Query 047352
Match_columns 182
No_of_seqs 165 out of 857
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 10:16:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02689 Herpes_Helicase: Heli 99.7 1.2E-17 2.6E-22 160.4 5.5 60 56-115 730-791 (818)
2 KOG0987 DNA helicase PIF1/RRM3 99.6 4.5E-17 9.7E-22 152.5 1.7 87 2-88 454-540 (540)
3 PHA03311 helicase-primase subu 99.5 2.1E-14 4.5E-19 138.4 4.8 60 57-116 741-802 (828)
4 COG0507 RecD ATP-dependent exo 99.2 1.1E-11 2.3E-16 118.4 2.4 90 4-109 576-668 (696)
5 TIGR02768 TraA_Ti Ti-type conj 99.1 1.4E-10 3E-15 112.6 5.5 89 3-113 620-709 (744)
6 TIGR01448 recD_rel helicase, p 98.9 1.6E-09 3.6E-14 104.9 5.4 90 3-114 599-698 (720)
7 PRK13826 Dtr system oriT relax 98.9 2.3E-09 5E-14 108.0 5.7 93 3-112 646-739 (1102)
8 PRK13889 conjugal transfer rel 98.8 2.7E-09 5.8E-14 106.6 4.2 88 3-110 613-701 (988)
9 TIGR01447 recD exodeoxyribonuc 98.8 1.6E-08 3.4E-13 96.3 7.0 91 3-114 477-571 (586)
10 PRK10875 recD exonuclease V su 98.8 6.7E-09 1.5E-13 99.3 4.4 94 3-115 493-590 (615)
11 PF13538 UvrD_C_2: UvrD-like h 98.0 3.6E-07 7.9E-12 66.4 -3.5 45 60-104 50-99 (104)
12 PRK13709 conjugal transfer nic 97.5 0.00012 2.7E-09 77.3 5.2 95 3-116 1347-1447(1747)
13 TIGR02760 TraI_TIGR conjugativ 97.1 0.0003 6.5E-09 75.2 2.8 88 3-107 1401-1491(1960)
14 PRK14712 conjugal transfer nic 97.1 0.0011 2.3E-08 70.0 6.4 96 3-117 1218-1319(1623)
15 PF01443 Viral_helicase1: Vira 96.4 0.0019 4E-08 52.7 2.3 38 67-104 184-228 (234)
16 TIGR02760 TraI_TIGR conjugativ 95.0 0.023 4.9E-07 61.3 4.1 93 3-116 759-852 (1960)
17 PRK13709 conjugal transfer nic 81.8 1.7 3.7E-05 47.1 4.3 92 3-113 723-816 (1747)
18 PF13087 AAA_12: AAA domain; P 74.3 0.39 8.5E-06 38.1 -2.4 39 66-104 144-191 (200)
19 TIGR01073 pcrA ATP-dependent D 73.7 1.7 3.6E-05 42.4 1.4 43 68-112 552-610 (726)
20 PRK10919 ATP-dependent DNA hel 72.0 1.4 2.9E-05 43.0 0.3 44 68-113 554-612 (672)
21 PF13361 UvrD_C: UvrD-like hel 69.3 3.2 7E-05 34.8 2.0 18 68-85 290-307 (351)
22 TIGR01075 uvrD DNA helicase II 67.1 3 6.4E-05 40.7 1.5 43 68-112 551-609 (715)
23 PRK11773 uvrD DNA-dependent he 59.8 4.3 9.4E-05 39.7 1.1 43 68-112 556-614 (721)
24 PRK13909 putative recombinatio 53.7 7.2 0.00016 39.4 1.6 17 68-84 610-626 (910)
25 KOG3310 Riboflavin synthase al 51.7 17 0.00037 30.5 3.2 21 8-28 43-63 (210)
26 COG1074 RecB ATP-dependent exo 41.1 15 0.00032 38.3 1.5 18 68-85 746-763 (1139)
27 TIGR02784 addA_alphas double-s 40.6 15 0.00032 38.0 1.4 17 68-84 778-794 (1141)
28 TIGR00609 recB exodeoxyribonuc 34.8 21 0.00047 36.8 1.6 18 68-85 655-672 (1087)
29 TIGR02785 addA_Gpos recombinat 33.0 23 0.0005 37.1 1.5 18 68-85 785-802 (1232)
30 PF08247 ENOD40: ENOD40 protei 28.1 35 0.00076 16.5 0.9 11 64-74 2-12 (12)
31 PF00677 Lum_binding: Lumazine 27.4 77 0.0017 22.7 3.0 23 8-30 41-63 (85)
32 PRK10876 recB exonuclease V su 24.6 40 0.00087 35.4 1.5 17 68-84 738-754 (1181)
33 TIGR01074 rep ATP-dependent DN 21.7 51 0.0011 31.7 1.5 43 68-112 554-611 (664)
34 COG0307 RibC Riboflavin syntha 21.7 99 0.0022 26.4 3.1 34 9-42 41-83 (204)
35 PLN02741 riboflavin synthase 20.7 1.1E+02 0.0025 25.5 3.2 34 9-42 44-86 (194)
36 PF14732 UAE_UbL: Ubiquitin/SU 20.4 1.3E+02 0.0028 21.7 3.1 16 7-22 57-72 (87)
37 PRK11054 helD DNA helicase IV; 20.1 55 0.0012 32.4 1.4 18 68-85 591-608 (684)
No 1
>PF02689 Herpes_Helicase: Helicase; InterPro: IPR003840 This entry consists of DNA helicases from a number of different organisms.; GO: 0004386 helicase activity, 0005524 ATP binding
Probab=99.70 E-value=1.2e-17 Score=160.44 Aligned_cols=60 Identities=40% Similarity=0.475 Sum_probs=56.3
Q ss_pred cceeeeeccceeeeeeccccccceeeEEEECCCC-CCCCCcE-EEEEeecCCCCeEEcccCc
Q 047352 56 LNRRQLPLAPCFAMTINKSQGQSLKYVGLYLPKQ-VFTNVFV-KALTNLLTEKTTCSLHNAL 115 (182)
Q Consensus 56 ~~R~QfPl~la~A~TIhKsQG~Tl~~v~i~l~~~-~F~~Gq~-VAlSRv~s~~gL~l~~~~~ 115 (182)
.++.|||+.++|||||||||||||++|+||++++ +|+|||+ |||||+++++||++..+..
