gi|254780391|r 14 EYNLLVLLQDEYEKGKRVSVQCGSERVRDSLN-----EYLWTWKKDGFLP-------HGVDVGDEGD------FSSFQPV 75 (141)
Q Consensus 14 ~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD-----~~LW~~~~~sFiP-------H~~~~~~~~~------~~~~~PV 75 (141)
..-+-+.+++.+++|++++|+||=.++++.|| ..+|..=...|.| ||...+++-+ -....-|
T Consensus 514 ~~~v~~~~~~E~~~GrQaYvv~PlI~ESE~lp~lk~A~~~~~~l~~~f~~~~~v~LlHGrm~~~eK~~vm~~F~~~~~~I 593 (721)
T TIGR00643 514 IDIVYEFIEEEIAKGRQAYVVYPLIEESEKLPDLKAAEALYERLKKAFLPKYNVGLLHGRMKSDEKEAVMEEFREGEVDI 593 (721)
T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEE
T ss_conf 68999999999832890899964403200471689999999998886122100113306898478999999852158369
Q ss_pred EEECC----CCCCCCCCEEEEEE
Q ss_conf 98328----66789981999981
Q gi|254780391|r 76 LLTIS----SLNANTSTIRFLVD 94 (141)
Q Consensus 76 ~i~~~----~~~~~~~~~~~lin 94 (141)
+++|. +-+.++|.+.|.-|
T Consensus 594 LVsTTVIEVGVDVPnAtvMVIe~ 616 (721)
T TIGR00643 594 LVSTTVIEVGVDVPNATVMVIED 616 (721)
T ss_pred EEEEEEEEEEEECCCCCEEEEEC
T ss_conf 99976899986179772788866
No 28
>PTZ00110 helicase; Provisional
Probab=53.42 E-value=19 Score=17.28 Aligned_cols=122 Identities=11% Similarity=0.168 Sum_probs=73.1
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC------CCCCCEEEEECCCC--
Q ss_conf 7489999999999997798499982998999999998521882333133224777654------44220699832866--
Q gi|254780391|r 11 NDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGD------FSSFQPVLLTISSL-- 82 (141)
Q Consensus 11 ~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~------~~~~~PV~i~~~~~-- 82 (141)
......+..++.+.. .+.+++|+|.....++.|...|....-.+..=|+-.....-. -....+|+++++-.
T Consensus 412 ~eK~~~L~~lL~~~~-~~~kvIIFvnTK~~ad~L~~~L~~~G~~a~~LHGd~~Q~eR~~~L~~Fr~G~~~ILVATDVAAR 490 (602)
T PTZ00110 412 HEKRAKLKELLGQIM-DGGKILIFSETKKGADTLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKHPIMIATDVASR 490 (602)
T ss_pred HHHHHHHHHHHHHCC-CCCCEEEEECCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCHHHC
T ss_conf 889999999998527-8996899929738999999999867995798208899999999999997699988988222331
Q ss_pred CCCCCCEEEEEECCCCCCCHHHCC----C---------EEEEEECCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 789981999981687782113117----5---------7999975989899999999999999889986
Q gi|254780391|r 83 NANTSTIRFLVDEASMHIGDVDYY----E---------KVVFIINTDDQGSLEWGRAHWRSLKNSGYAP 138 (141)
Q Consensus 83 ~~~~~~~~~linl~~~~p~~~~~f----~---------rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~ 138 (141)
...-.++...||- ..|...+.| . ..+-+|.+ |+. ..||+--+..++++-.+
T Consensus 491 GLDI~dV~~VINY--D~P~~~edYVHRIGRTGRAG~kG~A~TF~Tp-d~~--~~a~~Lv~~L~ea~q~v 554 (602)
T PTZ00110 491 GLDVRDVKYVINF--DFPNQIEDYVHRIGRTGRAGAKGASYTFLTP-DKY--RSARELVKLMREAKQEI 554 (602)
T ss_pred CCCCCCCCEEEEE--CCCCCCCCCCCCCCCCCCCCCCEEEEEEECC-CCH--HHHHHHHHHHHHCCCCC
T ss_conf 5551579879995--8979802210135615068993169999777-707--78999999999838999
No 29
>pfam11513 TA0956 Thermoplasma acidophilum protein TA0956. TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif.
Probab=51.29 E-value=11 Score=18.83 Aligned_cols=28 Identities=14% Similarity=0.171 Sum_probs=23.3
Q ss_pred ECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 7598989999999999999988998603
Q gi|254780391|r 113 INTDDQGSLEWGRAHWRSLKNSGYAPDV 140 (141)
Q Consensus 113 v~~~d~~~~~~aR~rwk~yk~~G~~~~~ 140 (141)
|...++..|+.-++--+.||+.||..+.
T Consensus 81 Fsd~~~~~K~~i~ei~~kykd~Gyk~E~ 108 (110)
T pfam11513 81 FSDIDENMKNSIEEIVKKYKDLGYKVEI 108 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEEC
T ss_conf 4254556899999999997537842442
No 30
>COG4221 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]
Probab=48.25 E-value=23 Score=16.79 Aligned_cols=85 Identities=18% Similarity=0.224 Sum_probs=53.0
Q ss_pred EEEECCCC-HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf 99631674-89999999999997798499982998999999998521882333133224777654442206998328667
Q gi|254780391|r 5 LFYRFKND-WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLN 83 (141)
Q Consensus 5 ~FY~l~~~-~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~~~~ 83 (141)
-+-...++ +-++.+ ++..++|.+++......+.+++|-+-|=. ..++|+.+...+.+.... .|. ...
