Query 023062
Match_columns 288
No_of_seqs 91 out of 93
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:10:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023062.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023062hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10483 Elong_Iki1: Elongator 99.9 3.6E-27 7.7E-32 220.0 15.6 214 17-285 10-244 (280)
2 PF09807 DUF2348: Uncharacteri 99.3 2.4E-10 5.3E-15 105.6 20.0 215 18-257 18-245 (249)
3 PF06745 KaiC: KaiC; InterPro 99.1 3.1E-09 6.7E-14 94.6 13.3 175 50-266 42-224 (226)
4 TIGR03877 thermo_KaiC_1 KaiC d 98.8 3.5E-07 7.7E-12 82.8 18.0 185 51-268 45-235 (237)
5 PRK06067 flagellar accessory p 98.8 5.4E-07 1.2E-11 80.9 17.6 177 53-269 51-231 (234)
6 PRK04328 hypothetical protein; 98.6 6.2E-06 1.3E-10 75.7 17.9 188 50-271 46-240 (249)
7 COG2874 FlaH Predicted ATPases 98.4 3.1E-05 6.7E-10 71.2 17.3 208 13-268 20-233 (235)
8 PRK09302 circadian clock prote 98.2 2.3E-05 5E-10 78.6 13.7 167 52-265 298-472 (509)
9 PRK09302 circadian clock prote 98.1 0.00017 3.7E-09 72.4 16.9 180 51-270 55-244 (509)
10 TIGR02655 circ_KaiC circadian 98.0 0.0001 2.2E-09 73.9 13.7 174 51-270 287-468 (484)
11 PRK08533 flagellar accessory p 98.0 0.00016 3.5E-09 65.8 13.5 173 53-269 50-228 (230)
12 TIGR03881 KaiC_arch_4 KaiC dom 98.0 0.00054 1.2E-08 61.0 16.2 173 53-263 46-226 (229)
13 TIGR02655 circ_KaiC circadian 97.8 0.0015 3.2E-08 65.7 17.7 182 50-271 44-235 (484)
14 TIGR03878 thermo_KaiC_2 KaiC d 97.8 0.00082 1.8E-08 62.1 14.6 131 51-209 60-203 (259)
15 TIGR03880 KaiC_arch_3 KaiC dom 97.8 0.0003 6.4E-09 62.7 11.2 171 53-267 42-220 (224)
16 COG0467 RAD55 RecA-superfamily 97.5 0.0029 6.2E-08 57.9 14.5 145 50-213 46-196 (260)
17 cd01124 KaiC KaiC is a circadi 97.4 0.0037 8E-08 53.2 12.5 134 52-211 24-165 (187)
18 cd01121 Sms Sms (bacterial rad 97.1 0.054 1.2E-06 53.2 18.2 150 54-266 109-269 (372)
19 TIGR02237 recomb_radB DNA repa 97.0 0.01 2.2E-07 52.0 11.4 153 54-262 39-208 (209)
20 PRK11823 DNA repair protein Ra 97.0 0.049 1.1E-06 54.5 17.5 149 54-265 107-266 (446)
21 cd01122 GP4d_helicase GP4d_hel 96.5 0.3 6.5E-06 44.5 17.3 110 144-267 140-271 (271)
22 PRK09361 radB DNA repair and r 96.5 0.18 3.9E-06 44.8 15.4 99 144-264 107-223 (225)
23 cd01123 Rad51_DMC1_radA Rad51_ 96.4 0.12 2.7E-06 45.8 13.9 40 55-94 53-94 (235)
24 cd01394 radB RadB. The archaea 96.4 0.2 4.3E-06 44.2 15.0 97 145-262 104-217 (218)
25 TIGR00416 sms DNA repair prote 96.2 0.29 6.3E-06 49.3 16.6 147 54-263 121-278 (454)
26 TIGR02238 recomb_DMC1 meiotic 96.0 0.47 1E-05 45.5 16.5 40 55-94 130-171 (313)
27 KOG4723 Uncharacterized conser 95.8 0.19 4E-06 46.4 12.2 185 16-211 16-218 (248)
28 PRK04301 radA DNA repair and r 95.7 0.84 1.8E-05 43.2 16.6 39 56-94 137-177 (317)
29 PTZ00035 Rad51 protein; Provis 95.5 1.1 2.4E-05 43.3 16.9 156 55-263 152-333 (337)
30 PLN03186 DNA repair protein RA 95.5 1.3 2.9E-05 43.1 17.4 155 56-263 158-338 (342)
31 PLN03187 meiotic recombination 95.3 0.93 2E-05 44.3 15.9 39 56-94 161-201 (344)
32 TIGR02239 recomb_RAD51 DNA rep 95.1 2.5 5.4E-05 40.5 18.0 155 56-263 131-312 (316)
33 cd01393 recA_like RecA is a b 95.1 0.26 5.7E-06 43.4 10.5 126 56-211 54-201 (226)
34 cd00984 DnaB_C DnaB helicase C 94.9 0.069 1.5E-06 47.6 6.5 146 55-211 42-208 (242)
35 TIGR02236 recomb_radA DNA repa 94.9 1.4 3.1E-05 41.3 15.4 39 56-94 130-170 (310)
36 PRK05973 replicative DNA helic 94.3 0.42 9.1E-06 44.3 10.2 62 15-83 59-120 (237)
37 PF05625 PAXNEB: PAXNEB protei 94.2 0.13 2.8E-06 50.3 6.9 69 146-214 202-280 (363)
38 PF08423 Rad51: Rad51; InterP 93.4 3.4 7.4E-05 38.3 14.4 156 55-263 72-253 (256)
39 cd01120 RecA-like_NTPases RecA 93.3 2 4.3E-05 34.6 11.4 67 143-209 84-164 (165)
40 cd01125 repA Hexameric Replica 92.8 2.2 4.8E-05 38.4 12.0 140 54-214 40-194 (239)
41 PF07088 GvpD: GvpD gas vesicl 91.6 13 0.00028 37.9 16.5 195 16-265 7-213 (484)
42 TIGR00665 DnaB replicative DNA 90.0 4 8.7E-05 40.2 11.5 222 16-267 191-432 (434)
43 PF05763 DUF835: Protein of un 90.0 1.4 3.1E-05 37.5 7.3 73 125-200 59-133 (136)
44 PHA02542 41 41 helicase; Provi 84.2 52 0.0011 33.5 17.2 217 15-268 185-429 (473)
45 PF03192 DUF257: Pyrococcus pr 81.8 15 0.00033 33.4 10.0 152 21-210 13-186 (210)
46 PRK09165 replicative DNA helic 78.7 43 0.00094 34.2 13.1 239 14-268 211-488 (497)
47 PF13481 AAA_25: AAA domain; P 78.1 2.3 4.9E-05 36.3 3.2 39 39-77 47-92 (193)
48 PF03796 DnaB_C: DnaB-like hel 77.5 8.4 0.00018 35.0 7.0 223 16-268 15-258 (259)
49 cd00983 recA RecA is a bacter 77.2 40 0.00086 32.9 11.8 139 29-213 64-226 (325)
50 PF14417 MEDS: MEDS: MEthanoge 73.4 63 0.0014 28.3 13.0 139 38-199 30-175 (191)
51 PRK09354 recA recombinase A; P 72.5 29 0.00064 34.1 9.6 61 16-90 56-117 (349)
52 TIGR02012 tigrfam_recA protein 71.9 26 0.00057 34.0 9.0 50 29-91 64-113 (321)
53 PRK05748 replicative DNA helic 71.5 57 0.0012 32.5 11.6 223 15-268 198-443 (448)
54 PRK08760 replicative DNA helic 70.6 91 0.002 31.7 13.0 224 15-267 224-467 (476)
55 TIGR03600 phage_DnaB phage rep 67.6 18 0.00039 35.5 7.1 181 15-211 189-389 (421)
56 PRK06321 replicative DNA helic 66.1 1.6E+02 0.0035 30.0 13.6 221 15-268 221-466 (472)
57 PRK08506 replicative DNA helic 64.4 1.7E+02 0.0036 29.7 13.7 180 15-211 187-387 (472)
58 PRK09519 recA DNA recombinatio 60.0 1.1E+02 0.0023 33.6 11.6 156 53-260 86-265 (790)
59 COG0144 Sun tRNA and rRNA cyto 53.0 39 0.00084 33.0 6.4 66 22-102 158-226 (355)
60 PRK05595 replicative DNA helic 52.8 2.5E+02 0.0054 28.0 13.0 221 15-267 196-438 (444)
61 PRK08840 replicative DNA helic 42.0 3.9E+02 0.0085 27.2 12.0 228 15-272 212-461 (464)
62 PRK08006 replicative DNA helic 38.6 4.4E+02 0.0096 26.8 12.2 223 15-268 219-464 (471)
63 PF11382 DUF3186: Protein of u 38.6 54 0.0012 31.4 4.9 61 37-100 65-129 (308)
64 PRK07004 replicative DNA helic 38.4 4.4E+02 0.0094 26.7 12.4 223 15-267 208-451 (460)
65 COG1066 Sms Predicted ATP-depe 38.4 4.7E+02 0.01 27.0 15.3 147 57-268 122-281 (456)
66 PF00004 AAA: ATPase family as 38.2 87 0.0019 24.2 5.3 57 19-75 58-120 (132)
67 KOG3949 RNA polymerase II elon 34.7 77 0.0017 31.5 5.3 73 165-246 231-307 (360)
68 PF11633 SUD-M: Single-strande 32.9 16 0.00036 31.6 0.3 65 25-95 6-70 (142)
69 PRK04296 thymidine kinase; Pro 27.0 4.2E+02 0.009 23.0 8.2 65 144-213 78-144 (190)
70 COG4544 Uncharacterized conser 26.4 1E+02 0.0022 29.3 4.3 53 36-95 66-118 (260)
71 PF00154 RecA: recA bacterial 25.2 1E+02 0.0022 30.1 4.3 56 23-92 57-112 (322)
72 COG3598 RepA RecA-family ATPas 23.4 6.4E+02 0.014 25.4 9.4 106 56-190 128-244 (402)
73 PF13911 AhpC-TSA_2: AhpC/TSA 23.1 81 0.0017 24.9 2.7 38 50-98 8-45 (115)
74 PF06574 FAD_syn: FAD syntheta 20.7 1.7E+02 0.0037 25.2 4.5 39 50-94 31-85 (157)
75 PF09967 DUF2201: VWA-like dom 20.2 2.7E+02 0.0058 23.0 5.3 39 23-65 3-41 (126)
No 1
>PF10483 Elong_Iki1: Elongator subunit Iki1; InterPro: IPR019519 Histone acetylation protein (Hap) 2 (also known as Elongator complex protein 5) is one of three histone acetyltransferases proteins that, in yeasts, are found associated with elongating forms of RNA polymerase II (Elongator). The Haps can be isolated in two forms, as a six-subunit complex with Elongator, and as a complex of the three proteins on their own. The role of the Hap complex in transcription is still speculative, being possibly to keep the histone acetylation activity of free Elongator in check, allowing histone acetylation only in the presence of a transcribing polymerase, or the interaction with Haps might render Elongator susceptible to modifications thereby altering its activity []. This protein family also contains Dermal papilla-derived protein 6, which also belong to the ELP5 family. ; PDB: 4A8J_B 4EJS_B.