T Consensus 730 ~t~~qfpi~~~~AmTIhKSQG~SL~kV~i~l~~~~~F~~gq~YVAlSRvts~~~L~i~~nPl 791 (818)
T PF02689_consen 730 CTRVQFPISSAFAMTIHKSQGQSLDKVAIDLGKPKVFSHGQLYVALSRVTSLEGLKINFNPL 791 (818)
T ss_pred eeecCCcceeeEEEEEeHhhccccceEEEECCCCcccCCCceEEEEEeeccccccEEecCcc
Confidence 5899999999999999999999999999999998 9999999 9999999999999865544
No 2
>KOG0987 consensus DNA helicase PIF1/RRM3 [Cell cycle control, cell division, chromosome partitioning]
Probab=99.64 E-value=4.5e-17 Score=152.52 Aligned_cols=87 Identities=53% Similarity=0.905 Sum_probs=83.7
Q ss_pred CCCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceee
Q 047352 2 LNQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKY 81 (182)
Q Consensus 2 LDv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~ 81 (182)
+|+..|||||||+.|+.+....+.+++++|+..|+.|.|||+.+.+++...++.+.|+|||+.+||||||||||||||.+
T Consensus 454 l~~~~gl~~~trl~it~l~~~~~~~~~~~g~r~~~~v~i~r~~~~~~~~~~~~~~~r~qfp~~~~~a~~i~ksqgqsl~~ 533 (540)
T KOG0987|consen 454 LDPKGGLCNGTRLQITLLGVFLLEARIVTGSRAGKFVLIPRFDISPSDTNLPFRMRRRQFPLSLAFAMTINKSQGQSLEK 533 (540)
T ss_pred cchhhhhhccchhhhhcccCcccceeeeecccccceEEecccccCccccCcccccccccccceeeeecccChhhhhhHHh
Confidence 58899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCC
Q 047352 82 VGLYLPK 88 (182)
Q Consensus 82 v~i~l~~ 88 (182)
|++||++
T Consensus 534 v~~~l~~ 540 (540)
T KOG0987|consen 534 VGLYLPR 540 (540)
T ss_pred hcCcCCC
Confidence 9999864
No 3
>PHA03311 helicase-primase subunit BBLF4; Provisional
Probab=99.48 E-value=2.1e-14 Score=138.35 Aligned_cols=60 Identities=25% Similarity=0.260 Sum_probs=54.5
Q ss_pred ceeeeeccceeeeeeccccccceeeEEEECCCC-CCCCCcE-EEEEeecCCCCeEEcccCcc
Q 047352 57 NRRQLPLAPCFAMTINKSQGQSLKYVGLYLPKQ-VFTNVFV-KALTNLLTEKTTCSLHNALE 116 (182)
Q Consensus 57 ~R~QfPl~la~A~TIhKsQG~Tl~~v~i~l~~~-~F~~Gq~-VAlSRv~s~~gL~l~~~~~~ 116 (182)
+---|=++++|||||||||||||++|+|+++++ .|+|||+ ||+||+++++||++..+..+
T Consensus 741 tt~DYGi~~~~AmTI~KSQG~sL~~V~i~f~~~k~~~~gq~YVAlSR~~s~~~L~i~~np~~ 802 (828)
T PHA03311 741 TTVDYGISSKLAMTIAKSQGLSLDKVAICFGNHKNLKLSHVYVAMSRVTSSNFLVMNLNPLR 802 (828)
T ss_pred eecccccchhheeeehHhhCCccceEEEECCCccccccCcEEEEEEeccCccccEEecCCcc
Confidence 344588999999999999999999999999887 9999999 99999999999999877553
No 4
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]
Probab=99.16 E-value=1.1e-11 Score=118.37 Aligned_cols=90 Identities=23% Similarity=0.299 Sum_probs=66.8
Q ss_pred CCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeEE
Q 047352 4 QIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYVG 83 (182)
Q Consensus 4 v~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v~ 83 (182)
...|+.||..|++..+...... ++.....+|..+.+ ..+.+.++.+|||||||||||.++++|.
T Consensus 576 ~~~~vfNGdiG~~~~~~~~~~~-~~~~~~~dg~~~~~---------------~~~~~~~~~~ayA~TIHKsQGSef~~v~ 639 (696)
T COG0507 576 RALGVFNGDIGVILSIVKRRQG-DVLVVDFDGREVVV---------------ARSELPELELAYAMTIHKSQGSEFDRVI 639 (696)
T ss_pred cccceecCccceEEeeccccCc-eEEEEecCCCEEEE---------------ehhhhhhhhhheeeeEecccCCCCCeEE
Confidence 3457999999999886433222 22222223332322 2477889999999999999999999999
Q ss_pred EECCC--CCCCCCcE-EEEEeecCCCCeE
Q 047352 84 LYLPK--QVFTNVFV-KALTNLLTEKTTC 109 (182)
Q Consensus 84 i~l~~--~~F~~Gq~-VAlSRv~s~~gL~ 109 (182)
+.|++ ++|+-+++ ||+||++..-.|.
T Consensus 640 v~l~~~~~~l~r~l~YtAiTRar~~l~l~ 668 (696)
T COG0507 640 VLLPSHSPMLSRELLYTAITRARDRLILY 668 (696)
T ss_pred EEcCCCchhhhhhHHHHHhhhhheeEEEE
Confidence 99975 47899999 9999999987776
No 5
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=99.07 E-value=1.4e-10 Score=112.61 Aligned_cols=89 Identities=21% Similarity=0.148 Sum_probs=68.5
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.|++||.+|+|+++..+.+.+++.. |..+.+|.-. --++.+|||+|||||||+|.++|
T Consensus 620 ~~~~gv~NGd~g~V~~i~~~~i~v~~~~----G~~v~~~~~~---------------~~~l~laYA~TvHKsQGst~~~v 680 (744)
T TIGR02768 620 NRDLGVKNGMLGTVEEIEDGRLVVQLDS----GELVIIPQAE---------------YDALDHGYATTIHKSQGVTVDRA 680 (744)
T ss_pred ccccCCcCCCEEEEEEecCCeEEEEECC----CCEEEECHHH---------------hCccCceEEeccccccCCccCcE
Confidence 5677999999999999987777666543 3455554211 12689999999999999999999
Q ss_pred EEECCCCCCCCCcE-EEEEeecCCCCeEEccc
Q 047352 83 GLYLPKQVFTNVFV-KALTNLLTEKTTCSLHN 113 (182)
Q Consensus 83 ~i~l~~~~F~~Gq~-VAlSRv~s~~gL~l~~~ 113 (182)
.+.. ...+...++ ||+||.+.. +.|...