T Consensus 9 ~lITGASSGiG~A~A---~~l~~~G~~vvl~aRR~drL~~la~~~~~---~~~~~~~~DVtD~~~~~~----~i~--~~~ 76 (246)
T COG4221 9 ALITGASSGIGEATA---RALAEAGAKVVLAARREERLEALADEIGA---GAALALALDVTDRAAVEA----AIE--ALP 76 (246)
T ss_pred EEEECCCCHHHHHHH---HHHHHCCCEEEEEECCHHHHHHHHHHHCC---CCEEEEEECCCCHHHHHH----HHH--HHH
T ss_conf 999468656889999---99997899699986368899999986256---743789613678899999----999--999
Q ss_pred CCCCCEEEEEECCCCCCC
Q ss_conf 899819999816877821
Q gi|254780391|r 84 ANTSTIRFLVDEASMHIG 101 (141)
Q Consensus 84 ~~~~~~~~linl~~~~p~ 101 (141)
.....+|+|+|-+...+.
T Consensus 77 ~~~g~iDiLvNNAGl~~g 94 (246)
T COG4221 77 EEFGRIDILVNNAGLALG 94 (246)
T ss_pred HHHCCCCEEEECCCCCCC
T ss_conf 751760589966877768
No 31
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=44.95 E-value=26 Score=16.48 Aligned_cols=82 Identities=16% Similarity=0.023 Sum_probs=36.8
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC------CCCCCCCEEEEECCC--CC
Q ss_conf 4899999999999977984999829989999999985218823331332247776------544422069983286--67
Q gi|254780391|r 12 DWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDE------GDFSSFQPVLLTISS--LN 83 (141)
Q Consensus 12 ~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~------~~~~~~~PV~i~~~~--~~ 83 (141)
+....+..|+.. ....+++|+|.+.+.++.+.+.|=...-....=|+-..... +-......|+++++- ..
T Consensus 318 dk~~~L~~ll~~--~~~~k~IIF~nt~~~~~~l~~~L~~~g~~~~~lhg~l~q~~R~~~l~~F~~g~~~iLVaTDvaaRG 395 (472)
T PRK01297 318 DKYKLLYNLVTQ--NPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRG 395 (472)
T ss_pred HHHHHHHHHHHH--CCCCCEEEECCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCHHHCC
T ss_conf 999999999984--798736896174999999998765449616864377899999999999976999699886613366
Q ss_pred CCCCCEEEEEEC
Q ss_conf 899819999816
Q gi|254780391|r 84 ANTSTIRFLVDE 95 (141)
Q Consensus 84 ~~~~~~~~linl 95 (141)
.+-.++...||.
T Consensus 396 LDi~~V~~VIny 407 (472)
T PRK01297 396 IHIDGISHVINF 407 (472)
T ss_pred CCCCCCCEEEEE
T ss_conf 775788889996
No 32
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=43.52 E-value=28 Score=16.34 Aligned_cols=111 Identities=14% Similarity=-0.001 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC------CCCCCCEEEEECCCC--CC
Q ss_conf 8999999999999779849998299899999999852188233313322477765------444220699832866--78
Q gi|254780391|r 13 WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEG------DFSSFQPVLLTISSL--NA 84 (141)
Q Consensus 13 ~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~------~~~~~~PV~i~~~~~--~~ 84 (141)
....+..|+.+. ...+++|+|...+.++.|.+.|=...-.+..=|+-.....- -......|+++++-. ..
T Consensus 232 k~~~L~~ll~~~--~~~~~iIF~~tk~~a~~l~~~L~~~g~~~~~lHg~~sq~~R~~~l~~F~~g~~~vLVaTDvaaRGi 309 (457)
T PRK10590 232 KRELLSQMIGKG--NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGL 309 (457)
T ss_pred HHHHHHHHHHHC--CCCCEEEEECHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCC
T ss_conf 999999998615--866335884119999999999855699823232478999999999999869982999577011556
Q ss_pred CCCCEEEEEECCCCCCCHHHCC-------------CEEEEEECCCCHHHHHHHHHHH
Q ss_conf 9981999981687782113117-------------5799997598989999999999
Q gi|254780391|r 85 NTSTIRFLVDEASMHIGDVDYY-------------EKVVFIINTDDQGSLEWGRAHW 128 (141)
Q Consensus 85 ~~~~~~~linl~~~~p~~~~~f-------------~rvieiv~~~d~~~~~~aR~rw 128 (141)
.-.++...||. ..|...+.| ...|-+|. .+|...-..=|++
T Consensus 310 Di~~V~~VIny--D~P~~~e~YvHRiGRTGRaG~~G~ait~v~-~~e~~~~~~ie~~ 363 (457)
T PRK10590 310 DIEELPHVVNY--ELPNVPEDYVHRIGRTGRAAATGEALSLVC-VDEHKLLRDIEKL 363 (457)
T ss_pred CCCCCCEEEEE--CCCCCHHHEECCCCCCCCCCCCEEEEEEEC-HHHHHHHHHHHHH
T ss_conf 63568879993--899974450022670605899536999866-8999999999999
No 33
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=42.15 E-value=29 Score=16.21 Aligned_cols=108 Identities=11% Similarity=0.071 Sum_probs=62.0
Q ss_pred CEEEEEECC--CCHHHHHHHHHHHH---HHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf 827996316--74899999999999---9779849998299899999999852188233313322477765444220699
Q gi|254780391|r 2 RTLLFYRFK--NDWEYNLLVLLQDE---YEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVL 76 (141)
Q Consensus 2 t~v~FY~l~--~~~~~~~~~L~~K~---~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~ 76 (141)
|...|+.+. .+..+-+...++++ ...|+|++++.+....... -++++||||-= +. +-|+
T Consensus 72 ~~~~f~~~sAv~~gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK-------~QQD~lLp~vE---~G------~iil 135 (436)
T COG2256 72 TNAAFEALSAVTSGVKDLREIIEEARKNRLLGRRTILFLDEIHRFNK-------AQQDALLPHVE---NG------TIIL 135 (436)
T ss_pred HCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHCCH-------HHHHHHHHHHC---CC------EEEE
T ss_conf 17766995152346799999999999987258834998722533374-------45655103324---88------6899
Q ss_pred EECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 8328667899819999816877821131175799997598989999999999999988998
Q gi|254780391|r 77 LTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYA 137 (141)
Q Consensus 77 i~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~ 137 (141)
|+...+||.. -+|- . +-.=.||+++= +=+.+....+=.|=-.-..+|+.