Probab=99.95 E-value=3.6e-27 Score=220.02 Aligned_cols=214 Identities=21% Similarity=0.254 Sum_probs=116.5
Q ss_pred CCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccC
Q 023062 17 EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD 96 (288)
Q Consensus 17 e~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsD 96 (288)
|..|+++|.||++.|+. .++++++ ...+.++..||+|+||.+++ .+ |+|.. ++|-
T Consensus 10 d~spl~Li~DSl~q~a~-~Ll~e~i-------~~a~~~~~~V~~lsfEt~~~--~~-----~~d~~--------~~~~-- 64 (280)
T PF10483_consen 10 DASPLTLILDSLEQSAR-PLLKEFI-------RRAKSRNEKVHFLSFETLNK--PE-----YADSF--------INAR-- 64 (280)
T ss_dssp S--SEEEEEEBTTB-SH-HHHHHHH-------HHHTS----EEEEESS--S----T-----T-SEE--------EETT--
T ss_pred CCCCeEEEEEcccccCH-HHHHHHH-------HHHHcCCCeEEEEEeEeCCC--cc-----cCCee--------cccc--
Confidence 37899999999999954 6666663 34467788999999999876 33 55532 2222
Q ss_pred CCCCcccccCccccccccccccccccccchhhHHHHHHHhh--cccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhc
Q 023062 97 PLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQG--LIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 174 (288)
Q Consensus 97 PlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~~~~--~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~ 174 (288)
+|+ +.+++..|...- ...+.+++++|+|||||||+.+.++ .+++||++|+.
T Consensus 65 --~~~------------------------~~~i~~~i~s~~~~~~~~~~~~~lVvIDSLn~ll~~~~~-~l~~fLssl~~ 117 (280)
T PF10483_consen 65 --GKS------------------------LQDIVKEIKSHLPSSSSSPTKKFLVVIDSLNYLLNHHPC-QLSQFLSSLLS 117 (280)
T ss_dssp --SS-------------------------HHHHHHHHHHTS--SS-SS---EEEEES-GGGS-GG----GHHHHHHHH--
T ss_pred --CCC------------------------HHHHHHHHHhhcccccccCCCCeEEEEEcchHHHHHHHH-HHHHHHHhccc
Confidence 332 122222223321 3355667899999999999999999 99999999998
Q ss_pred CCceeEEEEEeeCcc-------CCcchHhHHhhhceeEEEEeecCccccccccchhhhhhh------hhcccceeEEEEE
Q 023062 175 HDQVSSIFWLLHSDL-------HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSML------EQNFRKGKFHVRF 241 (288)
Q Consensus 175 ~~~v~SVv~llH~DL-------h~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~------~~n~~~~~~~Vr~ 241 (288)
++. ++|||+||+|+ |+|+++++|+|||||+++|+|..+.....++.-+++.-. +.|..+..+++++
T Consensus 118 ~p~-~svv~~~H~Dl~~~~~~~~~P~~l~lL~~LATtii~v~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~l~~ 196 (280)
T PF10483_consen 118 SPQ-SSVVGLYHTDLLPPSQNPYYPSPLSLLSYLATTIITVEPLSHISADKEALDRSLSKPEFGLGEGLNGVGFVLELEN 196 (280)
T ss_dssp -TT-EEEEEEEETTS---TTB-TS--HHHHHHHH-SEEEEEEE---SS--HHHHHHHHHTT---SS---S-SEEEEEEEE
T ss_pred CCC-cEEEEEEccCcCcccccccCcCHHHHHHHhceEEEEEcccCccchhHHHHHhhhhhcccChhhhccCceEEEEEEE
Confidence 777 78999999999 999999999999999999999988765555554544433 2566689999999
Q ss_pred ecCCCCeeeeEeEEEEEcCceEEEeCCC------cchhhhccCCcceEEE
Q 023062 242 KRRNGRVRVMCEEILVELAGIKFTPVLS------EDEIINQRLLPKVSII 285 (288)
Q Consensus 242 kRr~GRV~~~~E~f~i~~~~~~f~~~~~------~~~~~~~~~~~~v~~~ 285 (288)
|||+||+.. |||.|..++..+..+.. ...+...++.|+++|-
T Consensus 197 RrksGR~~~--e~~~~~~~~~~~~~~~~~~e~~~~~~~~p~~~~~~~TFN 244 (280)
T PF10483_consen 197 RRKSGRVVS--EWFVIDINSHIYEQVSEKKEVEEEPEEDPESLQPNLTFN 244 (280)
T ss_dssp E-TTS-EEE--EEEEEETTTTEEEE-------------------------
T ss_pred EcCCCCcEe--EEEEEecCCCcceeecccccccCCCCCCcccccccceEe
Confidence 999999766 46666666655544443 2234667888888884
No 2
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=99.32 E-value=2.4e-10 Score=105.61 Aligned_cols=215 Identities=18% Similarity=0.240 Sum_probs=146.8
Q ss_pred CCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEeccc
Q 023062 18 HAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYT 95 (288)
Q Consensus 18 ~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fs 95 (288)
..-+++|+|+ .+++. =+..|++ +..++ .+..|.+|+|..+.+.|..-++|-|.+-... +.+++++|+.+
T Consensus 18 ~g~~ili~d~-~~dgs-FLlh~~L---~~~Lk----~~~~V~fv~~~q~~~HY~~v~~KLG~NL~~~~~~gql~fiD~l~ 88 (249)
T PF09807_consen 18 PGKLILIEDC-ETDGS-FLLHHFL---SQYLK----AGCKVCFVAFSQSFSHYNNVAQKLGVNLSAAKEKGQLVFIDGLK 88 (249)
T ss_pred CCeEEEEEcC-CCCch-hHHHHHH---HHHhc----CCCcEEEEEccCCHHHHHHHHHhhEecchHhccCCcEEEeehhh
Confidence 4447999999 88855 5667773 33333 3458999999999999999999999997652 34799999999
Q ss_pred CCCCCcccccCccccccccccccccccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHh-hCChHHHHHHHHhhhc
Q 023062 96 DPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVR-HASISSVAGILSNLRS 174 (288)
Q Consensus 96 DPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~-~~s~~~l~~~L~~L~~ 174 (288)
++.+|--.....+.. .+..+.--.....|.+||..|.+.--.....++++|+||-|+.|+- ..+...+..|++.++.
T Consensus 89 ~~~~~l~~~~~~~~~--~~~~~l~~~~~~~L~~L~~~I~~~l~~~~~~~~~~liIDdls~Ll~lG~s~~~vldF~~ycra 166 (249)
T PF09807_consen 89 SSLDLLFDEDSSDEP--NPLKFLREDNASSLRSLYEFIQEALSPADSNGSVVLIIDDLSVLLSLGVSSNDVLDFIHYCRA 166 (249)
T ss_pred hhhhhhhccccccCC--ccccccccCCcchHHHHHHHHHHHHhhccCCCCeEEEEeCHHHHHHcCCCHHHHHHHHHHHHH
Confidence 888774221100000 0111111122346888888777655222234568999999999987 6677789999999885
Q ss_pred --CCc-eeEEEEEeeCccCCc----c-hHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecC--
Q 023062 175 --HDQ-VSSIFWLLHSDLHEI----K-FTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRR-- 244 (288)
Q Consensus 175 --~~~-v~SVv~llH~DLh~p----~-~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr-- 244 (288)
+.+ -.++|.+.|.|...+ . ....|+|+|+.+|+++|.+.. +++. =.|.+.|.+|+.