T Consensus 681 iv~~-~~~l~r~llYvAiTRar~~--~~l~~~ 709 (744)
T TIGR02768 681 FVLA-SKSMDRHLAYVAMTRHRES--VQLYAG 709 (744)
T ss_pred EEec-CCccccchhhhhhhcccce--eEEEEc
Confidence 9874 558999999 999999764 455543
No 6
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=98.89 E-value=1.6e-09 Score=104.87 Aligned_cols=90 Identities=21% Similarity=0.254 Sum_probs=64.0
Q ss_pred CCCCCeeecceEEEEEcCCce------eeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccc
Q 047352 3 NQIEGLCNDTRLIVTRLGKWS------IGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQG 76 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~------i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG 76 (182)
|.+.|+.||..|+|+++..+. +.+.+ .|+.+.++. ++ + -.+.+|||+|||||||
T Consensus 599 ~~~~~v~NGdiG~I~~i~~~~~~~~~~i~v~f-----~g~~v~~~~-----~~--~--------~~l~lAYAiTvHKsQG 658 (720)
T TIGR01448 599 DYNNEIFNGDLGMIVKIEGAKQGKKDQVVVDF-----DGNEVELTR-----AE--L--------FNLTLAYATSIHKSQG 658 (720)
T ss_pred cchhccccCCeeEEEeccccccCCCceEEEEE-----CCeEEEEcH-----HH--h--------hhhhhhheeeehhccC
Confidence 456799999999999985432 22322 344443321 11 1 1588999999999999
Q ss_pred cceeeEEEECCC---CCCCCCcE-EEEEeecCCCCeEEcccC
Q 047352 77 QSLKYVGLYLPK---QVFTNVFV-KALTNLLTEKTTCSLHNA 114 (182)
Q Consensus 77 ~Tl~~v~i~l~~---~~F~~Gq~-VAlSRv~s~~gL~l~~~~ 114 (182)
.+.++|.+.++. .++....+ ||++|++. .+.|+...
T Consensus 659 Se~~~Vii~l~~~~~~~l~r~llYTAiTRAk~--~l~lvg~~ 698 (720)
T TIGR01448 659 SEFPTVILPIHTAHMRMLYRNLLYTALTRAKK--RVILVGSA 698 (720)
T ss_pred ccCCEEEEECCcccchhhhhchheeeeeeece--EEEEEECH
Confidence 999999998754 35777788 99999986 56666543
No 7
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=98.87 E-value=2.3e-09 Score=107.96 Aligned_cols=93 Identities=20% Similarity=0.144 Sum_probs=68.4
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.|+.||++|+|+++..+.+.+.+..|. .+..|.++. .. + --+.++||+|||||||.|.++|
T Consensus 646 d~~lgV~NGd~GtV~~i~~~~i~v~~d~g~-~~r~V~~~~-----~~--~--------~~ldhaYA~TVHKSQGsT~d~V 709 (1102)
T PRK13826 646 EGSLGVKNGMIGKVVEAAPNRIVAEIGEGE-HRRQVTVEQ-----RF--Y--------NNLDHGYATTIHKSQGATVDRV 709 (1102)
T ss_pred cCccCccCCCeEEEEEecCCeEEEEEcCCC-CceEEEech-----hh--c--------cchhheeeeeeecccccccceE
Confidence 456799999999999998777766654443 223343321 10 0 0278999999999999999999
Q ss_pred EEECCCCCCCCCcE-EEEEeecCCCCeEEcc
Q 047352 83 GLYLPKQVFTNVFV-KALTNLLTEKTTCSLH 112 (182)
Q Consensus 83 ~i~l~~~~F~~Gq~-VAlSRv~s~~gL~l~~ 112 (182)
.+..+ ..+....+ ||+||.+..-.|..-.
T Consensus 710 ~vl~s-~~ldR~llYVA~TRaR~~~~ly~~~ 739 (1102)
T PRK13826 710 KVLAS-LSLDRHLTYVAMTRHREDLQLYYGR 739 (1102)
T ss_pred EEecc-cccccchhHHhhccccceEEEEEch
Confidence 98765 46787788 9999998877666544
No 8
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=98.82 E-value=2.7e-09 Score=106.62 Aligned_cols=88 Identities=16% Similarity=0.111 Sum_probs=64.2
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.|+.||+.|+|+++..+.+.+++- .|..|.++. .+ + -.+.++||+|||||||+|.++|
T Consensus 613 d~~lgV~NGd~GtV~~I~~~~i~V~~d----~gr~V~~~~-----~~--~--------~~ldlaYA~TIHKSQGsT~d~V 673 (988)
T PRK13889 613 ERGLGVKNGTLGTIEQVSAQSMSVRLD----DGRSVAFDL-----KD--Y--------DRIDHGYAATIHKAQGMTVDRT 673 (988)
T ss_pred CCcCCEeCCCeEEEEEecCCeEEEEEC----CCeEEEecH-----HH--c--------CcccchhhhhhHHhcCCCCCeE
Confidence 456799999999999998876666653 234443321 11 0 1478999999999999999999
Q ss_pred EEECCCCCCCCCcE-EEEEeecCCCCeEE
Q 047352 83 GLYLPKQVFTNVFV-KALTNLLTEKTTCS 110 (182)
Q Consensus 83 ~i~l~~~~F~~Gq~-VAlSRv~s~~gL~l 110 (182)
.+.... .+....+ ||+||.+..--|..
T Consensus 674 ~vl~~~-~~~r~l~YVAiTRar~~v~l~~ 701 (988)
T PRK13889 674 HVLATP-GMDAHSSYVALSRHRDGVDLHY 701 (988)
T ss_pred EEeccc-ccccchhHHhhhhhhheEEEEe
Confidence 887643 5666678 99999996544443
No 9
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.