T Consensus 136 IGATTENPsF-----~ln~-----A-LlSR~~vf~lk-~L~~~di~~~l~ra~~~~~rgl~ 184 (436)
T COG2256 136 IGATTENPSF-----ELNP-----A-LLSRARVFELK-PLSSEDIKKLLKRALLDEERGLG 184 (436)
T ss_pred EECCCCCCCE-----EECH-----H-HHHHHHEEEEE-CCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 9626789871-----4038-----8-86110415651-69989999999999865413777
No 34
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=42.12 E-value=28 Score=16.29 Aligned_cols=38 Identities=13% Similarity=0.201 Sum_probs=28.0
Q ss_pred HHCC-CEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 3117-57999975989899999999999999889986039
Q gi|254780391|r 103 VDYY-EKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDVI 141 (141)
Q Consensus 103 ~~~f-~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~v 141 (141)
+.++ .+++..+| +|+.-++++..-.+...+.|+.+.++
T Consensus 39 L~~~~~~vil~~D-~D~AG~~Aa~r~~~~l~~~g~~v~i~ 77 (79)
T cd03364 39 LKRLAKEVILAFD-GDEAGQKAALRALELLLKLGLNVRVL 77 (79)
T ss_pred HHCCCCCEEEEEC-CCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 7231586799978-98899999999999999779969999
No 35
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=40.59 E-value=31 Score=16.06 Aligned_cols=25 Identities=16% Similarity=0.142 Sum_probs=20.8
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 9899999999999999889986039
Q gi|254780391|r 117 DQGSLEWGRAHWRSLKNSGYAPDVI 141 (141)
Q Consensus 117 d~~~~~~aR~rwk~yk~~G~~~~~v 141 (141)
|...+++||.+-+.+.+.|..++++
T Consensus 144 ~~~~~~~a~~~a~DL~d~gI~iel~ 168 (218)
T cd01458 144 DSIKDSQAAVKAEDLKDKGIELELF 168 (218)
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 8799999999998898779689998
No 36
>pfam00782 DSPc Dual specificity phosphatase, catalytic domain. Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.
Probab=34.36 E-value=38 Score=15.46 Aligned_cols=22 Identities=27% Similarity=0.605 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHCCCEEEEEECC
Q ss_conf 9999999999779849998299
Q gi|254780391|r 16 NLLVLLQDEYEKGKRVSVQCGS 37 (141)
Q Consensus 16 ~~~~L~~K~~~~~~ri~I~~~d 37 (141)
.++..++++...|.+|+|+|..
T Consensus 59 ~~~~fI~~~~~~g~~VLVHC~~ 80 (131)
T pfam00782 59 EAVEFIDDAIQKGGKVLVHCQA 80 (131)
T ss_pred HHHHHHHHHHHCCCCEEEECCC
T ss_conf 9999999998649969999999
No 37
>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein; InterPro: IPR005285 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family includes transporters, whose physiological function is not yet established. These proteins are thought to confer resistance to the chemicals cycloheximide and sulphomethuron methyl, BFA, azole antifungal agents, other antifungal agents: amorolfine and terbinafine. Some of them could serve as an efflux pump of various antibiotics..
Probab=31.98 E-value=42 Score=15.23 Aligned_cols=38 Identities=16% Similarity=0.266 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHCCCEEE--EEECCHHHHHHHHHHHHCCC
Q ss_conf 999999999997798499--98299899999999852188
Q gi|254780391|r 15 YNLLVLLQDEYEKGKRVS--VQCGSERVRDSLNEYLWTWK 52 (141)
Q Consensus 15 ~~~~~L~~K~~~~~~ri~--I~~~d~~~~~~lD~~LW~~~ 52 (141)
-.+|+|+.|.-..|+-|+ |+=|+.--.++.|++|--.+
T Consensus 1004 Wsi~~l~RKLad~GQaILCTIHQPSA~L~~eFDrLLlLqk 1043 (1466)
T TIGR00956 1004 WSICKLLRKLADHGQAILCTIHQPSAILFEEFDRLLLLQK 1043 (1466)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHHHHHC
T ss_conf 9999999988755983886043024899998628977542
No 38
>pfam08350 DUF1724 Domain of unknown function (DUF1724). This domain of unknown function has so far only been found at the C-terminus of archaean proteins, including several transcriptional regulators of the ArsR family (see pfam01022).
