Query 047960
Match_columns 371
No_of_seqs 268 out of 1497
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 04:57:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1802 RNA helicase nonsense 100.0 7.4E-41 1.6E-45 338.2 13.5 201 1-206 635-840 (935)
2 PF13087 AAA_12: AAA domain; P 100.0 1.6E-38 3.4E-43 288.3 7.6 180 1-181 18-199 (200)
3 KOG1803 DNA helicase [Replicat 100.0 1.7E-37 3.7E-42 313.1 11.8 196 1-206 426-632 (649)
4 TIGR00376 DNA helicase, putati 100.0 9.1E-37 2E-41 321.6 17.6 197 1-206 426-634 (637)
5 COG1112 Superfamily I DNA and 100.0 1.6E-30 3.4E-35 279.7 15.0 196 1-207 555-754 (767)
6 KOG1807 Helicases [Replication 100.0 1.3E-29 2.9E-34 259.9 13.3 187 2-203 789-977 (1025)
7 KOG1801 tRNA-splicing endonucl 100.0 7.3E-29 1.6E-33 267.8 13.9 210 2-212 605-819 (827)
8 KOG1805 DNA replication helica 100.0 5.6E-29 1.2E-33 261.1 8.2 191 2-204 864-1077(1100)
9 KOG1804 RNA helicase [RNA proc 99.8 8.9E-21 1.9E-25 200.0 4.9 193 3-207 525-724 (775)
10 KOG1806 DEAD box containing he 99.5 1.3E-14 2.9E-19 153.7 5.7 178 1-186 1067-1248(1320)
11 PRK11054 helD DNA helicase IV; 98.6 2.9E-07 6.2E-12 98.8 12.0 86 94-182 559-664 (684)
12 PF13538 UvrD_C_2: UvrD-like h 97.9 5.1E-06 1.1E-10 67.3 1.1 50 126-178 55-104 (104)
13 PRK13909 putative recombinatio 97.6 0.00031 6.7E-09 78.2 10.1 60 124-183 605-704 (910)
14 COG1074 RecB ATP-dependent exo 97.6 0.00053 1.2E-08 77.9 12.2 63 125-187 742-842 (1139)
15 COG3973 Superfamily I DNA and 97.3 0.0012 2.6E-08 68.9 9.0 146 1-180 592-745 (747)
16 TIGR00609 recB exodeoxyribonuc 97.2 0.002 4.4E-08 73.1 11.4 56 126-181 652-737 (1087)
17 TIGR01448 recD_rel helicase, p 96.9 0.00042 9.2E-09 75.2 1.6 52 129-184 650-701 (720)
18 PF01443 Viral_helicase1: Vira 96.7 0.00066 1.4E-08 62.6 1.7 49 128-178 184-233 (234)
19 PF13361 UvrD_C: UvrD-like hel 96.7 0.0046 1E-07 59.6 7.6 94 1-117 1-99 (351)
20 TIGR01447 recD exodeoxyribonuc 96.7 0.00081 1.8E-08 71.3 2.5 55 126-184 520-574 (586)
21 PF13361 UvrD_C: UvrD-like hel 96.6 0.00079 1.7E-08 65.0 1.1 58 124-181 285-350 (351)
22 cd00221 Vsr Very Short Patch R 96.6 0.0006 1.3E-08 57.1 0.2 68 225-305 26-113 (115)
23 COG0507 RecD ATP-dependent exo 96.4 0.0017 3.7E-08 70.2 2.4 54 127-185 622-675 (696)
24 PRK10875 recD exonuclease V su 96.3 0.0023 5E-08 68.2 2.9 54 127-184 539-592 (615)
25 cd01038 Endonuclease_DUF559 Do 96.2 0.00064 1.4E-08 56.2 -1.9 91 210-322 13-107 (108)
26 TIGR02768 TraA_Ti Ti-type conj 96.1 0.0065 1.4E-07 66.3 4.7 56 129-192 666-721 (744)
27 PRK09767 hypothetical protein; 95.6 0.0018 4E-08 54.4 -1.5 79 231-326 34-114 (117)
28 TIGR01075 uvrD DNA helicase II 95.3 0.016 3.5E-07 63.0 4.3 56 125-180 547-610 (715)
29 PRK10919 ATP-dependent DNA hel 95.3 0.017 3.7E-07 62.4 4.2 56 125-180 550-612 (672)
30 TIGR02785 addA_Gpos recombinat 95.1 0.023 5E-07 65.4 4.8 60 125-184 781-882 (1232)
31 TIGR01073 pcrA ATP-dependent D 94.9 0.016 3.6E-07 63.0 2.6 57 125-181 548-612 (726)
32 PRK11773 uvrD DNA-dependent he 94.8 0.027 5.8E-07 61.3 4.1 56 125-180 552-615 (721)
33 TIGR02784 addA_alphas double-s 94.8 0.051 1.1E-06 62.2 6.5 73 125-197 774-891 (1141)
34 TIGR01073 pcrA ATP-dependent D 94.1 0.17 3.7E-06 55.2 8.4 94 1-117 273-366 (726)
35 TIGR01074 rep ATP-dependent DN 94.0 0.03 6.4E-07 60.3 2.3 58 124-181 549-613 (664)
36 KOG1804 RNA helicase [RNA proc 93.6 0.063 1.4E-06 58.3 3.7 188 3-202 339-542 (775)
37 PRK10876 recB exonuclease V su 93.3 0.047 1E-06 62.6 2.4 53 125-177 734-815 (1181)
38 PRK11773 uvrD DNA-dependent he 93.2 0.27 5.8E-06 53.6 7.9 93 1-117 277-369 (721)
39 TIGR01075 uvrD DNA helicase II 93.0 0.3 6.6E-06 53.2 8.0 93 1-117 272-364 (715)
40 PRK13889 conjugal transfer rel 91.6 0.14 3.1E-06 57.4 3.3 46 130-183 660-705 (988)
41 PRK13826 Dtr system oriT relax 91.5 0.17 3.6E-06 57.4 3.8 46 129-182 695-740 (1102)
42 TIGR01074 rep ATP-dependent DN 90.5 0.94 2E-05 48.8 8.3 94 1-117 270-363 (664)
43 PRK10876 recB exonuclease V su 90.3 1.2 2.6E-05 51.3 9.3 112 1-117 441-573 (1181)
44 PF04480 DUF559: Protein of un 89.6 0.0076 1.6E-07 49.8 -6.7 76 230-322 30-107 (108)
45 COG0210 UvrD Superfamily I DNA 89.6 0.16 3.6E-06 54.5 1.6 56 126-181 554-618 (655)
46 TIGR00632 vsr DNA mismatch end 87.2 0.14 3.1E-06 42.9 -0.6 60 241-302 34-113 (117)
47 PRK10919 ATP-dependent DNA hel 86.0 2.8 6.2E-05 45.4 8.4 94 1-117 271-364 (672)
48 TIGR02784 addA_alphas double-s 84.6 3.2 6.9E-05 47.8 8.3 46 72-117 555-607 (1141)
49 PF09848 DUF2075: Uncharacteri 84.4 0.51 1.1E-05 46.8 1.6 52 128-179 274-350 (352)
50 TIGR02785 addA_Gpos recombinat 82.6 3.7 8E-05 47.7 7.8 47 71-117 543-598 (1232)
51 PRK14712 conjugal transfer nic 81.1 0.91 2E-05 53.4 2.2 53 128-182 1265-1317(1623)
52 PRK13709 conjugal transfer nic 80.0 1.2 2.6E-05 53.0 2.7 53 128-182 1394-1446(1747)
53 PF00580 UvrD-helicase: UvrD/R 79.8 2.8 6E-05 39.7 4.8 50 88-137 38-102 (315)
54 TIGR02760 TraI_TIGR conjugativ 72.3 2.1 4.6E-05 51.8 2.1 49 129-182 1449-1497(1960)
55 COG3972 Superfamily I DNA and 69.1 7.7 0.00017 40.5 4.9 103 71-179 454-574 (660)
56 COG3410 Uncharacterized conser 68.8 3.6 7.9E-05 36.5 2.2 55 128-182 90-176 (191)
57 PRK10481 hypothetical protein; 66.0 17 0.00036 34.1 6.2 24 94-117 128-151 (224)
58 COG1724 Predicted RNA binding 64.6 2.3 4.9E-05 31.9 0.1 23 290-312 14-37 (66)
59 COG0210 UvrD Superfamily I DNA 61.2 24 0.00053 37.9 7.3 94 1-117 277-371 (655)
60 PF13245 AAA_19: Part of AAA d 51.8 37 0.00079 25.9 4.9 34 95-135 42-75 (76)
61 KOG2340 Uncharacterized conser 50.0 30 0.00066 36.5 5.3 82 91-172 289-376 (698)
62 TIGR02990 ectoine_eutA ectoine 49.3 49 0.0011 31.2 6.4 15 94-108 119-133 (239)
63 COG2852 Very-short-patch-repai 42.7 3.4 7.3E-05 35.0 -2.3 77 231-324 44-122 (129)
64 TIGR02773 addB_Gpos ATP-depend 42.5 88 0.0019 36.3 8.3 56 124-179 579-663 (1158)
65 cd00899 b4GalT Beta-4-Galactos 38.4 47 0.001 31.0 4.3 74 96-188 2-82 (219)
66 PF07302 AroM: AroM protein; 36.5 1.8E+02 0.0038 27.3 7.8 49 94-147 124-186 (221)
67 cd01037 Restriction_endonuclea 34.3 16 0.00035 26.3 0.5 51 249-302 24-78 (80)
68 PF04592 SelP_N: Selenoprotein 33.3 1.3E+02 0.0028 28.5 6.3 63 84-146 51-117 (238)
69 PRK11054 helD DNA helicase IV; 32.2 60 0.0013 35.5 4.5 43 90-135 236-278 (684)
70 KOG2108 3'-5' DNA helicase [Re 32.0 24 0.00052 39.0 1.5 53 126-178 674-740 (853)
71 cd00133 PTS_IIB PTS_IIB: subun 29.4 1E+02 0.0022 22.5 4.3 49 98-146 2-53 (84)
72 KOG3553 Tax interaction protei 28.2 28 0.00061 28.5 0.9 62 263-337 9-71 (124)
73 PF13778 DUF4174: Domain of un 27.8 2.7E+02 0.0059 23.0 6.9 59 138-198 40-109 (118)
74 PF13733 Glyco_transf_7N: N-te 27.3 33 0.00072 29.6 1.3 73 95-186 46-125 (136)
75 TIGR01447 recD exodeoxyribonuc 27.2 2.8E+02 0.0061 29.7 8.5 95 96-198 194-315 (586)
76 cd05568 PTS_IIB_bgl_like PTS_I 26.1 86 0.0019 23.5 3.4 50 97-146 2-53 (85)
77 COG4752 Uncharacterized protei 24.8 90 0.0019 27.5 3.4 87 94-184 42-146 (190)
78 PF13604 AAA_30: AAA domain; P 23.1 1.8E+02 0.004 26.0 5.5 85 95-197 46-149 (196)
79 KOG2924 Deoxyhypusine synthase 22.0 93 0.002 30.2 3.2 73 126-198 228-310 (366)
80 COG4474 Uncharacterized protei 21.3 1.1E+02 0.0024 27.5 3.3 18 92-109 68-85 (180)
No 1
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=100.00 E-value=7.4e-41 Score=338.17 Aligned_cols=201 Identities=37% Similarity=0.626 Sum_probs=171.2
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCC-CCcccCCCC-CCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINL-PDEVYYKDP-VLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGV 78 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~-~~~~~~~~~-~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv 78 (371)
|||.+||||||.|++|+|..||+|.|.++-..... +....++.| ...|+.|+... |.++...+++|+.|..||..+.
T Consensus 635 ~~L~vQYRmhP~lSefpsn~fY~G~LqnGVT~~~R~~~g~~~pwp~p~~pl~fy~~~-g~eeisasGtSf~Nr~Ea~~~e 713 (935)
T KOG1802|consen 635 IRLQVQYRMHPALSEFPSNMFYEGELQNGVTEIERSPLGVDFPWPQPDKPLFFYVCY-GQEEISASGTSFLNRTEAANCE 713 (935)
T ss_pred eEEEEeeeeChhhhhcchhhhccchhhcCcchhhhccCCCCCCCCCCCCccceEEec-cceeeeccccceecHHHHHHHH
Confidence 68999999999999999999999999987543322 222222222 24677777765 6777777788999999999999
Q ss_pred HHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhh--hccCCCCCeEEccccCCCCccccEEEEEccccCCC-Cc
Q 047960 79 CLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNV--LNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GV 155 (371)
Q Consensus 79 ~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~--~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~-~~ 155 (371)
.|+..|++. |+.+.+|||||||.+|+.+|-+.|... +..+....|.|.|||+|||+|+|+||+||||++.+ ++
T Consensus 714 kii~~l~~~----gv~~~qIGVITpYegQr~~i~~ym~~~gsl~~~ly~~veVasVDaFQGrEKdfIIlSCVRsn~~qgI 789 (935)
T KOG1802|consen 714 KIITKLLKS----GVKPSQIGVITPYEGQRSYIVNYMQTNGSLHKDLYKEVEVASVDAFQGREKDFIILSCVRSNEHQGI 789 (935)
T ss_pred HHHHHHHHc----CCCHHHeeeecccchhHHHHHHHHHhcCccccchhheeEEEeeccccCcccceEEEEEeeccccccc
Confidence 999988663 799999999999999999999987542 33333567899999999999999999999999975 49
Q ss_pred cCCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCceecc
Q 047960 156 GFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDM 206 (371)
Q Consensus 156 gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~~~ 206 (371)
||+.|+||||||+||||.+|+||||+..|++.++|.++|.|++++.+++..
T Consensus 790 GFl~d~RRlNVaLTRaK~glvivGN~~~L~k~~LW~~li~h~~eke~l~eg 840 (935)
T KOG1802|consen 790 GFLNDPRRLNVALTRAKYGLVIVGNPKVLRKHPLWGHLITHYKEKEVLVEG 840 (935)
T ss_pred ccccCchhhhhhhhhcccceEEecCHHHhhhchHHHHHHHHhhcccceeec
Confidence 999999999999999999999999999999999999999999999999874
No 2
>PF13087 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A 2XZL_A.
Probab=100.00 E-value=1.6e-38 Score=288.33 Aligned_cols=180 Identities=41% Similarity=0.629 Sum_probs=124.9
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCc-ccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDE-VYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVC 79 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~-~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~ 79 (371)
++|++||||||+|++|+|+.||+|+|.+.++....+.. .........|+.|+++.+.........+|+.|..||++|+.
T Consensus 18 ~~L~~qyR~~~~I~~~~s~~fY~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~s~~N~~Ea~~i~~ 97 (200)
T PF13087_consen 18 VMLTEQYRMHPEIADFSSRLFYNGKLVSGPSVKNRPAPLLKLLPSPQNPIVFIDVSGSESSSESSQTSYYNPDEAEFIVE 97 (200)
T ss_dssp EE--EE-SS-HHHHHHHHHHHSTT--EESS-TCCCS-T-----SSTTSSEEEEE----EEEETTC-SCEEEHHHHHHHHH
T ss_pred eecccccCCCHHHHHHHHHHHhchhcccCcccccccccccccccCCCCceEEEecccccccccccccceechhhHHHHHH
Confidence 47999999999999999999999999998876554433 11223345689999999766655544479999999999999
Q ss_pred HHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCC-CccCC
Q 047960 80 LYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GVGFV 158 (371)
Q Consensus 80 lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~-~~gfl 158 (371)
++..|....... ..+.+|||||||++|+.+|++.|.+.........+.|+|||+|||+|+||||||+|+++.. ..||+
T Consensus 98 ~~~~l~~~~~~~-~~~~~I~Iitpy~~Q~~~i~~~l~~~~~~~~~~~~~v~Tvd~~QG~E~diVi~s~v~~~~~~~~~f~ 176 (200)
T PF13087_consen 98 LVRDLLDNGPDS-NKPSSIGIITPYRAQVALIRKALRSRYPSSPIKDIKVSTVDSFQGQEADIVIVSLVRTNSSSNIGFL 176 (200)
T ss_dssp HHHHHHHTT--G----GGEEEEES-HHHHHHHHHHHHHCSTCHHHHCSEEEEHHHHTT--EEEEEEEE---STTS-SGGG
T ss_pred HHhhhhhccccc-cccCCceEEcCchHHHHHHHHHHhhhccccccceEEEecHHHhccccceEEEEEeccCCcccccccc
Confidence 998886632111 0247999999999999999999986543322223999999999999999999999999743 48999
Q ss_pred CCCCchhhhhHhhcccEEEEeec
Q 047960 159 ADIRRMNVALTRARRALWVMGNA 181 (371)
Q Consensus 159 ~d~rRLNVAlSRAK~~liVvGn~ 181 (371)
.+++|+|||+||||.++|||||.
T Consensus 177 ~~~~r~nVA~SRAk~~liiig~~ 199 (200)
T PF13087_consen 177 NDPNRLNVALSRAKSGLIIIGNP 199 (200)
T ss_dssp C-HHHHHHHHTSEEEEEEEEE-H
T ss_pred CCcCeeeeeHHHHhcCEEEEecC
Confidence 99999999999999999999986
No 3
>KOG1803 consensus DNA helicase [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-37 Score=313.14 Aligned_cols=196 Identities=33% Similarity=0.541 Sum_probs=162.8
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCC-----CCcccCCCCCCCcEEEEEcCCCee-eecCCC---CCccCH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINL-----PDEVYYKDPVLRPYVFFDVIHGRE-SHRGGS---VSYQNV 71 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~-----~~~~~~~~~~~~p~~f~~v~~g~~-~~~~~~---~S~~N~ 71 (371)
++|++|||||..|+.|+|..||+|+|+++.++... +... .......|++++|+.+... +.++.. .|+.|.
