Query psy16286
Match_columns 92
No_of_seqs 102 out of 1073
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 17:31:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16286.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16286hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1807|consensus 99.9 8.4E-23 1.8E-27 166.3 4.4 86 1-86 917-1003(1025)
2 KOG1802|consensus 99.7 1.6E-18 3.5E-23 140.2 3.7 62 1-63 778-839 (935)
3 TIGR00376 DNA helicase, putati 99.6 3.3E-16 7.1E-21 126.5 5.0 62 1-63 572-633 (637)
4 KOG1803|consensus 99.5 2.1E-14 4.5E-19 115.2 5.0 62 1-62 569-630 (649)
5 COG1112 Superfamily I DNA and 99.3 1.4E-12 3E-17 104.8 4.3 62 1-63 690-752 (767)
6 PF13087 AAA_12: AAA domain; P 99.2 1.3E-12 2.8E-17 89.9 0.2 39 1-39 162-200 (200)
7 KOG1801|consensus 99.1 3.4E-11 7.4E-16 100.0 1.6 65 1-65 750-814 (827)
8 KOG1805|consensus 99.1 3.3E-11 7.2E-16 100.8 1.0 61 1-62 1016-1077(1100)
9 KOG1804|consensus 96.8 0.00039 8.4E-09 58.2 0.7 60 1-61 655-720 (775)
10 PF01443 Viral_helicase1: Vira 95.5 0.015 3.2E-07 40.5 3.0 20 16-35 214-233 (234)
11 KOG1806|consensus 94.8 0.0035 7.7E-08 54.2 -2.0 55 1-58 1209-1266(1320)
12 TIGR02785 addA_Gpos recombinat 92.7 0.056 1.2E-06 47.4 1.5 30 21-50 862-891 (1232)
13 PF13538 UvrD_C_2: UvrD-like h 92.1 0.061 1.3E-06 33.1 0.7 18 18-35 87-104 (104)
14 PF13361 UvrD_C: UvrD-like hel 92.0 0.052 1.1E-06 39.1 0.4 17 21-37 333-349 (351)
15 PRK13909 putative recombinatio 89.5 0.16 3.5E-06 43.2 1.1 22 19-40 683-704 (910)
16 TIGR02784 addA_alphas double-s 89.4 0.24 5.2E-06 43.0 2.1 34 21-54 857-890 (1141)
17 TIGR01448 recD_rel helicase, p 85.7 0.46 9.9E-06 39.7 1.6 28 14-41 674-701 (720)
18 TIGR01447 recD exodeoxyribonuc 84.0 0.67 1.5E-05 37.9 1.8 27 15-41 548-574 (586)
19 COG1074 RecB ATP-dependent exo 81.8 0.38 8.3E-06 42.0 -0.4 25 21-45 819-843 (1139)
20 PRK11054 helD DNA helicase IV; 79.2 1.3 2.7E-05 37.0 1.8 34 19-59 644-677 (684)
21 PF09848 DUF2075: Uncharacteri 77.6 0.65 1.4E-05 35.1 -0.3 18 18-35 332-349 (352)
22 PRK10875 recD exonuclease V su 76.0 1.3 2.8E-05 36.6 1.0 26 17-42 568-593 (615)
23 TIGR02768 TraA_Ti Ti-type conj 74.2 2.3 5E-05 35.7 2.1 28 15-42 687-714 (744)
24 TIGR01075 uvrD DNA helicase II 66.6 2.1 4.6E-05 35.4 0.3 22 15-36 587-609 (715)
25 TIGR01073 pcrA ATP-dependent D 66.4 2.2 4.9E-05 35.3 0.4 24 15-38 588-612 (726)
26 COG0507 RecD ATP-dependent exo 66.2 2.7 5.9E-05 34.6 0.8 26 17-42 650-675 (696)
27 PRK11773 uvrD DNA-dependent he 65.5 2.3 5E-05 35.3 0.3 22 15-36 592-614 (721)
28 PRK10919 ATP-dependent DNA hel 62.9 2.4 5.2E-05 35.1 -0.0 23 15-37 589-612 (672)
29 COG3410 Uncharacterized conser 59.7 3 6.5E-05 29.6 -0.0 22 18-39 155-176 (191)
30 TIGR00609 recB exodeoxyribonuc 58.2 3.2 6.9E-05 36.3 -0.1 17 21-37 720-736 (1087)
31 TIGR01074 rep ATP-dependent DN 52.3 5.7 0.00012 32.4 0.5 23 16-38 590-613 (664)
32 PRK10876 recB exonuclease V su 49.5 4.6 0.0001 35.7 -0.5 14 21-34 802-815 (1181)
33 PF08727 P3A: Poliovirus 3A pr 43.8 18 0.0004 21.0 1.6 24 49-72 30-53 (57)
34 PF03089 RAG2: Recombination a 34.5 22 0.00047 27.5 1.2 37 18-54 90-129 (337)
35 KOG3992|consensus 32.4 25 0.00055 26.2 1.2 23 17-39 64-86 (314)
36 PF07057 TraI: DNA helicase Tr 31.6 16 0.00034 24.6 0.0 26 23-54 1-26 (126)
37 PF11772 EpuA: DNA-directed RN 31.2 66 0.0014 17.9 2.5 27 31-57 19-46 (47)
38 PHA02778 major capsid L1 prote 28.1 28 0.00062 28.4 0.9 33 16-51 140-172 (503)
39 KOG1624|consensus 27.6 34 0.00074 26.0 1.2 34 21-55 163-199 (290)
40 PRK02260 S-ribosylhomocysteina 26.5 92 0.002 21.7 3.1 50 21-71 75-127 (158)
41 COG1880 CdhB CO dehydrogenase/ 24.6 88 0.0019 22.0 2.7 36 20-59 27-62 (170)
42 PRK13826 Dtr system oriT relax 23.7 55 0.0012 29.3 1.9 27 15-41 716-742 (1102)
43 PRK13889 conjugal transfer rel 23.6 42 0.00092 29.6 1.2 23 16-38 681-703 (988)
44 PF02664 LuxS: S-Ribosylhomocy 22.9 1.4E+02 0.003 20.8 3.4 51 20-71 74-127 (157)
45 KOG1324|consensus 20.9 52 0.0011 23.6 1.0 18 13-30 62-79 (190)
46 KOG0545|consensus 20.1 48 0.001 25.4 0.7 58 29-90 57-122 (329)
No 1
>KOG1807|consensus
Probab=99.87 E-value=8.4e-23 Score=166.34 Aligned_cols=86 Identities=37% Similarity=0.726 Sum_probs=82.6
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCccccccccccccC-CCEEEeC
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINESFRLQCNKH-RAVTIIR 79 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~~~~~l~c~~h-~~~~~v~ 79 (92)
+|+||||..|++|||+..||++|||||||+|||||||..+++...++|.++++-+.+.+.|+..+|+.|..| +..+.+.