T Consensus 167 ~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h~a~l~i~v~~L~TG--~s~D------------VhGqL~v~~r~~~~ 232 (249)
T PF09807_consen 167 TLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAHMADLVITVEPLPTG--YSKD------------VHGQLTVLWRGNSS 232 (249)
T ss_pred HhccccCCCEEEEEecCCCCccchHHHHHHHHHHHhcEEEEecCCCCc--cccc------------ceEEEEEEEccCCc
Confidence 222 357999999987632 2 789999999999999998664 2221 248888877773
Q ss_pred CCCeeeeEeEEEE
Q 023062 245 NGRVRVMCEEILV 257 (288)
Q Consensus 245 ~GRV~~~~E~f~i 257 (288)
.|+-..+...|++
T Consensus 233 ~~~~~~~~~~~~y 245 (249)
T PF09807_consen 233 SGYHRPKTKTYQY 245 (249)
T ss_pred cccccccceEEEE
Confidence 3444444345554
No 3
>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....
Probab=99.06 E-value=3.1e-09 Score=94.64 Aligned_cols=175 Identities=20% Similarity=0.275 Sum_probs=107.7
Q ss_pred hhccc-cCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCCCCcccccCccccccccccccccccccch
Q 023062 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (288)
Q Consensus 50 a~~~q-~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (288)
+++.+ ++.+.++++|.+|+++.+.++..|+|.... +.++.++|+++...+|... ++
T Consensus 42 ~~~~~~ge~vlyvs~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~~~~~---------------------~~ 100 (226)
T PF06745_consen 42 NGLKNFGEKVLYVSFEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIGWSPN---------------------DL 100 (226)
T ss_dssp HHHHHHT--EEEEESSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST-TSC---------------------CH
T ss_pred HhhhhcCCcEEEEEecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccccccccc---------------------CH
Confidence 45556 789999999999999999999999876431 2359999999999888621 22
Q ss_pred hhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhcC---CceeEEEEEee-CccCCcchHhHHh-hh
Q 023062 127 DKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLH-SDLHEIKFTSVLE-YL 201 (288)
Q Consensus 127 ~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~~---~~v~SVv~llH-~DLh~p~~l~aL~-~L 201 (288)
+.+...+.+. ..+.+ +..||||||+.+....++..+-.+|+.|... ..++.+ .+.| .+-+++.....++ |+
T Consensus 101 ~~l~~~i~~~--i~~~~-~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~l-lt~~~~~~~~~~~~~~i~~~l 176 (226)
T PF06745_consen 101 EELLSKIREA--IEELK-PDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTL-LTSEMPSGSEDDGTFGIEHYL 176 (226)
T ss_dssp HHHHHHHHHH--HHHHT-SSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEE-EEEEESSSSSSSSSTSHHHHH
T ss_pred HHHHHHHHHH--HHhcC-CCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEE-EEEccccCcccccccchhhhc
Confidence 2222222211 11111 2589999999996677777777777777662 334444 4444 3444454555555 49
Q ss_pred ceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEe
Q 023062 202 SSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTP 266 (288)
Q Consensus 202 Attvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~ 266 (288)
|+++|.++-.... +...-.+.|..+|.. +.....-.|.|.++|+++.|
T Consensus 177 ~D~vI~L~~~~~~----------------~~~~R~l~I~K~Rg~-~~~~~~~~f~I~~~Gi~i~~ 224 (226)
T PF06745_consen 177 ADGVIELRYEEEG----------------GRIRRRLRIVKMRGS-RHSTGIHPFEITPGGIEIYP 224 (226)
T ss_dssp SSEEEEEEEEEET----------------TEEEEEEEEEEETTS-----BEEEEEEETTEEEEET
T ss_pred ccEEEEEEEEeeC----------------CEEEEEEEEEEcCCC-CCCCcEEEEEEECCeEEEec
Confidence 9999999853331 113344555555544 45566788999998888766
No 4
>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.
Probab=98.83 E-value=3.5e-07 Score=82.85 Aligned_cols=185 Identities=15% Similarity=0.112 Sum_probs=106.8
Q ss_pred hccccCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeEEEEecccCCCCCcccccCccccccccccccccccccchhh
Q 023062 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (288)
Q Consensus 51 ~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (288)
+..+++.+.+|++|-+|+++.+-+++.|+|... -..++.++|||++-.++..... .+ +.....+++.
T Consensus 45 ~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~~~~~~~g~l~~~d~~~~~~~~~~~~~----------~~-~~~~~~~~~~ 113 (237)
T TIGR03877 45 GLQMGEPGIYVALEEHPVQVRRNMAQFGWDVRKYEEEGKFAIVDAFTGGIGEAAERE----------KY-VVKDPTDVRE 113 (237)
T ss_pred HHHcCCcEEEEEeeCCHHHHHHHHHHhCCCHHHHhhcCCEEEEeccccccccccccc----------cc-cccCcccHHH
Confidence 335688999999999999999999999998532 1347999999998555433211 00 0111224444
Q ss_pred HHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhc---CCceeEEEEEeeCccCCcc-hHhHHhhhcee
Q 023062 129 LYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDLHEIK-FTSVLEYLSSM 204 (288)
Q Consensus 129 l~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~---~~~v~SVv~llH~DLh~p~-~l~aL~~LAtt 204 (288)
+...+.+. ..+.+. -.||||||+.++... +...-.++.+|.+ .-.+. ++.+.|.+..+.. ....++|+|++
T Consensus 114 ~~~~i~~~--i~~~~~-~~vVIDSls~l~~~~-~~~~r~~l~~l~~~lk~~~~t-~llt~~~~~~~~~~~~~~~~~~~D~ 188 (237)
T TIGR03877 114 LIDVLRQA--IRDINA-KRVVIDSVTTLYITK-PAMARSIVMQLKRVLSGLGCT-SIFVSQVSVGERGFGGPGVEHAVDG 188 (237)
T ss_pred HHHHHHHH--HHHhCC-CEEEEcChhHhhcCC-hHHHHHHHHHHHHHHHhCCCE-EEEEECcccccccccccceEEEEeE
Confidence 43333332 122233 379999999987643 2222233333332 12233 3334554433211 11347999999
Q ss_pred EEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 205 VASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 205 vitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
+|.++-.... |...-.+.| .|-|..+.....-.|.|..+|+.+-|..
T Consensus 189 vI~L~~~~~~----------------~~~~R~l~i-~K~Rg~~~~~~~~~~~It~~Gi~v~~~~ 235 (237)
T TIGR03877 189 IIRLDLDEID----------------GELKRSLIV-WKMRGTKHSMRRHPFEITDKGIIVYPDK 235 (237)
T ss_pred EEEEEEEeeC----------------CceEEEEEE-EECCCCCCCCceEEEEEcCCCEEEEeCC
Confidence 9999742221 111222333 3445555666667899999999877764
No 5
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=98.78 E-value=5.4e-07 Score=80.89 Aligned_cols=177 Identities=20% Similarity=0.232 Sum_probs=116.2
Q ss_pred cccCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHH
Q 023062 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (288)
Q Consensus 53 ~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (288)
.+++.+.++.+|.+|+++.+-+++.|++.... ..++.++|.+.....|... .++.++
T Consensus 51 ~~g~~~~y~~~e~~~~~~~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~---------------------~~~~ll 109 (234)
T PRK06067 51 KQGKKVYVITTENTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNST---------------------LANKLL 109 (234)
T ss_pred hCCCEEEEEEcCCCHHHHHHHHHHCCCChhHHHhCCCceEEeccccccccCcc---------------------hHHHHH
Confidence 46889999999999999999999999886431 2356777777666655432 112222
Q ss_pred HHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhcC-CceeEEEEEeeCccCCcchHhHHhhhceeEEEEe
Q 023062 131 SLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVE 209 (288)
Q Consensus 131 ~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~~-~~v~SVv~llH~DLh~p~~l~aL~~LAttvitv~ 209 (288)
..+.+ ...+. ++-.|+|||++.++...+...+..++..++.. ..-..++.+.|...........++|+++.+|.+.
T Consensus 110 ~~l~~--~i~~~-~~~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~~~~~~~~~~~~~~l~DgvI~L~ 186 (234)
T PRK06067 110 ELIIE--FIKSK-REDVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHPYAFSEELLSRIRSICDVYLKLR 186 (234)
T ss_pred HHHHH--HHHhc-CCCEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecCCcCCHHHHHHHHhheEEEEEEE
Confidence 22222 12222 23489999999998877777777876655431 1124567778887776677788999999999998
Q ss_pred ecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcC-ceEEEeCCC
Q 023062 210 PFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELA-GIKFTPVLS 269 (288)
Q Consensus 210 p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~-~~~f~~~~~ 269 (288)
..... |...-.+.|..+|.+....+..-.|.|.++ |+.+.|...