Probab=98.75 E-value=1.6e-08 Score=96.26 Aligned_cols=91 Identities=22% Similarity=0.202 Sum_probs=61.8
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.|+.||..|+|....+. +.+.+..+ .|+ +.++. +. . -.+.+|||||||||||.++++|
T Consensus 477 d~~~gl~NGdiG~i~~~~~~-~~v~f~~~--~g~-~~~~~-----~~--l--------~~~~~ayA~TvHKSQGsef~~V 537 (586)
T TIGR01447 477 DYTLGLFNGDIGVLLRDPDG-LTVWFHFA--DGS-KAVLP-----SR--L--------PNYETAFAMTVHKSQGSEFDHV 537 (586)
T ss_pred CcccCcCCCCeEEEEEeCCc-EEEEEEcC--CCe-EEech-----HH--c--------CccceEEEEEeeHhcCCcCCeE
Confidence 56779999999999875433 33333211 222 22211 10 0 1367899999999999999999
Q ss_pred EEECCC---CCCCCCcE-EEEEeecCCCCeEEcccC
Q 047352 83 GLYLPK---QVFTNVFV-KALTNLLTEKTTCSLHNA 114 (182)
Q Consensus 83 ~i~l~~---~~F~~Gq~-VAlSRv~s~~gL~l~~~~ 114 (182)
.+.++. ++++.-.+ ||++|++. .+.|...+
T Consensus 538 i~~l~~~~~~~l~r~llYTaiTRAk~--~l~i~~~~ 571 (586)
T TIGR01447 538 ILILPNGNSPVLTRELLYTGITRAKD--QLSVWSDK 571 (586)
T ss_pred EEECCCCCCcccccceeEEEeeehhC--eEEEEECH
Confidence 999865 45666677 99999885 56666543
No 10
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=98.75 E-value=6.7e-09 Score=99.34 Aligned_cols=94 Identities=23% Similarity=0.224 Sum_probs=63.9
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.||.||..|+|+...++.+.+.+.. ..|..+.++. +. . -++.+|||||||||||.++++|
T Consensus 493 d~~~gl~NGdiG~v~~~~~~~l~v~f~~--~~g~~~~~~~-----~~--l--------~~~~~ayA~TVHKSQGsEf~~V 555 (615)
T PRK10875 493 DSALGLFNGDIGIALDRGQGELRVWFQL--PDGNIKSVQP-----SR--L--------PEHETAWAMTVHKSQGSEFDHT 555 (615)
T ss_pred CcccCcccCceEEEeecCCCeEEEEEEC--CCCcEEEech-----Hh--c--------cccceEEEEehhhhcCCCCCeE
Confidence 5677999999999997665544444321 1233333321 10 0 1368899999999999999999
Q ss_pred EEECCCC---CCCCCcE-EEEEeecCCCCeEEcccCc
Q 047352 83 GLYLPKQ---VFTNVFV-KALTNLLTEKTTCSLHNAL 115 (182)
Q Consensus 83 ~i~l~~~---~F~~Gq~-VAlSRv~s~~gL~l~~~~~ 115 (182)
.+.++.. ++....+ ||++|++ +.+.|...+.
T Consensus 556 ilvlp~~~~~~l~R~LlYTaiTRAk--~~l~l~~~~~ 590 (615)
T PRK10875 556 ALVLPNQFTPVVTRELVYTAITRAR--RRLSLYADER 590 (615)
T ss_pred EEECCCccchhhhhhhHHhhhhhhh--ceEEEEeCHH
Confidence 9988753 4555667 9999998 4566665443
No 11
>PF13538 UvrD_C_2: UvrD-like helicase C-terminal domain; PDB: 1W36_G 3K70_G 3DMN_A 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=97.96 E-value=3.6e-07 Score=66.36 Aligned_cols=45 Identities=24% Similarity=0.366 Sum_probs=32.6
Q ss_pred eeeccceeeeeeccccccceeeEEEECCCCC-C---CCCcE-EEEEeecC
Q 047352 60 QLPLAPCFAMTINKSQGQSLKYVGLYLPKQV-F---TNVFV-KALTNLLT 104 (182)
Q Consensus 60 QfPl~la~A~TIhKsQG~Tl~~v~i~l~~~~-F---~~Gq~-VAlSRv~s 104 (182)
++....+||+|||||||++++.|.+..+... + ...++ ||+||++.
T Consensus 50 ~~~~~~~~~~Tih~akGle~d~V~v~~~~~~~~~~~~~~~lYva~TRA~~ 99 (104)
T PF13538_consen 50 SYQVSHAYAMTIHKAKGLEFDAVIVVDPDSSNFDELSRRLLYVAITRAKH 99 (104)
T ss_dssp CCTCCCCSEEETGGCTT--EEEEEEEEGGGGSGCGCHHHHHHHHHTTEEE
T ss_pred ccccCcEEEEEhHHhcCccccEEEEEcCCcccCCchhhccEEeeHhHhhh
Confidence 3344489999999999999999999987644 2 12246 99999874
No 12
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.49 E-value=0.00012 Score=77.31 Aligned_cols=95 Identities=19% Similarity=0.204 Sum_probs=63.4
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.|+.||.+++|+.+.++.|. +..|. |+.++ .+.+. ..+-.+.++||.|.|+|||+|-++|
T Consensus 1347 Dk~~G~~Ng~~~tV~~I~~~~I~--l~~~~--~~~~l------~~~~~-------~~~~hlD~gYA~T~h~AQG~T~~~v 1409 (1747)
T PRK13709 1347 DRERGYVANSVWTVTAVSGDSVT--LSDGQ--QTRVI------RPGQE-------RAEQHIDLAYAITAHGAQGASETYA 1409 (1747)
T ss_pred CcccccccCCEEEEEEEcCCeEE--EEcCC--ceEEe------cccch-------hhhhhhhhhhhhhhhhhcccccceE
Confidence 56789999999999999877643 33332 22222 11111 1223467899999999999999999
Q ss_pred EEECC-----CCCCCCCcE-EEEEeecCCCCeEEcccCcc
Q 047352 83 GLYLP-----KQVFTNVFV-KALTNLLTEKTTCSLHNALE 116 (182)
Q Consensus 83 ~i~l~-----~~~F~~Gq~-VAlSRv~s~~gL~l~~~~~~ 116 (182)
.+..+ ...+..-.+ ||+||.+. .+.|...+..
T Consensus 1410 i~~~~~~~~~~~l~~~~~fYVaiSRar~--~l~IyTDd~e 1447 (1747)
T PRK13709 1410 IALEGTEGGRKQMAGFESAYVALSRMKQ--HVQVYTDNRQ 1447 (1747)
T ss_pred EEEeccccccccccchhhhhhccccccc--ceEEEEcCHH
Confidence 87543 223444456 99999988 5666665543
No 13
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=97.09 E-value=0.0003 Score=75.24 Aligned_cols=88 Identities=11% Similarity=0.101 Sum_probs=58.8
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.|+.||.+++|+++..+.+.+.. ..|+.+.+ .+.. ...--+-.+||.|.|+|||.|-++|
T Consensus 1401 d~~~g~~n~~~~~V~~v~~~~~~~~~----~~~~~~~l-----~~~~--------~~~~h~d~~YA~T~h~aQG~T~~~v 1463 (1960)
T TIGR02760 1401 DKNRGIKANEVYTVTQVVNGLSVQLS----KVKNSLSL-----KPIQ--------AKDKHWDYAYTRTADSAQGATYTFV 1463 (1960)
T ss_pred CcccccccCCeEEEEEEcCCcEEEEc----CCCceEEe-----cCch--------hhhhccchhhhhhhhhhcccccceE
Confidence 56789999999999998665554442 22333333 2211 1123456799999999999999999
Q ss_pred EEECCC--CCCCCCcE-EEEEeecCCCC
Q 047352 83 GLYLPK--QVFTNVFV-KALTNLLTEKT 107 (182)
Q Consensus 83 ~i~l~~--~~F~~Gq~-VAlSRv~s~~g 107 (182)
.+.++. .....-++ ||+||.+.--.