T Consensus 917 lSLVRsn~~griGFL~~anRvCVALSRAr~glyiiGN~q~la~~~pLWnkivntLrenn~Ig~~lpl~c~~h~~~~t~v~ 996 (1025)
T KOG1807|consen 917 LSLVRSNISGRIGFLRQANRVCVALSRARWGLYIIGNVQILADTPPLWNKIVNTLRENNAIGEALPLICSTHKDGTTYVN 996 (1025)
T ss_pred EEEEeccCCceeeeeeccchhhhhhhhhhcceEEecceeecccCchhHHHHHHHHHhccccccccccceeecCCceEEEc
Confidence 599999999999999999999999999999999999999998789999999999999999999999999999 8888899
Q ss_pred Cccchhh
Q psy16286 80 AVEDFEA 86 (92)
Q Consensus 80 ~~~df~~ 86 (92)
..++|++
T Consensus 997 k~~~fqk 1003 (1025)
T KOG1807|consen 997 KSKQFQK 1003 (1025)
T ss_pred hHHhhcc
Confidence 8888887
No 2
>KOG1802|consensus
Probab=99.73 E-value=1.6e-18 Score=140.23 Aligned_cols=62 Identities=35% Similarity=0.592 Sum_probs=58.9
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCcccc
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINE 63 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~~ 63 (92)
+||||+|....||||.|++||||||||||+||+|+||+..| ..+++|..+|.|+++++++..
T Consensus 778 lSCVRsn~~qgIGFl~d~RRlNVaLTRaK~glvivGN~~~L-~k~~LW~~li~h~~eke~l~e 839 (935)
T KOG1802|consen 778 LSCVRSNEHQGIGFLNDPRRLNVALTRAKYGLVIVGNPKVL-RKHPLWGHLITHYKEKEVLVE 839 (935)
T ss_pred EEEeecccccccccccCchhhhhhhhhcccceEEecCHHHh-hhchHHHHHHHHhhcccceee
Confidence 69999999999999999999999999999999999999999 669999999999999998754
No 3
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=99.62 E-value=3.3e-16 Score=126.54 Aligned_cols=62 Identities=26% Similarity=0.500 Sum_probs=58.6
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCcccc
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINE 63 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~~ 63 (92)
+|+||+|..+.+||+.+.+|+|||+||||++|+||||..+| ..++.|++++++++++|++..
T Consensus 572 ~S~vrsn~~~~~gFl~d~rRLNVAlTRAK~~LiIvGn~~~l-~~~~~~~~li~~~~~~~~~~~ 633 (637)
T TIGR00376 572 ISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTL-SNHKFYKRLIEWCKQHGEVRE 633 (637)
T ss_pred EEEEecCCCCCcccccCcceeeeehhhhhCceEEEECHHHh-ccChHHHHHHHHHHHCCCEEc
Confidence 58999999889999999999999999999999999999999 789999999999999998753
No 4
>KOG1803|consensus
Probab=99.50 E-value=2.1e-14 Score=115.22 Aligned_cols=62 Identities=21% Similarity=0.406 Sum_probs=58.1
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCccc
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSIN 62 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~ 62 (92)
||+||||..+.+|||.+.+|||||+||||+++.+|||..++...+..+.++++++++++.+.
T Consensus 569 fsmVRSN~k~evGFL~e~RRLNVAiTRaRRh~~vIgds~tl~~~~~~l~k~~~f~~~~~~~~ 630 (649)
T KOG1803|consen 569 FSLVRSNDKGEVGFLGETRRLNVAITRARRHFVVIGDSRTLKEGNEFLKKLVEFLEENKLVF 630 (649)
T ss_pred EEEEeecCcccccccCCcceeeEEEEeccceEEEEcCcHHHHhhHHHHHHHHHHhhhcceec
Confidence 69999999999999999999999999999999999999999448999999999999988764
No 5
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]
Probab=99.32 E-value=1.4e-12 Score=104.84 Aligned_cols=62 Identities=29% Similarity=0.483 Sum_probs=57.8
Q ss_pred CeeeeeCCC-CCcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCcccc
Q psy16286 1 MAGSTNNVH-NNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINE 63 (92)
Q Consensus 1 ~S~VRsn~~-~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~~ 63 (92)
+|+||||.. +.+||+.+.+|+|||+||||++|+|+|+...+ ...+.|..++.+++..+.+..
T Consensus 690 ~S~v~s~~~~~~i~~l~d~rRLNVAlTRAk~~livvg~~~~l-~~~~~~~~~~~~~~~~~~~~~ 752 (767)
T COG1112 690 LSLVRSNDDKGEIGFLGDPRRLNVALTRAKRKLIVVGSSSTL-ESDPLYKRLINDLKRKGLLAE 752 (767)
T ss_pred EEEEeecCCCccccccCchhhhhhhhhcccceEEEEcChhHh-hhchhHHHHHHHHHhcCcEee
Confidence 699999988 69999999999999999999999999999999 889999999999999987643
No 6
>PF13087 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A 2XZL_A.
Probab=99.24 E-value=1.3e-12 Score=89.92 Aligned_cols=39 Identities=49% Similarity=0.709 Sum_probs=30.2
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccch
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMK 39 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~ 39 (92)
+|+||++....+||+.+.+|+|||+||||.+|+||||.+
T Consensus 162 ~s~v~~~~~~~~~f~~~~~r~nVA~SRAk~~liiig~~~ 200 (200)
T PF13087_consen 162 VSLVRTNSSSNIGFLNDPNRLNVALSRAKSGLIIIGNPE 200 (200)
T ss_dssp EEE---STTS-SGGGC-HHHHHHHHTSEEEEEEEEE-H-
T ss_pred EEeccCCccccccccCCcCeeeeeHHHHhcCEEEEecCC
Confidence 589999977889999999999999999999999999864
No 7
>KOG1801|consensus
Probab=99.08 E-value=3.4e-11 Score=100.01 Aligned_cols=65 Identities=20% Similarity=0.369 Sum_probs=60.3
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCcccccc
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINESF 65 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~~~~ 65 (92)
+|+||++..+.+||+.+..|+||||||||++++++||...|...++.|..++...+..++..+..