T Consensus 426 ~~Ln~QYRMn~~Im~wsn~~fY~~qlka~~~v~~~lL~dl~~v~-~t~~t~~PlvlvDT~~~~~~e~~~e~~~~~S~~N~ 504 (649)
T KOG1803|consen 426 ILLNEQYRMNEKIMNWSNEVFYNGQLKAASSVASHLLRDLPNVL-ATESTKSPLVLVDTQGEKDEEKRGEEEELGSKYNE 504 (649)
T ss_pred hhhhhhhcchHHHhhCcHhhhcCCeeeecchhhhhhhhcccCCC-CccccCCcEEEEecccchhhhhccchhhccccCCH
Confidence 58999999999999999999999999998876642 2211 1223578999999986432 222222 288999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccC
Q 047960 72 DEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRAS 151 (371)
Q Consensus 72 ~EA~~Vv~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~ 151 (371)
.||+.|...+..|.. .|+++.+|||||||++|+.+|+... ......+.|+|||.|||+|+|+||||+||+|
T Consensus 505 gEa~Iv~~Hv~~L~~----~gV~p~dIaVIsPY~aQv~llR~~~-----~~~~~~veV~TVD~fQGrEkdvVIfsmVRSN 575 (649)
T KOG1803|consen 505 GEAKIVMEHVKRLLE----AGVQPSDIAVISPYNAQVSLLREED-----EEDFRDVEVGTVDGFQGREKDVVIFSLVRSN 575 (649)
T ss_pred HHHHHHHHHHHHHHH----cCCChhHeEEeccchHHHHHHhhcc-----cccCccceeecccccccceeeEEEEEEEeec
Confidence 999988877666644 4899999999999999999998321 1334568999999999999999999999999
Q ss_pred CCC-ccCCCCCCchhhhhHhhcccEEEEeeccccc-CCchHHHHHHHHHhCCceecc
Q 047960 152 NHG-VGFVADIRRMNVALTRARRALWVMGNAGALT-QSDDWAALIADSKARNCYMDM 206 (371)
Q Consensus 152 ~~~-~gfl~d~rRLNVAlSRAK~~liVvGn~~~L~-~~~~w~~ll~~a~~~~~~~~~ 206 (371)
+.+ +||+.+.||||||+||||+++.||||..++. .+..+++++.|+.+++.++.+
T Consensus 576 ~k~evGFL~e~RRLNVAiTRaRRh~~vIgds~tl~~~~~~l~k~~~f~~~~~~~~~p 632 (649)
T KOG1803|consen 576 DKGEVGFLGETRRLNVAITRARRHFVVIGDSRTLKEGNEFLKKLVEFLEENKLVFGP 632 (649)
T ss_pred CcccccccCCcceeeEEEEeccceEEEEcCcHHHHhhHHHHHHHHHHhhhcceeccc
Confidence 876 9999999999999999999999999999999 888999999999988877644
No 4
>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=100.00 E-value=9.1e-37 Score=321.64 Aligned_cols=197 Identities=38% Similarity=0.564 Sum_probs=165.2
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCC-----CCcccC----CCCCCCcEEEEEcCCCee--eecCCCCCcc
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINL-----PDEVYY----KDPVLRPYVFFDVIHGRE--SHRGGSVSYQ 69 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~-----~~~~~~----~~~~~~p~~f~~v~~g~~--~~~~~~~S~~ 69 (371)
.||++||||||+|++|+|+.||+|+|++++++... |..... ......|++|+++.+... .....+.|+.
T Consensus 426 ~~L~~QYRMh~~I~~f~s~~fY~g~L~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~p~~fidt~g~~~~e~~~~~~~S~~ 505 (637)
T TIGR00376 426 RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATDSEDDLETEIPLLFIDTSGCELFELKEADSTSKY 505 (637)
T ss_pred eecchhcCCCHHHHhhhHHhhcCCccccCcchhhhhhhhcccccccccccccCCCCCEEEEECCCccccccccCCCCCcC
Confidence 48999999999999999999999999988765432 111100 011235899999986432 1233456899
Q ss_pred CHHHHHHHHHHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccc
Q 047960 70 NVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVR 149 (371)
Q Consensus 70 N~~EA~~Vv~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vr 149 (371)
|..||..|+.++..+.+ .|+++.+|||||||++|+.+|++.|.+. ..++.|.|||+|||+|+|+||+|+|+
T Consensus 506 N~~EA~~V~~~v~~l~~----~g~~~~~IgVItPY~aQv~~L~~~l~~~-----~~~i~v~TVd~fQG~E~DvIi~S~vr 576 (637)
T TIGR00376 506 NPGEAELVSEIIQALVK----MGVPANDIGVITPYDAQVDLLRQLLEHR-----HIDIEVSSVDGFQGREKEVIIISFVR 576 (637)
T ss_pred CHHHHHHHHHHHHHHHh----cCCCcceEEEEcccHHHHHHHHHHHHhh-----CCCeEEccccccCCccccEEEEEEEe
Confidence 99999999999888755 3788999999999999999999988542 34699999999999999999999999
Q ss_pred cCCC-CccCCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCceecc
Q 047960 150 ASNH-GVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDM 206 (371)
Q Consensus 150 s~~~-~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~~~ 206 (371)
++.. .+||+.+.||||||+||||.+||||||..+|..++.|+.|++||++++++..+
T Consensus 577 sn~~~~~gFl~d~rRLNVAlTRAK~~LiIvGn~~~l~~~~~~~~li~~~~~~~~~~~~ 634 (637)
T TIGR00376 577 SNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVREA 634 (637)
T ss_pred cCCCCCcccccCcceeeeehhhhhCceEEEECHHHhccChHHHHHHHHHHHCCCEEcC
Confidence 9874 48999999999999999999999999999999999999999999999998765
No 5
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]
Probab=99.97 E-value=1.6e-30 Score=279.72 Aligned_cols=196 Identities=37% Similarity=0.557 Sum_probs=165.4
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCC--CCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDP--VLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGV 78 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~--~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv 78 (371)
.+|++||||||.|+.|+|+.||+++|..+............... ...|+.++++.+..+ ...+.++.|..||..+.
T Consensus 555 ~~L~~qyRm~~~i~~f~s~~~y~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~n~~e~~~~~ 632 (767)
T COG1112 555 YLLRVQYRMHPDIIAFSSKVFYNGRLEVHTSFLAFTLLDGEIPEVVISNPLEFYDTLGAEE--FFESKSKLNELEAEIVK 632 (767)
T ss_pred eeeeeecccChhhhhCchhhccCCccccCcchhhhhhhccccccccccCceEEEEecCccc--ccCccceecHHHHHHHH
Confidence 47999999999999999999999999988765443221111111 246888998875544 34456889999999999
Q ss_pred HHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCC--Ccc
Q 047960 79 CLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH--GVG 156 (371)
Q Consensus 79 ~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~--~~g 156 (371)
.++..+.+. +..+.+|||||||++|+.+|++.+.... ..+.|+|||+|||+|+||||+|+|+++.. ++|
T Consensus 633 ~~~~~~~~~----~~~~~~igvis~y~~q~~~i~~~~~~~~-----~~v~v~tvd~fQG~EkdvIi~S~v~s~~~~~~i~ 703 (767)
T COG1112 633 VIVDELLKD----GLEENDIGVISPYRAQVSLIRRLLNEAG-----KGVEVGTVDGFQGREKDVIILSLVRSNDDKGEIG 703 (767)
T ss_pred HHHHHHHHc----CCcHHHcceecccHHHHHHHHHHHHhcC-----CceEEeeccccCCccCcEEEEEEEeecCCCcccc
Confidence 988887653 6777789999999999999999886533 57999999999999999999999999976 699
Q ss_pred CCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCceeccC
Q 047960 157 FVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMD 207 (371)
Q Consensus 157 fl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~~~~ 207 (371)
|+.++||||||+||||.+|||||+...+...+.|+.++.+++..+++....
T Consensus 704 ~l~d~rRLNVAlTRAk~~livvg~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 754 (767)
T COG1112 704 FLGDPRRLNVALTRAKRKLIVVGSSSTLESDPLYKRLINDLKRKGLLAELN 754 (767)
T ss_pred ccCchhhhhhhhhcccceEEEEcChhHhhhchhHHHHHHHHHhcCcEeecc
Confidence 999999999999999999999999999999999999999999998887665
No 6
>KOG1807 consensus Helicases [Replication, recombination and repair]
Probab=99.96 E-value=1.3e-29 Score=259.89 Aligned_cols=187 Identities=30% Similarity=0.443 Sum_probs=161.4
Q ss_pred ccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHHH
Q 047960 2 LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLY 81 (371)
Q Consensus 2 ~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~lv 81 (371)
+|+.||||||.|+......||++ |.+++++...|+..++. ..+.|+.+....+ .....|+.|..||.++++++
T Consensus 789 rLn~QhRM~p~IsrllvpsiYdd-l~d~esvk~yedI~gms----~nlfFv~hnspee--~~de~S~~NlhEa~mlv~l~ 861 (1025)
T KOG1807|consen 789 RLNLQHRMRPCISRLLVPSIYDD-LLDSESVKEYEDIRGMS----KNLFFVQHNSPEE--CMDEMSIGNLHEAGMLVKLT 861 (1025)
T ss_pred hhhHHhhhchHHHHHhhHHHhhh-hhcchhhcccccccccc----ceeeEEecCCccc--CcchhhhhhHHHHHHHHHHH
Confidence 68999999999999999999986 88899998888766543 3455665543222 22337999999999999999
Q ss_pred HHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCCC-ccCCCC
Q 047960 82 EHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHG-VGFVAD 160 (371)
Q Consensus 82 ~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~-~gfl~d 160 (371)
++|++ .++.+.+|.|+|+|.+|..+|+++|.+.+.. .|.|.|||+|||.|+|||++|+||++..+ +||+.-
T Consensus 862 kyli~----q~y~psdIviLttY~gQk~ci~rllp~~~~s----tv~VatVDsfQGeEndIVLlSLVRsn~~griGFL~~ 933 (1025)
T KOG1807|consen 862 KYLIQ----QQYKPSDIVILTTYNGQKECIKRLLPQNYRS----TVQVATVDSFQGEENDIVLLSLVRSNISGRIGFLRQ 933 (1025)
T ss_pred HHHHh----cCCCccceEEEeechhHHHHHHHHhHHHhcC----cceEEEeccccCccccEEEEEEEeccCCceeeeeec
Confidence 99866 4899999999999999999999999876644 49999999999999999999999999876 999999
Q ss_pred CCchhhhhHhhcccEEEEeecccccC-CchHHHHHHHHHhCCce
Q 047960 161 IRRMNVALTRARRALWVMGNAGALTQ-SDDWAALIADSKARNCY 203 (371)
Q Consensus 161 ~rRLNVAlSRAK~~liVvGn~~~L~~-~~~w~~ll~~a~~~~~~ 203 (371)
++|++||+||||.+|+||||...+.. .++|.++++-.++.+.+
T Consensus 934 anRvCVALSRAr~glyiiGN~q~la~~~pLWnkivntLrenn~I 977 (1025)
T KOG1807|consen 934 ANRVCVALSRARWGLYIIGNVQILADTPPLWNKIVNTLRENNAI 977 (1025)
T ss_pred cchhhhhhhhhhcceEEecceeecccCchhHHHHHHHHHhcccc
Confidence 99999999999999999999999877 68999999999887654
No 7
>KOG1801 consensus tRNA-splicing endonuclease positive effector (SEN1) [RNA processing and modification]
Probab=99.96 E-value=7.3e-29 Score=267.77 Aligned_cols=210 Identities=43% Similarity=0.721 Sum_probs=184.7
Q ss_pred ccccccCCchhhhhcchhhccCCccccCcccc-CCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 2 LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVI-NLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 2 ~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~-~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
+|+.||||||+|+.|+|+.||+++|++.+.+. ......++.++...|+.|+++..|.+...++ .|..|..|+.++..+
T Consensus 605 ~L~vqyrmhp~Is~fP~~~fy~~~i~d~~~vs~~~~~~~~~~~~~~~~y~f~~v~~g~e~~~~~-~s~~n~~E~~~~~~~ 683 (827)
T KOG1801|consen 605 LLTVQYRMHPEISRFPSKEFYGGRLKDVNNVSESNTVKLWHSGETFGPYPFFNVHYGKERAGGG-KSPVNNEEVRFVGAI 683 (827)
T ss_pred eecceeecCCccccCccccccccccccCcccchhhccccCcCCCccCceEEEEecccccccCCC-CCcccHHHHHHHHHH
Confidence 69999999999999999999999999888877 4455566777888999999999888776554 688999999999999
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCC--CCeEEccccCCCCccccEEEEEccccCCCC-ccC
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEG--KDLYINTVDAFQGQERDVIIMSCVRASNHG-VGF 157 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~--~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~-~gf 157 (371)
+.++.+...+....+..+|||+||+.|+..+++.+...+..-.. ..+.+.|||.|||.|+||||+|+|+++..+ +||
T Consensus 684 ~~~l~~~~~~~~~~~~~vGvisPY~~q~~~l~~~~~~~~~~~~~~~~~i~v~tvD~fqg~e~diii~s~vrs~~~g~igf 763 (827)
T KOG1801|consen 684 YSRLYKVSQPQVSVPGSVGVISPYKNQVKALRERFPEAYSLLLANNVDLSVSTVDSFQGGERDIIIISTVRSIDEGSIGF 763 (827)
T ss_pred HHHHHhhccccCCCCcceeeECchHHHHHHHHHHHHHHhcchhcccceeEEEecccccCCCCceeEEEEEEecccCccch
Confidence 99999887776666789999999999999999988776653332 478999999999999999999999999877 799
Q ss_pred CCCCCchhhhhHhhcccEEEEeecccccCCch-HHHHHHHHHhCCceeccCCCChh
Q 047960 158 VADIRRMNVALTRARRALWVMGNAGALTQSDD-WAALIADSKARNCYMDMDSLPKE 212 (371)
Q Consensus 158 l~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~-w~~ll~~a~~~~~~~~~~~~~~~ 212 (371)
+.+.+|+|||+||||.++|++||...|..... |..++..++.++|+++.......
T Consensus 764 ~~~~~RlnvALtra~~~l~v~Gne~~L~~~~~~w~~li~da~~r~~~~~~~~~~~~ 819 (827)
T KOG1801|consen 764 ECNLRRLNVALTRARTCFWLVGNEITLAPSCSIWASLILDAKGRGCFMDRAADVND 819 (827)
T ss_pred hhhHHHHHHhhcccccceEEecCccccccccchhhhhcchhcccccccccccccch
Confidence 99999999999999999999999999988776 99999999999999987653333
No 8
>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]
Probab=99.95 E-value=5.6e-29 Score=261.12 Aligned_cols=191 Identities=30% Similarity=0.446 Sum_probs=150.1
Q ss_pred ccccccCCchhhhhcchhhccCCccccCccccC------CCCc----------ccCCC---CCCCcEEEEEcCCC--eee
Q 047960 2 LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVIN------LPDE----------VYYKD---PVLRPYVFFDVIHG--RES 60 (371)
Q Consensus 2 ~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~------~~~~----------~~~~~---~~~~p~~f~~v~~g--~~~ 60 (371)
.|+.||||..+|..++|.+||+|+|+++..... .+.. ..|-. ...++.+|+++... .++
T Consensus 864 ~Lt~QYRMn~~I~~LSN~L~Yg~~L~Cgs~eVs~~~~~~~~~~~~~~~~~s~s~~wl~~v~~p~~~v~f~~~D~~~~ie~ 943 (1100)
T KOG1805|consen 864 SLTLQYRMNREIMRLSNKLIYGNRLKCGSKEVSRASELDRKGALSVYMDDSSSDHWLQAVLEPTRDVCFVNTDTCSTIES 943 (1100)
T ss_pred hHHHHHhhcchHHhhhhhheECCeeeecChhhhhhhccccchhhhhhcccccchHHHHHhhcCCccceEEecCcccchhh
Confidence 488999999999999999999999998753221 0000 00100 12345677665532 222
Q ss_pred ecCCCCCccCHHHHHHHHHHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccc
Q 047960 61 HRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQER 140 (371)
Q Consensus 61 ~~~~~~S~~N~~EA~~Vv~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~Er 140 (371)
.+......|..||..|++++..+++. |+++.+|||||||++|+.+|++.+... .+.|.|||.|||+++
T Consensus 944 -~~e~~~i~N~~EA~li~~~~~~fv~s----Gv~~~dIGIis~YraQv~Li~~~l~~~-------~lEinTVD~yQGRDK 1011 (1100)
T KOG1805|consen 944 -QGEKGGITNHGEAKLISELVEDFVKS----GVKPSDIGIISPYRAQVELIRKILSSA-------VLEINTVDRYQGRDK 1011 (1100)
T ss_pred -hccccCcCchhHHHHHHHHHHHHHHc----CCCHHHeeeeehHHHHHHHHHhhcccc-------ceeeeehhhhcCCCC
Confidence 12222356999999999999888663 899999999999999999999877431 289999999999999
Q ss_pred cEEEEEccccCCCC-c-cCCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCcee
Q 047960 141 DVIIMSCVRASNHG-V-GFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYM 204 (371)
Q Consensus 141 DVIIiS~vrs~~~~-~-gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~ 204 (371)
|+||+|+|+++... . ..+.|+||+|||+||||..||+||+..+|...+.+++|+++...+..++
T Consensus 1012 d~IivSfvrsn~~~~~~eLLkD~rRlNVAlTRAK~KLIlvGs~s~l~~~~~~~~l~~~l~~~~~l~ 1077 (1100)
T KOG1805|consen 1012 DCIIVSFVRSNKKSKVGELLKDWRRLNVALTRAKKKLILVGSKSTLESYPPFRQLLKLLENRIELL 1077 (1100)
T ss_pred CEEEEEEEecCCcccHHHHHHhhHHHHHHHHhhhceEEEEecccccccCchHHHHHhhhhhhhhHH
Confidence 99999999999753 2 3678999999999999999999999999999999999999987766543
No 9
>KOG1804 consensus RNA helicase [RNA processing and modification]
Probab=99.81 E-value=8.9e-21 Score=200.05 Aligned_cols=193 Identities=28% Similarity=0.384 Sum_probs=153.9
Q ss_pred cccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHHHH
Q 047960 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYE 82 (371)
Q Consensus 3 L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~lv~ 82 (371)
|-.+||+||.|....|+.||.+.|....+.........|.. .++|+-+. |.....+++.|+.|..||..|..++.