T Consensus 1464 i~~~~s~~~l~~~~~~YVaiSRar~~~~ 1491 (1960)
T TIGR02760 1464 IALIKGRLALTNYRSAYIDLTRASHHVE 1491 (1960)
T ss_pred EEEecchhhhhhhhhHhhhhhhcccceE
Confidence 887643 22333345 99999876533
No 14
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.06 E-value=0.0011 Score=69.99 Aligned_cols=96 Identities=17% Similarity=0.154 Sum_probs=64.0
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|.+.||+||.+.+|+.+..+.+..+ .|. ....+ .+.+. ...--+-++||.|.|.|||+|-+++
T Consensus 1218 D~~~G~~Ng~~~tV~~i~~~~i~l~--~g~---~~~~i-----~~~~~-------~~~~hlD~aYA~Tah~AQG~T~~~v 1280 (1623)
T PRK14712 1218 DRERGYVANSVWTVTAVSGDSVTLS--DGQ---QTRVI-----RPGQE-------RAEQHIDLAYAITAHGAQGASETFA 1280 (1623)
T ss_pred CcccccccCceEEEEEEcCCeEEEe--cCc---eeEee-----cCccc-------chhhhhhhhhhhhhhhccCCccceE
Confidence 6678999999999999987765543 331 11111 11111 1223467899999999999998888
Q ss_pred EEECCC----CC-CCCCcE-EEEEeecCCCCeEEcccCccc
Q 047352 83 GLYLPK----QV-FTNVFV-KALTNLLTEKTTCSLHNALEF 117 (182)
Q Consensus 83 ~i~l~~----~~-F~~Gq~-VAlSRv~s~~gL~l~~~~~~~ 117 (182)
....+. .. ...-.+ ||+||.+. .+.|..++...
T Consensus 1281 I~~~~s~~~~~~lt~~rsfYVaiSRAr~--~v~IYTDd~~~ 1319 (1623)
T PRK14712 1281 IALEGTEGNRKLMAGFESAYVALSRMKQ--HVQVYTDNRQG 1319 (1623)
T ss_pred EEecccccchhhcccchhheeeeeeccc--eEEEEECCHHH
Confidence 664432 12 244455 99999987 77777766654
No 15
>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases. Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity
Probab=96.44 E-value=0.0019 Score=52.68 Aligned_cols=38 Identities=26% Similarity=0.348 Sum_probs=31.3
Q ss_pred eeeeeccccccceeeEEEECCCC----CCC--CCcE-EEEEeecC
Q 047352 67 FAMTINKSQGQSLKYVGLYLPKQ----VFT--NVFV-KALTNLLT 104 (182)
Q Consensus 67 ~A~TIhKsQG~Tl~~v~i~l~~~----~F~--~Gq~-VAlSRv~s 104 (182)
-++|+|.+||+|+++|.+++... .+. .-++ |||||.+.
T Consensus 184 ~~~T~~e~qG~tf~~V~l~~~~~~~~~~~~~~~~~~~VALTR~~~ 228 (234)
T PF01443_consen 184 RVFTVHESQGLTFDNVTLVLLSDTDNELYSESRNHLYVALTRHTK 228 (234)
T ss_pred ceechHHcceEEeCCEEEEECCCcccccccCCcccEEEEcccccc
Confidence 48999999999999999998754 343 5577 99999875
No 16
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=95.03 E-value=0.023 Score=61.34 Aligned_cols=93 Identities=14% Similarity=0.043 Sum_probs=61.8
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|...||-||.+++|.++....+.++.- .|+...+|. +. ...-++..+||.|.|+|||+|-+.+
T Consensus 759 ~~~~gl~ng~~~tV~~i~~~~i~l~~~----~g~~~~L~~-----~~--------~~~~~ldh~Ya~T~h~aQG~T~~~~ 821 (1960)
T TIGR02760 759 HFHSRVRNGELLTVSSINNEGITLITE----DGQTLHLPH-----GA--------LEDAHLDYGYVLTPYHTQPDDAKVF 821 (1960)
T ss_pred CcccCccCCCEEEEEEEcCCeEEEEeC----CCceEEccC-----CC--------cccccccccccCCCcccCCCcceEE
Confidence 456789999999999998776665542 233333321 11 1345778899999999999998865
Q ss_pred EEECCCCCCCCCcE-EEEEeecCCCCeEEcccCcc
Q 047352 83 GLYLPKQVFTNVFV-KALTNLLTEKTTCSLHNALE 116 (182)
Q Consensus 83 ~i~l~~~~F~~Gq~-VAlSRv~s~~gL~l~~~~~~ 116 (182)
.+. ...- .+.++ |++||.++ .+.|...+..