T Consensus 750 ~s~vrs~~~g~igf~~~~~RlnvALtra~~~l~v~Gne~~L~~~~~~w~~li~da~~r~~~~~~~ 814 (827)
T KOG1801|consen 750 ISTVRSIDEGSIGFECNLRRLNVALTRARTCFWLVGNEITLAPSCSIWASLILDAKGRGCFMDRA 814 (827)
T ss_pred EEEEEecccCccchhhhHHHHHHhhcccccceEEecCccccccccchhhhhcchhcccccccccc
Confidence 58999999999999999999999999999999999999999777888999999999999986543
No 8
>KOG1805|consensus
Probab=99.06 E-value=3.3e-11 Score=100.80 Aligned_cols=61 Identities=28% Similarity=0.392 Sum_probs=55.7
Q ss_pred CeeeeeCCCCCcC-CccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCccc
Q psy16286 1 MAGSTNNVHNNVG-FLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSIN 62 (92)
Q Consensus 1 ~S~VRsn~~~~~G-Fl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i~ 62 (92)
+|+||+|...+.| .|+|++|+||||||||+.|+++|+.++| .+.+.++++++++.++..+.
T Consensus 1016 vSfvrsn~~~~~~eLLkD~rRlNVAlTRAK~KLIlvGs~s~l-~~~~~~~~l~~~l~~~~~l~ 1077 (1100)
T KOG1805|consen 1016 VSFVRSNKKSKVGELLKDWRRLNVALTRAKKKLILVGSKSTL-ESYPPFRQLLKLLENRIELL 1077 (1100)
T ss_pred EEEEecCCcccHHHHHHhhHHHHHHHHhhhceEEEEeccccc-ccCchHHHHHhhhhhhhhHH
Confidence 5899999988888 9999999999999999999999999999 77888999999998776653
No 9
>KOG1804|consensus
Probab=96.81 E-value=0.00039 Score=58.20 Aligned_cols=60 Identities=20% Similarity=0.145 Sum_probs=51.6
Q ss_pred CeeeeeCCCC------CcCCccCCccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCCcc
Q psy16286 1 MAGSTNNVHN------NVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSI 61 (92)
Q Consensus 1 ~S~VRsn~~~------~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i 61 (92)
+|+|||.... ..+|++.++|+|||.+||+.-++++||+..+ ..++.|+.++....++|..
T Consensus 655 iStVrS~~~~~~~~~~~~~fls~pk~l~v~V~rp~~l~i~~~~~h~~-~~~~~~~~~l~~~~~n~~y 720 (775)
T KOG1804|consen 655 GSTVRSFALPLLDDRYFGLFLSRPKRLLVAVGRPRALLINLGNPHLL-GGDPPWGLLLLLRVENGRY 720 (775)
T ss_pred eecccccCCCcccccccceeecCcccceeeccCccccccccCCcccc-cCCCChhhheeeeecCCcc
Confidence 5899997651 2238999999999999999999999999999 8899999999888777654
No 10
>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=95.48 E-value=0.015 Score=40.55 Aligned_cols=20 Identities=35% Similarity=0.576 Sum_probs=18.2
Q ss_pred cCCccceeeccccceeEEEE
Q psy16286 16 KTVNRVCVALSRAKQGLFIM 35 (92)
Q Consensus 16 ~~~~RinVAlSRAk~gl~Ii 35 (92)
.+.+++.||||||++.|+|+
T Consensus 214 ~~~~~~~VALTR~~~~l~i~ 233 (234)
T PF01443_consen 214 ESRNHLYVALTRHTKSLVIL 233 (234)
T ss_pred CCcccEEEEccccccEEEEE
Confidence 36999999999999999986
No 11
>KOG1806|consensus
Probab=94.82 E-value=0.0035 Score=54.17 Aligned_cols=55 Identities=24% Similarity=0.428 Sum_probs=44.1
Q ss_pred CeeeeeCCCCCcCCccCCccceeeccccceeEEEEccchhhhhc---cHHHHHHHHHHHhC
Q psy16286 1 MAGSTNNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSAD---SQLWQEIKNKLVTR 58 (92)
Q Consensus 1 ~S~VRsn~~~~~GFl~~~~RinVAlSRAk~gl~IiGn~~~L~~~---~~~w~~ll~~~~~~ 58 (92)
+|+||+- -+|.+.|.+|+-||+|||+.|+|+.++.+.+++. -+.|+.+.+.=...
T Consensus 1209 lslv~tr---~~gh~rdvrrlvva~srarlglyv~~r~~lf~~c~eLtp~~~~l~k~p~~l 1266 (1320)
T KOG1806|consen 1209 LSLVRTR---EVGHLRDVRRLVVAMSRARLGLYVLCRRSLFRSCRELTPAFNELEKRPDKL 1266 (1320)
T ss_pred eeehhhh---hhhhhccHHHHHHHHHHhhccchhHHHHHHHHHHHhccHHHHHHhhCcchh
Confidence 4777774 6999999999999999999999999999988543 56677775554433
No 12
>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=92.71 E-value=0.056 Score=47.36 Aligned_cols=30 Identities=37% Similarity=0.620 Sum_probs=21.5
Q ss_pred ceeeccccceeEEEEccchhhhhccHHHHH
Q psy16286 21 VCVALSRAKQGLFIMGNMKCLSADSQLWQE 50 (92)
Q Consensus 21 inVAlSRAk~gl~IiGn~~~L~~~~~~w~~ 50 (92)
+=|||||||..|||+|....+.+.-.-|..
T Consensus 862 LYVAlTRAke~Lil~g~~~~~~~~~~~~~~ 891 (1232)
T TIGR02785 862 LYVALTRAKEKLILVGSVKDEKKESKKWLA 891 (1232)
T ss_pred HHhhhhhhhheEEEEecHHHHHHHHHHHHH
Confidence 369999999999999986655333333433
No 13
>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=92.10 E-value=0.061 Score=33.12 Aligned_cols=18 Identities=39% Similarity=0.610 Sum_probs=15.3
Q ss_pred CccceeeccccceeEEEE
Q psy16286 18 VNRVCVALSRAKQGLFIM 35 (92)
Q Consensus 18 ~~RinVAlSRAk~gl~Ii 35 (92)
.+.+=||+||||+.|+||
T Consensus 87 ~~~lYva~TRA~~~L~iv 104 (104)
T PF13538_consen 87 RRLLYVAITRAKHELYIV 104 (104)
T ss_dssp HHHHHHHHTTEEEEEEEE
T ss_pred hccEEeeHhHhhhhhCCC
Confidence 345789999999999986
No 14
>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=92.00 E-value=0.052 Score=39.10 Aligned_cols=17 Identities=35% Similarity=0.516 Sum_probs=15.1
Q ss_pred ceeeccccceeEEEEcc
Q psy16286 21 VCVALSRAKQGLFIMGN 37 (92)
Q Consensus 21 inVAlSRAk~gl~IiGn 37 (92)
+=||+||||+.|||++.