T Consensus 187 ~~~~~----------------~~~~r~l~i~K~Rg~~~~~~~~~~~~I~~~~Gi~v~~~~~ 231 (234)
T PRK06067 187 AEQIG----------------GRYVKVLEVVKLRGARKTTGNIISFDVDPAFGIKIIPLSL 231 (234)
T ss_pred eeccC----------------CEEeEEEEEEhhcCCCCCCCCEEEEEEcCCCCeEEEEeec
Confidence 53221 123344555555555443335667888874 898877654
No 6
>PRK04328 hypothetical protein; Provisional
Probab=98.56 E-value=6.2e-06 Score=75.66 Aligned_cols=188 Identities=15% Similarity=0.086 Sum_probs=108.1
Q ss_pred hhccccCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeEEEEecccCCCCCcccccCccccccccccccccccccchh
Q 023062 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (288)
Q Consensus 50 a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (288)
.+..+++.+.++++|-+|+.+++.+++.|+|... -+.++.++|+|+.-.+...... .+ +.....+++
T Consensus 46 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~~~l~iid~~~~~~~~~~~~~----------~~-~~~~~~~~~ 114 (249)
T PRK04328 46 NGLQMGEPGVYVALEEHPVQVRRNMRQFGWDVRKYEEEGKFAIVDAFTGGIGSAAKRE----------KY-VVKDPDDVR 114 (249)
T ss_pred HHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCHHHHhhcCCEEEEeccccccccccccc----------cc-cccCcccHH
Confidence 3446688999999999999999999999987532 1347999999998766532111 01 011122334
Q ss_pred hHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHH----HHHHHHhhhcCCceeEEEEEeeCccCCcc-hHhHHhhhc
Q 023062 128 KLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISS----VAGILSNLRSHDQVSSIFWLLHSDLHEIK-FTSVLEYLS 202 (288)
Q Consensus 128 sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~----l~~~L~~L~~~~~v~SVv~llH~DLh~p~-~l~aL~~LA 202 (288)
.+...|.+ ...+.+ +-.||||||+.+... .+.. +.++.+.+++. .++ ++.+.|.+..+.. .-..++|+|
T Consensus 115 ~~~~~i~~--~i~~~~-~~~vVIDSlt~l~~~-~~~~~r~~~~~l~~~lk~~-g~t-~llt~e~~~~~~~~~~~~~~~~~ 188 (249)
T PRK04328 115 ELIDVLRQ--AIKDIG-AKRVVIDSVSTLYLT-KPAMARSIVMQLKRVLSGL-GCT-AIFVSQVSVGERGFGGPGVEHAV 188 (249)
T ss_pred HHHHHHHH--HHHhhC-CCEEEEeChhHhhcC-ChHHHHHHHHHHHHHHHhC-CCE-EEEEECccccccccCCCCcEEEE
Confidence 43332222 112222 337999999998764 3322 23333334432 223 3334455433211 112469999
Q ss_pred eeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeCCCcc
Q 023062 203 SMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPVLSED 271 (288)
Q Consensus 203 ttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~~~~~ 271 (288)
+++|.++-.... |...-.+.|+.+ |........-.|.|.++|+.+-|...+.
T Consensus 189 D~vI~L~~~~~~----------------~~~~R~l~I~K~-Rg~~~~~~~~~~~It~~Gi~v~~~~~~~ 240 (249)
T PRK04328 189 DGIIRLDLDEID----------------GELKRSLIVWKM-RGTKHSMRRHPFEITDKGIVVYPDKVLK 240 (249)
T ss_pred EEEEEEEEEecC----------------CcEEEEEEEEEc-cCCCCCCceEEEEEcCCCEEEEecceEE
Confidence 999999742211 112233444433 4444555556799999999988876655
No 7
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=98.38 E-value=3.1e-05 Score=71.21 Aligned_cols=208 Identities=15% Similarity=0.119 Sum_probs=142.3
Q ss_pred cc-cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccc-cCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeE
Q 023062 13 GL-EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWI 88 (288)
Q Consensus 13 ~~-~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q-~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v 88 (288)
+| .|=+.|.|++-.-=..++-+. |+...+-+..+ +..+.++.-|.+--+|..-|..-+.|..- ++.++
T Consensus 20 rLGGGiP~GsL~lIEGd~~tGKSv--------Lsqr~~YG~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l 91 (235)
T COG2874 20 RLGGGIPVGSLILIEGDNGTGKSV--------LSQRFAYGFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRL 91 (235)
T ss_pred hccCCCccCeEEEEECCCCccHHH--------HHHHHHHHHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhccee
Confidence 45 346666665443333443322 22333334443 55999999999999999999988887643 45567
Q ss_pred EEEecccCCCCCcccccCccccccccccccccccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHH
Q 023062 89 HILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGI 168 (288)
Q Consensus 89 ~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~ 168 (288)
.|+-.-.+|.+|+...+ -+-|+.+ .+ +.+ ....-+|+|||||..+.+.+..++.+|
T Consensus 92 ~~~~~~~~~~~~~~~~~-----------------~~~L~~l----~~--~~k-~~~~dViIIDSls~~~~~~~~~~vl~f 147 (235)
T COG2874 92 LFFPVNLEPVNWGRRSA-----------------RKLLDLL----LE--FIK-RWEKDVIIIDSLSAFATYDSEDAVLNF 147 (235)
T ss_pred EEEEecccccccChHHH-----------------HHHHHHH----Hh--hHH-hhcCCEEEEecccHHhhcccHHHHHHH
Confidence 77777678999987644 1122222 11 112 223348999999999999999999999
Q ss_pred HHhhhc-CCceeEEEEEeeCccCCcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCC
Q 023062 169 LSNLRS-HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGR 247 (288)
Q Consensus 169 L~~L~~-~~~v~SVv~llH~DLh~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GR 247 (288)
+..+|. +..=.-|+..+|.+.-...++.-++..+++.++++-..-. +.....+.++.-+-.++
T Consensus 148 m~~~r~l~d~gKvIilTvhp~~l~e~~~~rirs~~d~~l~L~~~~~G----------------g~~~~~~~i~K~~ga~~ 211 (235)
T COG2874 148 MTFLRKLSDLGKVIILTVHPSALDEDVLTRIRSACDVYLRLRLEELG----------------GDLIKVLEIVKYRGARK 211 (235)
T ss_pred HHHHHHHHhCCCEEEEEeChhhcCHHHHHHHHHhhheeEEEEhhhhC----------------CeeeEEEEEeeecCchh
Confidence 999998 3344558999999999999999999999999999842221 11335556665555666
Q ss_pred eeeeEeEEEEEcCc-eEEEeCC
Q 023062 248 VRVMCEEILVELAG-IKFTPVL 268 (288)
Q Consensus 248 V~~~~E~f~i~~~~-~~f~~~~ 268 (288)
-..+.=-|.|+++- +...|++
T Consensus 212 s~~~~I~F~V~P~~Glkvep~S 233 (235)
T COG2874 212 SFQNIISFRVEPGFGLKVEPAS 233 (235)
T ss_pred hcCCceeEEecCCCceEEEEee
Confidence 66778889999987 4555543
No 8
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=98.20 E-value=2.3e-05 Score=78.58 Aligned_cols=167 Identities=15% Similarity=0.154 Sum_probs=102.1
Q ss_pred ccccCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCCCCcccccCccccccccccccccccccchhhH
Q 023062 52 KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL 129 (288)
Q Consensus 52 ~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl 129 (288)
..+++.+.++.||-+|+.+.+.+++.|+|.+.. ..++.+++.+.++.++... +..+
T Consensus 298 ~~~g~~~~yis~e~~~~~i~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~----------------------~~~i 355 (509)
T PRK09302 298 CRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLEDH----------------------LIII 355 (509)
T ss_pred HhCCCcEEEEEecCCHHHHHHHHHHcCCChHHHhhcCCceeecCCcccCCHHHH----------------------HHHH
Confidence 456889999999999999999999999875331 2356778877666555321 1111
Q ss_pred HHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhcC---CceeEEEEEeeCcc---CCcchHhHHhhhce
Q 023062 130 YSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDL---HEIKFTSVLEYLSS 203 (288)
Q Consensus 130 ~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~~---~~v~SVv~llH~DL---h~p~~l~aL~~LAt 203 (288)
.+.+. +.+ +-.||||||+.+....+...+-++|..|... ..++.++. .+..- +.+.....++|+++
T Consensus 356 ~~~i~------~~~-~~~vVIDslt~l~~~~~~~~~~~~l~~l~~~~k~~~~t~l~t-~~~~~~~g~~~~~~~~~~~l~D 427 (509)
T PRK09302 356 KREIE------EFK-PSRVAIDPLSALARGGSLNEFRQFVIRLTDYLKSEEITGLFT-NLTPDFMGSHSITESHISSLTD 427 (509)
T ss_pred HHHHH------HcC-CCEEEEcCHHHHHHhCCHHHHHHHHHHHHHHHHhCCCeEEEE-eccccccCCCCCCcCceEEeee
Confidence 11111 222 3479999999998877766666666555441 23333333 33321 22333345899999
Q ss_pred eEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEE
Q 023062 204 MVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFT 265 (288)
Q Consensus 204 tvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~ 265 (288)
++|.+.-.... |..+-.+.|..+ |..+.....-.|.|..+|+.+-
T Consensus 428 ~vI~L~~~~~~----------------~~~~R~l~I~K~-Rg~~~~~~~~~f~It~~Gi~v~ 472 (509)
T PRK09302 428 TWILLQYVEIN----------------GEMNRALYVLKM-RGSWHSNQIREFVITDKGIHIK 472 (509)
T ss_pred EEEEEEEeecC----------------CeeEEEEEEEEc-CCCCCCCceEEEEEeCCcEEEc
Confidence 99999742221 112233444444 4444566677789999998774
No 9
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=98.08 E-value=0.00017 Score=72.36 Aligned_cols=180 Identities=17% Similarity=0.124 Sum_probs=106.8
Q ss_pred hccc-cCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCCCCcccccCccccccccccccccccccchh
Q 023062 51 GKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (288)
Q Consensus 51 ~~~q-~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (288)
++.+ ++.++++++|-+++++.+-++..|+|.... +.++.++|.|.+|..|... . -.+++
T Consensus 55 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~~~~~-~-----------------~~~~~ 116 (509)
T PRK09302 55 GIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEEA-G-----------------EYDLE 116 (509)
T ss_pred HHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCccccccccc-c-----------------cccHH
Confidence 3444 789999999999999999999999885442 3469999999999888542 1 01233
Q ss_pred hHHHHHHHhhcccCCCCcEEEEEechhHHHhhCCh-H----HHHHHHHhhhcCCceeEEEEEeeCccCCc--chHhHHhh
Q 023062 128 KLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASI-S----SVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEY 200 (288)
Q Consensus 128 sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~-~----~l~~~L~~L~~~~~v~SVv~llH~DLh~p--~~l~aL~~ 200 (288)
.++..+.++ ..+.+ +-.|||||++.+...... . .+.++++.++.. .++ ++..-|..-..+ ......+|
T Consensus 117 ~l~~~l~~~--i~~~~-~~~vVIDSls~l~~~~d~~~~~r~~l~~L~~~Lk~~-g~T-vLlt~~~~~~~~~~~~~~~~~~ 191 (509)
T PRK09302 117 ALFIRIEYA--IDKIG-AKRVVLDSIEALFSGFSNEAVVRRELRRLFAWLKQK-GVT-AVITGERGDEYGPLTRYGVEEF 191 (509)
T ss_pred HHHHHHHHH--HHhhC-CCEEEECCHHHHHhhccCHHHHHHHHHHHHHHHHhC-CCE-EEEEECCccCcCCccccCceEE
Confidence 333322221 12222 236999999998664332 2 234444444432 223 344456543111 22235689
Q ss_pred hceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeCCCc
Q 023062 201 LSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPVLSE 270 (288)
Q Consensus 201 LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~~~~ 270 (288)
+|+++|.++-... ++...-.+.|+..|.. +.....-.|.|.+.|+.+-|....