T Consensus 822 ~~~-~~~~-~~~~~~~~lsRa~~--~l~IyTd~~~ 852 (1960)
T TIGR02760 822 LGV-KQYA-LSKALLNSLNRSAS--RVDLFTDLDE 852 (1960)
T ss_pred EEe-cchh-hhHHHHHHHhhCcc--eeEEEECCHH
Confidence 443 2111 33356 99999666 6777765543
No 17
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=81.82 E-value=1.7 Score=47.07 Aligned_cols=92 Identities=13% Similarity=-0.003 Sum_probs=60.5
Q ss_pred CCCCCeeecceEEEEEcCCceeeEEEeecCcCceEEEeeeEEeccCCCCCccccceeeeeccceeeeeeccccccceeeE
Q 047352 3 NQIEGLCNDTRLIVTRLGKWSIGGDIISGTNIGQNVTIPRIIMSPNESRWPFKLNRRQLPLAPCFAMTINKSQGQSLKYV 82 (182)
Q Consensus 3 Dv~~GLcNGTRgvV~~l~~~~i~~~iitg~~~G~~V~IpRi~l~~s~~~~~~~~~R~QfPl~la~A~TIhKsQG~Tl~~v 82 (182)
|...||-||.+++|+++....+.++.-. .|+.+.+|- +. + ...-.|+..+||.|.|++ |-+++
T Consensus 723 d~~~~l~Ngd~~tV~~i~~~~i~l~~~~---~gk~~~L~~------~~--~---~~~~~~ldhaYa~T~~~a---t~~~~ 785 (1747)
T PRK13709 723 IPGLRLKGGDRLQVTSVSEDGLTVVVPG---RAEPATLPV------DD--S---PFTALKLEHGWVETPGHS---VSDSA 785 (1747)
T ss_pred CcccCccCCCEEEEEEecCCeEEEEECC---CceEEEeCC------cc--c---ccccCceeeeeecccccc---cCcee
Confidence 5667999999999999988877765321 233333321 10 0 011246888999999999 44666
Q ss_pred EEECCCCCCCCCc-E-EEEEeecCCCCeEEccc
Q 047352 83 GLYLPKQVFTNVF-V-KALTNLLTEKTTCSLHN 113 (182)
Q Consensus 83 ~i~l~~~~F~~Gq-~-VAlSRv~s~~gL~l~~~ 113 (182)
.+....+.....+ . |+++|... .+.|..+
T Consensus 786 ~v~~~~~~~~~s~~~~v~ltrs~~--~l~IyTd 816 (1747)
T PRK13709 786 TVFASVTQRAMDNATLNGLARSGR--DVRLYSS 816 (1747)
T ss_pred EEEEecCchhhhHHHHHHHhhccc--eEEEEcC
Confidence 6655555565444 4 99999855 7777765
No 18
>PF13087 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A 2XZL_A.
Probab=74.31 E-value=0.39 Score=38.09 Aligned_cols=39 Identities=26% Similarity=0.177 Sum_probs=26.1
Q ss_pred eeeeeeccccccceeeEEEECCCC------CCCCC--cE-EEEEeecC
Q 047352 66 CFAMTINKSQGQSLKYVGLYLPKQ------VFTNV--FV-KALTNLLT 104 (182)
Q Consensus 66 a~A~TIhKsQG~Tl~~v~i~l~~~------~F~~G--q~-VAlSRv~s 104 (182)
-...|||+.||+=.|-|.+++-.. -|-.. .+ ||+||++.
T Consensus 144 ~~v~Tvd~~QG~E~diVi~s~v~~~~~~~~~f~~~~~r~nVA~SRAk~ 191 (200)
T PF13087_consen 144 IKVSTVDSFQGQEADIVIVSLVRTNSSSNIGFLNDPNRLNVALSRAKS 191 (200)
T ss_dssp SEEEEHHHHTT--EEEEEEEE---STTS-SGGGC-HHHHHHHHTSEEE
T ss_pred EEEecHHHhccccceEEEEEeccCCccccccccCCcCeeeeeHHHHhc
Confidence 457999999999999999987543 13333 35 99999875
No 19
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=73.68 E-value=1.7 Score=42.41 Aligned_cols=43 Identities=21% Similarity=0.248 Sum_probs=31.8
Q ss_pred eeeeccccccceeeEEE-ECCCCCCCCC--------------cE-EEEEeecCCCCeEEcc
Q 047352 68 AMTINKSQGQSLKYVGL-YLPKQVFTNV--------------FV-KALTNLLTEKTTCSLH 112 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i-~l~~~~F~~G--------------q~-VAlSRv~s~~gL~l~~ 112 (182)
-||||+|+|+=++.|.| .+..+.|.+. -+ ||++|++. .|.|..
T Consensus 552 LmTiH~sKGLEf~vVfv~gl~eg~~P~~~~~~~~~~~eEERRL~YVAiTRAk~--~L~ls~ 610 (726)
T TIGR01073 552 LMTLHAAKGLEFPVVFLIGMEEGVFPHSRSLMDEKELEEERRLAYVGITRAEE--ELYLTH 610 (726)
T ss_pred EEeeeeccCccCCEEEEeCCcCCCCCcccccCCchhHHHHHhhHHhhhhhhhh--eEEEEe
Confidence 38999999999999975 4666777542 15 99999984 455543
No 20
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=71.96 E-value=1.4 Score=43.01 Aligned_cols=44 Identities=20% Similarity=0.229 Sum_probs=33.8
Q ss_pred eeeeccccccceeeEEE-ECCCCCCCCC-------------cE-EEEEeecCCCCeEEccc
Q 047352 68 AMTINKSQGQSLKYVGL-YLPKQVFTNV-------------FV-KALTNLLTEKTTCSLHN 113 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i-~l~~~~F~~G-------------q~-VAlSRv~s~~gL~l~~~ 113 (182)
-||||+|+|+=++.|-| .+..+.|.|. -+ ||+.|++ +.|.|...
T Consensus 554 L~TiH~sKGLEf~~Vfi~gl~eg~~P~~~~~~~~~leEERRLfYVA~TRAk--~~L~Ls~~ 612 (672)
T PRK10919 554 LMTLHASKGLEFPYVYLVGMEEGLLPHQSSIDEDNIDEERRLAYVGITRAQ--KELTFTLC 612 (672)
T ss_pred EEeeecccCcCCCEEEEeCCcCCCCCCcccCCcccHHHHHHHHHHhHhhhh--hheEEeeh
Confidence 48999999999999974 5777778763 14 9999998 45666543
No 21
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A ....
Probab=69.30 E-value=3.2 Score=34.76 Aligned_cols=18 Identities=39% Similarity=0.408 Sum_probs=14.1
Q ss_pred eeeeccccccceeeEEEE
Q 047352 68 AMTINKSQGQSLKYVGLY 85 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i~ 85 (182)
=||||||+|+-++.|.|-
T Consensus 290 i~TiH~sKGLEf~~V~v~ 307 (351)
T PF13361_consen 290 IMTIHKSKGLEFDIVFVP 307 (351)
T ss_dssp EEECGGGTT--EEEEEEE
T ss_pred EeeheeccccCCCeEEEe
Confidence 399999999999999764
No 22
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=67.08 E-value=3 Score=40.70 Aligned_cols=43 Identities=16% Similarity=0.247 Sum_probs=32.1
Q ss_pred eeeeccccccceeeEEEE-CCCCCCCCC--------------cE-EEEEeecCCCCeEEcc
Q 047352 68 AMTINKSQGQSLKYVGLY-LPKQVFTNV--------------FV-KALTNLLTEKTTCSLH 112 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i~-l~~~~F~~G--------------q~-VAlSRv~s~~gL~l~~ 112 (182)
=||||+|+|+=++.|.|- +..+.|.+. .+ ||+.|++. .|.|..