T Consensus 333 ~YVA~TRAk~~L~l~~~ 349 (351)
T PF13361_consen 333 FYVAMTRAKERLYLSYP 349 (351)
T ss_dssp HHHHHHTEEEEEEEEEE
T ss_pred heEecchhhceEEEEEe
Confidence 36999999999999975
No 15
>PRK13909 putative recombination protein RecB; Provisional
Probab=89.49 E-value=0.16 Score=43.25 Aligned_cols=22 Identities=32% Similarity=0.478 Sum_probs=18.2
Q ss_pred ccceeeccccceeEEEEccchh
Q psy16286 19 NRVCVALSRAKQGLFIMGNMKC 40 (92)
Q Consensus 19 ~RinVAlSRAk~gl~IiGn~~~ 40 (92)
|-+=|||||||..|||+|....
T Consensus 683 rlLYVAlTRA~~~L~i~~~~~~ 704 (910)
T PRK13909 683 NVLYVAFTRAKNSLIVVKKDES 704 (910)
T ss_pred hhHheeccchhhceEEEecccc
Confidence 4457999999999999997543
No 16
>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=89.39 E-value=0.24 Score=43.02 Aligned_cols=34 Identities=21% Similarity=0.422 Sum_probs=23.3
Q ss_pred ceeeccccceeEEEEccchhhhhccHHHHHHHHH
Q psy16286 21 VCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNK 54 (92)
Q Consensus 21 inVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~ 54 (92)
+=||+||||..|||+|...--......|..++..
T Consensus 857 LYVAlTRA~~~L~l~g~~~~~~~~~~~w~~~~~~ 890 (1141)
T TIGR02784 857 LYVAMTRAEDRLIVCGYRGKRTSPKDTWYALVKR 890 (1141)
T ss_pred HHHhhhhhhheeEEEeecCCCccchhhHHHHHHH
Confidence 4699999999999999754211113358876654
No 17
>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=85.74 E-value=0.46 Score=39.68 Aligned_cols=28 Identities=25% Similarity=0.393 Sum_probs=24.5
Q ss_pred CccCCccceeeccccceeEEEEccchhh
Q psy16286 14 FLKTVNRVCVALSRAKQGLFIMGNMKCL 41 (92)
Q Consensus 14 Fl~~~~RinVAlSRAk~gl~IiGn~~~L 41 (92)
.+-+.+-+=+|+||||+.++|+|+.+.|
T Consensus 674 ~~l~r~llYTAiTRAk~~l~lvg~~~a~ 701 (720)
T TIGR01448 674 RMLYRNLLYTALTRAKKRVILVGSAEAF 701 (720)
T ss_pred hhhhhchheeeeeeeceEEEEEECHHHH
Confidence 4556777899999999999999998887
No 18
>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=84.03 E-value=0.67 Score=37.94 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=23.3
Q ss_pred ccCCccceeeccccceeEEEEccchhh
Q psy16286 15 LKTVNRVCVALSRAKQGLFIMGNMKCL 41 (92)
Q Consensus 15 l~~~~RinVAlSRAk~gl~IiGn~~~L 41 (92)
+-+.+-+-||+||||+.++|+|+.+.|
T Consensus 548 ~l~r~llYTaiTRAk~~l~i~~~~~~l 574 (586)
T TIGR01447 548 VLTRELLYTGITRAKDQLSVWSDKETL 574 (586)
T ss_pred ccccceeEEEeeehhCeEEEEECHHHH
Confidence 456777899999999999999988766
No 19
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=81.81 E-value=0.38 Score=42.05 Aligned_cols=25 Identities=36% Similarity=0.473 Sum_probs=19.9
Q ss_pred ceeeccccceeEEEEccchhhhhcc
Q psy16286 21 VCVALSRAKQGLFIMGNMKCLSADS 45 (92)
Q Consensus 21 inVAlSRAk~gl~IiGn~~~L~~~~ 45 (92)
+=|||||||..|||+|-...-.+..
T Consensus 819 LYVAlTRAk~~L~l~g~~~~~~~~~ 843 (1139)
T COG1074 819 LYVALTRAKEQLILIGAPSKREKSS 843 (1139)
T ss_pred HHHHHHHHHHheEEEeecccccccc
Confidence 4699999999999999777663333
No 20
>PRK11054 helD DNA helicase IV; Provisional
Probab=79.21 E-value=1.3 Score=37.01 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=23.1
Q ss_pred ccceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCC
Q psy16286 19 NRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRR 59 (92)
Q Consensus 19 ~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~ 59 (92)
+-+=||+||||+.++|+.+... ...++..+.+.+
T Consensus 644 RLlYVAlTRAr~~l~i~~~~~~-------~S~fv~el~~~~ 677 (684)
T PRK11054 644 RLLYVALTRAKHRVWLLFNKGN-------PSPFVEELKNLD 677 (684)
T ss_pred HHHHHHhhhhhcEEEEEEcCCC-------CCHHHHHHhhCC
Confidence 3457999999999999975331 244555555543
No 21
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function. It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].
Probab=77.61 E-value=0.65 Score=35.11 Aligned_cols=18 Identities=33% Similarity=0.425 Sum_probs=16.2
Q ss_pred CccceeeccccceeEEEE
Q psy16286 18 VNRVCVALSRAKQGLFIM 35 (92)
Q Consensus 18 ~~RinVAlSRAk~gl~Ii 35 (92)
.|..+|.|||+++|+||-
T Consensus 332 ~N~y~VLLTRG~~G~~iy 349 (352)
T PF09848_consen 332 KNIYRVLLTRGIKGTYIY 349 (352)
T ss_pred HHHHHHHHhcccceEEEE
Confidence 677899999999999984
No 22
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=76.04 E-value=1.3 Score=36.58 Aligned_cols=26 Identities=31% Similarity=0.418 Sum_probs=22.1
Q ss_pred CCccceeeccccceeEEEEccchhhh
Q psy16286 17 TVNRVCVALSRAKQGLFIMGNMKCLS 42 (92)
Q Consensus 17 ~~~RinVAlSRAk~gl~IiGn~~~L~ 42 (92)
+.+-+=||+||||+.+.|+|+...|.