T Consensus 192 laDgVI~L~~~~~----------------~~~~~R~l~I~K~Rg~-~~~~~~~~f~I~~~Gi~v~p~~~~ 244 (509)
T PRK09302 192 VSDCVIILRNRLE----------------GEKRTRTLRILKYRGT-THGKNEYPFTITEDGISVLPLTAM 244 (509)
T ss_pred EeeEEEEEeEEcc----------------CCeEEEEEEEEECCCC-CcCCccEEEEECCCcEEEEecccc
Confidence 9999999973211 1112344444444432 333335668888888888776554
No 10
>TIGR02655 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.
Probab=98.00 E-value=0.0001 Score=73.92 Aligned_cols=174 Identities=16% Similarity=0.191 Sum_probs=102.4
Q ss_pred hccccCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeEEEEecccCCCCCcccccCccccccccccccccccccchhh
Q 023062 51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (288)
Q Consensus 51 ~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (288)
++.+++.+.+++||-|++++..-+++-|+|... ...++.+++.+....+... .+..
T Consensus 287 ~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~~~~~----------------------~~~~ 344 (484)
T TIGR02655 287 ACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGLED----------------------HLQI 344 (484)
T ss_pred HHHCCCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccCChHH----------------------HHHH
Confidence 445678999999999999999999999988532 1235888887643332211 1222
Q ss_pred HHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhc---CCceeEEEE-EeeCcc-CCcchHhHHhhhce
Q 023062 129 LYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFW-LLHSDL-HEIKFTSVLEYLSS 203 (288)
Q Consensus 129 l~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~---~~~v~SVv~-llH~DL-h~p~~l~aL~~LAt 203 (288)
+.+.|.+ . ++-.||||||+.+....+..++-.++..|.+ ...++.++. ..|.-. ..+-+-.-++|||+
T Consensus 345 i~~~i~~------~-~~~~vvIDsi~~~~~~~~~~~~r~~~~~l~~~lk~~~it~~~t~~~~~~~~~~~~~~~~~s~l~D 417 (484)
T TIGR02655 345 IKSEIAD------F-KPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGFFTNTSDQFMGSHSITDSHISTITD 417 (484)
T ss_pred HHHHHHH------c-CCCEEEEcCHHHHHHhcCHHHHHHHHHHHHHHHhhCCCeEEEeecccccccCCccCCCCeeEeee
Confidence 2222221 1 2347999999999765555544443433333 233444333 223211 11122235799999
Q ss_pred eEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEE-eCCCc
Q 023062 204 MVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFT-PVLSE 270 (288)
Q Consensus 204 tvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~-~~~~~ 270 (288)
++|.+.-.... +..+-.+. ..|.|.+....+.-+|.|...|++.. |....
T Consensus 418 ~ii~l~~~e~~----------------g~~~r~i~-V~K~R~~~~~~~~~~~~It~~Gi~v~~~~~~~ 468 (484)
T TIGR02655 418 TILMLQYVEIR----------------GEMSRAIN-VFKMRGSWHDKGIREFMISDKGPEIKDSFRNF 468 (484)
T ss_pred EEEEEEEEecC----------------CEEEEEEE-EEEccCCCCCCceEEEEEcCCcEEEcccccCC
Confidence 99999632221 01122233 35667777788888899999999884 44433
No 11
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=97.99 E-value=0.00016 Score=65.77 Aligned_cols=173 Identities=13% Similarity=0.061 Sum_probs=104.9
Q ss_pred cccCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHH
Q 023062 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY 130 (288)
Q Consensus 53 ~q~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~ 130 (288)
.+++.+.++.+|.+++++.+.+++.|++.+. ....+.++++|..-.++. +.+..+
T Consensus 50 ~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~~-----------------------~~~~~l 106 (230)
T PRK08533 50 QNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGNS-----------------------EKRKFL 106 (230)
T ss_pred hCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccChH-----------------------HHHHHH
Confidence 3568999999999999999999999987542 134577777763211110 011111
Q ss_pred HHHHHhhcccCCCCcEEEEEechhHHHhhC-C---hHHHHHHHHhhhcCCceeEEEEEeeCccCCcchHhHHhhhceeEE
Q 023062 131 SLIIEQGLIGQGKDRFSIAIDSVSEMVRHA-S---ISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVA 206 (288)
Q Consensus 131 ~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~-s---~~~l~~~L~~L~~~~~v~SVv~llH~DLh~p~~l~aL~~LAttvi 206 (288)
..+.+ ..... .+-.++|||++.++... + ...+.++|+.++.. .. .++...|.+.-.......++|+|+++|
T Consensus 107 ~~il~--~~~~~-~~~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~~-g~-tvi~t~~~~~~~~~~~~~~~~~~DgvI 181 (230)
T PRK08533 107 KKLMN--TRRFY-EKDVIIIDSLSSLISNDASEVAVNDLMAFFKRISSL-NK-VIILTANPKELDESVLTILRTAATMLI 181 (230)
T ss_pred HHHHH--HHHhc-CCCEEEEECccHHhcCCcchHHHHHHHHHHHHHHhC-CC-EEEEEecccccccccceeEEEeeeEEE
Confidence 11111 11112 33479999999998542 2 23456666666543 22 344444433322223346899999999
Q ss_pred EEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeCCC
Q 023062 207 SVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPVLS 269 (288)
Q Consensus 207 tv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~~~ 269 (288)
.++-... +|..+-.+.|..+|..++.....=-|.|.++.+-.+.+.|
T Consensus 182 ~L~~~~~----------------~~~~~R~i~V~KmR~~~~~~~~~~~f~i~~~~g~~~~~~~ 228 (230)
T PRK08533 182 RLEVKVF----------------GGDLKNSAKIVKYNMAKGSFQKSIPFRVEPKIGLAVEIAS 228 (230)
T ss_pred EEEEeec----------------CCEEEEEEEEEEecCCccccCCEEEEEEcCCccEEEEEee
Confidence 9984322 1234566888888888887777788999988654444443
No 12
>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.
Probab=97.96 E-value=0.00054 Score=61.03 Aligned_cols=173 Identities=14% Similarity=0.112 Sum_probs=95.7
Q ss_pred cccCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCC--CCcccccCccccccccccccccccccchhh
Q 023062 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPL--GWKNWLIDKDISQEASSLSSFCQDVRNLDK 128 (288)
Q Consensus 53 ~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPl--gW~~~~~~~~~~~~~s~~~~~~~~v~~L~s 128 (288)
.+++.+.++.+|.+++.+.+.+++.|++.... +.++.++|.+.... .|.-. . -+++.
T Consensus 46 ~~g~~~~~is~e~~~~~i~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~~~~~------------------~-~~~~~ 106 (229)
T TIGR03881 46 RDGDPVIYVTTEESRESIIRQAAQFGMDFEKAIEEGKLVIIDALMKEKEDEWSLR------------------E-LSIEE 106 (229)
T ss_pred hcCCeEEEEEccCCHHHHHHHHHHhCCCHHHHhhcCCEEEEEccccccccccccc------------------c-CCHHH
Confidence 45789999999999999999899999886532 24688899776431 12110 0 02233
Q ss_pred HHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhcC--CceeEEEEEeeCcc-CCcchHhHHhhhceeE
Q 023062 129 LYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH--DQVSSIFWLLHSDL-HEIKFTSVLEYLSSMV 205 (288)
Q Consensus 129 l~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~~--~~v~SVv~llH~DL-h~p~~l~aL~~LAttv 205 (288)
+...+.++. ...+.++-.|+|||++.++...+ ...-.++..|+.. ..=..++.+.|... .++.....++|+|+++
T Consensus 107 ~~~~i~~~~-~~~~~~~~~vvIDsl~~l~~~~~-~~~r~~~~~l~~~l~~~~~tvil~~~~~~~~~~~~~~~~~~l~D~v 184 (229)
T TIGR03881 107 LLNKVIEAK-KYLGYGHARLVIDSMSAFWLDKP-AMARKYSYYLKRVLNRWNFTILLTSQYAITTSQAFGFGIEHVADGI 184 (229)
T ss_pred HHHHHHHHH-HhhccCceEEEecCchhhhccCh-HHHHHHHHHHHHHHHhCCCEEEEEecccccCCCCcccceEEEEeEE
Confidence 322233221 11112345789999999976533 2223333333331 11233445556332 2222224589999999
Q ss_pred EEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEc-CceE
Q 023062 206 ASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVEL-AGIK 263 (288)
Q Consensus 206 itv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~-~~~~ 263 (288)
|.++-.... |..+-.+.|+.+|.++ .....-.|.|.+ .|+.