T Consensus 525 l~rnyrshp~il~l~~~l~y~~eL~~~~~~~~v~~~~~w~~----liif~g~~-G~~~r~~~s~S~~n~~Ea~~V~~~~k 599 (775)
T KOG1804|consen 525 LCRNYRSHPIILCLENRLYYLGELTAEASEVDVRGLELWSG----LILFYGAP-GFTERAGNSPSWLNLEEAAVVVRMTK 599 (775)
T ss_pred hHHHHhhhhHhhhcccccccccceeeeccHHHHHHHHhccc----ceeccccc-cccccccCChhhccHHHHHHHHHHHh
Confidence 56789999999999999999999986654333222111211 14454444 66667777889999999999987766
Q ss_pred HHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCCC-------c
Q 047960 83 HLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHG-------V 155 (371)
Q Consensus 83 ~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~-------~ 155 (371)
.+.. +......+|||||||++|++.|+..+.. .+...+.|++|+.|||+|+.|||+|+|++.... .
T Consensus 600 ~l~~---~~~~~~~DIgvitpy~aq~~~i~~~l~~----~~~~~~~vgsVe~fqGqE~~viiiStVrS~~~~~~~~~~~~ 672 (775)
T KOG1804|consen 600 ALPL---GEVAQPQDIGVITPYTAQVSEIRKALRR----LGVPGVKVGSVEEFQGQEPWVILGSTVRSFALPLLDDRYFG 672 (775)
T ss_pred ccCC---CCccccccceeeCcHHHHHHHHHHHhcc----cCCCCCcccceeeeccccceeeEeecccccCCCcccccccc
Confidence 5532 2234445899999999999999888765 567789999999999999999999999998632 2
Q ss_pred cCCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCceeccC
Q 047960 156 GFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMD 207 (371)
Q Consensus 156 gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~~~~ 207 (371)
+|+.++++||||+|||+..++++|+...+...+.|+.++.++..++.+..-.
T Consensus 673 ~fls~pk~l~v~V~rp~~l~i~~~~~h~~~~~~~~~~~l~~~~~n~~y~~c~ 724 (775)
T KOG1804|consen 673 LFLSRPKRLLVAVGRPRALLINLGNPHLLGGDPPWGLLLLLRVENGRYPGCD 724 (775)
T ss_pred eeecCcccceeeccCccccccccCCcccccCCCChhhheeeeecCCcccCCC
Confidence 3889999999999999999999999999999999999999998887765543
No 10
>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]
Probab=99.50 E-value=1.3e-14 Score=153.70 Aligned_cols=178 Identities=29% Similarity=0.427 Sum_probs=146.9
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCC--CeeeecCCCCCccCHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIH--GRESHRGGSVSYQNVDEAKFGV 78 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~--g~~~~~~~~~S~~N~~EA~~Vv 78 (371)
|-|+.|+|..+.|+++.| .-|.+ |...+.+..+|...........+++|++++. |..+...+..-+.|..||+.++
T Consensus 1067 i~lnaqgrar~sI~~Ly~-wry~l-Lg~l~~v~~lp~f~~aNagf~~~~qlinv~Df~g~gEt~p~p~fyQnlgeaey~v 1144 (1320)
T KOG1806|consen 1067 IDLNAQGRARASIASLYN-WRYPL-LGNLPHVSPLPRFQYANAGFAYEFQFINVPDFKGSGETEPSPGFYQNLGEAEYAV 1144 (1320)
T ss_pred ecchhhhhHHHHHHHHHH-hhhcc-cccCcCCccchhhhccccCceeeEEEecchhhccccccCCCcccccCCchhhhHH
Confidence 358899999999999997 66754 6666666677766666667778899999875 4444444555689999999999
Q ss_pred HHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCC--CCCeEEccccCCCCccccEEEEEccccCCCCcc
Q 047960 79 CLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEE--GKDLYINTVDAFQGQERDVIIMSCVRASNHGVG 156 (371)
Q Consensus 79 ~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~--~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~g 156 (371)
++..++.- .|++...|.|+|.|.+|+.+|++.+..+..... +.+-+|.|||.|||+..|.||+|+|++.. +|
T Consensus 1145 Aly~YMr~----Lgypa~Kisilttyngq~~lirdii~rrc~~nPfig~pAkv~tvdk~qgqqndfiIlslv~tr~--~g 1218 (1320)
T KOG1806|consen 1145 ALFQYMRL----LGYPANKISILTTYNGQKSLIRDIINRRCSHNPFIGQPAKVTTVDKFQGQQNDFIILSLVRTRE--VG 1218 (1320)
T ss_pred HHHHHHHH----hCCchhHeeEEEeecchHHHHHHHHHHhccCCCccCCcccCCccccccccccceEEeeehhhhh--hh
Confidence 99887644 389999999999999999999998877655443 45668999999999999999999999875 78
Q ss_pred CCCCCCchhhhhHhhcccEEEEeecccccC
Q 047960 157 FVADIRRMNVALTRARRALWVMGNAGALTQ 186 (371)
Q Consensus 157 fl~d~rRLNVAlSRAK~~liVvGn~~~L~~ 186 (371)
.+.|.+|+-||+|||+.+++|++......+
T Consensus 1219 h~rdvrrlvva~srarlglyv~~r~~lf~~ 1248 (1320)
T KOG1806|consen 1219 HLRDVRRLVVAMSRARLGLYVLCRRSLFRS 1248 (1320)
T ss_pred hhccHHHHHHHHHHhhccchhHHHHHHHHH
Confidence 999999999999999999999988876543
No 11
>PRK11054 helD DNA helicase IV; Provisional
Probab=98.60 E-value=2.9e-07 Score=98.76 Aligned_cols=86 Identities=23% Similarity=0.371 Sum_probs=60.8
Q ss_pred CCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCCCc------------------
Q 047960 94 GKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGV------------------ 155 (371)
Q Consensus 94 ~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~------------------ 155 (371)
+..+|+||+.|..+...+.+.+...+ ....|.+.|++..-|.|+|.|||--+.....++
T Consensus 559 ~~~~I~IL~R~~~~~~~~l~~~~~~~---~~~~i~~~T~h~sKGLEfD~ViI~g~~~g~~gfP~~~~~~~~~~~~~~~~~ 635 (684)
T PRK11054 559 PDERILLLARYHHLRPALLDKAATRW---PKLQIDFMTIHASKGQQADYVIILGLQEGQDGFPAPARESIMEEALLPPPE 635 (684)
T ss_pred CCCcEEEEEechhhHHHHHHHHHhhc---ccCCeEEEehhhhcCCcCCEEEEecCCcCcccCCcccccchhhhccccccc
Confidence 35799999999887755444443332 224799999999999999999986543221100
Q ss_pred cC--CCCCCchhhhhHhhcccEEEEeecc
Q 047960 156 GF--VADIRRMNVALTRARRALWVMGNAG 182 (371)
Q Consensus 156 gf--l~d~rRLNVAlSRAK~~liVvGn~~ 182 (371)
.| ....|.|.||+||||+.++|+.+..
T Consensus 636 ~~~~~eERRLlYVAlTRAr~~l~i~~~~~ 664 (684)
T PRK11054 636 DFPDAEERRLLYVALTRAKHRVWLLFNKG 664 (684)
T ss_pred ccccHHHHHHHHHHhhhhhcEEEEEEcCC
Confidence 01 1135779999999999999998643
No 12
>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=97.85 E-value=5.1e-06 Score=67.27 Aligned_cols=50 Identities=30% Similarity=0.348 Sum_probs=38.9
Q ss_pred CeEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEE
Q 047960 126 DLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVM 178 (371)
Q Consensus 126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVv 178 (371)
.+.+.|++.+||.|+|.||+....... .-....+.|.||+||||+.|+||
T Consensus 55 ~~~~~Tih~akGle~d~V~v~~~~~~~---~~~~~~~~lYva~TRA~~~L~iv 104 (104)
T PF13538_consen 55 HAYAMTIHKAKGLEFDAVIVVDPDSSN---FDELSRRLLYVAITRAKHELYIV 104 (104)
T ss_dssp CCSEEETGGCTT--EEEEEEEEGGGGS---GCGCHHHHHHHHHTTEEEEEEEE
T ss_pred cEEEEEhHHhcCccccEEEEEcCCccc---CCchhhccEEeeHhHhhhhhCCC
Confidence 788999999999999999998765541 11334577999999999999986
No 13
>PRK13909 putative recombination protein RecB; Provisional
Probab=97.57 E-value=0.00031 Score=78.18 Aligned_cols=60 Identities=27% Similarity=0.336 Sum_probs=42.9
Q ss_pred CCCeEEccccCCCCccccEEEEEccccCC---C--------CccCC-----------------------------CCCCc
Q 047960 124 GKDLYINTVDAFQGQERDVIIMSCVRASN---H--------GVGFV-----------------------------ADIRR 163 (371)
Q Consensus 124 ~~~i~V~TVd~fQG~ErDVIIiS~vrs~~---~--------~~gfl-----------------------------~d~rR 163 (371)
...|+|.|||..-|.|++|||+.-..... . +.+.. ...|.
T Consensus 605 ~daV~imTIHkSKGLEfpvVil~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~rl 684 (910)
T PRK13909 605 SKGVQIMTVHKSKGLEFEHVIVCDRLGKPNSDSSNLLFEYDGIELWQIYYRIKGRENFDKDYARALEKEKALKYEEEINV 684 (910)
T ss_pred cCceEEEEeeccCCCCCcEEEEccCccCCCCCCCcEEEccCCCCcceeccchhhhhcCcHHHHHHHHHHHHHHHHHHHhh
Confidence 34688999999999999999995432111 0 11100 01378
Q ss_pred hhhhhHhhcccEEEEeeccc
Q 047960 164 MNVALTRARRALWVMGNAGA 183 (371)
Q Consensus 164 LNVAlSRAK~~liVvGn~~~ 183 (371)
|.||+||||+.|+|+|....
T Consensus 685 LYVAlTRA~~~L~i~~~~~~ 704 (910)
T PRK13909 685 LYVAFTRAKNSLIVVKKDES 704 (910)
T ss_pred HheeccchhhceEEEecccc
Confidence 99999999999999998654
No 14
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=97.57 E-value=0.00053 Score=77.93 Aligned_cols=63 Identities=24% Similarity=0.397 Sum_probs=46.2
Q ss_pred CCeEEccccCCCCccccEEEEEccccCCC------------Ccc--CC------------------------CCCCchhh
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRASNH------------GVG--FV------------------------ADIRRMNV 166 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs~~~------------~~g--fl------------------------~d~rRLNV 166 (371)
..|+|-|||..-|.|+++||+...-+.+. +.+ +. .+.|.|.|
T Consensus 742 ~~VrImTIHkSKGLEfPiVflp~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~k~~~~~e~~~E~~RLLYV 821 (1139)
T COG1074 742 DLVRIMTIHKSKGLEFPIVFLPFILSKRFNDSDVPLLVYYDGLRFELFDDLKSYPTPESQANKELAEEEALAEELRLLYV 821 (1139)
T ss_pred CeEEEEEEeccCCCCCCEEEecCCCCcccccccccceeecCCCceeeEeccccCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34889999999999999999987444321 000 00 02478999
Q ss_pred hhHhhcccEEEEeecccccCC
Q 047960 167 ALTRARRALWVMGNAGALTQS 187 (371)
Q Consensus 167 AlSRAK~~liVvGn~~~L~~~ 187 (371)
|+||||.+|||+|....-+..
T Consensus 822 AlTRAk~~L~l~g~~~~~~~~ 842 (1139)
T COG1074 822 ALTRAKEQLILIGAPSKREKS 842 (1139)
T ss_pred HHHHHHHheEEEeeccccccc
Confidence 999999999999988764433
No 15
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=97.25 E-value=0.0012 Score=68.85 Aligned_cols=146 Identities=21% Similarity=0.229 Sum_probs=91.8
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
|-|..+||+.-+|.+|.|.+.= ..-..+|-+ ...-.|.+.. +-.|..=.+.+-.+
T Consensus 592 v~l~~syrSt~eI~efan~~l~-d~~~~~p~~----------rsge~p~~i~--------------~~~ne~l~qr~~~i 646 (747)
T COG3973 592 VGLIASYRSTAEIDEFANSLLP-DRFRIHPLT----------RSGEKPAVIM--------------SVANEELVQRNPDI 646 (747)
T ss_pred hhhhhhhcChHHHHHHHHHhcc-CCCccchhh----------cCCCCceeee--------------ccchHHHHHhhHHH
Confidence 3578899999999999986443 211111110 0011222221 22344444444455
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhc-----cC---CCCCeEEccccCCCCccccEEEEEccccCC
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLN-----SE---EGKDLYINTVDAFQGQERDVIIMSCVRASN 152 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~-----~~---~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~ 152 (371)
+..+.+ ....+|+||++...|...+.+.|++.-. .. -.....|-.++-..|-|+|-||+--.. +.
T Consensus 647 i~~mkk------~~~etiaVi~kt~~d~~~~~d~lre~~~~r~I~k~nq~f~~~~~vipvy~aKGlEFD~viv~d~s-~~ 719 (747)
T COG3973 647 IPRMKK------RGSETIAVICKTDHDCKAVMDSLREKDSQRTIAKENQRFHHGSDVIPVYDAKGLEFDHVIVVDPS-IV 719 (747)
T ss_pred HHHHHh------cCCCceEEECCcHHHHHHHHHHHhhcchhhHHHhhcccccCCceEEEeeecccceeeeEEEecch-hh
Confidence 554433 2457899999999999999988875311 11 123556788999999999988874321 11
Q ss_pred CCccCCCCCCchhhhhHhhcccEEEEee
Q 047960 153 HGVGFVADIRRMNVALTRARRALWVMGN 180 (371)
Q Consensus 153 ~~~gfl~d~rRLNVAlSRAK~~liVvGn 180 (371)
----.+.+.|.||+|||-+.++|||-
T Consensus 720 --e~te~~~r~LYva~TRAlh~l~if~~ 745 (747)
T COG3973 720 --EETEQDLRDLYVAVTRALHSLYIFGE 745 (747)
T ss_pred --cccccchhhHHHHHHHHHHHHHHhhc
Confidence 01235789999999999999998863
No 16
>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=97.23 E-value=0.002 Score=73.06 Aligned_cols=56 Identities=23% Similarity=0.355 Sum_probs=41.1
Q ss_pred CeEEccccCCCCccccEEEEEccccCCCC------------ccC---C---------------CCCCchhhhhHhhcccE
Q 047960 126 DLYINTVDAFQGQERDVIIMSCVRASNHG------------VGF---V---------------ADIRRMNVALTRARRAL 175 (371)
Q Consensus 126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~~~------------~gf---l---------------~d~rRLNVAlSRAK~~l 175 (371)
.|+|-|||...|-|++|||+......... .+. . .+.|.|.||+||||+.|
T Consensus 652 aV~ImTIHkSKGLEfPvVflp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~E~lRLLYVAlTRA~~~l 731 (1087)
T TIGR00609 652 LVKIVTIHKSKGLEYPIVFLPFITDAKKSNFASLHDQHSHEYQLYDFNQSEENQKLARVERLAEDLRLLYVALTRAKKQL 731 (1087)
T ss_pred cEEEEEEEccCCCCCCEEEEeccccccCCccceeeeccCCceeecCCcccHHHHHHHHHHHHhHHHHHHHHHHHHHhHee
Confidence 58899999999999999998765332110 001 1 12478999999999999
Q ss_pred EEEeec
Q 047960 176 WVMGNA 181 (371)
Q Consensus 176 iVvGn~ 181 (371)
+|....