Probab=31.92 E-value=42 Score=15.22 Aligned_cols=29 Identities=17% Similarity=0.483 Sum_probs=22.2
Q ss_pred CCCEEEEEECCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 1757999975989899999999999999889
Q gi|254780391|r 105 YYEKVVFIINTDDQGSLEWGRAHWRSLKNSG 135 (141)
Q Consensus 105 ~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G 135 (141)
+|.+ =.|+ ..+|.+++.|++-|.+||++-
T Consensus 33 ~~d~-~~li-S~e~~Al~WG~eLF~yyk~~s 61 (64)
T pfam08350 33 RFDH-ESLI-SFEPSALKWGEELFEYYKDRS 61 (64)
T ss_pred CCCC-CCEE-ECCHHHHHHHHHHHHHHHHHC
T ss_conf 4446-5337-768789899999999999746
No 39
>PRK05580 primosome assembly protein PriA; Validated
Probab=31.85 E-value=42 Score=15.21 Aligned_cols=50 Identities=12% Similarity=0.017 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHC-CCCCCCCCCCCC
Q ss_conf 89999999999997798499982998999999998521-882333133224
Q gi|254780391|r 13 WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWT-WKKDGFLPHGVD 62 (141)
Q Consensus 13 ~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~-~~~~sFiPH~~~ 62 (141)
..+...+++++++++|++++|++|+.....++-+.|=. |...-.+=|+-.
T Consensus 199 KTevYl~li~~~l~~GkqvLiLvPEI~lt~q~~~rl~~~fg~~v~v~HS~l 249 (699)
T PRK05580 199 KTEVYLQAIAEALAQGKQALVLVPEIALTPQLLARFRARFGARVAVLHSGL 249 (699)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf 799999999999973997899917678789999999987099579964889
No 40
>KOG3350 consensus
Probab=31.25 E-value=43 Score=15.15 Aligned_cols=40 Identities=15% Similarity=0.227 Sum_probs=32.5
Q ss_pred HHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 99999977984999829989999999985218823331332
Q gi|254780391|r 20 LLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHG 60 (141)
Q Consensus 20 L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~ 60 (141)
..-|.+.++++-+|+|.-+-+.+.++++| .....||.|-.
T Consensus 156 ~tik~L~r~~~kvilCtGeimee~~s~~l-~~~~~sF~PeH 195 (217)
T KOG3350 156 ETIKRLQRNQKKVILCTGEIMEEWASALL-PVLKCSFRPEH 195 (217)
T ss_pred HHHHHHHCCCCEEEEECHHHHHHHHHHHH-HHHHCCCCCHH
T ss_conf 99999706885399834067689999875-33210013544
No 41
>cd00127 DSPc Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
Probab=30.41 E-value=45 Score=15.07 Aligned_cols=21 Identities=33% Similarity=0.562 Sum_probs=11.7
Q ss_pred HHHHHHHHHHCCCEEEEEECC
Q ss_conf 999999999779849998299
Q gi|254780391|r 17 LLVLLQDEYEKGKRVSVQCGS 37 (141)
Q Consensus 17 ~~~L~~K~~~~~~ri~I~~~d 37 (141)
++..++++.++|.+|+|+|..
T Consensus 70 ~~~fI~~~~~~~~~VLVHC~~ 90 (139)
T cd00127 70 AVDFIDDAREKGGKVLVHCLA 90 (139)
T ss_pred HHHHHHHHHHHCCCEEEECCC
T ss_conf 999999999728968998998
No 42
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=28.75 E-value=48 Score=14.89 Aligned_cols=131 Identities=15% Similarity=0.210 Sum_probs=68.4
Q ss_pred EEEEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHH--------HHHHHHHCCCCC--CCCCCCCCCCCCCCC----
Q ss_conf 799631674899999999999977984999829989999--------999985218823--331332247776544----
Q gi|254780391|r 4 LLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRD--------SLNEYLWTWKKD--GFLPHGVDVGDEGDF---- 69 (141)
Q Consensus 4 v~FY~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~--------~lD~~LW~~~~~--sFiPH~~~~~~~~~~---- 69 (141)
|.=|........-+-..+.+.+.+|+++++.|+=.+..+ .+-+.||++=++ -.|=||....++-+.
T Consensus 449 I~T~~i~~~~~~~v~e~i~~ei~~GrQaY~VcPLIeeSE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~ 528 (677)
T COG1200 449 ITTVVIPHERRPEVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEA 528 (677)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHH
T ss_conf 08999644447999999999997499799995253543311365499999999987054636777568986779999999
Q ss_pred -CC-CCEEEEECC----CCCCCCCCEEEEEECCCC-CCCHHH----------CCCEEEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf -42-206998328----667899819999816877-821131----------1757999975989899999999999999
Q gi|254780391|r 70 -SS-FQPVLLTIS----SLNANTSTIRFLVDEASM-HIGDVD----------YYEKVVFIINTDDQGSLEWGRAHWRSLK 132 (141)
Q Consensus 70 -~~-~~PV~i~~~----~~~~~~~~~~~linl~~~-~p~~~~----------~f~rvieiv~~~d~~~~~~aR~rwk~yk 132 (141)
.+ ..-|++++. +-+.+++.+.+.-| +.- -.+.+. .=.-|+.+.. .+.. ..|++|.+..+
T Consensus 529 Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~-AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~--~~~~-~~a~~RL~im~ 604 (677)
T COG1200 529 FKEGEIDILVATTVIEVGVDVPNATVMVIEN-AERFGLAQLHQLRGRVGRGDLQSYCVLLYK--PPLS-EVAKQRLKIMR 604 (677)
T ss_pred HHCCCCCEEEEEEEEEECCCCCCCEEEEEEC-HHHHHHHHHHHHCCCCCCCCCCEEEEEEEC--CCCC-HHHHHHHHHHH
T ss_conf 9808876899813899523578870799965-433037888875265578875448999967--9877-56899999887
Q ss_pred H--CCCCC
Q ss_conf 8--89986
Q gi|254780391|r 133 N--SGYAP 138 (141)
Q Consensus 133 ~--~G~~~ 138 (141)
+ .||.+
T Consensus 605 ~t~DGF~I 612 (677)
T COG1200 605 ETTDGFVI 612 (677)
T ss_pred HCCCCCEE
T ss_conf 44876010
No 43
>PRK06196 oxidoreductase; Provisional
Probab=27.23 E-value=51 Score=14.73 Aligned_cols=64 Identities=13% Similarity=0.121 Sum_probs=35.1
Q ss_pred HHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCC
Q ss_conf 977984999829989999999985218823331332247776544422069983286678998199998168778
Q gi|254780391|r 25 YEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMH 99 (141)
Q Consensus 25 ~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~~~~~~~~~~~~linl~~~~ 99 (141)
.+.|.+|++.|.|.+.+++.-+.+ +...|++=-+. ... -|-=..+.-......+++|||-+...