T Consensus 185 I~L~~~~~~----------------~~~~R~i~i~K~R~~~-~~~~~~~~~I~~~~Gi~ 226 (229)
T TIGR03881 185 IRFRKVVVD----------------GELRRYLIVEKMRQTN-HDKRAWEIDIVPGKGLV 226 (229)
T ss_pred EEEEEeccC----------------CcEEEEEEEEeccCCC-CCCceeEEEEcCCCceE
Confidence 999843221 1233445555554443 444455677875 4554
No 13
>TIGR02655 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.
Probab=97.79 E-value=0.0015 Score=65.67 Aligned_cols=182 Identities=18% Similarity=0.176 Sum_probs=104.1
Q ss_pred hhccc-cCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCCCCcccccCccccccccccccccccccch
Q 023062 50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (288)
Q Consensus 50 a~~~q-~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (288)
+++.+ ++.+++++||-+|+++.+.+++.|+|.... ..++.++|.+..+ |..... .. -++
T Consensus 44 ~g~~~~ge~~lyvs~eE~~~~l~~~~~~~G~~~~~~~~~g~l~~~~~~~~~--~~~~~~---------------~~-~~l 105 (484)
T TIGR02655 44 NGIIHFDEPGVFVTFEESPQDIIKNARSFGWDLQKLVDEGKLFILDASPDP--EGQDVV---------------GG-FDL 105 (484)
T ss_pred HHHHhCCCCEEEEEEecCHHHHHHHHHHcCCCHHHHhhcCceEEEecCchh--cccccc---------------cc-CCH
Confidence 44455 789999999999999999999999986431 3468888875433 221100 00 122
Q ss_pred hhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCCh-----HHHHHHHHhhhcCCceeEEEEEeeC-ccCCc-chHhHHh
Q 023062 127 DKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHS-DLHEI-KFTSVLE 199 (288)
Q Consensus 127 ~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~-----~~l~~~L~~L~~~~~v~SVv~llH~-DLh~p-~~l~aL~ 199 (288)
+.++..+.+ ....+..+ .|+|||++.+....+. ..+.++++.|+.. .++.++ +-|. +...+ ...+..+
T Consensus 106 ~~~l~~i~~--~ls~g~~q-RVvIDSl~aL~~~~~~~~~~r~~l~~Li~~L~~~-g~TvLL-tsh~~~~~~~~~~~~~~e 180 (484)
T TIGR02655 106 SALIERINY--AIRKYKAK-RVSIDSVTAVFQQYDAVSVVRREIFRLVARLKQI-GVTTVM-TTERIEEYGPIARYGVEE 180 (484)
T ss_pred HHHHHHHHH--HHHHhCCc-EEEEeehhHhhhhcCchHHHHHHHHHHHHHHHHC-CCEEEE-EecCcccccccccCCcee
Confidence 222111111 11223333 6899999998764333 2345566666542 333333 4443 32221 2223459
Q ss_pred hhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeCCCcc
Q 023062 200 YLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPVLSED 271 (288)
Q Consensus 200 ~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~~~~~ 271 (288)
|+++++|.+.-... ++...-.+.|+.+|.+ +.....-.|.|..+|+.+.|.....
T Consensus 181 ~laDgVI~L~~~~~----------------~~~~~R~l~I~K~Rgs-~~~~~~~~~~It~~Gi~v~p~~~~~ 235 (484)
T TIGR02655 181 FVSDNVVILRNVLE----------------GERRRRTLEILKLRGT-SHMKGEYPFTITDHGINIFPLGAMR 235 (484)
T ss_pred EeeeeEEEEEEEec----------------CCEEEEEEEEEECCCC-CcCCceEEEEEcCCcEEEEeccccc
Confidence 99999999973211 1112234555555533 3334445689999999987765544
No 14
>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family. This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.
Probab=97.78 E-value=0.00082 Score=62.13 Aligned_cols=131 Identities=13% Similarity=0.105 Sum_probs=68.4
Q ss_pred hccccCcEEEEEecCChHHHHHH----HHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccch
Q 023062 51 GKSQSRGLVVVAYSRSPSFYVDL----LKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL 126 (288)
Q Consensus 51 ~~~q~~~V~vlafe~spe~y~~~----lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L 126 (288)
++.+++.+.++.+|-++++..+. .++.|+|.+...++++++|..+.+.- . .++
T Consensus 60 ~a~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~g~d~~~~~~~l~~id~~~~~~~-----~------------------~~~ 116 (259)
T TIGR03878 60 QASRGNPVLFVTVESPANFVYTSLKERAKAMGVDFDKIEENIILIDAASSTEL-----R------------------ENV 116 (259)
T ss_pred HHhCCCcEEEEEecCCchHHHHHHHHHHHHcCCCHHHHhCCEEEEECCCchhh-----h------------------hhH
Confidence 34568899999999777643333 45667775444457888887653210 0 112
Q ss_pred hhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHH----HHHhhhcCCceeE-EEEEeeCccCC----cchHhH
Q 023062 127 DKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAG----ILSNLRSHDQVSS-IFWLLHSDLHE----IKFTSV 197 (288)
Q Consensus 127 ~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~----~L~~L~~~~~v~S-Vv~llH~DLh~----p~~l~a 197 (288)
+.++..+.+ ...+.+ +-.||||||+.+..... ...-+ +++.++... +.. ++.-.+.+.++ +..-..
T Consensus 117 ~~l~~~l~~--~i~~~~-~~~vVIDSls~l~~~~~-~~~r~~~~~L~~~lk~~~-~t~ll~~e~~~~~~~~~~~~~~~~~ 191 (259)
T TIGR03878 117 PNLLATLAY--AIKEYK-VKNTVIDSITGLYEAKE-MMAREIVRQLFNFMKKWY-QTALFVSQKRSGHEELSAEAAGGYA 191 (259)
T ss_pred HHHHHHHHH--HHHhhC-CCEEEEcCchHhcccch-HHHHHHHHHHHHHHHHcC-CeEEEEeccccCcccccccccCCcc
Confidence 222211111 112222 33789999998765422 22222 333333322 222 22223332211 111125
Q ss_pred HhhhceeEEEEe
Q 023062 198 LEYLSSMVASVE 209 (288)
Q Consensus 198 L~~LAttvitv~ 209 (288)
++|+++++|.+.
T Consensus 192 ~~~l~D~vI~L~ 203 (259)
T TIGR03878 192 VSHIVDGTIVLA 203 (259)
T ss_pred eeEeeccEEEEe
Confidence 899999999997
No 15
>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Probab=97.77 E-value=0.0003 Score=62.69 Aligned_cols=171 Identities=13% Similarity=0.131 Sum_probs=97.5
Q ss_pred cccCcEEEEEecCChHHHHHHHHhcCCCcCC-CCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHH
Q 023062 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS-SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS 131 (288)
Q Consensus 53 ~q~~~V~vlafe~spe~y~~~lk~~G~d~~~-~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~ 131 (288)
.+++.+.++.+|-+++.+.+-++..|++... .++++.++|....-. . ..++.+..
T Consensus 42 ~~g~~~~y~s~e~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~------~------------------~~~~~l~~ 97 (224)
T TIGR03880 42 KNGEKAMYISLEEREERILGYAKSKGWDLEDYIDKSLYIVRLDPSDF------K------------------TSLNRIKN 97 (224)
T ss_pred hCCCeEEEEECCCCHHHHHHHHHHcCCChHHHHhCCeEEEecCHHHH------H------------------hhHHHHHH
Confidence 4578999999999999999999999887533 122466666321100 0 01112111
Q ss_pred HHHHhhcccCCCCcEEEEEechhHH--HhhCCh---HHHHHHHHhhhcCCceeEEEEEeeCccCCc--chHhHHhhhcee
Q 023062 132 LIIEQGLIGQGKDRFSIAIDSVSEM--VRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEYLSSM 204 (288)
Q Consensus 132 ~i~~~~~~~~~~~~~~VvIDSLs~L--L~~~s~---~~l~~~L~~L~~~~~v~SVv~llH~DLh~p--~~l~aL~~LAtt 204 (288)
.+.. +..+.+ .-.|||||++.+ +...+. ..+..+++.++.. . ..++.+.|.+-..+ .....++|+|+.
T Consensus 98 ~~~~--~i~~~~-~~~vVIDsls~l~~~~~~~~~~r~~l~~l~~~lk~~-~-~tvll~s~~~~~~~~~~~~~~~~~l~D~ 172 (224)
T TIGR03880 98 ELPI--LIKELG-ASRVVIDPISLLETLFDDDAERRTELFRFYSSLRET-G-VTTILTSEADKTNVFASKYGLIEYLADG 172 (224)
T ss_pred HHHH--HHHHhC-CCEEEEcChHHHhhhcCCHHHHHHHHHHHHHHHHhC-C-CEEEEEEcccCCCCCccCCCceEEEEeE
Confidence 1111 112222 236889999987 222211 3456677777643 2 34666677665433 335668999999
Q ss_pred EEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeC
Q 023062 205 VASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPV 267 (288)
Q Consensus 205 vitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~ 267 (288)
+|.+.-.... + .+.....+.|..+ |..+.....-.|.|..+|+...|-
T Consensus 173 vI~L~~~~~~---------~-----~~~~~r~l~v~K~-Rg~~~~~~~~~~~i~~~Gi~v~~~ 220 (224)
T TIGR03880 173 VIILKYVRNS---------D-----LRDVRLAVEVVKM-RRSKHSREIKPYEITDSGITVYSE 220 (224)
T ss_pred EEEEeeeecc---------c-----CcceEEEEEEEEc-cCCCCCCceEEEEEcCCcEEEecc
Confidence 9999622110 0 0001123444333 445566667779999999887663
No 16
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=97.55 E-value=0.0029 Score=57.91 Aligned_cols=145 Identities=19% Similarity=0.234 Sum_probs=87.0
Q ss_pred hhccccCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeEEEEecccCCCCCcccccCccccccccccccccccccchh
Q 023062 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD 127 (288)
Q Consensus 50 a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~ 127 (288)
.++..++.++++++|-+|+++++.+++.|.|... -+..+.++|.|+...+-..... ....++.