T Consensus 732 ~l~~~~ 737 (1087)
T TIGR00609 732 FIGIAP 737 (1087)
T ss_pred EEEecc
Confidence 997553
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=96.86 E-value=0.00042 Score=75.16 Aligned_cols=52 Identities=25% Similarity=0.294 Sum_probs=44.0
Q ss_pred EccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecccc
Q 047960 129 INTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGAL 184 (371)
Q Consensus 129 V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L 184 (371)
.-|||..||.|.|.||+-+..+. ..+.+.+.+.||+||||+.++|+|+...+
T Consensus 650 AiTvHKsQGSe~~~Vii~l~~~~----~~~l~r~llYTAiTRAk~~l~lvg~~~a~ 701 (720)
T TIGR01448 650 ATSIHKSQGSEFPTVILPIHTAH----MRMLYRNLLYTALTRAKKRVILVGSAEAF 701 (720)
T ss_pred eeeehhccCccCCEEEEECCccc----chhhhhchheeeeeeeceEEEEEECHHHH
Confidence 35999999999999999865432 24678899999999999999999998865
No 18
>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=96.74 E-value=0.00066 Score=62.63 Aligned_cols=49 Identities=22% Similarity=0.286 Sum_probs=38.9
Q ss_pred EEccccCCCCccccEEEEEccccCCCCccCC-CCCCchhhhhHhhcccEEEE
Q 047960 128 YINTVDAFQGQERDVIIMSCVRASNHGVGFV-ADIRRMNVALTRARRALWVM 178 (371)
Q Consensus 128 ~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl-~d~rRLNVAlSRAK~~liVv 178 (371)
.+.|++++||.|+|.|++-...... .... .+.++++||+||||..|.++
T Consensus 184 ~~~T~~e~qG~tf~~V~l~~~~~~~--~~~~~~~~~~~~VALTR~~~~l~i~ 233 (234)
T PF01443_consen 184 RVFTVHESQGLTFDNVTLVLLSDTD--NELYSESRNHLYVALTRHTKSLVIL 233 (234)
T ss_pred ceechHHcceEEeCCEEEEECCCcc--cccccCCcccEEEEccccccEEEEE
Confidence 5999999999999999886543322 1223 36899999999999999986
No 19
>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=96.73 E-value=0.0046 Score=59.61 Aligned_cols=94 Identities=16% Similarity=0.286 Sum_probs=57.2
Q ss_pred CccccccCCchhhhhcchhhc-----cCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHF-----YQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAK 75 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~F-----Y~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~ 75 (371)
|.|+++|||+|.|+++.|..| ..+.-........ .......++.++... ....|++
T Consensus 1 i~L~~NyRS~~~Iv~~~N~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~-------------~~~~e~~ 61 (351)
T PF13361_consen 1 ITLTTNYRSSPNIVDFANRLFENILPNDNKDRYEKEIQS------AENSEDGKISIIEFD-------------NEEEEAE 61 (351)
T ss_dssp EEE-EESSS-HHHHHHHHHHHCC---TTSSSSCCCEEEE------SSTCEESSEEEEEES-------------SHHHHHH
T ss_pred CCCCCCcCcCHHHHHHHHHHHHhhhhhhccchhhhhhcc------ccccccCCceeeccC-------------CHHHHHH
Confidence 569999999999999999888 2222111110000 000111223333322 2456788
Q ss_pred HHHHHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 76 FGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 76 ~Vv~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
.|+..+..+.. .+++..+|+|++....|...|.+.|.+
T Consensus 62 ~i~~~I~~l~~----~~~~~~diAVL~R~~~~~~~i~~~L~~ 99 (351)
T PF13361_consen 62 YIAEEIKELIR----NGIPPSDIAVLVRTNSQIKEIEDALKE 99 (351)
T ss_dssp HHHHHHHHHHH----TTS-GGGEEEEESSGGHHHHHHHHHHH
T ss_pred HHHHHHHHHhh----cCCCcccEEEEEECchhHHHHHHHHhh
Confidence 77776655433 278899999999999999999998876
No 20
>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=96.73 E-value=0.00081 Score=71.26 Aligned_cols=55 Identities=25% Similarity=0.264 Sum_probs=45.0
Q ss_pred CeEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecccc
Q 047960 126 DLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGAL 184 (371)
Q Consensus 126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L 184 (371)
...+.|||..||.|+|.||+.+.... ..+.+.+.++||+||||+.++|+|+...+
T Consensus 520 ~ayA~TvHKSQGsef~~Vi~~l~~~~----~~~l~r~llYTaiTRAk~~l~i~~~~~~l 574 (586)
T TIGR01447 520 TAFAMTVHKSQGSEFDHVILILPNGN----SPVLTRELLYTGITRAKDQLSVWSDKETL 574 (586)
T ss_pred eEEEEEeeHhcCCcCCeEEEECCCCC----CcccccceeEEEeeehhCeEEEEECHHHH
Confidence 34578999999999999999875432 23567789999999999999999987643
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=96.58 E-value=0.00079 Score=64.96 Aligned_cols=58 Identities=21% Similarity=0.316 Sum_probs=41.5
Q ss_pred CCCeEEccccCCCCccccEEEEEccccCCCC----c----cCCCCCCchhhhhHhhcccEEEEeec
Q 047960 124 GKDLYINTVDAFQGQERDVIIMSCVRASNHG----V----GFVADIRRMNVALTRARRALWVMGNA 181 (371)
Q Consensus 124 ~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~----~----gfl~d~rRLNVAlSRAK~~liVvGn~ 181 (371)
...|.|.|+|..-|.|+|+||+-......-+ . .+....|.+.||+||||+.|+|++..
T Consensus 285 ~~~V~i~TiH~sKGLEf~~V~v~~~~~~~~p~~~~~~~~~~~~Ee~rl~YVA~TRAk~~L~l~~~~ 350 (351)
T PF13361_consen 285 DDGVQIMTIHKSKGLEFDIVFVPGLNEGTFPSYRSIEDRQELEEERRLFYVAMTRAKERLYLSYPK 350 (351)
T ss_dssp CGSEEEEECGGGTT--EEEEEEETTBTBTTTCHHHHHHHHHHHHHHHHHHHHHHTEEEEEEEEEEC
T ss_pred ccCcEEeeheeccccCCCeEEEecccCCcChHHHHHhhHhhhHHHHhHheEecchhhceEEEEEec
Confidence 3579999999999999999999765433211 0 11123477999999999999998753
No 22
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=96.57 E-value=0.0006 Score=57.13 Aligned_cols=68 Identities=9% Similarity=-0.071 Sum_probs=49.5
Q ss_pred CCCCCCCCccccCcccCCcccccccCCCCCCCCCCCCCCCc-cccCCCCCCCCCCc-------------------ccccc
Q 047960 225 GPLQGKIPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEK-VSRNGNYRPFKPPL-------------------ENSLD 284 (371)
Q Consensus 225 ~~l~~~g~~v~~~v~~~g~r~~~~~~~~~~r~~~~~~~~~~-~~~~g~~~~~~~~~-------------------e~~~~ 284 (371)
..|.+.|+.+.+|+++. +++.|+..++-.- |+|||..+ |... ++..+
T Consensus 26 ~~L~~~Gl~~r~~~~~~-----------~~~~D~~~~~~klaIe~DG~~w--H~~~~~~~~~~~~~~~~w~~k~~~~~~r 92 (115)
T cd00221 26 SALWELGYRFRKQDKDL-----------PGKPDIVVPGYRLAIFVDGCFW--HGHPCHKRKPPPKNTEFWLEKIERNVER 92 (115)
T ss_pred HHHHHCCCEEEeCCCCC-----------CcccCEEecCCCEEEEEcCccc--cCCccccccCCCccHHHHHHHHHHHHHH
Confidence 44555666655555543 4577777764332 99999987 4444 78899
Q ss_pred ccccccccccccccccccccc
Q 047960 285 DFDQSGEKYRDAWQHGIQKKQ 305 (371)
Q Consensus 285 ~~~~~~~~~r~~~~~~~~~~~ 305 (371)
|..++..|++.||.+.|+...
T Consensus 93 D~~r~~~L~~~GW~ViRvw~~ 113 (115)
T cd00221 93 DRRVQAALERLGWRVLRVWEC 113 (115)
T ss_pred HHHHHHHHHHCcCEEEEEeCC
Confidence 999999999999999987654
No 23
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]
Probab=96.40 E-value=0.0017 Score=70.19 Aligned_cols=54 Identities=28% Similarity=0.324 Sum_probs=45.9
Q ss_pred eEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeeccccc
Q 047960 127 LYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALT 185 (371)
Q Consensus 127 i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L~ 185 (371)
-.+.|||..||.|.|.|++-... .. -+.+...+.||+||||+.++++|+...++
T Consensus 622 ayA~TIHKsQGSef~~v~v~l~~-~~----~~l~r~l~YtAiTRar~~l~l~~~~~~~~ 675 (696)
T COG0507 622 AYAMTIHKSQGSEFDRVIVLLPS-HS----PMLSRELLYTAITRARDRLILYGDEKAFA 675 (696)
T ss_pred heeeeEecccCCCCCeEEEEcCC-Cc----hhhhhhHHHHHhhhhheeEEEEcChHHHH
Confidence 35789999999999999999877 22 25678899999999999999998888754
No 24
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=96.34 E-value=0.0023 Score=68.18 Aligned_cols=54 Identities=28% Similarity=0.226 Sum_probs=43.2
Q ss_pred eEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecccc
Q 047960 127 LYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGAL 184 (371)
Q Consensus 127 i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L 184 (371)
..+.|||..||.|+|.|++-..... ..+.+.+.+.||+||||+.+.|+|+...+
T Consensus 539 ayA~TVHKSQGsEf~~Vilvlp~~~----~~~l~R~LlYTaiTRAk~~l~l~~~~~~l 592 (615)
T PRK10875 539 AWAMTVHKSQGSEFDHTALVLPNQF----TPVVTRELVYTAITRARRRLSLYADERVL 592 (615)
T ss_pred EEEEehhhhcCCCCCeEEEECCCcc----chhhhhhhHHhhhhhhhceEEEEeCHHHH
Confidence 3578999999999999988754321 12456788999999999999999998754
No 25
>cd01038 Endonuclease_DUF559 Domain of unknown function, appears to be related to a diverse group of endonucleases.
Probab=96.16 E-value=0.00064 Score=56.16 Aligned_cols=91 Identities=10% Similarity=-0.069 Sum_probs=63.5
Q ss_pred ChhhHHHHhhcCCCCCCCCCC---CCccccCcccCCcccccccCCCCCCCCCCCCCCC-ccccCCCCCCCCCCccccccc
Q 047960 210 PKEFSVALAAKAPGYGPLQGK---IPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDE-KVSRNGNYRPFKPPLENSLDD 285 (371)
Q Consensus 210 ~~~~~~~~~~~~~~~~~l~~~---g~~v~~~v~~~g~r~~~~~~~~~~r~~~~~~~~~-~~~~~g~~~~~~~~~e~~~~~ 285 (371)
++.++..+. ..|... |+.+.+|+.+++| +.|+...+.. .|||||.+ |.+.. ..|
T Consensus 13 ~S~~E~~l~------~~L~~~~~~g~~~~~q~~i~~~-----------~vD~~~~~~kl~IE~DG~~---H~~~~--~~D 70 (108)
T cd01038 13 QTDAERLLW------QELRRRRLNGFKFRRQAPIGRY-----------IVDFACPEAKLVVELDGGQ---HDEQI--AYD 70 (108)
T ss_pred CCHHHHHHH------HHHHhcccCCCceeeccCCCCc-----------EeeeEccccCEEEEEeCcc---cCchH--HHH
Confidence 445555444 334444 7777777766555 5555544322 29999984 34443 899
Q ss_pred ccccccccccccccccccccCCCCCCCCchHHHHHhh
Q 047960 286 FDQSGEKYRDAWQHGIQKKQSSGGKGSPRLEDLVDAF 322 (371)
Q Consensus 286 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 322 (371)
..|+..+...||.+.+.....-..+|+..+..+..+|
T Consensus 71 ~~R~~~L~~~Gw~vlR~~~~dv~~~~~~~~~~I~~~l 107 (108)
T cd01038 71 AERDAWLEARGFRVLRFWNNEVLRNIEAVLEAILAAL 107 (108)
T ss_pred HHHHHHHHHCCCEEEEEEHHHHhhCHHHHHHHHHHHh
Confidence 9999999999999999999888888888887776554
No 26
>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=96.06 E-value=0.0065 Score=66.31 Aligned_cols=56 Identities=20% Similarity=0.183 Sum_probs=45.6
Q ss_pred EccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecccccCCchHHH
Q 047960 129 INTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAA 192 (371)
Q Consensus 129 V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ 192 (371)
..||+..||.|.|.||+.. ..+.+.+.++||+||||+.++|+|+...+.....|..
T Consensus 666 A~TvHKsQGst~~~viv~~--------~~~l~r~llYvAiTRar~~~~l~~~~~~~~~~~~l~~ 721 (744)
T TIGR02768 666 ATTIHKSQGVTVDRAFVLA--------SKSMDRHLAYVAMTRHRESVQLYAGKEDFTDRGALVK 721 (744)
T ss_pred EeccccccCCccCcEEEec--------CCccccchhhhhhhcccceeEEEEchhhccChHHHHH
Confidence 5599999999999999862 2346788999999999999999999988765544433
No 27
>PRK09767 hypothetical protein; Provisional
Probab=95.60 E-value=0.0018 Score=54.37 Aligned_cols=79 Identities=9% Similarity=-0.077 Sum_probs=60.9
Q ss_pred CCccccCcccCCcccccccCCCCCCCCCCCCCCCc--cccCCCCCCCCCCcccccccccccccccccccccccccccCCC
Q 047960 231 IPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEK--VSRNGNYRPFKPPLENSLDDFDQSGEKYRDAWQHGIQKKQSSG 308 (371)
Q Consensus 231 g~~v~~~v~~~g~r~~~~~~~~~~r~~~~~~~~~~--~~~~g~~~~~~~~~e~~~~~~~~~~~~~r~~~~~~~~~~~~~~ 308 (371)
|+..-+|..+++| -.|.+.. ..+ |||||+.. . ++...|..|+..|+++||.+.|.......
T Consensus 34 g~kFrRQ~pig~y-----------i~DF~c~-~~rLaIE~DG~~H----~-~~~~~D~~R~~~L~~~G~~VlRf~n~dV~ 96 (117)
T PRK09767 34 DFKFRRQHPVGSY-----------ILDFACC-SARVVVELDGGQH----D-LAVAYDTRRTSWLESQGWTVLRFWNNEID 96 (117)
T ss_pred CCeeEecccccCe-----------eeceecc-ccCEEEEEeCccc----c-hhHHHHHHHHHHHHHCCCEEEEEEHHHHH
Confidence 5666666666555 4555543 334 99999744 2 23578999999999999999999999999
Q ss_pred CCCCCchHHHHHhhhhcc
Q 047960 309 GKGSPRLEDLVDAFWWVG 326 (371)
Q Consensus 309 ~~~~~~~~~~~~~~~~~g 326 (371)
.+++..++.+..++....
T Consensus 97 ~~~~~Vl~~I~~~l~~~~ 114 (117)
T PRK09767 97 CNEEAVLEIILQELNRRS 114 (117)
T ss_pred hCHHHHHHHHHHHHhccC
Confidence 999999999988887653
No 28
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=95.35 E-value=0.016 Score=63.01 Aligned_cols=56 Identities=18% Similarity=0.221 Sum_probs=40.8
Q ss_pred CCeEEccccCCCCccccEEEEEccccCCCC----c---cCCC-CCCchhhhhHhhcccEEEEee
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRASNHG----V---GFVA-DIRRMNVALTRARRALWVMGN 180 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~----~---gfl~-d~rRLNVAlSRAK~~liVvGn 180 (371)
..|.+.|+|+.-|.|.++||+.-.....-+ . +-+. ..|.+.||+||||+.|++...
T Consensus 547 ~~V~lmTiH~sKGLEf~~Vfl~gl~eg~~P~~~~~~~~~~leEERRL~YVAiTRAk~~L~ls~~ 610 (715)
T TIGR01075 547 DAVQLMTLHSAKGLEFPLVFLVGMEEGMFPSQMSLDEGGRLEEERRLAYVGITRAMQKLTITYA 610 (715)
T ss_pred CcEEEEEeeeccCCcCCEEEEeCCcCCCCCCccccCccccHHHHHhHHhhhhhhhhhheEEEec
Confidence 359999999999999999998765332110 0 0011 237799999999999999754
No 29
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=95.30 E-value=0.017 Score=62.43 Aligned_cols=56 Identities=18% Similarity=0.129 Sum_probs=41.3
Q ss_pred CCeEEccccCCCCccccEEEEEccccCCCCcc------CCC-CCCchhhhhHhhcccEEEEee
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRASNHGVG------FVA-DIRRMNVALTRARRALWVMGN 180 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~g------fl~-d~rRLNVAlSRAK~~liVvGn 180 (371)
..|.+.|+|+..|.|.|+|||.-+....-+.. -+. ..|.+.||+||||+.|++...
T Consensus 550 ~~V~L~TiH~sKGLEf~~Vfi~gl~eg~~P~~~~~~~~~leEERRLfYVA~TRAk~~L~Ls~~ 612 (672)
T PRK10919 550 DQVQLMTLHASKGLEFPYVYLVGMEEGLLPHQSSIDEDNIDEERRLAYVGITRAQKELTFTLC 612 (672)
T ss_pred CcEEEEeeecccCcCCCEEEEeCCcCCCCCCcccCCcccHHHHHHHHHHhHhhhhhheEEeeh
Confidence 45999999999999999999976544321100 011 146799999999999999754
No 30
>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=95.10 E-value=0.023 Score=65.43 Aligned_cols=60 Identities=23% Similarity=0.328 Sum_probs=44.3
Q ss_pred CCeEEccccCCCCccccEEEEEccccCC------------CCccCCC------------------------------CCC
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRASN------------HGVGFVA------------------------------DIR 162 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs~~------------~~~gfl~------------------------------d~r 162 (371)
..|.|.|||..-|.|++|||+.-...+. ...|+.. ..|
T Consensus 781 daV~IMTIHkSKGLEFPvVfl~~l~~~fn~~d~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~Ee~R 860 (1232)
T TIGR02785 781 NAVRLMTIHKSKGLEFPVVFVLGMGKQFNKQDLNSSYLLNRQLGLGITYIDPQERLSYPSLPKVAIKQKMKRELLSEEMR 860 (1232)
T ss_pred CeEEEEeeecccCCCCCEEEEeCCCCCCCccccccceEeccccCCCCceecchhccCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 3599999999999999999997653210 0012110 137
Q ss_pred chhhhhHhhcccEEEEeecccc
Q 047960 163 RMNVALTRARRALWVMGNAGAL 184 (371)
Q Consensus 163 RLNVAlSRAK~~liVvGn~~~L 184 (371)
.|.||+||||+.|+|+|....+
T Consensus 861 lLYVAlTRAke~Lil~g~~~~~ 882 (1232)
T TIGR02785 861 VLYVALTRAKEKLILVGSVKDE 882 (1232)
T ss_pred HHHhhhhhhhheEEEEecHHHH
Confidence 7999999999999999986544
No 31
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=94.86 E-value=0.016 Score=63.01 Aligned_cols=57 Identities=19% Similarity=0.225 Sum_probs=41.4
Q ss_pred CCeEEccccCCCCccccEEEEEccccCCCC-ccC------C-CCCCchhhhhHhhcccEEEEeec
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRASNHG-VGF------V-ADIRRMNVALTRARRALWVMGNA 181 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~-~gf------l-~d~rRLNVAlSRAK~~liVvGn~ 181 (371)
..|.+.|+|+.-|.|+|+||+.......-+ ..- + ...|.+.||+||||+.|++....