T Consensus 551 lmTiH~sKGLEf~~Vfl~gl~eg~~P~~~~~~~~~~leEERRL~YVAiTRAk~--~L~ls~ 609 (715)
T TIGR01075 551 LMTLHSAKGLEFPLVFLVGMEEGMFPSQMSLDEGGRLEEERRLAYVGITRAMQ--KLTITY 609 (715)
T ss_pred EEEeeeccCCcCCEEEEeCCcCCCCCCccccCccccHHHHHhHHhhhhhhhhh--heEEEe
Confidence 389999999999999753 566677652 24 99999984 455543
No 23
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=59.79 E-value=4.3 Score=39.70 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=32.4
Q ss_pred eeeeccccccceeeEEE-ECCCCCCCCC--------------cE-EEEEeecCCCCeEEcc
Q 047352 68 AMTINKSQGQSLKYVGL-YLPKQVFTNV--------------FV-KALTNLLTEKTTCSLH 112 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i-~l~~~~F~~G--------------q~-VAlSRv~s~~gL~l~~ 112 (182)
=||||+|+|+=++.|.| .+..+.|.+. -+ ||++|++. .|.|..
T Consensus 556 LmTiH~AKGLEf~~Vfl~gl~eg~~P~~~~~~~~~~leEERRL~YVAiTRAk~--~L~ls~ 614 (721)
T PRK11773 556 LMTLHSAKGLEFPLVFIVGMEEGLFPSQMSLEEGGRLEEERRLAYVGITRAMQ--KLTLTY 614 (721)
T ss_pred EEechhccCCcCCEEEEeCCccCCCCCccccccchhhHHHHhHHHhhhhhhhh--eeEEEe
Confidence 48999999999999975 4667777642 14 99999884 566654
No 24
>PRK13909 putative recombination protein RecB; Provisional
Probab=53.66 E-value=7.2 Score=39.36 Aligned_cols=17 Identities=35% Similarity=0.473 Sum_probs=15.8
Q ss_pred eeeeccccccceeeEEE
Q 047352 68 AMTINKSQGQSLKYVGL 84 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i 84 (182)
-||||||+|+-++.|.+
T Consensus 610 imTIHkSKGLEfpvVil 626 (910)
T PRK13909 610 IMTVHKSKGLEFEHVIV 626 (910)
T ss_pred EEEeeccCCCCCcEEEE
Confidence 59999999999999977
No 25
>KOG3310 consensus Riboflavin synthase alpha chain [Coenzyme transport and metabolism]
Probab=51.68 E-value=17 Score=30.53 Aligned_cols=21 Identities=29% Similarity=0.181 Sum_probs=16.8
Q ss_pred eeecceEEEEEcCCceeeEEE
Q 047352 8 LCNDTRLIVTRLGKWSIGGDI 28 (182)
Q Consensus 8 LcNGTRgvV~~l~~~~i~~~i 28 (182)
-||||.++|++|.++...+-+
T Consensus 43 AVNGtCLTVTeFn~~~FtVGi 63 (210)
T KOG3310|consen 43 AVNGTCLTVTEFNAEEFTVGI 63 (210)
T ss_pred EEccEEEEEEeecccceEEec
Confidence 489999999999887665543
No 26
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=41.08 E-value=15 Score=38.27 Aligned_cols=18 Identities=44% Similarity=0.429 Sum_probs=15.7
Q ss_pred eeeeccccccceeeEEEE
Q 047352 68 AMTINKSQGQSLKYVGLY 85 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i~ 85 (182)
-||||||+|+=.+-|-+-
T Consensus 746 ImTIHkSKGLEfPiVflp 763 (1139)
T COG1074 746 IMTIHKSKGLEFPIVFLP 763 (1139)
T ss_pred EEEEeccCCCCCCEEEec
Confidence 599999999999988653
No 27
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=40.63 E-value=15 Score=38.03 Aligned_cols=17 Identities=29% Similarity=0.339 Sum_probs=15.6
Q ss_pred eeeeccccccceeeEEE
Q 047352 68 AMTINKSQGQSLKYVGL 84 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i 84 (182)
-||||||+|+=++.|.+
T Consensus 778 ImTIH~SKGLEfpvV~l 794 (1141)
T TIGR02784 778 VMTVHGAKGLEAPVVFL 794 (1141)
T ss_pred EEeccccCCCCCCEEEE
Confidence 59999999999999976
No 28
>TIGR00609 recB exodeoxyribonuclease V, beta subunit. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.84 E-value=21 Score=36.85 Aligned_cols=18 Identities=39% Similarity=0.342 Sum_probs=15.8
Q ss_pred eeeeccccccceeeEEEE
Q 047352 68 AMTINKSQGQSLKYVGLY 85 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i~ 85 (182)
-||||||+|+=.+-|.+-
T Consensus 655 ImTIHkSKGLEfPvVflp 672 (1087)
T TIGR00609 655 IVTIHKSKGLEYPIVFLP 672 (1087)
T ss_pred EEEEEccCCCCCCEEEEe
Confidence 599999999999988764
No 29
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=33.04 E-value=23 Score=37.12 Aligned_cols=18 Identities=39% Similarity=0.431 Sum_probs=15.9
Q ss_pred eeeeccccccceeeEEEE
Q 047352 68 AMTINKSQGQSLKYVGLY 85 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i~ 85 (182)
-||||||+|+=++-|.+-
T Consensus 785 IMTIHkSKGLEFPvVfl~ 802 (1232)
T TIGR02785 785 LMTIHKSKGLEFPVVFVL 802 (1232)
T ss_pred EEeeecccCCCCCEEEEe
Confidence 599999999999999764
No 30
>PF08247 ENOD40: ENOD40 protein; InterPro: IPR013186 The soybean early nodulin 40 (ENOD40) mRNA contains two short overlapping ORFs; in vitro translation yields two peptides of 12 and 24 amino acids []. The putative role of the ENOD40 genes has been in favour of organogenesis, such as induction of the cortical cell divisions that lead to initiation of nodule primordia, in developing lateral roots and embryonic tissues. This supports the hypothesis for a role of ENOD40 in lateral organ development [].
Probab=28.06 E-value=35 Score=16.54 Aligned_cols=11 Identities=27% Similarity=0.576 Sum_probs=8.7
Q ss_pred cceeeeeeccc
Q 047352 64 APCFAMTINKS 74 (182)
Q Consensus 64 ~la~A~TIhKs 74 (182)
+++|--+||-|
T Consensus 2 ~l~wqksihgs 12 (12)
T PF08247_consen 2 ELCWQKSIHGS 12 (12)
T ss_pred ceeEeeeecCC
Confidence 57899999864
No 31
>PF00677 Lum_binding: Lumazine binding domain; InterPro: IPR001783 The following proteins have been shown [, ] to be structurally and evolutionary related: Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN. These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process; PDB: 3DDY_A 1KZL_A 3A3G_B 3A35_B 3A3B_B 1I8D_C 1PKV_B 1HZE_B 1I18_B.