T Consensus 47 a~~Ga~Vil~~R~~~k~~~a~~~i---~~~~~~~lDLs-----~~~---sVr~~a~~~~~~~~~lDvLInNAGi~ 110 (316)
T PRK06196 47 AQAGAHVVVPARRPDAAREALAGI---DGVEVVALDLA-----DLA---SVRAFAERFLDSGRRIDILINNAGVM 110 (316)
T ss_pred HHCCCEEEEEECCHHHHHHHHHHH---CCCCEEECCCC-----CHH---HHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf 978998999949999999999874---17857983688-----999---99999999997579832999578767
No 44
>KOG0391 consensus
Probab=27.08 E-value=51 Score=14.71 Aligned_cols=36 Identities=28% Similarity=0.360 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHH
Q ss_conf 899999999999977984999829989999999985
Q gi|254780391|r 13 WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYL 48 (141)
Q Consensus 13 ~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~L 48 (141)
.+++++-|+.+-+..|+|++|++....++..|-.+|
T Consensus 1261 KLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLEqFL 1296 (1958)
T KOG0391 1261 KLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFL 1296 (1958)
T ss_pred HHHHHHHHHHHHHHCCCEEEEHHHHHHHHHHHHHHH
T ss_conf 599999999999855854885168899999999998
No 45
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=26.87 E-value=52 Score=14.69 Aligned_cols=53 Identities=17% Similarity=0.237 Sum_probs=32.7
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHH
Q ss_conf 9983286678998199998168778211311757999975989899999999999
Q gi|254780391|r 75 VLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWR 129 (141)
Q Consensus 75 V~i~~~~~~~~~~~~~~linl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk 129 (141)
+.+..+-.+.++ -++---|....|-+.-.|.+.+.+||++|+..++.|...+.
T Consensus 91 ~tl~~DI~d~~G--~via~aGt~vNPLd~v~~~~~LvF~DgdD~~Qv~Wa~~~~~ 143 (210)
T PRK13738 91 VRLAADIRDNEG--RVFARQGEVMNPLQYVPFNQTLYFINGDDPAQVAWMKRQTP 143 (210)
T ss_pred EEECCCCCCCCC--CEEECCCCEECCCCCCCCCCEEEEEECCCHHHHHHHHHHCC
T ss_conf 884575238999--89975887778641246887289995989999999997400
No 46
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=26.32 E-value=53 Score=14.63 Aligned_cols=118 Identities=15% Similarity=0.101 Sum_probs=56.2
Q ss_pred EEECCCCH---HHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC------CCCCCCCEEE
Q ss_conf 96316748---99999999999977984999829989999999985218823331332247776------5444220699
Q gi|254780391|r 6 FYRFKNDW---EYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDE------GDFSSFQPVL 76 (141)
Q Consensus 6 FY~l~~~~---~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~------~~~~~~~PV~ 76 (141)
+|+..++. ...++.|+.+. ...+++|+|.+.+.++.|...|=...-....=|+-..... .-......|+
T Consensus 224 ~~~~~~~~~~k~~~L~~ll~~~--~~~k~iIF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~q~~R~~~l~~F~~g~~~vL 301 (417)
T PRK11192 224 WYYRADDLEHKTALLCHLLKQE--EVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQKKRNEAIKRLTDGRVNVL 301 (417)
T ss_pred EEEEECCHHHHHHHHHHHHHCC--CCCCCEEEECCHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEE
T ss_conf 9999376899999999998534--76652153112466768988653148835754001799999999999976999899
Q ss_pred EECCC--CCCCCCCEEEEEECCCCCCCHHHCC-------------CEEEEEECCCCHHHHHHHHHHH
Q ss_conf 83286--6789981999981687782113117-------------5799997598989999999999
Q gi|254780391|r 77 LTISS--LNANTSTIRFLVDEASMHIGDVDYY-------------EKVVFIINTDDQGSLEWGRAHW 128 (141)
Q Consensus 77 i~~~~--~~~~~~~~~~linl~~~~p~~~~~f-------------~rvieiv~~~d~~~~~~aR~rw 128 (141)
++++- ...+-.++...||- ..|.....| ..++-+|. .+|...-..=++|
T Consensus 302 VaTDvaaRGiDi~~V~~VIny--d~P~~~~~YvHRiGRTGR~G~~G~ait~v~-~~d~~~~~~ie~~ 365 (417)
T PRK11192 302 VATDVAARGIDIDDISHVINF--DMPRSADTYLHRIGRTGRAGKKGTAISLVE-AHDHLLLGKIERY 365 (417)
T ss_pred EECCHHHCCCCCCCCCEEEEE--CCCCCHHHHHHHCCHHHCCCCCEEEEEEEC-HHHHHHHHHHHHH
T ss_conf 981243467770469889997--999988892330677234899548999874-8999999999999
No 47
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=26.13 E-value=53 Score=14.61 Aligned_cols=22 Identities=27% Similarity=0.579 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHCCCEEEEEECC
Q ss_conf 9999999999779849998299
Q gi|254780391|r 16 NLLVLLQDEYEKGKRVSVQCGS 37 (141)
Q Consensus 16 ~~~~L~~K~~~~~~ri~I~~~d 37 (141)
.++..++++...|.+|+|+|..