T Consensus 548 ~~V~LmTiH~sKGLEf~vVfv~gl~eg~~P~~~~~~~~~~~eEERRL~YVAiTRAk~~L~ls~~~ 612 (726)
T TIGR01073 548 GAVTLMTLHAAKGLEFPVVFLIGMEEGVFPHSRSLMDEKELEEERRLAYVGITRAEEELYLTHAT 612 (726)
T ss_pred CceEEEeeeeccCccCCEEEEeCCcCCCCCcccccCCchhHHHHHhhHHhhhhhhhheEEEEehh
Confidence 459999999999999999999765332110 000 1 12477999999999999997543
No 32
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=94.80 E-value=0.027 Score=61.34 Aligned_cols=56 Identities=16% Similarity=0.130 Sum_probs=40.9
Q ss_pred CCeEEccccCCCCccccEEEEEccccCCCC-ccC------CCC-CCchhhhhHhhcccEEEEee
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRASNHG-VGF------VAD-IRRMNVALTRARRALWVMGN 180 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~-~gf------l~d-~rRLNVAlSRAK~~liVvGn 180 (371)
..|.+.|+|+.-|.|+++||+.-.....-+ ..- +.. .|.+.||+||||+.|++...
T Consensus 552 ~~V~LmTiH~AKGLEf~~Vfl~gl~eg~~P~~~~~~~~~~leEERRL~YVAiTRAk~~L~ls~~ 615 (721)
T PRK11773 552 DAVQLMTLHSAKGLEFPLVFIVGMEEGLFPSQMSLEEGGRLEEERRLAYVGITRAMQKLTLTYA 615 (721)
T ss_pred CceEEEechhccCCcCCEEEEeCCccCCCCCccccccchhhHHHHhHHHhhhhhhhheeEEEeh
Confidence 359999999999999999999765332210 000 111 36789999999999999754
No 33
>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=94.78 E-value=0.051 Score=62.18 Aligned_cols=73 Identities=29% Similarity=0.403 Sum_probs=49.2
Q ss_pred CCeEEccccCCCCccccEEEEEcccc---CCCC---------ccC-------C-------------------------CC
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRA---SNHG---------VGF-------V-------------------------AD 160 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs---~~~~---------~gf-------l-------------------------~d 160 (371)
..|.|.|||..-|.|+++||+.-... +... .|. + ..
T Consensus 774 daV~ImTIH~SKGLEfpvV~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~ 853 (1141)
T TIGR02784 774 DEVRVMTVHGAKGLEAPVVFLVDTGSAPFASQHAPKLLFTGGSGEASDGKAPLWRPPSAFDPALSAAARERLKERAEDEY 853 (1141)
T ss_pred CeEEEEeccccCCCCCCEEEEeCCCCCCCCccccccccccccCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHH
Confidence 45999999999999999999954421 1100 010 0 01
Q ss_pred CCchhhhhHhhcccEEEEeecccccC-CchHHHHHHHH
Q 047960 161 IRRMNVALTRARRALWVMGNAGALTQ-SDDWAALIADS 197 (371)
Q Consensus 161 ~rRLNVAlSRAK~~liVvGn~~~L~~-~~~w~~ll~~a 197 (371)
.|.|.||+||||+.|+|+|....-.. ...|..++..+
T Consensus 854 ~RLLYVAlTRA~~~L~l~g~~~~~~~~~~~w~~~~~~~ 891 (1141)
T TIGR02784 854 RRLLYVAMTRAEDRLIVCGYRGKRTSPKDTWYALVKRA 891 (1141)
T ss_pred hhHHHHhhhhhhheeEEEeecCCCccchhhHHHHHHHH
Confidence 27799999999999999998642211 22588766554
No 34
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=94.13 E-value=0.17 Score=55.18 Aligned_cols=94 Identities=15% Similarity=0.193 Sum_probs=59.7
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
+.|.++|||++.|.++.|..+-.+.-.. +.......+...++.++... .-..||+.|+..
T Consensus 273 i~L~~NyRS~~~Il~~an~li~~~~~r~-------~~~l~~~~~~g~~v~~~~~~-------------~~~~Ea~~ia~~ 332 (726)
T TIGR01073 273 ILLEQNYRSTKNILQAANEVIEHNSNRK-------PKNLWTENSSGDKITYYEAD-------------TERDEAQFVAGE 332 (726)
T ss_pred EECccCCCCCHHHHHHHHHHHHhccccc-------ccccccCCCCCcceEEEeCC-------------CHHHHHHHHHHH
Confidence 3689999999999999998876543211 10000011111223333221 124688888877
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
+..+.. ..+++..+|+|++..+.|...|...|.+
T Consensus 333 I~~l~~---~~~~~~~diAVL~R~~~~~~~l~~~L~~ 366 (726)
T TIGR01073 333 IDKLVK---NGERKYGDFAILYRTNAQSRVFEETLLK 366 (726)
T ss_pred HHHHHH---cCCCCcCCEEEEEeCchhHHHHHHHHHH
Confidence 666643 2336788999999999999988888865
No 35
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=94.03 E-value=0.03 Score=60.28 Aligned_cols=58 Identities=17% Similarity=0.111 Sum_probs=42.5
Q ss_pred CCCeEEccccCCCCccccEEEEEccccCCCC--cc-----CCCCCCchhhhhHhhcccEEEEeec
Q 047960 124 GKDLYINTVDAFQGQERDVIIMSCVRASNHG--VG-----FVADIRRMNVALTRARRALWVMGNA 181 (371)
Q Consensus 124 ~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~--~g-----fl~d~rRLNVAlSRAK~~liVvGn~ 181 (371)
...|.+.|+|...|.|.++|||.-.....-+ .. .....|.+.||+||||+.|++....
T Consensus 549 ~d~V~l~TiH~sKGLEf~~Vfv~gl~eg~~P~~~~~~~~~~~EErRlfYVA~TRAk~~L~Ls~~~ 613 (664)
T TIGR01074 549 LDQVQLMTLHASKGLEFPYVFIVGMEEGILPHQSSIEEDNVEEERRLAYVGITRAQKELTFTLCK 613 (664)
T ss_pred CCeEEEEeeecccCccCCeEEEeCCcCCCCCCccccccchHHHHHHHHHHhhhhhhheeEEEehh
Confidence 3469999999999999999999765433210 00 1123467999999999999998653
No 36
>KOG1804 consensus RNA helicase [RNA processing and modification]
Probab=93.55 E-value=0.063 Score=58.31 Aligned_cols=188 Identities=20% Similarity=0.178 Sum_probs=112.4
Q ss_pred cccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHHHH
Q 047960 3 LSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYE 82 (371)
Q Consensus 3 L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~lv~ 82 (371)
.+.+||+|-.+..|.+..||....-...+-.+.+.. ....|..|.+... ......++..+.|..|...++.-++
T Consensus 339 ~~~n~~~a~~~v~~~~~~~~il~~~p~~a~~k~~~~-----rl~~p~~~~~~~~-~~~~~~~~~~~~~~~~v~~~~~~~e 412 (775)
T KOG1804|consen 339 KTENYREAIAIVSFTSPHFYILVCAPSNASGKQPAH-----RLHYPLTFSTARG-EDVRAKSSTAWYNNAEVSEVVEKVE 412 (775)
T ss_pred CccchHHHHHHHHhcchHHHhhcccccccccccccc-----ccccccccccccc-ccccccchhHHhhhHHHHHHHHHHH
Confidence 467899999999999999996433322222222222 2245667766542 2222334445678888877777666
Q ss_pred HHHHHHHhc-C-CCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCcccc---EEEEEccccCCCC---
Q 047960 83 HLQKTLKSM-G-LGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERD---VIIMSCVRASNHG--- 154 (371)
Q Consensus 83 ~l~~~l~~~-~-~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErD---VIIiS~vrs~~~~--- 154 (371)
.+.+..... + -.-.++|++++|..|+..++..|... -...+......+|...- .|++|+....-+.
T Consensus 413 ~~~~~~~~~i~i~t~~sag~~~~~g~~v~~f~hil~De------Ag~stEpe~lv~i~~~~~~~~vvLsgdh~Qlgpv~~ 486 (775)
T KOG1804|consen 413 ELRKVWPYRWGITTCTSAGCVTSYGFQVGHFRHILVDE------AGVSTEPELLVPGKQFRQPFQVVLSGDHTQLGPVSK 486 (775)
T ss_pred HHhhccceEEEEeeccceeeeecccccccceeeeeecc------cccccCcccccccccccceeEEEEccCccccccccc
Confidence 665322111 1 12237899999999999888776221 12223333344444444 5555543322110
Q ss_pred ----ccCCCCCCchhhhhHhhcccEEEEeecccccCCc----hHHHHHHHHHhCCc
Q 047960 155 ----VGFVADIRRMNVALTRARRALWVMGNAGALTQSD----DWAALIADSKARNC 202 (371)
Q Consensus 155 ----~gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~----~w~~ll~~a~~~~~ 202 (371)
-.+..+...+|-|+|||....-++|+.+.+...+ .|.++...+-.+..
T Consensus 487 s~~A~~~gl~rsLler~l~r~~~~~~~~g~~~~l~~t~l~rnyrshp~il~l~~~l 542 (775)
T KOG1804|consen 487 SARAEELGLDRSLLERALTRAQSLVAVVGDYNALCSTGLCRNYRSHPIILCLENRL 542 (775)
T ss_pred chhhhhhcccHHHHHHHHHHHhhccccCCCcccccchhhHHHHhhhhHhhhccccc
Confidence 1133356789999999999999999999986654 46665555554444
No 37
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=93.30 E-value=0.047 Score=62.63 Aligned_cols=53 Identities=21% Similarity=0.258 Sum_probs=39.0
Q ss_pred CCeEEccccCCCCccccEEEEEcccc--CCCCc------c------C---------------CCCCCchhhhhHhhcccE
Q 047960 125 KDLYINTVDAFQGQERDVIIMSCVRA--SNHGV------G------F---------------VADIRRMNVALTRARRAL 175 (371)
Q Consensus 125 ~~i~V~TVd~fQG~ErDVIIiS~vrs--~~~~~------g------f---------------l~d~rRLNVAlSRAK~~l 175 (371)
..|.|.|||..-|.|++|||+..... ...+. + + -.+.|.+.||+||||..|
T Consensus 734 ~~V~ImTIH~SKGLEfPvVflp~l~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~E~l~Ee~RLlYVAlTRAk~~l 813 (1181)
T PRK10876 734 HLVQIVTIHKSKGLEYPLVWLPFITNFRVQDQAFYHDRHSFEAVLDLNAAEESVALAEEERLAEDLRLLYVALTRSVWHC 813 (1181)
T ss_pred CcEEEEEEeccCCcCCCEEEecccccccCCccceeecCCCCeeEeecCCcHHHHHHHHHHHHHHHHHHHHHHhhhHhhhh
Confidence 35999999999999999999876531 10000 0 0 123488999999999999
Q ss_pred EE
Q 047960 176 WV 177 (371)
Q Consensus 176 iV 177 (371)
+|
T Consensus 814 ~l 815 (1181)
T PRK10876 814 SL 815 (1181)
T ss_pred ee
Confidence 98
No 38
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=93.16 E-value=0.27 Score=53.64 Aligned_cols=93 Identities=16% Similarity=0.167 Sum_probs=59.5
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
+.|..+|||.++|.++.|..+-.+.-...... ....+...++.++... ....||..|++.
T Consensus 277 i~L~~NyRSt~~Il~~an~li~~n~~r~~k~~-------~~~~~~g~~v~~~~~~-------------~~~~Ea~~ia~~ 336 (721)
T PRK11773 277 IRLEQNYRSTANILKAANALIANNNGRLGKEL-------WTDGGDGEPISLYCAF-------------NELDEARFVVER 336 (721)
T ss_pred EECCcCCCCCHHHHHHHHHHHHhcccccCccc-------ccCCCCCCeeEEEeCC-------------CHHHHHHHHHHH
Confidence 36899999999999999987765432211100 0000111122222111 134788888877
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
+..+.. .|++..+|+|++.-+.|...|.+.|.+
T Consensus 337 I~~l~~----~g~~~~diAVL~R~~~~~~~le~~L~~ 369 (721)
T PRK11773 337 IKTWQD----NGGALSDCAILYRSNAQSRVLEEALLQ 369 (721)
T ss_pred HHHHHH----cCCCcccEEEEEecchhHHHHHHHHHH
Confidence 766543 367888999999999999999888865
No 39
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=93.00 E-value=0.3 Score=53.17 Aligned_cols=93 Identities=16% Similarity=0.218 Sum_probs=59.8
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
+.|..+||+.++|.++.|..+-.+.-..... .....+...++.++... ....||+.|++.
T Consensus 272 ~~L~~NyRS~~~Il~~an~li~~~~~r~~~~-------~~~~~~~g~~i~~~~~~-------------~~~~Ea~~ia~~ 331 (715)
T TIGR01075 272 IRLEQNYRSTANILAAANALIANNDERLGKN-------LWTDGEVGEPISLYSAF-------------NELDEARFVVSR 331 (715)
T ss_pred EECcccCCCCHHHHHHHHHHHHhcccccccc-------ccCCCCCCCceEEEeCC-------------CHHHHHHHHHHH
Confidence 3689999999999999998876543211100 00001111223332211 124688888877
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
+..+.. .|++..+|+|++.-+.|...|...|.+
T Consensus 332 I~~l~~----~g~~~~diAVL~R~~~~~~~le~~L~~ 364 (715)
T TIGR01075 332 IKTWQR----NGGALDECAVLYRSNAQSRVLEEALLQ 364 (715)
T ss_pred HHHHHH----cCCCccCEEEEEecCchHHHHHHHHHH
Confidence 766543 367888999999999999999888865
No 40
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=91.56 E-value=0.14 Score=57.44 Aligned_cols=46 Identities=22% Similarity=0.115 Sum_probs=35.3
Q ss_pred ccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeeccc
Q 047960 130 NTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGA 183 (371)
Q Consensus 130 ~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~ 183 (371)
.||+..||.+.|-|++... ...+.+.++||+||||+.+.++.+...
T Consensus 660 ~TIHKSQGsT~d~V~vl~~--------~~~~r~l~YVAiTRar~~v~l~~~~~~ 705 (988)
T PRK13889 660 ATIHKAQGMTVDRTHVLAT--------PGMDAHSSYVALSRHRDGVDLHYGRDD 705 (988)
T ss_pred hhhHHhcCCCCCeEEEecc--------cccccchhHHhhhhhhheEEEEecCcc
Confidence 3888889999997776531 124567899999999999999975543
No 41
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=91.50 E-value=0.17 Score=57.39 Aligned_cols=46 Identities=24% Similarity=0.216 Sum_probs=38.1
Q ss_pred EccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecc
Q 047960 129 INTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAG 182 (371)
Q Consensus 129 V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~ 182 (371)
..||+..||.+.|.|++-. +.+.+.+.++||+||||+.+.|+.+..
T Consensus 695 A~TVHKSQGsT~d~V~vl~--------s~~ldR~llYVA~TRaR~~~~ly~~~~ 740 (1102)
T PRK13826 695 ATTIHKSQGATVDRVKVLA--------SLSLDRHLTYVAMTRHREDLQLYYGRR 740 (1102)
T ss_pred eeeeecccccccceEEEec--------ccccccchhHHhhccccceEEEEEchh
Confidence 3488999999999888752 224677899999999999999999886
No 42
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=90.49 E-value=0.94 Score=48.79 Aligned_cols=94 Identities=11% Similarity=-0.071 Sum_probs=55.8
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
+.|.++||++|+|.++.|..|-.+.-... +.. ....+...++.++... ....||+.|+..
T Consensus 270 ~~L~~NyRs~~~Il~~~n~l~~~~~~~~~---~~~----~~~~~~g~~v~~~~~~-------------~~~~Ea~~ia~~ 329 (664)
T TIGR01074 270 IKLEQNYRSTGRILKAANILIANNPHVFE---KKL----FSELGYGEKIKVIECN-------------NEEHEAERIAGE 329 (664)
T ss_pred EECCCCCCChHHHHHHHHHHHhcCccccc---ccc----cccCCCCCceEEEeCC-------------CHHHHHHHHHHH
Confidence 35899999999999999986543221000 000 0000111123332221 134678877765
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
+... ....+++..+|+|++....|...|...|.+
T Consensus 330 I~~~---~~~~~~~~~diAVL~R~~~~~~~l~~~l~~ 363 (664)
T TIGR01074 330 IIAH---KLVNKTQYKDYAILYRGNHQSRLLEKALMQ 363 (664)
T ss_pred HHHH---HHcCCCCcccEEEEEecCchHHHHHHHHHH
Confidence 4321 112367888999999999999988888865
No 43
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=90.30 E-value=1.2 Score=51.33 Aligned_cols=112 Identities=12% Similarity=0.068 Sum_probs=59.5
Q ss_pred CccccccCCchhhhhcchhhccCCccc------cCccccC---CCCcccC-CCCCCCcEEEEEcCCCeeeecCCCCCccC
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLT------DSESVIN---LPDEVYY-KDPVLRPYVFFDVIHGRESHRGGSVSYQN 70 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~------~~~s~~~---~~~~~~~-~~~~~~p~~f~~v~~g~~~~~~~~~S~~N 70 (371)
+.|.++|||.|+|+++.|..|-...-. +...+.. ....... ......++.++... +. +.......