Probab=27.40 E-value=77 Score=22.71 Aligned_cols=23 Identities=26% Similarity=0.208 Sum_probs=18.7
Q ss_pred eeecceEEEEEcCCceeeEEEee
Q 047352 8 LCNDTRLIVTRLGKWSIGGDIIS 30 (182)
Q Consensus 8 LcNGTRgvV~~l~~~~i~~~iit 30 (182)
-|||..++|+++.++.....++.
T Consensus 41 avnGvcLTV~~~~~~~f~~~l~~ 63 (85)
T PF00677_consen 41 AVNGVCLTVTDINEDWFEVDLIP 63 (85)
T ss_dssp EETTEEEEEEEEETTEEEEEEEH
T ss_pred EECCeeeEEEEecCCEEEEechH
Confidence 37999999999988887777664
No 32
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=24.65 E-value=40 Score=35.35 Aligned_cols=17 Identities=41% Similarity=0.460 Sum_probs=15.0
Q ss_pred eeeeccccccceeeEEE
Q 047352 68 AMTINKSQGQSLKYVGL 84 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i 84 (182)
-||||||+|+=.+-|-+
T Consensus 738 ImTIH~SKGLEfPvVfl 754 (1181)
T PRK10876 738 IVTIHKSKGLEYPLVWL 754 (1181)
T ss_pred EEEEeccCCcCCCEEEe
Confidence 49999999999998864
No 33
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=21.66 E-value=51 Score=31.67 Aligned_cols=43 Identities=19% Similarity=0.240 Sum_probs=30.6
Q ss_pred eeeeccccccceeeEEE-ECCCCCCCCC-------------cE-EEEEeecCCCCeEEcc
Q 047352 68 AMTINKSQGQSLKYVGL-YLPKQVFTNV-------------FV-KALTNLLTEKTTCSLH 112 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i-~l~~~~F~~G-------------q~-VAlSRv~s~~gL~l~~ 112 (182)
-||||+|+|+-.+.|.| .+..+.|.+. .+ ||++|++ +.|.+..
T Consensus 554 l~TiH~sKGLEf~~Vfv~gl~eg~~P~~~~~~~~~~~EErRlfYVA~TRAk--~~L~Ls~ 611 (664)
T TIGR01074 554 LMTLHASKGLEFPYVFIVGMEEGILPHQSSIEEDNVEEERRLAYVGITRAQ--KELTFTL 611 (664)
T ss_pred EEeeecccCccCCeEEEeCCcCCCCCCccccccchHHHHHHHHHHhhhhhh--heeEEEe
Confidence 38999999999999975 4666667421 24 8999887 4455543
No 34
>COG0307 RibC Riboflavin synthase alpha chain [Coenzyme metabolism]
Probab=21.66 E-value=99 Score=26.42 Aligned_cols=34 Identities=26% Similarity=0.431 Sum_probs=25.2
Q ss_pred eecceEEEEEcCCceeeEEEeecC---------cCceEEEeee
Q 047352 9 CNDTRLIVTRLGKWSIGGDIISGT---------NIGQNVTIPR 42 (182)
Q Consensus 9 cNGTRgvV~~l~~~~i~~~iitg~---------~~G~~V~IpR 42 (182)
|||..++|+++.++...+.+...+ ..|..|-++|
T Consensus 41 vnGvCLTVt~~~~~~f~~dv~~ETl~~TnL~~~~~G~~VNLER 83 (204)
T COG0307 41 VNGVCLTVTEFNEDGFSVDVMPETLRRTNLGDLKVGDKVNLER 83 (204)
T ss_pred ECCEEEEEEEECCCcEEEEecHHHhhhcchhhcccCCEEeeeh
Confidence 899999999999888877666432 3555666665
No 35
>PLN02741 riboflavin synthase
Probab=20.71 E-value=1.1e+02 Score=25.50 Aligned_cols=34 Identities=26% Similarity=0.253 Sum_probs=24.9
Q ss_pred eecceEEEEEcCCceeeEEEeecC---------cCceEEEeee
Q 047352 9 CNDTRLIVTRLGKWSIGGDIISGT---------NIGQNVTIPR 42 (182)
Q Consensus 9 cNGTRgvV~~l~~~~i~~~iitg~---------~~G~~V~IpR 42 (182)
|||..++|+++.++...+.++..+ ..|..|-++|
T Consensus 44 vnGvCLTV~~~~~~~f~vdvipETl~~T~L~~l~~G~~VNLEr 86 (194)
T PLN02741 44 VNGTCLTVTEFDGDEFTVGLAPETLRKTSLGELKTGSLVNLER 86 (194)
T ss_pred ECcEEEEEEEECCCEEEEEEEHHHhhhCccccCCCCCEEeecc
Confidence 899999999998887777766431 2566666655
No 36
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=20.40 E-value=1.3e+02 Score=21.74 Aligned_cols=16 Identities=25% Similarity=0.362 Sum_probs=12.1
Q ss_pred CeeecceEEEEEcCCc
Q 047352 7 GLCNDTRLIVTRLGKW 22 (182)
Q Consensus 7 GLcNGTRgvV~~l~~~ 22 (182)
|+.||+.+.|.++..+
T Consensus 57 gi~~gs~L~v~D~~q~ 72 (87)
T PF14732_consen 57 GIVNGSILTVDDFDQD 72 (87)
T ss_dssp T--TT-EEEEEETTTT
T ss_pred CCCCCCEEEEEEcCCC
Confidence 8999999999999877
No 37
>PRK11054 helD DNA helicase IV; Provisional
Probab=20.15 E-value=55 Score=32.36 Aligned_cols=18 Identities=44% Similarity=0.580 Sum_probs=16.6
Q ss_pred eeeeccccccceeeEEEE
Q 047352 68 AMTINKSQGQSLKYVGLY 85 (182)
Q Consensus 68 A~TIhKsQG~Tl~~v~i~ 85 (182)
-||+|.|+|+.+|.|.|.
T Consensus 591 ~~T~h~sKGLEfD~ViI~ 608 (684)
T PRK11054 591 FMTIHASKGQQADYVIIL 608 (684)
T ss_pred EEehhhhcCCcCCEEEEe
Confidence 589999999999999985
Done!