T Consensus 568 ~R~LlYTaiTRAk~~l~l~~~~~~l~ 593 (615)
T PRK10875 568 TRELVYTAITRARRRLSLYADERVLS 593 (615)
T ss_pred hhhhHHhhhhhhhceEEEEeCHHHHH
Confidence 45567899999999999999988763
No 23
>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=74.18 E-value=2.3 Score=35.70 Aligned_cols=28 Identities=11% Similarity=0.177 Sum_probs=24.6
Q ss_pred ccCCccceeeccccceeEEEEccchhhh
Q psy16286 15 LKTVNRVCVALSRAKQGLFIMGNMKCLS 42 (92)
Q Consensus 15 l~~~~RinVAlSRAk~gl~IiGn~~~L~ 42 (92)
+-+.+-+-||+||||+.+.|+|+.+.+.
T Consensus 687 ~l~r~llYvAiTRar~~~~l~~~~~~~~ 714 (744)
T TIGR02768 687 SMDRHLAYVAMTRHRESVQLYAGKEDFT 714 (744)
T ss_pred ccccchhhhhhhcccceeEEEEchhhcc
Confidence 4567788999999999999999988883
No 24
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=66.56 E-value=2.1 Score=35.44 Aligned_cols=22 Identities=36% Similarity=0.398 Sum_probs=17.6
Q ss_pred ccCCccc-eeeccccceeEEEEc
Q psy16286 15 LKTVNRV-CVALSRAKQGLFIMG 36 (92)
Q Consensus 15 l~~~~Ri-nVAlSRAk~gl~IiG 36 (92)
+..++|+ =||+||||+.||+.-
T Consensus 587 leEERRL~YVAiTRAk~~L~ls~ 609 (715)
T TIGR01075 587 LEEERRLAYVGITRAMQKLTITY 609 (715)
T ss_pred HHHHHhHHhhhhhhhhhheEEEe
Confidence 4555666 699999999999964
No 25
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=66.41 E-value=2.2 Score=35.31 Aligned_cols=24 Identities=25% Similarity=0.499 Sum_probs=18.3
Q ss_pred ccCCccc-eeeccccceeEEEEccc
Q psy16286 15 LKTVNRV-CVALSRAKQGLFIMGNM 38 (92)
Q Consensus 15 l~~~~Ri-nVAlSRAk~gl~IiGn~ 38 (92)
+..++|+ =||+||||+.||+....
T Consensus 588 ~eEERRL~YVAiTRAk~~L~ls~~~ 612 (726)
T TIGR01073 588 LEEERRLAYVGITRAEEELYLTHAT 612 (726)
T ss_pred HHHHHhhHHhhhhhhhheEEEEehh
Confidence 3445665 69999999999997543
No 26
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]
Probab=66.16 E-value=2.7 Score=34.57 Aligned_cols=26 Identities=23% Similarity=0.477 Sum_probs=21.7
Q ss_pred CCccceeeccccceeEEEEccchhhh
Q psy16286 17 TVNRVCVALSRAKQGLFIMGNMKCLS 42 (92)
Q Consensus 17 ~~~RinVAlSRAk~gl~IiGn~~~L~ 42 (92)
+.+-+=||+||||..++++|..+.+.
T Consensus 650 ~r~l~YtAiTRar~~l~l~~~~~~~~ 675 (696)
T COG0507 650 SRELLYTAITRARDRLILYGDEKAFA 675 (696)
T ss_pred hhhHHHHHhhhhheeEEEEcChHHHH
Confidence 34556799999999999999988883
No 27
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=65.45 E-value=2.3 Score=35.32 Aligned_cols=22 Identities=32% Similarity=0.380 Sum_probs=17.8
Q ss_pred ccCCccc-eeeccccceeEEEEc
Q psy16286 15 LKTVNRV-CVALSRAKQGLFIMG 36 (92)
Q Consensus 15 l~~~~Ri-nVAlSRAk~gl~IiG 36 (92)
+..++|+ =||+||||+.||+.-
T Consensus 592 leEERRL~YVAiTRAk~~L~ls~ 614 (721)
T PRK11773 592 LEEERRLAYVGITRAMQKLTLTY 614 (721)
T ss_pred hHHHHhHHHhhhhhhhheeEEEe
Confidence 4556676 699999999999974
No 28
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=62.88 E-value=2.4 Score=35.10 Aligned_cols=23 Identities=22% Similarity=0.307 Sum_probs=18.0
Q ss_pred ccCCccc-eeeccccceeEEEEcc
Q psy16286 15 LKTVNRV-CVALSRAKQGLFIMGN 37 (92)
Q Consensus 15 l~~~~Ri-nVAlSRAk~gl~IiGn 37 (92)
+..++|+ =||+||||.-||+...
T Consensus 589 leEERRLfYVA~TRAk~~L~Ls~~ 612 (672)
T PRK10919 589 IDEERRLAYVGITRAQKELTFTLC 612 (672)
T ss_pred HHHHHHHHHHhHhhhhhheEEeeh
Confidence 3445666 6999999999999854
No 29
>COG3410 Uncharacterized conserved protein [Function unknown]
Probab=59.72 E-value=3 Score=29.63 Aligned_cols=22 Identities=27% Similarity=0.480 Sum_probs=18.8
Q ss_pred CccceeeccccceeEEEEccch
Q psy16286 18 VNRVCVALSRAKQGLFIMGNMK 39 (92)
Q Consensus 18 ~~RinVAlSRAk~gl~IiGn~~ 39 (92)
.||+||.|||.=+|+||.--..
T Consensus 155 kNsinvlmtRGIrGlyiyaeDp 176 (191)
T COG3410 155 KNSINVLMTRGIRGLYIYAEDP 176 (191)
T ss_pred HHHHHHHHhcccceEEEEEeCH
Confidence 6899999999999999985433
No 30
>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=58.19 E-value=3.2 Score=36.30 Aligned_cols=17 Identities=53% Similarity=0.591 Sum_probs=14.4
Q ss_pred ceeeccccceeEEEEcc
Q psy16286 21 VCVALSRAKQGLFIMGN 37 (92)
Q Consensus 21 inVAlSRAk~gl~IiGn 37 (92)
+=|||||||+.+||...