T Consensus 441 ~~L~~NyRS~~~Iv~~~N~lf~~~~~~~~~~~i~~~~v~a~~~~~~~~~~~~~~~~~~~~l~~~~-~~----~~~~~~~~ 515 (1181)
T PRK10876 441 YTLDTNWRSAPGMVNSVNKLFSQTDDPFLFREIPFIPVKAAGKNQALRFVVKGETQPAMKFWLME-GE----GVGVGDYQ 515 (1181)
T ss_pred eECCCCcCcCHHHHHHHHHHHhcccccccCCCCCccccccccccccccccccCCCCCceeeeecC-CC----ccCcchHH
Confidence 358999999999999999988653210 0000000 0000000 00111223333222 11 00111123
Q ss_pred HHHHHHHHHHHHHHHHHH-----------HhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 71 VDEAKFGVCLYEHLQKTL-----------KSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 71 ~~EA~~Vv~lv~~l~~~l-----------~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
..||+.|+.-+..++..- ...+++..+|+|++..+.|...|++.|.+
T Consensus 516 ~~eA~~iA~~I~~ll~~g~~~~~~~~~~~~~r~~~~~DIAVLvRs~~~a~~i~~aL~~ 573 (1181)
T PRK10876 516 QTMAQQCAAQIRDWLQAGQRGEALLMNGDDSRPVRASDITVLVRSRQEAALIRDALTL 573 (1181)
T ss_pred HHHHHHHHHHHHHHHhcccccceeeccCCCcCCCCcccEEEEEecCchHHHHHHHHHh
Confidence 457777776555543210 01235678999999999999999998875
No 44
>PF04480 DUF559: Protein of unknown function (DUF559); InterPro: IPR007569 This entry represents a protein of unknown function, but is thought to be a DNA mismatch repair endonuclease. ; PDB: 3R3P_B 3HRL_A.
Probab=89.64 E-value=0.0076 Score=49.81 Aligned_cols=76 Identities=11% Similarity=-0.002 Sum_probs=50.0
Q ss_pred CCCccccCcccCCcccccccCCCCCCCCCCCCCCCc--cccCCCCCCCCCCcccccccccccccccccccccccccccCC
Q 047960 230 KIPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEK--VSRNGNYRPFKPPLENSLDDFDQSGEKYRDAWQHGIQKKQSS 307 (371)
Q Consensus 230 ~g~~v~~~v~~~g~r~~~~~~~~~~r~~~~~~~~~~--~~~~g~~~~~~~~~e~~~~~~~~~~~~~r~~~~~~~~~~~~~ 307 (371)
.|+...+|+.+++|++ |.... ..+ ||+||... ++. ...|..|+..+...||...|.-...-
T Consensus 30 ~g~~f~~q~~ig~y~~-----------Df~~~-~~kl~IE~DG~~H---~~~--~~~D~~R~~~L~~~Gw~VlR~~~~~v 92 (108)
T PF04480_consen 30 GGYKFRRQVPIGRYRV-----------DFACP-EAKLAIEIDGRQH---STP--RERDRRRDNWLEALGWTVLRFTAEDV 92 (108)
T ss_dssp TT--EEEEEEETTEEE-----------EEEET-CTTEEEEEE-S-T---T----HHHHHHHHHHHHHTT-EEEEEEHHHH
T ss_pred CCceEEEecCCCCEEE-----------eeccC-cccEEEEEcCccc---cch--HHhhHHHHHHHHHCCCEEEEeeHHHH
Confidence 3455566666666644 44443 244 99999753 443 77899999999999999999988887
Q ss_pred CCCCCCchHHHHHhh
Q 047960 308 GGKGSPRLEDLVDAF 322 (371)
Q Consensus 308 ~~~~~~~~~~~~~~~ 322 (371)
..+|+..++.+..++
T Consensus 93 ~~~~~~vv~~I~~~i 107 (108)
T PF04480_consen 93 REDPEAVVEQIRAAI 107 (108)
T ss_dssp HHGHHHHHHHHHHHH
T ss_pred HhCHHHHHHHHHHHh
Confidence 777777777766554
No 45
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=89.61 E-value=0.16 Score=54.47 Aligned_cols=56 Identities=21% Similarity=0.272 Sum_probs=40.8
Q ss_pred CeEEccccCCCCccccEEEEEccccCC-CC------ccC-CC-CCCchhhhhHhhcccEEEEeec
Q 047960 126 DLYINTVDAFQGQERDVIIMSCVRASN-HG------VGF-VA-DIRRMNVALTRARRALWVMGNA 181 (371)
Q Consensus 126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~-~~------~gf-l~-d~rRLNVAlSRAK~~liVvGn~ 181 (371)
.|.+.|+|...|.|+++||+...-... +. .+. +. ..|.+.||+||||+.|++....
T Consensus 554 ~V~lmT~H~aKGlEf~~Vfl~g~~eg~~P~~~~~~~~~~~~eEERRL~YVaiTRA~~~L~~t~~~ 618 (655)
T COG0210 554 QVNLMTIHAAKGLEFPYVFLVGLEEGLFPADRSLDEGDEPLEEERRLLYVAITRAKKKLYLTYAA 618 (655)
T ss_pred ceEEEechhccCCCCCeEEEecccCCCCCChhhcccCCCCccHHHHHHHHHHHHHHHhhhhhHHH
Confidence 599999999999999999997653321 10 111 33 3356899999999999986443
No 46
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=87.18 E-value=0.14 Score=42.91 Aligned_cols=60 Identities=13% Similarity=0.075 Sum_probs=48.8
Q ss_pred CCcccccccCCCCCCCCCCCCCCCc-cccCCCCCCCCC-------------------Ccccccccccccccccccccccc
Q 047960 241 AGQRHRSFDMNMESRSGTPSEDDEK-VSRNGNYRPFKP-------------------PLENSLDDFDQSGEKYRDAWQHG 300 (371)
Q Consensus 241 ~g~r~~~~~~~~~~r~~~~~~~~~~-~~~~g~~~~~~~-------------------~~e~~~~~~~~~~~~~r~~~~~~ 300 (371)
.|++.+-+.+..++..|.+-..-.. |+.||.+| |+ ..++...|-.+.+.|+..||...
T Consensus 34 ~G~rfR~q~~~lpg~pD~~~~~~klaIfVDGcfW--Hgh~c~~~~~pk~n~~fW~~Ki~~n~~rD~~~~~~L~~~Gw~Vl 111 (117)
T TIGR00632 34 LGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFW--HGHHCYLGKVPKTRTDFWSPKIEKNVERDRRVNSRLQELGWRVL 111 (117)
T ss_pred CCCEEEEecCCCCCcccEEecCCCEEEEEccccc--ccCCcccccCCCccHHHHHHHHHHHHHHHHHHHHHHHHCcCEEE
Confidence 5788888888899999988876555 99999987 31 13567889999999999999988
Q ss_pred cc
Q 047960 301 IQ 302 (371)
Q Consensus 301 ~~ 302 (371)
+.
T Consensus 112 r~ 113 (117)
T TIGR00632 112 RV 113 (117)
T ss_pred EE
Confidence 75
No 47
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=86.05 E-value=2.8 Score=45.42 Aligned_cols=94 Identities=9% Similarity=-0.089 Sum_probs=54.5
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCCCCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCL 80 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~l 80 (371)
+.|.++|||.++|.++.|..+=.+.-.- +.......+...++.++... .-..||..|+..
T Consensus 271 ~~L~~NyRs~~~I~~~an~li~~n~~~~-------~k~~~~~~~~g~~~~~~~~~-------------~~~~ea~~i~~~ 330 (672)
T PRK10919 271 IKLEQNYRSSGRILKAANILIANNPHVF-------EKRLFSELGYGDELKVLSAN-------------NEEHEAERVTGE 330 (672)
T ss_pred EECCCCCCCcHHHHHHHHHHHhhCcccc-------ccccccCCCCCCceEEEcCC-------------CHHHHHHHHHHH
Confidence 3699999999999999998764432110 00000000111122222111 123677776543
Q ss_pred HHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 81 YEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 81 v~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
+... ....+.+..+|+|++--+.|...|.+.|.+
T Consensus 331 i~~~---~~~~~~~~~diAVL~Rs~~~~~~le~~L~~ 364 (672)
T PRK10919 331 LIAH---HFVNKTQYKDYAILYRGNHQSRVFEKFLMQ 364 (672)
T ss_pred HHHH---HHhcCCCcCcEEEEEeCchhHHHHHHHHHH
Confidence 2221 112357778999999999999989888865
No 48
>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=84.59 E-value=3.2 Score=47.79 Aligned_cols=46 Identities=4% Similarity=-0.075 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHH------hcCCCCceEEEEcccHHH-HHHHHHHHHh
Q 047960 72 DEAKFGVCLYEHLQKTLK------SMGLGKVTVGIITPYKLQ-LKCLQHEFRN 117 (371)
Q Consensus 72 ~EA~~Vv~lv~~l~~~l~------~~~~~~~sIgVITpy~aQ-~~~I~~~L~~ 117 (371)
.||+.|++.+..+...-. ...++..+|+|++.-+.+ ...|.+.|.+
T Consensus 555 ~eA~~Ia~~I~~ll~~g~~~~~~~~r~~~~~DIAILvRs~~~~~~~i~~aL~~ 607 (1141)
T TIGR02784 555 RLAERIAATIRDWLDRGTPIPKGRGRAARPGDILVLVRKRDAFVSALIRALKR 607 (1141)
T ss_pred HHHHHHHHHHHHHHhCCCccccCCcCCCCCCcEEEEEeCCchhHHHHHHHHHH
Confidence 578888877766543100 011466799999999887 5678887765
No 49
>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=84.41 E-value=0.51 Score=46.83 Aligned_cols=52 Identities=17% Similarity=0.153 Sum_probs=37.5
Q ss_pred EEccccCCCCccccEEEEEccccC-----CC----------C-ccCCCC---------CCchhhhhHhhcccEEEEe
Q 047960 128 YINTVDAFQGQERDVIIMSCVRAS-----NH----------G-VGFVAD---------IRRMNVALTRARRALWVMG 179 (371)
Q Consensus 128 ~V~TVd~fQG~ErDVIIiS~vrs~-----~~----------~-~gfl~d---------~rRLNVAlSRAK~~liVvG 179 (371)
.|+++++.||-|.|.+.+....+- .. . -++... .|.+||.|||++++++|..
T Consensus 274 evgsi~t~QG~eldy~GVi~G~dl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~i~N~y~VLLTRG~~G~~iy~ 350 (352)
T PF09848_consen 274 EVGSIYTIQGFELDYVGVIIGPDLRYDPEDGRWVVDPEKYKDKKGKKKRSDEELDRYIKNIYRVLLTRGIKGTYIYA 350 (352)
T ss_pred cceeEEEecccccceeEEEECCCeEEECCCCeEEEchhhccccchhcccchHHHHHHHHHHHHHHHhcccceEEEEe
Confidence 699999999999999988664221 00 0 111111 3779999999999999864
No 50
>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=82.60 E-value=3.7 Score=47.71 Aligned_cols=47 Identities=17% Similarity=-0.003 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHH---H------hcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 71 VDEAKFGVCLYEHLQKTL---K------SMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 71 ~~EA~~Vv~lv~~l~~~l---~------~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
..||+.|+..+..+...- . ..+++..+|+|++..+.+...|.+.|.+
T Consensus 543 ~~EA~~IA~~I~~l~~~g~~v~d~~~~~~r~~~~~DIAIL~Rs~~~~~~i~~aL~~ 598 (1232)
T TIGR02785 543 QQEATMVAERIKALIKEGFKVYDKKTGEYRPVTYRDIVILTRSRGWNLQIMEEFKK 598 (1232)
T ss_pred HHHHHHHHHHHHHHHhcCCccccccccccCCCCcCCEEEEEeccccHHHHHHHHHH
Confidence 568888888777664320 0 0235678999999999999999888865
No 51
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=81.08 E-value=0.91 Score=53.41 Aligned_cols=53 Identities=23% Similarity=0.229 Sum_probs=41.9
Q ss_pred EEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecc
Q 047960 128 YINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAG 182 (371)
Q Consensus 128 ~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~ 182 (371)
.+.|++..||...|.+|+....... -+.+.+.+.++|++||||+.+.|+.+-.
T Consensus 1265 YA~Tah~AQG~T~~~vI~~~~s~~~--~~~lt~~rsfYVaiSRAr~~v~IYTDd~ 1317 (1623)
T PRK14712 1265 YAITAHGAQGASETFAIALEGTEGN--RKLMAGFESAYVALSRMKQHVQVYTDNR 1317 (1623)
T ss_pred hhhhhhhccCCccceEEEecccccc--hhhcccchhheeeeeeccceEEEEECCH
Confidence 4789999999999999986432211 2345688999999999999999997654
No 52
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=79.99 E-value=1.2 Score=52.97 Aligned_cols=53 Identities=21% Similarity=0.172 Sum_probs=42.0
Q ss_pred EEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecc
Q 047960 128 YINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAG 182 (371)
Q Consensus 128 ~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~ 182 (371)
.+.|++..||...|.+|+.+..... -..+.+.+.++|++||||+.+.|+.+-.
T Consensus 1394 YA~T~h~AQG~T~~~vi~~~~~~~~--~~~l~~~~~fYVaiSRar~~l~IyTDd~ 1446 (1747)
T PRK13709 1394 YAITAHGAQGASETYAIALEGTEGG--RKQMAGFESAYVALSRMKQHVQVYTDNR 1446 (1747)
T ss_pred hhhhhhhhcccccceEEEEeccccc--cccccchhhhhhcccccccceEEEEcCH
Confidence 4779999999999999987532111 1246788999999999999999997754
No 53
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....
Probab=79.84 E-value=2.8 Score=39.73 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=38.3
Q ss_pred HHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCC---------------CCCeEEccccCCCC
Q 047960 88 LKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEE---------------GKDLYINTVDAFQG 137 (371)
Q Consensus 88 l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~---------------~~~i~V~TVd~fQG 137 (371)
+...++++.+|.++||.++-+..|++.|...+.... ...+.|.|+|+|-.
T Consensus 38 l~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~T~hsf~~ 102 (315)
T PF00580_consen 38 LYEGGVPPERILVLTFTNAAAQEMRERIRELLEEEQQESSDNERLRRQLSNIDRIYISTFHSFCY 102 (315)
T ss_dssp HHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHCCTT-HHHHHHHHHCTTSEEEEHHHHHH
T ss_pred hccccCChHHheecccCHHHHHHHHHHHHHhcCcccccccccccccccccccchheeehhhhhhh
Confidence 444458999999999999988888888877655432 45788999887643
No 54
>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=72.29 E-value=2.1 Score=51.79 Aligned_cols=49 Identities=20% Similarity=0.191 Sum_probs=39.6
Q ss_pred EccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecc
Q 047960 129 INTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAG 182 (371)
Q Consensus 129 V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~ 182 (371)
..|++..||...|-||+.... . .-+.+.+.++|++||||+.+.|+.+..
T Consensus 1449 A~T~h~aQG~T~~~vi~~~~s-~----~~l~~~~~~YVaiSRar~~~~iyTd~~ 1497 (1960)
T TIGR02760 1449 TRTADSAQGATYTFVIALIKG-R----LALTNYRSAYIDLTRASHHVELYTDNK 1497 (1960)
T ss_pred hhhhhhhcccccceEEEEecc-h----hhhhhhhhHhhhhhhcccceEEEeCCH
Confidence 568999999999999987422 1 235678999999999999999998753
No 55
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=69.09 E-value=7.7 Score=40.49 Aligned_cols=103 Identities=15% Similarity=0.170 Sum_probs=64.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCceEEEEcccHHHH-H---HHHHHHHhh-hccC-------------CCCCeEEccc
Q 047960 71 VDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQL-K---CLQHEFRNV-LNSE-------------EGKDLYINTV 132 (371)
Q Consensus 71 ~~EA~~Vv~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~-~---~I~~~L~~~-~~~~-------------~~~~i~V~TV 132 (371)
..|+..|+ ..+.+ ....+....+|.||.+=.... . .|.+.|... ...+ ....+.+.+|
T Consensus 454 ~deivwi~---~qI~~-~~edeLe~dDIiVi~lDp~t~Rgy~~~li~sL~s~giq~hl~gvd~s~e~~f~~dgkvtis~I 529 (660)
T COG3972 454 PDEIVWII---IQIKE-FREDELEQDDIIVIFLDPGTMRGYIYELIHSLKSKGIQQHLWGVDISHETKFKQDGKVTISRI 529 (660)
T ss_pred chhhHHHH---HHHHH-hcccccccCCEEEEecCCccccchHHHHHHHHHHhhhhhhccccCcccccccccCceEEeeee
Confidence 34555444 44444 344567788999998742211 1 122222111 1000 1126889999
Q ss_pred cCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEe
Q 047960 133 DAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMG 179 (371)
Q Consensus 133 d~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvG 179 (371)
-+.-|.|+.+|+.--+..-+ .|+....|-+-+|+||.|.-+-|+|
T Consensus 530 yrAKGnEapfV~aL~a~~ls--~~la~~RN~LfTamTRSkawvrv~g 574 (660)
T COG3972 530 YRAKGNEAPFVYALGAAYLS--TGLADWRNILFTAMTRSKAWVRVVG 574 (660)
T ss_pred hhccCCCCcEEEEehhhhhC--ccchhHHhHHHHHHhhhhhhhhhhc
Confidence 99999999999976543332 4555566789999999999998988
No 56
>COG3410 Uncharacterized conserved protein [Function unknown]
Probab=68.77 E-value=3.6 Score=36.54 Aligned_cols=55 Identities=22% Similarity=0.277 Sum_probs=42.0
Q ss_pred EEccccCCCCccccEEEEEccccCC----------------CCccCCCC----------------CCchhhhhHhhcccE
Q 047960 128 YINTVDAFQGQERDVIIMSCVRASN----------------HGVGFVAD----------------IRRMNVALTRARRAL 175 (371)
Q Consensus 128 ~V~TVd~fQG~ErDVIIiS~vrs~~----------------~~~gfl~d----------------~rRLNVAlSRAK~~l 175 (371)
.|++|-..||-|.|.|=+-+.++-. ...||... .|++||.+||.-.++
T Consensus 90 evgSVYtaQGFdlnYvGvVlGrs~~yd~d~d~i~~dp~~ytD~~gfr~slkk~~~k~~eik~kiIkNsinvlmtRGIrGl 169 (191)
T COG3410 90 EVGSVYTAQGFDLNYVGVVLGRSVIYDEDKDEIVIDPSKYTDTGGFRSSLKKTPEKNQEIKEKIIKNSINVLMTRGIRGL 169 (191)
T ss_pred HhhhhheecccccceeEEEeccceeeccCCCeEecCcceeeccccchhhhhhhhhhCHHHHHHHHHHHHHHHHhcccceE
Confidence 4899999999999999887776531 01344431 289999999999999
Q ss_pred EEEeecc
Q 047960 176 WVMGNAG 182 (371)
Q Consensus 176 iVvGn~~ 182 (371)
+|+.--.