T Consensus 66 ~~~~fI~~~~~~~~~VLVHC~~ 87 (138)
T smart00195 66 EAVEFIEDAEKKGGKVLVHCQA 87 (138)
T ss_pred HHHHHHHHHHHCCCEEEEECCC
T ss_conf 9999999999769979999998
No 48
>KOG0327 consensus
Probab=25.89 E-value=54 Score=14.58 Aligned_cols=108 Identities=19% Similarity=0.160 Sum_probs=67.3
Q ss_pred EEEEECC--CCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC------CCCCCEE
Q ss_conf 7996316--7489999999999997798499982998999999998521882333133224777654------4422069
Q gi|254780391|r 4 LLFYRFK--NDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGD------FSSFQPV 75 (141)
Q Consensus 4 v~FY~l~--~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~------~~~~~PV 75 (141)
.-||... ......+|.|.. .-....|+|...+.+..|++.|=.+.-+...=|+-..++.-. ....+-|
T Consensus 241 kq~~i~v~k~~k~~~l~dl~~----~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~i~~d~~q~~R~~~~~~f~~g~srv 316 (397)
T KOG0327 241 KQFYINVEKEEKLDTLCDLYR----RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRV 316 (397)
T ss_pred EEEEEECCCCCCCCHHHHHHH----HHHCCEEEECCHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCCEE
T ss_conf 022201054311227999998----6431057851045677789998627733787634643003468999864587237
Q ss_pred EEECCCCCC--CCCCEEEEEECCCCCCCH-------------HHCCCEEEEEECCCC
Q ss_conf 983286678--998199998168778211-------------311757999975989
Q gi|254780391|r 76 LLTISSLNA--NTSTIRFLVDEASMHIGD-------------VDYYEKVVFIINTDD 117 (141)
Q Consensus 76 ~i~~~~~~~--~~~~~~~linl~~~~p~~-------------~~~f~rvieiv~~~d 117 (141)
+|+++-..+ .-..+..++|. ..|.. |.+=...+-+|...|
T Consensus 317 lIttdl~argidv~~~slviny--dlP~r~~~yihR~gr~gr~grkg~~in~v~~~d 371 (397)
T KOG0327 317 LITTDLLARGIDVQQVSLVVNY--DLPARKENYIHRIGRAGRFGRKGVAINFVTEED 371 (397)
T ss_pred EEECCCCCCCCCHHHCCEEEEE--CCCCCHHHHHHHCCCCCCCCCCCEEEEEEHHHH
T ss_conf 7412212465411101225650--165206666652554565677713555201756
No 49
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=25.53 E-value=55 Score=14.54 Aligned_cols=129 Identities=15% Similarity=0.190 Sum_probs=61.7
Q ss_pred EECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHH--------HHHHHHHC-CCC-CCCCCCCCCCCCCCC------CC
Q ss_conf 631674899999999999977984999829989999--------99998521-882-333133224777654------44
Q gi|254780391|r 7 YRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRD--------SLNEYLWT-WKK-DGFLPHGVDVGDEGD------FS 70 (141)
Q Consensus 7 Y~l~~~~~~~~~~L~~K~~~~~~ri~I~~~d~~~~~--------~lD~~LW~-~~~-~sFiPH~~~~~~~~~------~~ 70 (141)
|....+....+...+.+.+.+|++++|+|+-.+..+ ..-+.|-. |+. .--+-||.....+-+ ..
T Consensus 446 ~~~~~~~~~~~~~~i~~~~~~g~q~y~v~p~ieese~~~~~~~~~~~~~l~~~~~~~~v~~~hG~m~~~ek~~~m~~F~~ 525 (677)
T PRK10917 446 VVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQKALPELRVGLLHGRMKPAEKDAVMAAFKA 525 (677)
T ss_pred EEECHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHC
T ss_conf 99762568999999999997599289994131123320177799999999844899759983078987899999999983
Q ss_pred CCCEEEEECC----CCCCCCCCEEEEEECCCCC-CCHH---------HCCCEEEEEECCCCHHHHHHHHHHHHHHHH--C
Q ss_conf 2206998328----6678998199998168778-2113---------117579999759898999999999999998--8
Q gi|254780391|r 71 SFQPVLLTIS----SLNANTSTIRFLVDEASMH-IGDV---------DYYEKVVFIINTDDQGSLEWGRAHWRSLKN--S 134 (141)
Q Consensus 71 ~~~PV~i~~~----~~~~~~~~~~~linl~~~~-p~~~---------~~f~rvieiv~~~d~~~~~~aR~rwk~yk~--~ 134 (141)
....|++++. +-+.+++.+.+.-| ++.. .+.+ +..+=.|.++... + .-..|++|-+...+ .