T Consensus 46 ~~~~~ge~vlyvs~~e~~~~l~~~~~~~g~d~~~~~~~g~l~i~d~~~~~~~~~~~~~---------------~~~~~~~ 110 (260)
T COG0467 46 EGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVV---------------GDPLDLE 110 (260)
T ss_pred HHHhcCCcEEEEEecCCHHHHHHHHHHcCCCHHHHhhcCCEEEEEccccccccccccc---------------cCCccHH
Confidence 4445589999999999999999999999998742 1335889999888775322000 0112333
Q ss_pred hHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHH-HHHHHhhhcC-CceeEEEEEeeCccCC-cchH-hHHhhhce
Q 023062 128 KLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSV-AGILSNLRSH-DQVSSIFWLLHSDLHE-IKFT-SVLEYLSS 203 (288)
Q Consensus 128 sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l-~~~L~~L~~~-~~v~SVv~llH~DLh~-p~~l-~aL~~LAt 203 (288)
++...|.++. ...+ ...+||||++.+......... -.++..+.+. ..-. +.+++.+|... +... +..+|++.
T Consensus 111 ~l~~~I~~~~--~~~~-~~~~ViDsi~~~~~~~~~~~~~r~~~~~l~~~~~~~~-~t~~~~~~~~~~~~~~~~~~~~~vd 186 (260)
T COG0467 111 ELLDRIREIV--EKEG-ADRVVIDSITELTLYLNDPALVRRILLLLKRFLKKLG-VTSLLTTEAPVEERGESGVEEYIVD 186 (260)
T ss_pred HHHHHHHHHH--HHhC-CCEEEEeCCchHhhhcCchHHHHHHHHHHHHHHHhCC-CEEEEEecccccCCCccceEEEEEE
Confidence 4433333322 2222 558999999976554333333 3555555542 1222 44455555432 2222 57778999
Q ss_pred eEEEEeecCc
Q 023062 204 MVASVEPFNQ 213 (288)
Q Consensus 204 tvitv~p~~~ 213 (288)
.+|.+.....
T Consensus 187 gvI~l~~~~~ 196 (260)
T COG0467 187 GVIRLDLKEI 196 (260)
T ss_pred EEEEEeeecc
Confidence 9999986433
No 17
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=97.41 E-value=0.0037 Score=53.18 Aligned_cols=134 Identities=18% Similarity=0.144 Sum_probs=80.1
Q ss_pred ccccCcEEEEEecCChHHHHHHHHhcCCCcCCC--CCeEEEEecccCCCCCcccccCccccccccccccccccccch-hh
Q 023062 52 KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL-DK 128 (288)
Q Consensus 52 ~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L-~s 128 (288)
..+++.+.++++|-+++.+.+-+++.|++...+ ...+.+.|.+...+..... ++ ..
T Consensus 24 ~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~~---------------------~~~~~ 82 (187)
T cd01124 24 LARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAES---------------------SLRLE 82 (187)
T ss_pred HHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhhh---------------------hhhHH
Confidence 345789999999999999999999999885431 2346677755444321110 00 01
Q ss_pred HHHHHHHhhcccCCCCcEEEEEechhHHHh---hCChHHHHHHHHhhhcCCceeEEEEEeeCccC--CcchHhHHhhhce
Q 023062 129 LYSLIIEQGLIGQGKDRFSIAIDSVSEMVR---HASISSVAGILSNLRSHDQVSSIFWLLHSDLH--EIKFTSVLEYLSS 203 (288)
Q Consensus 129 l~~~i~~~~~~~~~~~~~~VvIDSLs~LL~---~~s~~~l~~~L~~L~~~~~v~SVv~llH~DLh--~p~~l~aL~~LAt 203 (288)
++..+.. .... .++-+|+||+++.++. ......+..++..|+.. .+ .++.+-|..-. .+.....++|+|+
T Consensus 83 ~~~~i~~--~~~~-~~~~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~-g~-tvi~v~~~~~~~~~~~~~~~~~~~aD 157 (187)
T cd01124 83 LIQRLKD--AIEE-FKAKRVVIDSVSGLLLMEQSTARLEIRRLLFALKRF-GV-TTLLTSEQSGLEGTGFGGGDVEYLVD 157 (187)
T ss_pred HHHHHHH--HHHH-hCCCEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHC-CC-EEEEEeccccCCCcccCcCceeEeee
Confidence 1111111 1111 2345899999999987 33344455677777654 23 34444453322 1233467899999
Q ss_pred eEEEEeec
Q 023062 204 MVASVEPF 211 (288)
Q Consensus 204 tvitv~p~ 211 (288)
.+|.++-.
T Consensus 158 ~ii~l~~~ 165 (187)
T cd01124 158 GVIRLRLD 165 (187)
T ss_pred EEEEEEEE
Confidence 99999843
No 18
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=97.08 E-value=0.054 Score=53.20 Aligned_cols=150 Identities=19% Similarity=0.154 Sum_probs=85.5
Q ss_pred ccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHH
Q 023062 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (288)
Q Consensus 54 q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (288)
+++.|.++.+|-+++.+..-.++.|++. +++.+++. .+++.+...+
T Consensus 109 ~g~~VlYvs~EEs~~qi~~Ra~rlg~~~----~~l~l~~e------------------------------~~le~I~~~i 154 (372)
T cd01121 109 RGGKVLYVSGEESPEQIKLRADRLGIST----ENLYLLAE------------------------------TNLEDILASI 154 (372)
T ss_pred cCCeEEEEECCcCHHHHHHHHHHcCCCc----ccEEEEcc------------------------------CcHHHHHHHH
Confidence 3578999999999988877677766662 33433321 0122222222
Q ss_pred HHhhcccCCCCcEEEEEechhHHHhhC------ChHHHHHHHHhhhcC---CceeEEEEEeeCccCC--cchHhHHhhhc
Q 023062 134 IEQGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRSH---DQVSSIFWLLHSDLHE--IKFTSVLEYLS 202 (288)
Q Consensus 134 ~~~~~~~~~~~~~~VvIDSLs~LL~~~------s~~~l~~~L~~L~~~---~~v~SVv~llH~DLh~--p~~l~aL~~LA 202 (288)
. ..++-+|||||++.+.... +..++-.++..|++. .. ..++.+-|..-.. .++ ..|+|++
T Consensus 155 ~-------~~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~-itvilvghvtk~g~~aG~-~~leh~v 225 (372)
T cd01121 155 E-------ELKPDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERN-IPIFIVGHVTKEGSIAGP-KVLEHMV 225 (372)
T ss_pred H-------hcCCcEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcC-CeEEEEeeccCCCcccCc-ccchhhc
Confidence 2 1245589999999986431 123343444444441 22 3344454543221 232 6899999
Q ss_pred eeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEe
Q 023062 203 SMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTP 266 (288)
Q Consensus 203 ttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~ 266 (288)
++++.++-.... ..-.+++ .|.|.|. ..+...|.|..+|+..++
T Consensus 226 D~Vi~le~~~~~------------------~~R~Lri-~KnR~g~-~~ei~~F~i~~~Gl~~v~ 269 (372)
T cd01121 226 DTVLYFEGDRHS------------------EYRILRS-VKNRFGS-TNELGVFEMRENGLREVS 269 (372)
T ss_pred eEEEEEEcCCCC------------------cEEEEEE-EeCCCCC-CCCEEEEEECCCCeEEcc
Confidence 999998842210 1122332 3445564 557788999999988544
No 19
>TIGR02237 recomb_radB DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
Probab=97.01 E-value=0.01 Score=51.98 Aligned_cols=153 Identities=15% Similarity=0.180 Sum_probs=78.7
Q ss_pred ccCcEEEEEecC-ChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHH
Q 023062 54 QSRGLVVVAYSR-SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (288)
Q Consensus 54 q~~~V~vlafe~-spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (288)
+++.+.++.+|. +++.+.+..+.+ .+. ..+++++++++ |+. ++...+..
T Consensus 39 ~g~~v~yi~~e~~~~~rl~~~~~~~-~~~--~~~~i~~~~~~-~~~--------------------------~~~~~~~~ 88 (209)
T TIGR02237 39 QGKKVVYIDTEGLSPERFKQIAEDR-PER--ALSNFIVFEVF-DFD--------------------------EQGVAIQK 88 (209)
T ss_pred CCCeEEEEECCCCCHHHHHHHHHhC-hHH--HhcCEEEEECC-CHH--------------------------HHHHHHHH
Confidence 467999999996 888888866543 121 13568887763 111 01111111
Q ss_pred HHHhhcccCCCCcEEEEEechhHHHhhC--C-----hHHHHHHHHhhhc---CCceeEEEEEee--CccC----CcchHh
Q 023062 133 IIEQGLIGQGKDRFSIAIDSVSEMVRHA--S-----ISSVAGILSNLRS---HDQVSSIFWLLH--SDLH----EIKFTS 196 (288)
Q Consensus 133 i~~~~~~~~~~~~~~VvIDSLs~LL~~~--s-----~~~l~~~L~~L~~---~~~v~SVv~llH--~DLh----~p~~l~ 196 (288)
+.+ ...+. ++-+||||||+.+.+.. + ...+...+..|++ ...+. ++.+-| .+.. .|.--.