T Consensus 170 yiyaeDp 176 (191)
T COG3410 170 YIYAEDP 176 (191)
T ss_pred EEEEeCH
Confidence 9986544
No 57
>PRK10481 hypothetical protein; Provisional
Probab=65.99 E-value=17 Score=34.05 Aligned_cols=24 Identities=29% Similarity=0.458 Sum_probs=19.2
Q ss_pred CCceEEEEcccHHHHHHHHHHHHh
Q 047960 94 GKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 94 ~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
...+|||||||..|.....+++.+
T Consensus 128 ~g~riGVitP~~~qi~~~~~kw~~ 151 (224)
T PRK10481 128 GGHQVGVIVPVEEQLAQQAQKWQV 151 (224)
T ss_pred CCCeEEEEEeCHHHHHHHHHHHHh
Confidence 357999999999999877766544
No 58
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=64.55 E-value=2.3 Score=31.88 Aligned_cols=23 Identities=17% Similarity=-0.002 Sum_probs=17.6
Q ss_pred ccccccccccccccccCC-CCCCC
Q 047960 290 GEKYRDAWQHGIQKKQSS-GGKGS 312 (371)
Q Consensus 290 ~~~~r~~~~~~~~~~~~~-~~~~~ 312 (371)
..|+.+||++.|+|||-. |+.|.
T Consensus 14 k~Le~~Gf~~vrqkGSH~q~kHp~ 37 (66)
T COG1724 14 KALEKDGFQLVRQKGSHRQYKHPD 37 (66)
T ss_pred HHHHhCCcEEEEeecceeEEEcCC
Confidence 468899999999999854 34443
No 59
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=61.20 E-value=24 Score=37.86 Aligned_cols=94 Identities=14% Similarity=0.184 Sum_probs=59.8
Q ss_pred CccccccCCchhhhhcchhhccCCccccCccccCCCCcccCC-CCCCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHHH
Q 047960 1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYK-DPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVC 79 (371)
Q Consensus 1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~~~~~-~~~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv~ 79 (371)
|.|.++||+.|.|....|...=.++-.... ..... ......+.++. ......||..++.
T Consensus 277 i~Le~NyRSt~~Il~~An~~i~~n~~r~~k-------~l~~~~~~~~~~~~~~~-------------~~~~~~ea~~i~~ 336 (655)
T COG0210 277 IKLEQNYRSTPNILAAANKVIANNKKRQAK-------TLRTEVEGSGEKVVLLL-------------ANDEEDEARWIAS 336 (655)
T ss_pred EEecCCCCCcHHHHHHHHHHHhcCCccCCC-------cceeccCCCCCCceEEe-------------CCChHHHHHHHHH
Confidence 468999999999999999765533211111 00000 11111122221 2246789999998
Q ss_pred HHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHh
Q 047960 80 LYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRN 117 (371)
Q Consensus 80 lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~ 117 (371)
.+..+... ...+..+|+|+.-...|...+...|..
T Consensus 337 ~I~~l~~~---~~~~~~d~aiL~R~n~~s~~~e~~l~~ 371 (655)
T COG0210 337 EIDALIEI---GKVNYSDIAILYRTNAQSRLIEEALRA 371 (655)
T ss_pred HHHHHHHc---CCCChhhEEEEEecCcchHHHHHHHHH
Confidence 77766442 126778999999999999999888863
No 60
>PF13245 AAA_19: Part of AAA domain
Probab=51.78 E-value=37 Score=25.91 Aligned_cols=34 Identities=12% Similarity=0.137 Sum_probs=25.4
Q ss_pred CceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCC
Q 047960 95 KVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAF 135 (371)
Q Consensus 95 ~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~f 135 (371)
+++|.|+||-+..++.|.+.+ .....++.|+++|
T Consensus 42 ~~~vlv~a~t~~aa~~l~~rl-------~~~~~~~~T~h~~ 75 (76)
T PF13245_consen 42 GKRVLVLAPTRAAADELRERL-------GLGVPFAMTIHSL 75 (76)
T ss_pred CCeEEEECCCHHHHHHHHHHH-------cCCCcchhhHHHh
Confidence 789999999999999888777 1112347777765
No 61
>KOG2340 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.98 E-value=30 Score=36.48 Aligned_cols=82 Identities=17% Similarity=0.246 Sum_probs=59.3
Q ss_pred cCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCCC------ccCCCCCCch
Q 047960 91 MGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHG------VGFVADIRRM 164 (371)
Q Consensus 91 ~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~------~gfl~d~rRL 164 (371)
.|...-.|.|++|++.-+-.|-++|...+...+.....|.+-..|+|.=.---...+.+...+. .|=..|.-|+
T Consensus 289 QG~tRpkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~Fri 368 (698)
T KOG2340|consen 289 QGFTRPKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRI 368 (698)
T ss_pred cCCCCceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhh
Confidence 3555557999999999988888888888776666678899999999975532333333333221 4556788999
Q ss_pred hhhhHhhc
Q 047960 165 NVALTRAR 172 (371)
Q Consensus 165 NVAlSRAK 172 (371)
-||+||--
T Consensus 369 Gl~ftkKt 376 (698)
T KOG2340|consen 369 GLAFTKKT 376 (698)
T ss_pred hHHHHHHH
Confidence 99999954
No 62
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=49.27 E-value=49 Score=31.16 Aligned_cols=15 Identities=27% Similarity=0.620 Sum_probs=11.1
Q ss_pred CCceEEEEcccHHHH
Q 047960 94 GKVTVGIITPYKLQL 108 (371)
Q Consensus 94 ~~~sIgVITpy~aQ~ 108 (371)
.-+.|+|+|||..-+
T Consensus 119 g~~RIalvTPY~~~v 133 (239)
T TIGR02990 119 GVRRISLLTPYTPET 133 (239)
T ss_pred CCCEEEEECCCcHHH
Confidence 346899999995443
No 63
>COG2852 Very-short-patch-repair endonuclease [Replication, recombination, and repair]
Probab=42.67 E-value=3.4 Score=35.04 Aligned_cols=77 Identities=12% Similarity=-0.086 Sum_probs=60.1
Q ss_pred CCccccCcccCCcccccccCCCCCCCCCCCCCCCc--cccCCCCCCCCCCcccccccccccccccccccccccccccCCC
Q 047960 231 IPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEK--VSRNGNYRPFKPPLENSLDDFDQSGEKYRDAWQHGIQKKQSSG 308 (371)
Q Consensus 231 g~~v~~~v~~~g~r~~~~~~~~~~r~~~~~~~~~~--~~~~g~~~~~~~~~e~~~~~~~~~~~~~r~~~~~~~~~~~~~~ 308 (371)
|+...+|..+++|.+ |-.-. +.| +|-||... .+...-|..|...|...||.-.|.+-..-.
T Consensus 44 g~KFrRQ~~ig~yiv-----------DF~c~-~~klIvElDG~qH-----~~~~~~Da~Rd~~L~~~G~~VLRf~N~ev~ 106 (129)
T COG2852 44 GFKFRRQQPIGRYIV-----------DFACR-DAKLIVELDGGQH-----EEREEYDAERDAFLESQGFTVLRFWNDEVL 106 (129)
T ss_pred CeeEEEeeeccCEEE-----------EEEcC-CccEEEEecCccc-----hhhhhhhHHHHHHHHhCCceEEEeccHHHH
Confidence 466677777777755 33333 445 89999876 455668999999999999999999999999
Q ss_pred CCCCCchHHHHHhhhh
Q 047960 309 GKGSPRLEDLVDAFWW 324 (371)
Q Consensus 309 ~~~~~~~~~~~~~~~~ 324 (371)
.+++..++++...+..
T Consensus 107 ~n~~~vl~~I~~~l~~ 122 (129)
T COG2852 107 QNIDRVLEEILAVLEE 122 (129)
T ss_pred hHHHHHHHHHHHHHHh
Confidence 9999999988777654
No 64
>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B. DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.
Probab=42.55 E-value=88 Score=36.28 Aligned_cols=56 Identities=16% Similarity=0.159 Sum_probs=40.4
Q ss_pred CCCeEEccccCCCCccccEEEEEccccCC-----CCccCCC------------------------CCCchhhhhHhhccc
Q 047960 124 GKDLYINTVDAFQGQERDVIIMSCVRASN-----HGVGFVA------------------------DIRRMNVALTRARRA 174 (371)
Q Consensus 124 ~~~i~V~TVd~fQG~ErDVIIiS~vrs~~-----~~~gfl~------------------------d~rRLNVAlSRAK~~ 174 (371)
...|.|.|++..+|.+.++|++--+.... ..-|++. +...+.+|+|||++.
T Consensus 579 ~d~V~v~~~~~~r~~~~k~v~vlG~ndg~~P~~~~~~~ll~d~er~~L~~~g~~l~~~~~~~~~~e~~~~y~alt~a~~~ 658 (1158)
T TIGR02773 579 LDQVSVGTMDRAKSDNTKVIYLLGMNDGVMPARSKEEGILSDEERELLEQQGVELSPTSKIKIFDEQFLVYTAFTSASER 658 (1158)
T ss_pred cCEEEEeccccccccCcCEEEEeCCCCCcCCCCCCCCCCcCHHHHHHHHHCCCCCCCChHHHhhcCcHHHHHHhcCccce
Confidence 35799999999999999999996543321 1123322 123488999999999
Q ss_pred EEEEe
Q 047960 175 LWVMG 179 (371)
Q Consensus 175 liVvG 179 (371)
|++--
T Consensus 659 L~lSy 663 (1158)
T TIGR02773 659 LKISY 663 (1158)
T ss_pred EEEEE
Confidence 99854
No 65
>cd00899 b4GalT Beta-4-Galactosyltransferase is involved in the formation of the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. Beta-4-Galactosyltransferase transfers galactose from uridine diphosphogalactose to the terminal beta-N-acetylglucosamine residues, hereby forming the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. At least seven homologous beta-4-galactosyltransferase isoforms have been identified that use different types of glycoproteins and glycolipids as substrates. Of the seven identified members of the beta-1,4-galactosyltransferase subfamily (beta1,4-Gal-T1 to -T7), b1,4-Gal-T1 is most characterized (biochemically). It is a Golgi-resident type II membrane enzyme with a cytoplasmic domain, membrane spanning region, and a stem region and catalytic domain facing the lumen.
Probab=38.38 E-value=47 Score=30.98 Aligned_cols=74 Identities=18% Similarity=0.259 Sum_probs=47.1
Q ss_pred ceEEEEcccHHHHHHHHHHHH---hhhccCCCCCeEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhc
Q 047960 96 VTVGIITPYKLQLKCLQHEFR---NVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRAR 172 (371)
Q Consensus 96 ~sIgVITpy~aQ~~~I~~~L~---~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK 172 (371)
..++||.||+...+.|+..|. ..+. =|+-+.-|.|+--+.. .-.+-...|||+++-|.
T Consensus 2 ~~~aiivpyr~R~~~l~~~l~~~~~~L~--------------rq~~~~~i~vi~Q~~~-----~~FNR~~llNvG~~~a~ 62 (219)
T cd00899 2 HKVAIIVPFRNRFEHLLIFLPHLHPFLQ--------------RQQLDYRIFVIEQVGN-----FRFNRAKLLNVGFLEAL 62 (219)
T ss_pred cceEEEEecCCHHHHHHHHHHHHHHHHH--------------hcCCcEEEEEEEecCC-----ccchhhhhhhHHHHHHh
Confidence 369999999877766665443 2332 1455555555543221 12344578999888886
Q ss_pred cc----EEEEeecccccCCc
Q 047960 173 RA----LWVMGNAGALTQSD 188 (371)
Q Consensus 173 ~~----liVvGn~~~L~~~~ 188 (371)
+. ++|+.+.+.+-.+.
T Consensus 63 k~~~~dc~i~hDVDllP~~~ 82 (219)
T cd00899 63 KDGDWDCFIFHDVDLLPEND 82 (219)
T ss_pred hcCCccEEEEecccccccCc
Confidence 64 89999999875544
No 66
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=36.49 E-value=1.8e+02 Score=27.26 Aligned_cols=49 Identities=22% Similarity=0.537 Sum_probs=31.5
Q ss_pred CCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCC--------------CCccccEEEEEc
Q 047960 94 GKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAF--------------QGQERDVIIMSC 147 (371)
Q Consensus 94 ~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~f--------------QG~ErDVIIiS~ 147 (371)
...+||||+|-..|.....++.... ..++.+....-| +.+..|+|++.|
T Consensus 124 ~~~~vGVivP~~eQ~~~~~~kW~~l-----~~~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDC 186 (221)
T PF07302_consen 124 GGHQVGVIVPLPEQIAQQAEKWQPL-----GNPVVVAAASPYEGDEEELAAAARELAEQGADLIVLDC 186 (221)
T ss_pred CCCeEEEEecCHHHHHHHHHHHHhc-----CCCeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEEC
Confidence 4479999999999999777665442 123333333333 334568888887
No 67
>cd01037 Restriction_endonuclease_like Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI
Probab=34.28 E-value=16 Score=26.28 Aligned_cols=51 Identities=8% Similarity=-0.128 Sum_probs=32.5
Q ss_pred cCCCCCCCCCCCCCCCc-cccCCCCCCCCCCcccccccc---cccccccccccccccc
Q 047960 249 DMNMESRSGTPSEDDEK-VSRNGNYRPFKPPLENSLDDF---DQSGEKYRDAWQHGIQ 302 (371)
Q Consensus 249 ~~~~~~r~~~~~~~~~~-~~~~g~~~~~~~~~e~~~~~~---~~~~~~~r~~~~~~~~ 302 (371)
.+..++..|.+.....- |+|||..+ +....-..+. .+...+...||++.+.
T Consensus 24 ~~~~~~~pDf~~~~~~~~ie~kg~~~---~~~~~~~~~~~~~~~~~~l~~~g~~~~~~ 78 (80)
T cd01037 24 VPIGSYIPDFVCPSAKLVIELKGTFH---DGLLRKLRTSEKQERIAFLEADGKKVLRF 78 (80)
T ss_pred CCCCCCccCEEccCCCEEEEEECccc---cCchhhhhhcchHHHHHHHHHCCCEEEEE
Confidence 34445556665552222 99999988 4433333444 5788899999988764
No 68
>PF04592 SelP_N: Selenoprotein P, N terminal region; InterPro: IPR007671 SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues, and accounts for more than 50% of the selenium content of rat and human plasma []. It is thought to be glycosylated []. SelP may have antioxidant properties. It can attach to epithelial cells, and may protect vascular endothelial cells against peroxynitrite toxicity []. The high selenium content of SelP suggests that it may be involved in selenium intercellular transport or storage []. The promoter structure of bovine SelP suggests that it may be involved in countering heavy metal intoxication, and may also have a developmental function []. The N-terminal region of SelP can exist independently of the C-terminal region. Zebrafish selenoprotein Pb (Q98SV0 from SWISSPROT) lacks the C-terminal Sec-rich region, and a protein encoded by the rat SelP gene and lacking this region has also been reported []. The N-terminal region contains a conserved SecxxCys motif, which is similar to the CysxxCys found in thioredoxins. It is speculated that the N-terminal region may adopt a thioredoxin fold and catalyse redox reactions []. The N-terminal region also contains a His-rich region, which is thought to mediate heparin binding. Binding to heparan proteoglycans could account for the membrane binding properties of SelP []. The function of the bacterial members of this family is uncharacterised.; GO: 0008430 selenium binding
Probab=33.33 E-value=1.3e+02 Score=28.46 Aligned_cols=63 Identities=13% Similarity=0.240 Sum_probs=44.7
Q ss_pred HHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCC----CCCeEEccccCCCCccccEEEEE
Q 047960 84 LQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEE----GKDLYINTVDAFQGQERDVIIMS 146 (371)
Q Consensus 84 l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~----~~~i~V~TVd~fQG~ErDVIIiS 146 (371)
|...|...|++.-++.||.+...+.+++...|+++.+... -+.......+.+-|...|++|+.