T Consensus 526 g~~~iLvsTtviEvGvdvpna~~mvi~~-aerfGlsqLhQLRGRVgRg~~~~~c~l~~~~-~-~~~~~~~Rl~~~~~~~d 602 (677)
T PRK10917 526 GEIDILVATTVIEVGVDVPNATVMVIEN-AERFGLAQLHQLRGRVGRGAAQSYCVLLYKD-P-LSETARERLKIMRETND 602 (677)
T ss_pred CCCCEEEECCEEECCCCCCCCCEEEEEC-CCCCCHHHHHHHCCCCCCCCCCEEEEEEECC-C-CCHHHHHHHHHHHHHCC
T ss_conf 9999999898975586788885899977-0105367887742743678884589998389-9-99789999999998587
Q ss_pred CCCC
Q ss_conf 9986
Q gi|254780391|r 135 GYAP 138 (141)
Q Consensus 135 G~~~ 138 (141)
||.+
T Consensus 603 Gf~i 606 (677)
T PRK10917 603 GFEI 606 (677)
T ss_pred CHHH
T ss_conf 4999
No 50
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=25.51 E-value=55 Score=14.54 Aligned_cols=40 Identities=25% Similarity=0.424 Sum_probs=33.9
Q ss_pred HHHHHHHHHHCCCEEEEEE-------------CCHHHHHHHH--HHHHCCCCCCCC
Q ss_conf 9999999997798499982-------------9989999999--985218823331
Q gi|254780391|r 17 LLVLLQDEYEKGKRVSVQC-------------GSERVRDSLN--EYLWTWKKDGFL 57 (141)
Q Consensus 17 ~~~L~~K~~~~~~ri~I~~-------------~d~~~~~~lD--~~LW~~~~~sFi 57 (141)
+-+|.....+.|.||-|.+ +|.-+++.++ ..||+ +|.-||
T Consensus 55 ~~~l~~~lrRrG~~VaViAvDP~SPfTGGsiLGDr~Rm~~~asrkqlW~-dPg~FI 109 (333)
T TIGR00750 55 VEKLIMELRRRGLKVAVIAVDPSSPFTGGSILGDRLRMQRLASRKQLWT-DPGVFI 109 (333)
T ss_pred HHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHC-CCCCEE
T ss_conf 9999899976597689998879759755145456887754422223322-898567
No 51
>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]
Probab=25.00 E-value=56 Score=14.48 Aligned_cols=47 Identities=23% Similarity=0.204 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 999999999999779849998299899999999852188233313322477
Q gi|254780391|r 14 EYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVG 64 (141)
Q Consensus 14 ~~~~~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~ 64 (141)
..+...-+......|+.|+|-+.+.+.++.++.+|=. .=|||.+...
T Consensus 415 ~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~----~~i~h~VLNA 461 (822)
T COG0653 415 FKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRK----AGIPHNVLNA 461 (822)
T ss_pred HHHHHHHHHHHHHCCCCEEECCCCEECCHHHHHHHHH----CCCCCEEECC
T ss_conf 9999999999996599889767314225267789986----4997404404
No 52
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=23.11 E-value=61 Score=14.26 Aligned_cols=103 Identities=16% Similarity=0.220 Sum_probs=57.0
Q ss_pred HHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEC--
Q ss_conf 999999997798499982998999999998521882333133224777654442206998328667899819999816--
Q gi|254780391|r 18 LVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDE-- 95 (141)
Q Consensus 18 ~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~~~~~~~~~~~~linl-- 95 (141)
+-++.+..++|..+-+.....---.-.+++-+.. ..|+-+.- +-+.++.+ -.+ +.+ +..+.
T Consensus 154 p~l~~el~~kg~~vslIlT~~V~er~~~~~~~el--~~~l~~~n-----------~~~~v~~~-~~~--~~~-~VTD~f~ 216 (260)
T COG4742 154 PSLYLELAEKGIDVSLILTEPVFERLKSDYKEEL--KEFLKLEN-----------TKLYVCDG-IKL--ASL-IVTDRFM 216 (260)
T ss_pred HHHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHH--HHHHHCCC-----------CEEEEECC-CCE--EEE-EEECHHH
T ss_conf 7999999975997799956889999999989999--99984578-----------74998469-854--268-8861146
Q ss_pred CCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 87782113117579999759898999999999999998899860
Q gi|254780391|r 96 ASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPD 139 (141)
Q Consensus 96 ~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~ 139 (141)
+-..+..=.+|.+-. ++ +-++.++++|++-|.+|+++--.+.
T Consensus 217 ~L~Lf~k~G~~d~~~-l~-s~e~~Ai~WG~eLf~yy~~~S~~i~ 258 (260)
T COG4742 217 ALSLFDKDGRYDRQY-LV-SFEPSALKWGEELFEYYKDRSEEIK 258 (260)
T ss_pred HHCCCCCCCCCCCCE-EE-ECCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 400415699807641-57-5586898999999999997436414
No 53
>cd02429 PTH2_like Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes. There is no functional information for this eukaryote-specific subgroup.
Probab=22.64 E-value=62 Score=14.20 Aligned_cols=48 Identities=13% Similarity=0.228 Sum_probs=36.0
Q ss_pred HHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf 97798499982998999999998521882333133224777654442206998328
Q gi|254780391|r 25 YEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTIS 80 (141)
Q Consensus 25 ~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~ 80 (141)
+..=++|..-++|+.++..|.+.|= ++.|-|-++.+.++. .|.-|++.
T Consensus 52 ld~MhKVVLe~~~e~~L~~Lse~L~----~~~i~hklWiEQPEn----ipTclA~k 99 (116)
T cd02429 52 LDNMHKVVLEVPDEAALKNLSSKLT----ENSIKHKLWIEQPEN----IPTCIALK 99 (116)
T ss_pred HHHCEEEEEECCCHHHHHHHHHHHH----HCCCCEEEEEECCCC----CCEEEEEC
T ss_conf 4002489896499899999999998----769743445506788----74045644
No 54
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=22.12 E-value=64 Score=14.14 Aligned_cols=46 Identities=24% Similarity=0.179 Sum_probs=24.1
Q ss_pred HHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 9999999977984999829989999999985218823331332247
Q gi|254780391|r 18 LVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDV 63 (141)
Q Consensus 18 ~~L~~K~~~~~~ri~I~~~d~~~~~~lD~~LW~~~~~sFiPH~~~~ 63 (141)
..+..+....|.+++|.|..-..|..+=+.|=.-.+..++=|++..