T Consensus 720 LYVAlTRA~~~l~l~~~ 736 (1087)
T TIGR00609 720 LYVALTRAKKQLFIGIA 736 (1087)
T ss_pred HHHHHHHHhHeeEEEec
Confidence 46999999999999654
No 31
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=52.26 E-value=5.7 Score=32.40 Aligned_cols=23 Identities=22% Similarity=0.257 Sum_probs=17.6
Q ss_pred cCCccc-eeeccccceeEEEEccc
Q psy16286 16 KTVNRV-CVALSRAKQGLFIMGNM 38 (92)
Q Consensus 16 ~~~~Ri-nVAlSRAk~gl~IiGn~ 38 (92)
..++|+ =||+||||+-||+....
T Consensus 590 ~EErRlfYVA~TRAk~~L~Ls~~~ 613 (664)
T TIGR01074 590 EEERRLAYVGITRAQKELTFTLCK 613 (664)
T ss_pred HHHHHHHHHhhhhhhheeEEEehh
Confidence 345554 69999999999998643
No 32
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=49.55 E-value=4.6 Score=35.75 Aligned_cols=14 Identities=29% Similarity=0.266 Sum_probs=12.8
Q ss_pred ceeeccccceeEEE
Q psy16286 21 VCVALSRAKQGLFI 34 (92)
Q Consensus 21 inVAlSRAk~gl~I 34 (92)
+=|||||||+.+||
T Consensus 802 lYVAlTRAk~~l~l 815 (1181)
T PRK10876 802 LYVALTRSVWHCSL 815 (1181)
T ss_pred HHHHhhhHhhhhee
Confidence 46999999999998
No 33
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=43.80 E-value=18 Score=21.05 Aligned_cols=24 Identities=8% Similarity=0.040 Sum_probs=15.3
Q ss_pred HHHHHHHHhCCccccccccccccC
Q psy16286 49 QEIKNKLVTRRSINESFRLQCNKH 72 (92)
Q Consensus 49 ~~ll~~~~~~~~i~~~~~l~c~~h 72 (92)
.++++|++++|+|.+..+.+...|
T Consensus 30 ~eV~~YC~~~GWIip~~~~~iER~ 53 (57)
T PF08727_consen 30 PEVREYCEEQGWIIPATPTNIERD 53 (57)
T ss_dssp HHHHHHHHHHT--TT-SS--SSSS
T ss_pred HHHHHHHHHCCccccCccceeeec
Confidence 579999999999988766655555
No 34
>PF03089 RAG2: Recombination activating protein 2; InterPro: IPR004321 The variable portion of the genes encoding immunoglobulins and T cell receptors are assembled from component V, D, and J DNA segments by a site-specific recombination reaction termed V(D)J recombination. V(D)J recombination is targeted to specific sites on the chromosome by recombination signal sequences (RSSs) that flank antigen receptor gene segments. The RSS consists of a conserved heptamer (consensus, 5'-CACAGTG-3') and nonamer (consensus, 5'-ACAAAAACC-3') separated by a spacer of either 12 or 23 bp. Efficient recombination occurs between a 12-RSS and a 23-RSS, a restriction known as the 12/23 rule. V(D)J recombination can be divided into two phases, DNA cleavage and DNA joining. DNA cleavage requires two lymphocyte-specific factors, the products of the recombination activating genes, RAG1 and RAG2, which together recognise the RSSs and create double strand breaks at the RSS-coding segment junctions []. RAG-mediated DNA cleavage occurs in a synaptic complex termed the paired complex, which is constituted from two distinct RSS-RAG complexes, a 12-SC and a 23-SC (where SC stands for signal complex). The DNA cleavage reaction involves two distinct enzymatic steps, initial nicking that creates a 3'-OH between a coding segment and its RSS, followed by hairpin formation in which the newly created 3'-OH attacks a phosphodiester bond on the opposite DNA strand. This generates a blunt, 5' phosphorylated signal end containing all of the RSS elements, and a covalently sealed hairpin coding end. The second phase of V(D)J recombination, in which broken DNA fragments are processed and joined, is less well characterised. Signal ends are typically joined precisely to form a signal joint, whereas joining of the coding ends requires the hairpin structure to be opened and typically involves nucleotide addition and deletion before formation of the coding joint. The factors involved in these processes include ubiquitously expressed proteins involved in the repair of DNA double strand breaks by nonhomologous end joining, terminal deoxynucleotidyl transferase, and Artemis protein. In addition to their critical roles in RSS recognition and DNA cleavage, the RAG proteins may perform two distinct types of functions in the postcleavage phase of V(D)J. A structural function has been inferred from the finding that, after DNA cleavage in vitro, the DNA ends remain associated with the RAG proteins in a "four end" complex known as the cleaved signal complex. After release of the coding ends in vitro, and after coding joint formation in vivo, the RAG proteins remain in a stable signal end complex (SEC) containing the two signal ends. These postcleavage complexes may serve as essential scaffolds for the second phase of the reaction, with the RAG proteins acting to organise the DNA processing and joining events. The second type of RAG protein-mediated postcleavage activity is the catalysis of phosphodiester bond hydrolysis and strand transfer reactions. The RAG proteins are capable of opening hairpin coding ends in vitro. The RAG proteins also show 3' flap endonuclease activity that may contribute to coding end processing/joining and can utilise the 3' OH group on the signal ends to attack hairpin coding ends (forming hybrid or open/shut joints) or virtually any DNA duplex (forming a transposition product).; GO: 0003677 DNA binding, 0006310 DNA recombination, 0005634 nucleus
Probab=34.48 E-value=22 Score=27.48 Aligned_cols=37 Identities=16% Similarity=0.355 Sum_probs=30.1
Q ss_pred CccceeeccccceeEEEEccchhhhh---ccHHHHHHHHH
Q psy16286 18 VNRVCVALSRAKQGLFIMGNMKCLSA---DSQLWQEIKNK 54 (92)
Q Consensus 18 ~~RinVAlSRAk~gl~IiGn~~~L~~---~~~~w~~ll~~ 54 (92)
-.-|||--||-|.+.+++|-.+++-. .-+.|+.+++=
T Consensus 90 GHt~~vV~SrGKta~VlFGGRSY~P~~qRTTenWNsVvDC 129 (337)
T PF03089_consen 90 GHTINVVHSRGKTACVLFGGRSYMPPGQRTTENWNSVVDC 129 (337)
T ss_pred cceEEEEEECCcEEEEEECCcccCCccccchhhcceeccC
Confidence 45689999999999999999988842 36779988653
No 35
>KOG3992|consensus
Probab=32.42 E-value=25 Score=26.19 Aligned_cols=23 Identities=39% Similarity=0.465 Sum_probs=19.8
Q ss_pred CCccceeeccccceeEEEEccch
Q psy16286 17 TVNRVCVALSRAKQGLFIMGNMK 39 (92)
Q Consensus 17 ~~~RinVAlSRAk~gl~IiGn~~ 39 (92)
-.+++|||.|.|+.-=||+|+.+
T Consensus 64 cdE~lnvavsh~kqEkf~L~srs 86 (314)
T KOG3992|consen 64 CDEGLNVAVSHAKQEKFILGSRS 86 (314)
T ss_pred cccCcchhhhcccceeeEeeccc
Confidence 46799999999999999999554
No 36
>PF07057 TraI: DNA helicase TraI; InterPro: IPR009767 This entry represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI. TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [].; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0000746 conjugation; PDB: 3FLD_B.