T Consensus 51 Lr~kL~~~g~~~I~f~vVN~~~~~s~~~~~~l~~r~~~~ipVyqq~~~q~dvW~~L~G~kdD~~iyD 117 (238)
T PF04592_consen 51 LREKLENEGLSNISFMVVNHQGEHSRLKYWELKRRVSEHIPVYQQDENQPDVWELLNGSKDDFLIYD 117 (238)
T ss_pred HHHHHHHCCCCceEEEEEcCCCcchhHHHHHHHHhCCCCCceecCCccccCHHHHhCCCcCcEEEEe
Confidence 3344566799999999999998888888777877654322 01233455667789999999986
No 69
>PRK11054 helD DNA helicase IV; Provisional
Probab=32.17 E-value=60 Score=35.48 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=34.8
Q ss_pred hcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCC
Q 047960 90 SMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAF 135 (371)
Q Consensus 90 ~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~f 135 (371)
..+.++.+|.++|+-+.-+..+++.|.+.+. ...+.|+|.|+|
T Consensus 236 ~~~~~~~~IL~ltft~~AA~em~eRL~~~lg---~~~v~v~TFHSl 278 (684)
T PRK11054 236 RGQAQPEQILLLAFGRQAAEEMDERIRERLG---TEDITARTFHAL 278 (684)
T ss_pred hCCCCHHHeEEEeccHHHHHHHHHHHHHhcC---CCCcEEEeHHHH
Confidence 3457789999999999999989988887764 357888888875
No 70
>KOG2108 consensus 3'-5' DNA helicase [Replication, recombination and repair]
Probab=32.00 E-value=24 Score=38.97 Aligned_cols=53 Identities=21% Similarity=0.299 Sum_probs=39.3
Q ss_pred CeEEccccCCCCccccEEEEEccccCCCC-------cc------CCC-CCCchhhhhHhhcccEEEE
Q 047960 126 DLYINTVDAFQGQERDVIIMSCVRASNHG-------VG------FVA-DIRRMNVALTRARRALWVM 178 (371)
Q Consensus 126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~~~-------~g------fl~-d~rRLNVAlSRAK~~liVv 178 (371)
.+..+|++..-|.|.|++-++..+....+ ++ +.. .++-+.|++||||..+|.-
T Consensus 674 ~~~l~Tih~akglefd~v~~~n~~~~~~~s~~~~~r~~~~r~~t~~~~e~n~lyV~vtRakkrl~~~ 740 (853)
T KOG2108|consen 674 NVILGTIHQAKGLEFDNVHLQNDFVKVFGSVSNFERLPSFRVETYNEDEWNFLYVAVTRAKKRLIMC 740 (853)
T ss_pred hhhhHHHHhccCcccceeecccCcccccccccchhhcchhhhhhhhhhhhhheeeeecchhhhcccc
Confidence 36789999999999999999987665422 11 111 2477899999999977654
No 71
>cd00133 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby r
Probab=29.38 E-value=1e+02 Score=22.47 Aligned_cols=49 Identities=8% Similarity=0.044 Sum_probs=32.0
Q ss_pred EEEEcccH-HHHHHHHHHHHhhhccCCC-CCeEEccccC-CCCccccEEEEE
Q 047960 98 VGIITPYK-LQLKCLQHEFRNVLNSEEG-KDLYINTVDA-FQGQERDVIIMS 146 (371)
Q Consensus 98 IgVITpy~-aQ~~~I~~~L~~~~~~~~~-~~i~V~TVd~-fQG~ErDVIIiS 146 (371)
|.++|+.. +-..++...|++.++.... ..+....++. ....+.|+||-.
T Consensus 2 il~vc~~G~~~s~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dliitt 53 (84)
T cd00133 2 ILVVCGSGIGSSSMLAEKLEKAAKELGIEVKVEAQGLSEVIDLADADLIIST 53 (84)
T ss_pred EEEECCCcHhHHHHHHHHHHHHHHHCCCeEEEEEcccchhhhcCCccEEEEC
Confidence 67888764 7777788888887765443 2344555555 555777766544
No 72
>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]
Probab=28.25 E-value=28 Score=28.50 Aligned_cols=62 Identities=21% Similarity=0.186 Sum_probs=48.5
Q ss_pred CCccccCCCCCCCCCCcccccccccccc-cccccccccccccccCCCCCCCCchHHHHHhhhhcccccceeccCcc
Q 047960 263 DEKVSRNGNYRPFKPPLENSLDDFDQSG-EKYRDAWQHGIQKKQSSGGKGSPRLEDLVDAFWWVGLYYTLTLTGSE 337 (371)
Q Consensus 263 ~~~~~~~g~~~~~~~~~e~~~~~~~~~~-~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~ 337 (371)
+..++|---...+|.. +|.|+++ +--++|+..|-.=-+-+..+|-+ --++|||-+++..||-
T Consensus 9 G~aveclsi~velHK~-----~~~d~~Gre~l~~GFkIGGGIDQDp~k~Pf~--------ytD~GiYvT~V~eGsP 71 (124)
T KOG3553|consen 9 GQAVECLSIRVELHKL-----RDYDQQGRENLILGFKIGGGIDQDPSKNPFS--------YTDKGIYVTRVSEGSP 71 (124)
T ss_pred CCceEEEEEEEEeeee-----hhhhcCCcEEEEEEEEeccccCCCcccCCCC--------cCCccEEEEEeccCCh
Confidence 3447776666655665 8888888 78899999998888888888876 3578999999988774
No 73
>PF13778 DUF4174: Domain of unknown function (DUF4174)
Probab=27.78 E-value=2.7e+02 Score=22.98 Aligned_cols=59 Identities=17% Similarity=0.298 Sum_probs=32.7
Q ss_pred ccccEEEEEccccCCCCccCCCCCCchhhhhHhhc-------ccEEEEeeccccc--CC--chHHHHHHHHH
Q 047960 138 QERDVIIMSCVRASNHGVGFVADIRRMNVALTRAR-------RALWVMGNAGALT--QS--DDWAALIADSK 198 (371)
Q Consensus 138 ~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK-------~~liVvGn~~~L~--~~--~~w~~ll~~a~ 198 (371)
.|||++++..+.......+ .......+.--|.+ ..+++||--...+ .. -.|..++....
T Consensus 40 ~eRdi~v~~i~~~~~~~~~--~~~~~~~~~~lr~~l~~~~~~f~~vLiGKDG~vK~r~~~p~~~~~lf~~ID 109 (118)
T PF13778_consen 40 DERDIVVIVITGDGARSPG--KPLSPEDIQALRKRLRIPPGGFTVVLIGKDGGVKLRWPEPIDPEELFDTID 109 (118)
T ss_pred ccCceEEEEEeCCcccccc--CcCCHHHHHHHHHHhCCCCCceEEEEEeCCCcEEEecCCCCCHHHHHHHHh
Confidence 5999999998765543222 22222333333333 4488888766532 12 24777766653
No 74
>PF13733 Glyco_transf_7N: N-terminal region of glycosyl transferase group 7; PDB: 2AGD_B 3EE5_A 2AE7_B 2AEC_A 2FYA_A 2AES_B 2AH9_A 2FYB_A 2FY7_A 3LW6_A ....
Probab=27.29 E-value=33 Score=29.58 Aligned_cols=73 Identities=21% Similarity=0.314 Sum_probs=42.8
Q ss_pred CceEEEEcccHHHHHHHHHHHHh---hhccCCCCCeEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhh
Q 047960 95 KVTVGIITPYKLQLKCLQHEFRN---VLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRA 171 (371)
Q Consensus 95 ~~sIgVITpy~aQ~~~I~~~L~~---~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRA 171 (371)
...++||.||+...+.|+..|.. .+.. |..+..|.|+--+.+ +..+-...+||++.-|
T Consensus 46 ~~kvAiIIPyRdR~~hL~~fl~~l~~~L~r--------------Q~~~y~I~vieQ~~~-----~~FNRg~L~NvGf~eA 106 (136)
T PF13733_consen 46 RHKVAIIIPYRDREEHLRIFLPHLHPFLQR--------------QQLDYRIFVIEQVDN-----GPFNRGKLMNVGFLEA 106 (136)
T ss_dssp S-EEEEEEEESS-HHHHHHHHHHHHHHHHH--------------TT-EEEEEEEEE-SS-----S---HHHHHHHHHHHH
T ss_pred ccceEEEEEeCCHHHHHHHHHHHHHHHHhh--------------CcceEEEEEEeeccC-----CCCchhhhhhHHHHHH
Confidence 45899999998777766665542 2221 334555555543321 1233446799999888
Q ss_pred cc----cEEEEeecccccC
Q 047960 172 RR----ALWVMGNAGALTQ 186 (371)
Q Consensus 172 K~----~liVvGn~~~L~~ 186 (371)
.+ -++||.+.++|-.
T Consensus 107 ~~~~~~dc~ifHDVDllP~ 125 (136)
T PF13733_consen 107 LKDDDFDCFIFHDVDLLPE 125 (136)
T ss_dssp HHHS--SEEEEE-TTEEES
T ss_pred hhccCCCEEEEeccccccc
Confidence 76 4889999988743
No 75
>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=27.24 E-value=2.8e+02 Score=29.73 Aligned_cols=95 Identities=16% Similarity=0.225 Sum_probs=54.1
Q ss_pred ceEEEEcccHHHHHHHHHHHHhhhccCC-------CCCeEEccccCCCCccc---------------cEEEEEccccCCC
Q 047960 96 VTVGIITPYKLQLKCLQHEFRNVLNSEE-------GKDLYINTVDAFQGQER---------------DVIIMSCVRASNH 153 (371)
Q Consensus 96 ~sIgVITpy~aQ~~~I~~~L~~~~~~~~-------~~~i~V~TVd~fQG~Er---------------DVIIiS~vrs~~~ 153 (371)
..|.+.+|-..-+..|.+.+......-. ..+....|++++-|... |++|+.=
T Consensus 194 ~~I~l~APTGkAA~rL~e~~~~~~~~l~~~~~~~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDE------ 267 (586)
T TIGR01447 194 LRIALAAPTGKAAARLAESLRKAVKNLAAAEALIAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDE------ 267 (586)
T ss_pred CcEEEECCcHHHHHHHHHHHHhhhcccccchhhhhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcc------
Confidence 4799999997777777777654321100 01344778877766533 4555521
Q ss_pred CccCCCCCCchhhhhH--hhcccEEEEeecccccC---CchHHHHHHHHH
Q 047960 154 GVGFVADIRRMNVALT--RARRALWVMGNAGALTQ---SDDWAALIADSK 198 (371)
Q Consensus 154 ~~gfl~d~rRLNVAlS--RAK~~liVvGn~~~L~~---~~~w~~ll~~a~ 198 (371)
.+.+ |...+.-.+. +.-..+|++|+.+.|.. +..+..++....
T Consensus 268 -aSMv-d~~l~~~ll~al~~~~rlIlvGD~~QLpsV~~G~vl~dl~~~~~ 315 (586)
T TIGR01447 268 -ASMV-DLPLMAKLLKALPPNTKLILLGDKNQLPSVEAGAVLGDLCELAS 315 (586)
T ss_pred -cccC-CHHHHHHHHHhcCCCCEEEEECChhhCCCCCCChhHHHHHHhhc
Confidence 1111 1112221111 23457999999998753 457888887654
No 76
>cd05568 PTS_IIB_bgl_like PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved in sugar utilization. The domain architecture of the IIB-containing protein includes a region N-terminal to the IIB domain which is homologous to the BglG transcription antiterminator with an RNA-binding domain followed by two homologous domains, PRD1 and PRD2 (PTS Regulation Domains). C-terminal to the IIB domain is a domain similar to the PTS IIA domain. In this system, the BglG-like region and the IIB and IIA-like domains are all expressed together as a single multidomain protein. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include this sensory system with similarity to the bacterial
Probab=26.06 E-value=86 Score=23.50 Aligned_cols=50 Identities=12% Similarity=0.204 Sum_probs=30.2
Q ss_pred eEEEEccc-HHHHHHHHHHHHhhhccCCC-CCeEEccccCCCCccccEEEEE
Q 047960 97 TVGIITPY-KLQLKCLQHEFRNVLNSEEG-KDLYINTVDAFQGQERDVIIMS 146 (371)
Q Consensus 97 sIgVITpy-~aQ~~~I~~~L~~~~~~~~~-~~i~V~TVd~fQG~ErDVIIiS 146 (371)
.|.|+|+. .+-..+|...|++.++.... ..+.....+...-.+.|+||-+
T Consensus 2 kilivC~~G~~~s~~l~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~DlIitT 53 (85)
T cd05568 2 KALVVCPSGIGTSRLLKSKLKKLFPEIEIIDVISLRELEEVDLDDYDLIIST 53 (85)
T ss_pred eEEEECCCCHHHHHHHHHHHHHHCCCceEEEEEeHHHHhhCcccCCCEEEEc
Confidence 47888886 66677888999888754322 1112223334445678866543
No 77
>COG4752 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.78 E-value=90 Score=27.49 Aligned_cols=87 Identities=18% Similarity=0.216 Sum_probs=54.8
Q ss_pred CCceEEEEcccHHHHHHHHHHHHhhhccCCC-------CCe-----------EEccccCCCCccccEEEEEccccCCCCc
Q 047960 94 GKVTVGIITPYKLQLKCLQHEFRNVLNSEEG-------KDL-----------YINTVDAFQGQERDVIIMSCVRASNHGV 155 (371)
Q Consensus 94 ~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~-------~~i-----------~V~TVd~fQG~ErDVIIiS~vrs~~~~~ 155 (371)
.-+.--|++|-.+|+.++++.+.-.+...+. +.+ .+..++...| ++..||....+.-+..+
T Consensus 42 eikgYyiV~pidAQ~~~~~r~i~yW~~g~G~~yNp~R~e~~~lv~l~~~le~ViEdIEk~eG-~rPLi~~TsAr~~~N~i 120 (190)
T COG4752 42 EIKGYYIVQPIDAQRIVIQRQINYWLSGEGRKYNPTRYEIVQLVRLAYTLEEVIEDIEKEEG-RRPLIVGTSARTYPNTI 120 (190)
T ss_pred eeccEEEEeecHHHHHHHHHHHHHHhcccCCcCCcCHHHHHHHHhHHHHHHHHHHHHHhhcC-CCceEEeccccccCCcc
Confidence 3345668889999998888877543322211 111 2445677777 57888877666655444
Q ss_pred cCCCCCCchhhhhHhhcccEEEEeecccc
Q 047960 156 GFVADIRRMNVALTRARRALWVMGNAGAL 184 (371)
Q Consensus 156 gfl~d~rRLNVAlSRAK~~liVvGn~~~L 184 (371)
.|-. .=|--+-|-|--|++||.-.-|
T Consensus 121 sy~~---lr~~I~e~dkp~LilfGTGwGl 146 (190)
T COG4752 121 SYSW---LRNEIQERDKPWLILFGTGWGL 146 (190)
T ss_pred cHHH---HHHHHhhcCCcEEEEecCCCCC
Confidence 4433 3344577889999999977654
No 78
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=23.14 E-value=1.8e+02 Score=26.04 Aligned_cols=85 Identities=20% Similarity=0.276 Sum_probs=44.5
Q ss_pred CceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCC-------------CccccEEEEEccccCCCCccCCCCC
Q 047960 95 KVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQ-------------GQERDVIIMSCVRASNHGVGFVADI 161 (371)
Q Consensus 95 ~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQ-------------G~ErDVIIiS~vrs~~~~~gfl~d~ 161 (371)
...|.+++|-...+..|.+.+. +.+.|+++|- -...+++|+.= .+.+ +.
T Consensus 46 g~~v~~~apT~~Aa~~L~~~~~----------~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDE-------asmv-~~ 107 (196)
T PF13604_consen 46 GKRVIGLAPTNKAAKELREKTG----------IEAQTIHSFLYRIPNGDDEGRPELPKKDVLIVDE-------ASMV-DS 107 (196)
T ss_dssp T--EEEEESSHHHHHHHHHHHT----------S-EEEHHHHTTEECCEECCSSCC-TSTSEEEESS-------GGG--BH
T ss_pred CCeEEEECCcHHHHHHHHHhhC----------cchhhHHHHHhcCCcccccccccCCcccEEEEec-------cccc-CH
Confidence 3789999999998888777641 2334443331 23356777741 2222 22
Q ss_pred Cchh---hhhHhhcccEEEEeeccccc---CCchHHHHHHHH
Q 047960 162 RRMN---VALTRARRALWVMGNAGALT---QSDDWAALIADS 197 (371)
Q Consensus 162 rRLN---VAlSRAK~~liVvGn~~~L~---~~~~w~~ll~~a 197 (371)
+.+. -++..+...++++|++..|. .+..|..+....
T Consensus 108 ~~~~~ll~~~~~~~~klilvGD~~QL~pV~~g~~~~~l~~~~ 149 (196)
T PF13604_consen 108 RQLARLLRLAKKSGAKLILVGDPNQLPPVGAGSPFADLQESG 149 (196)
T ss_dssp HHHHHHHHHS-T-T-EEEEEE-TTSHHHCSTTCHHHHHCGCS
T ss_pred HHHHHHHHHHHhcCCEEEEECCcchhcCCcCCcHHHHHHhcC
Confidence 2333 33334445899999998753 445555554443
No 79
>KOG2924 consensus Deoxyhypusine synthase [Posttranslational modification, protein turnover, chaperones]
Probab=21.99 E-value=93 Score=30.18 Aligned_cols=73 Identities=21% Similarity=0.347 Sum_probs=48.0
Q ss_pred CeEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhc-ccEEEEee---------cccccCCchHHHHHH
Q 047960 126 DLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRAR-RALWVMGN---------AGALTQSDDWAALIA 195 (371)
Q Consensus 126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK-~~liVvGn---------~~~L~~~~~w~~ll~ 195 (371)
.|-|-...---|.=-|.+.|-+.++..-.+....|.|++|...-.|. .++||+|. .+++++...|.-||+
T Consensus 228 ~IPvf~PaltDGSlGDmlyFHs~k~~~L~~DIv~Dir~iNt~av~a~~tgmIIlGgGvvKHHI~NAnLmrNGad~~VyIN 307 (366)
T KOG2924|consen 228 HIPVFSPALTDGSLGDMLYFHSFKNSGLVLDIVEDIRRINTEAVFANKTGMIILGGGVVKHHICNANLMRNGADYAVYIN 307 (366)
T ss_pred CCceecccccCCcccceEEEeeccCCCeEEeHHHHHHhhhhhhhhccccceEEEcCchhhhhcchhhhhhcCcceEEEec
Confidence 34444444455888899999888876534566789999998877765 58888864 344444444554544
Q ss_pred HHH
Q 047960 196 DSK 198 (371)
Q Consensus 196 ~a~ 198 (371)
-+.
T Consensus 308 taq 310 (366)
T KOG2924|consen 308 TAQ 310 (366)
T ss_pred ccc
Confidence 443
No 80
>COG4474 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.31 E-value=1.1e+02 Score=27.47 Aligned_cols=18 Identities=28% Similarity=0.480 Sum_probs=15.3
Q ss_pred CCCCceEEEEcccHHHHH
Q 047960 92 GLGKVTVGIITPYKLQLK 109 (371)
Q Consensus 92 ~~~~~sIgVITpy~aQ~~ 109 (371)
.+|...++|||||..|-+
T Consensus 68 eyp~ik~avitpFe~q~~ 85 (180)
T COG4474 68 EYPHIKLAVITPFEEQGK 85 (180)
T ss_pred hCCCeeEEEEechhhhcc
Confidence 478889999999988864
Done!