T Consensus 430 ~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~ 475 (733)
T COG1203 430 IELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFT 475 (733)
T ss_pred HHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHCCCCCEEEEECCCC
T ss_conf 6556776425882899992789999999998555895799886355
No 55
>COG4063 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A [Coenzyme metabolism]
Probab=21.78 E-value=41 Score=15.30 Aligned_cols=89 Identities=15% Similarity=0.161 Sum_probs=51.3
Q ss_pred HHHHHHC-----CCEEEEEECCHHHHHHHH---HHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCEEEE
Q ss_conf 9999977-----984999829989999999---98521882333133224777654442206998328667899819999
Q gi|254780391|r 21 LQDEYEK-----GKRVSVQCGSERVRDSLN---EYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFL 92 (141)
Q Consensus 21 ~~K~~~~-----~~ri~I~~~d~~~~~~lD---~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~~~~~~~~~~~~l 92 (141)
+||.... ..|-+|+|..+-+.+--- ..||+ +++. +.. =+|+....-| ++
T Consensus 58 IEKvianvIsNpNiRflvvcGaEv~GHitGq~~~alh~--------NGvd----d~g-----~IiGa~GAIP------yi 114 (238)
T COG4063 58 IEKVIANVISNPNIRFLVVCGAEVQGHITGQSMKALHA--------NGVD----DKG-----RIIGATGAIP------YI 114 (238)
T ss_pred HHHHHHHHCCCCCCEEEEEECCHHCCEEHHHHHHHHHH--------CCCC----CCC-----CEECCCCCCH------HH
T ss_conf 89998875069970599994522304123688999996--------3888----668-----5732445652------34
Q ss_pred EECCCCCCCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 8168778211311757999975989899999999999999889
Q gi|254780391|r 93 VDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSG 135 (141)
Q Consensus 93 inl~~~~p~~~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G 135 (141)
=|. +-+...||+|.+|+||--|-+....-+.+-+.|.+.+
T Consensus 115 ENi---~~eaveRfqqqvelvdlid~eD~~~I~~~v~ecv~kd 154 (238)
T COG4063 115 ENI---PDEAVERFQQQVELVDLIDVEDPDEITAKVEECVEKD 154 (238)
T ss_pred HCC---CHHHHHHHHHHEEEEHHCCCCCHHHHHHHHHHHHHCC
T ss_conf 229---9999999987700000216678799999999998559
No 56
>KOG3661 consensus
Probab=21.05 E-value=23 Score=16.86 Aligned_cols=96 Identities=18% Similarity=0.314 Sum_probs=58.7
Q ss_pred CCCEEEEEECCHHHHHH-HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCC---CEEEEEECCCCCCCH
Q ss_conf 79849998299899999-99985218823331332247776544422069983286678998---199998168778211
Q gi|254780391|r 27 KGKRVSVQCGSERVRDS-LNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTS---TIRFLVDEASMHIGD 102 (141)
Q Consensus 27 ~~~ri~I~~~d~~~~~~-lD~~LW~~~~~sFiPH~~~~~~~~~~~~~~PV~i~~~~~~~~~~---~~~~linl~~~~p~~ 102 (141)
...||+|++.|.-.-+- ..|.||+-- ........+|.++.+.+.+..+ +-++-+.+.-..|++
T Consensus 420 aSErvIVRAtNPGsFEp~d~Dv~Wqrn-------------gg~l~t~g~v~vG~~~~~p~a~LtV~Gdiy~sGr~m~PSD 486 (1019)
T KOG3661 420 ASERVIVRATNPGSFEPQDSDVLWQRN-------------GGPLTTFGHVRVGINTDRPDAALTVHGDIYVSGRLMHPSD 486 (1019)
T ss_pred CCCEEEEECCCCCCCCCCCCCHHHHHC-------------CCCCEECCCEEEECCCCCCCCCEEEECCEEEECEECCHHH
T ss_conf 144169963688878887542123215-------------8842421665650367787521477143676123326222
Q ss_pred HHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 31175799997598989999999999999988998603
Q gi|254780391|r 103 VDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSGYAPDV 140 (141)
Q Consensus 103 ~~~f~rvieiv~~~d~~~~~~aR~rwk~yk~~G~~~~~ 140 (141)
+.-=+.|-| ++ .-|......|.|--.|+ |.|||
T Consensus 487 iRlKe~itE-~~-t~ealenl~klR~VdYr---YKPEv 519 (1019)
T KOG3661 487 IRLKEHITE-VD-TTEALENLSKLRLVDYR---YKPEV 519 (1019)
T ss_pred HHHHHHHCH-HH-HHHHHHHHHHHEEEEEE---ECHHH
T ss_conf 006664000-02-89999876642533453---07034
No 57
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase; InterPro: IPR010039 This entry describes a small family of highly conserved proteins (>60 0dentity). Two of these, BcbF and EcbF of Pasteurella multocida are believed to be part of the capsule polysaccharide biosynthesis machinery because they are co-transcribed from a locus devoted to that purpose . In P. multocida there are six different variant capsules (A-F), and these proteins are found only in B and E. The other two species in which this gene is (currently) found are both also pathogenic. These proteins are also members of the IIIC subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterised enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in this subfamily..
Probab=20.54 E-value=49 Score=14.81 Aligned_cols=15 Identities=20% Similarity=0.180 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHCCCC
Q ss_conf 999999999988998
Q gi|254780391|r 123 WGRAHWRSLKNSGYA 137 (141)
Q Consensus 123 ~aR~rwk~yk~~G~~ 137 (141)
+-=++-|+||+.||+
T Consensus 28 ~Vi~~L~~YK~lGF~ 42 (126)
T TIGR01689 28 AVIEKLREYKALGFE 42 (126)
T ss_pred HHHHHHHHHHHCCCE
T ss_conf 999999988746878
Done!