Probab=31.63 E-value=16 Score=24.61 Aligned_cols=26 Identities=31% Similarity=0.432 Sum_probs=0.0
Q ss_pred eeccccceeEEEEccchhhhhccHHHHHHHHH
Q psy16286 23 VALSRAKQGLFIMGNMKCLSADSQLWQEIKNK 54 (92)
Q Consensus 23 VAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~ 54 (92)
|++||||..+-|--+- -+-|-..+..
T Consensus 1 V~lSRaKeHVQvYTDn------~~~W~~~~~~ 26 (126)
T PF07057_consen 1 VSLSRAKEHVQVYTDN------LEKWLAALEK 26 (126)
T ss_dssp --------------------------------
T ss_pred CcchhhhheeeeEeCC------HHHHHHHHHc
Confidence 7899999998876422 2336655544
No 37
>PF11772 EpuA: DNA-directed RNA polymerase subunit beta; InterPro: IPR024596 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the short 60-residue long bacterial family that is the beta subunit of the DNA-directed RNA polymerase, likely to be 2.7.7.6 from EC It is membrane-bound and is referred to by the name EpuA.
Probab=31.17 E-value=66 Score=17.86 Aligned_cols=27 Identities=19% Similarity=0.368 Sum_probs=18.6
Q ss_pred eEEEEccchhhh-hccHHHHHHHHHHHh
Q psy16286 31 GLFIMGNMKCLS-ADSQLWQEIKNKLVT 57 (92)
Q Consensus 31 gl~IiGn~~~L~-~~~~~w~~ll~~~~~ 57 (92)
|.-++|+.+.+. -+.+.|+++++.+..
T Consensus 19 GY~viG~G~p~~vf~~~tW~hi~d~~~g 46 (47)
T PF11772_consen 19 GYGVIGDGNPFDVFSPDTWQHIIDFFTG 46 (47)
T ss_pred eeeeeCCCCHHHhCCHHHHHHHHHHHcC
Confidence 556788765441 257889999988753
No 38
>PHA02778 major capsid L1 protein; Provisional
Probab=28.15 E-value=28 Score=28.35 Aligned_cols=33 Identities=27% Similarity=0.493 Sum_probs=28.0
Q ss_pred cCCccceeeccccceeEEEEccchhhhhccHHHHHH
Q psy16286 16 KTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEI 51 (92)
Q Consensus 16 ~~~~RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~l 51 (92)
...+|.||++===+..|+|||..-.+ +++|.+-
T Consensus 140 ~~D~R~nvs~DpKQ~Ql~ivGC~P~~---GehWd~a 172 (503)
T PHA02778 140 GTDDRQNVSFDPKQTQLFIVGCTPAL---GEHWDKA 172 (503)
T ss_pred CCCcceecccCccceeEEEEeccCCC---CCccCCC
Confidence 36899999999989999999988855 6788764
No 39
>KOG1624|consensus
Probab=27.59 E-value=34 Score=26.02 Aligned_cols=34 Identities=21% Similarity=0.256 Sum_probs=23.2
Q ss_pred ceeeccccce---eEEEEccchhhhhccHHHHHHHHHH
Q psy16286 21 VCVALSRAKQ---GLFIMGNMKCLSADSQLWQEIKNKL 55 (92)
Q Consensus 21 inVAlSRAk~---gl~IiGn~~~L~~~~~~w~~ll~~~ 55 (92)
+++||| ||. .|.|+++...-......|-.++++.
T Consensus 163 l~~ALS-~~~a~~~l~I~d~~~L~t~~pk~~~~l~~~~ 199 (290)
T KOG1624|consen 163 LKIALS-AKLAQDDLHIVDELGLPTGKPKYLLNLLAQR 199 (290)
T ss_pred HHHHHH-HHHhCCceEEecccCCCCCCcHHHHHHHHHH
Confidence 589999 554 8999999983323455666665554
No 40
>PRK02260 S-ribosylhomocysteinase; Provisional
Probab=26.47 E-value=92 Score=21.65 Aligned_cols=50 Identities=8% Similarity=0.230 Sum_probs=37.4
Q ss_pred ceeeccccceeEEEE--ccchhhhhccHHHHHHHHHH-HhCCcccccccccccc
Q psy16286 21 VCVALSRAKQGLFIM--GNMKCLSADSQLWQEIKNKL-VTRRSINESFRLQCNK 71 (92)
Q Consensus 21 inVAlSRAk~gl~Ii--Gn~~~L~~~~~~w~~ll~~~-~~~~~i~~~~~l~c~~ 71 (92)
|-+..=-+|-|+|++ |+.+.- .--+.|++.++++ ...+-|.-.-+.+|-+
T Consensus 75 I~~sPMGCrTGFYli~~g~~~~~-~i~~l~~~~l~~i~~~~~eVPga~~~~CGn 127 (158)
T PRK02260 75 IDISPMGCRTGFYLILIGTPDEE-DVADALKATLEDVLDDQEEVPGANEYQCGN 127 (158)
T ss_pred EEECCCccccccEEEEeCCCCHH-HHHHHHHHHHHHHHhhcCCCCCCChhcCCC
Confidence 556666788998874 544433 3467899999999 4788888888889977
No 41
>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]
Probab=24.56 E-value=88 Score=22.04 Aligned_cols=36 Identities=22% Similarity=0.385 Sum_probs=24.1
Q ss_pred cceeeccccceeEEEEccchhhhhccHHHHHHHHHHHhCC
Q psy16286 20 RVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRR 59 (92)
Q Consensus 20 RinVAlSRAk~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~ 59 (92)
-+-..++|||+-|.|+|..-. ++.|...+-.+.++.
T Consensus 27 v~ammIkkAkrPLlivGp~~~----dee~~E~~vKi~ekf 62 (170)
T COG1880 27 VVAMMIKKAKRPLLIVGPLAL----DEELLELAVKIIEKF 62 (170)
T ss_pred HHHHHHHhcCCceEEeccccc----CHHHHHHHHHHHHhc
Confidence 344568999999999994332 556666665555543
No 42
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=23.74 E-value=55 Score=29.27 Aligned_cols=27 Identities=15% Similarity=0.178 Sum_probs=22.3
Q ss_pred ccCCccceeeccccceeEEEEccchhh
Q psy16286 15 LKTVNRVCVALSRAKQGLFIMGNMKCL 41 (92)
Q Consensus 15 l~~~~RinVAlSRAk~gl~IiGn~~~L 41 (92)
+.+.+-+-||+||||+.+.|..+...+
T Consensus 716 ~ldR~llYVA~TRaR~~~~ly~~~~~~ 742 (1102)
T PRK13826 716 SLDRHLTYVAMTRHREDLQLYYGRRSF 742 (1102)
T ss_pred ccccchhHHhhccccceEEEEEchhhh
Confidence 345667899999999999999988744
No 43
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=23.64 E-value=42 Score=29.56 Aligned_cols=23 Identities=26% Similarity=0.260 Sum_probs=18.7
Q ss_pred cCCccceeeccccceeEEEEccc
Q psy16286 16 KTVNRVCVALSRAKQGLFIMGNM 38 (92)
Q Consensus 16 ~~~~RinVAlSRAk~gl~IiGn~ 38 (92)
.+.+-+-||+||||+.+.++...
T Consensus 681 ~~r~l~YVAiTRar~~v~l~~~~ 703 (988)
T PRK13889 681 MDAHSSYVALSRHRDGVDLHYGR 703 (988)
T ss_pred cccchhHHhhhhhhheEEEEecC
Confidence 35567899999999999998643
No 44
>PF02664 LuxS: S-Ribosylhomocysteinase (LuxS); InterPro: IPR003815 In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. For example, enteric bacteria use quorum sensing to regulate several traits that allow them to establish and maintain infection in their host, including motility, biofilm formation, and virulence-specific genes []. The LuxS/AI-2 system is one of several quorum sensing mechanisms. AI-2 (autoinducer-2) is a signalling molecule that functions in interspecies communication by regulating niche-specific genes with diverse functions in various bacteria, often in response to population density. LuxS (S-ribosylhomocysteinase; 4.4.1.21 from EC) is an autoinducer-production protein that has a metabolic function as a component of the activated methyl cycle. LuxS converts S-ribosylhomocysteine to homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD); DPD can then spontaneously cyclise to active AI-2 [, ]. LuxS is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases []. ; GO: 0005506 iron ion binding, 0009372 quorum sensing; PDB: 1J6X_B 1VGX_A 1INN_B 1VJE_B 1J6V_A 1VH2_A 1J6W_B 1JOE_B 1J98_A 1IE0_A ....
Probab=22.95 E-value=1.4e+02 Score=20.78 Aligned_cols=51 Identities=14% Similarity=0.257 Sum_probs=33.0
Q ss_pred cceeeccccceeEEEE--ccchhhhhccHHHHHHHHHHHhC-Ccccccccccccc
Q psy16286 20 RVCVALSRAKQGLFIM--GNMKCLSADSQLWQEIKNKLVTR-RSINESFRLQCNK 71 (92)
Q Consensus 20 RinVAlSRAk~gl~Ii--Gn~~~L~~~~~~w~~ll~~~~~~-~~i~~~~~l~c~~ 71 (92)
=|-+..=-+|-|+|++ |..+.- .-.+.|++.++++.+- |.|.-.-+.+|-+
T Consensus 74 iI~~gPMGCrTGFYli~~g~~~~~-~i~~l~~~~l~~i~~~~~eIPga~~~qCGn 127 (157)
T PF02664_consen 74 IIDFGPMGCRTGFYLILWGDPSSE-DIADLLKETLEFILEFEGEIPGANEVQCGN 127 (157)
T ss_dssp EEEEEE-TTSSEEEEEEESS--HH-HHHHHHHHHHHHHHT-SSSSTT-STTTSTT
T ss_pred EEEecCcccccccEEEEeCCCCHH-HHHHHHHHHHHHHHhcCCCCCCcChhcCCC
Confidence 3455666789999985 665433 3367899998888764 4777777788876
No 45
>KOG1324|consensus
Probab=20.88 E-value=52 Score=23.57 Aligned_cols=18 Identities=33% Similarity=0.396 Sum_probs=14.3
Q ss_pred CCccCCccceeeccccce
Q psy16286 13 GFLKTVNRVCVALSRAKQ 30 (92)
Q Consensus 13 GFl~~~~RinVAlSRAk~ 30 (92)
.|..-++||||-|||.-.
T Consensus 62 k~RPL~gRiNiVLSR~~~ 79 (190)
T KOG1324|consen 62 KFRPLPGRINVVLSRSLK 79 (190)
T ss_pred ccCCCCCceEEEEecccC
Confidence 366778999999999543
No 46
>KOG0545|consensus
Probab=20.12 E-value=48 Score=25.37 Aligned_cols=58 Identities=16% Similarity=0.340 Sum_probs=35.8
Q ss_pred ceeEEEEccchhhhhccHHHHHHHHHHHhCCcc----cc----ccccccccCCCEEEeCCccchhhhccc
Q psy16286 29 KQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSI----NE----SFRLQCNKHRAVTIIRAVEDFEACCCL 90 (92)
Q Consensus 29 k~gl~IiGn~~~L~~~~~~w~~ll~~~~~~~~i----~~----~~~l~c~~h~~~~~v~~~~df~~~~~~ 90 (92)
|--=+|||+..-| +.|..+++.|.-...- .. ..|+....-..+..=++|.+|..+||.
T Consensus 57 kPmeiiiGkkFkL----~VwE~il~tM~v~EvaqF~~d~~~~vqYPfvsksLRdia~GK~p~e~~~H~Cg 122 (329)
T KOG0545|consen 57 KPMEIIIGKKFKL----EVWEIILTTMRVHEVAQFWCDTIHTVQYPFVSKSLRDIAQGKDPTEWHRHCCG 122 (329)
T ss_pred CCeEEeecccccc----HHHHHHHHHHhhhhHHHhhhhhhheeechhHHHHHHHHhcCCCcchhhhhhhh
Confidence 3355789987766 7899999999754221 01 111111111444556889999998884
Done!