T Consensus 89 l~~--~~~~~-~~~lvVIDSis~l~~~~~~~~~~~~~~~l~~~~~~L~~~~~~~~v~-vl~t~~~~~~~~~~~~~~~gg~ 164 (209)
T TIGR02237 89 TSK--FIDRD-SASLVVVDSFTALYRLELSDDRISRNRELARQLTLLLSLARKKNLA-VVITNQVYTDVNNGTLRPLGGH 164 (209)
T ss_pred HHH--HHhhc-CccEEEEeCcHHHhHHHhCCccHHHHHHHHHHHHHHHHHHHHcCCE-EEEEcccEEecCCCCCcCCCcc
Confidence 111 11222 34589999999986522 1 1133333444433 22222 222222 2222 222123
Q ss_pred HHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCce
Q 023062 197 VLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGI 262 (288)
Q Consensus 197 aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~ 262 (288)
.++|.++++|.++-. . +.-.+ + .||+++......-+|.|.++|+
T Consensus 165 ~~~~~~d~vi~l~~~-~-------------------~~r~~-~-i~k~~~~~~~~~~~f~It~~Gi 208 (209)
T TIGR02237 165 LLEHWSKVILRLEKF-R-------------------GRRLA-T-LEKHRSRPEGESVYFRITDDGI 208 (209)
T ss_pred hhheeeeEEEEEEec-C-------------------CEEEE-E-EEECCCCCCCCeEEEEEeCCcc
Confidence 689999999999742 1 11122 2 3443333345556799988875
No 20
>PRK11823 DNA repair protein RadA; Provisional
Probab=97.01 E-value=0.049 Score=54.54 Aligned_cols=149 Identities=21% Similarity=0.171 Sum_probs=85.0
Q ss_pred ccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHH
Q 023062 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (288)
Q Consensus 54 q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (288)
+++.|.++.+|-+++.+..-.++.|++. +++.+.+ . .+++.+...+
T Consensus 107 ~g~~vlYvs~Ees~~qi~~ra~rlg~~~----~~l~~~~----e--------------------------~~l~~i~~~i 152 (446)
T PRK11823 107 AGGKVLYVSGEESASQIKLRAERLGLPS----DNLYLLA----E--------------------------TNLEAILATI 152 (446)
T ss_pred cCCeEEEEEccccHHHHHHHHHHcCCCh----hcEEEeC----C--------------------------CCHHHHHHHH
Confidence 4679999999999998888777777763 3333221 0 1223332222
Q ss_pred HHhhcccCCCCcEEEEEechhHHHhh------CChHHHHHHHHhhhcC---CceeEEEEEeeCccCC--cchHhHHhhhc
Q 023062 134 IEQGLIGQGKDRFSIAIDSVSEMVRH------ASISSVAGILSNLRSH---DQVSSIFWLLHSDLHE--IKFTSVLEYLS 202 (288)
Q Consensus 134 ~~~~~~~~~~~~~~VvIDSLs~LL~~------~s~~~l~~~L~~L~~~---~~v~SVv~llH~DLh~--p~~l~aL~~LA 202 (288)
.+ .++-+|||||++.+... .+..++-.++..|++. .. ..++.+-|..-.. .++ ..++|++
T Consensus 153 ~~-------~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~-itvilv~hvtk~~~~ag~-~~lehlv 223 (446)
T PRK11823 153 EE-------EKPDLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRG-IAVFLVGHVTKEGAIAGP-RVLEHMV 223 (446)
T ss_pred Hh-------hCCCEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcC-CEEEEEeeccCCCCcCCc-chhhhhC
Confidence 21 23458999999998652 1223344444444442 22 3344444544332 233 5699999
Q ss_pred eeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEE
Q 023062 203 SMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFT 265 (288)
Q Consensus 203 ttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~ 265 (288)
++++.++..... ..-.+++ .|.|.|. ..+...|.|..+|+.-+
T Consensus 224 D~Vi~le~~~~~------------------~~R~l~i-~K~R~g~-~~e~~~f~it~~Gi~~v 266 (446)
T PRK11823 224 DTVLYFEGDRHS------------------RYRILRA-VKNRFGA-TNEIGVFEMTEQGLREV 266 (446)
T ss_pred eEEEEEEcCCCC------------------ceEEEEE-ccCCCCC-CCceEEEEEcCCCceEC
Confidence 999988731110 1222333 3444454 44667899999998743
No 21
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=96.48 E-value=0.3 Score=44.46 Aligned_cols=110 Identities=19% Similarity=0.212 Sum_probs=61.2
Q ss_pred CcEEEEEechhHHHhhC-----ChHHHHHHHHhhhcC-Cce-eEEEEEeeCccC--C--------c-----chHhHHhhh
Q 023062 144 DRFSIAIDSVSEMVRHA-----SISSVAGILSNLRSH-DQV-SSIFWLLHSDLH--E--------I-----KFTSVLEYL 201 (288)
Q Consensus 144 ~~~~VvIDSLs~LL~~~-----s~~~l~~~L~~L~~~-~~v-~SVv~llH~DLh--~--------p-----~~l~aL~~L 201 (288)
++-+||||+|+.+.... ....+-++++.|+.. .+. ..++.+-|..-. . | .-..++++.
T Consensus 140 ~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~~L~~la~~~~vtvll~sq~~~~~~~~~~~~~~~~~~~d~~gs~~i~~~ 219 (271)
T cd01122 140 GIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSHLRRPDGDKTHEEGGEVSLSDFRGSAAIGQL 219 (271)
T ss_pred CceEEEECCHHHHhccCCCchhHHHHHHHHHHHHHHHHHHhCCEEEEEecccCccCCCccccCCCceEEeccCcHhHhhh
Confidence 34589999999997542 112234555555442 111 235555554322 1 1 113489999
Q ss_pred ceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeC
Q 023062 202 SSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPV 267 (288)
Q Consensus 202 Attvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~ 267 (288)
|++++.++..... + + .+.....++|..+|.+|..-.. -.++++....+|.|.
T Consensus 220 aD~vi~l~r~~~~----e--~-------~~~~~~~i~v~K~R~~~~~g~~-~~~~~~~~t~~~~~~ 271 (271)
T cd01122 220 ADNVIALERNQQA----E--L-------DERNTTYLRILKNRFTGGTGVA-GPLEYDKETGRLSPP 271 (271)
T ss_pred ccEEEEEEecCcc----c--c-------ccCCcEEEEEEeeccCCCccce-eeEEEECCCceecCC
Confidence 9999999853321 0 1 1123355666666666543222 346667888888773
No 22
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=96.47 E-value=0.18 Score=44.77 Aligned_cols=99 Identities=20% Similarity=0.193 Sum_probs=53.4
Q ss_pred CcEEEEEechhHHHhhC-----C----hHHHHHHHHhhhcC---CceeEEEEE--eeCccCC----cchHhHHhhhceeE
Q 023062 144 DRFSIAIDSVSEMVRHA-----S----ISSVAGILSNLRSH---DQVSSIFWL--LHSDLHE----IKFTSVLEYLSSMV 205 (288)
Q Consensus 144 ~~~~VvIDSLs~LL~~~-----s----~~~l~~~L~~L~~~---~~v~SVv~l--lH~DLh~----p~~l~aL~~LAttv 205 (288)
++-+|||||++.+.... . ...+.+.++.|++. ..+. ++.+ ++.+.+. +---..++|+++++
T Consensus 107 ~~~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~v~-vi~tnq~~~~~~~~~~~~~gg~~~~~~~d~i 185 (225)
T PRK09361 107 NVGLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLA-VVITNQVYSDIDSDGLRPLGGHTLEHWSKTI 185 (225)
T ss_pred cccEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCE-EEEEccceecCCCCcccCCCcchhhhhccEE
Confidence 34589999999886531 1 12345544445441 1222 2223 2333332 21123789999999
Q ss_pred EEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceEE
Q 023062 206 ASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIKF 264 (288)
Q Consensus 206 itv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f 264 (288)
|.++.... .+-.+ +..|+| +......-+|.|...|+..
T Consensus 186 i~l~~~~~-------------------~~r~~-~i~k~~-~~~~~~~~~f~It~~Gi~~ 223 (225)
T PRK09361 186 LRLEKFRN-------------------GKRRA-TLEKHR-SRPEGESAEFRITDRGIEI 223 (225)
T ss_pred EEEEEccC-------------------CeEEE-EEEECC-CCCCCCeEEEEEeCCcEec
Confidence 99985111 12222 334444 3344455679999888753
No 23
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=96.40 E-value=0.12 Score=45.77 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=30.1
Q ss_pred cCcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecc
Q 023062 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 55 ~~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
.+++.++..|. +++.+.+.++++|.+....-+++++.++|
T Consensus 53 ~~~viyi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~ 94 (235)
T cd01123 53 EGKAVYIDTEGTFRPERLVQIAERFGLDPEEVLDNIYVARAY 94 (235)
T ss_pred CccEEEEeCCCCcCHHHHHHHHHHhccChHhHhcCEEEEecC
Confidence 36899999988 57888888888877765545667777664
No 24
>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=96.37 E-value=0.2 Score=44.22 Aligned_cols=97 Identities=16% Similarity=0.059 Sum_probs=51.6
Q ss_pred cEEEEEechhHHHhhCCh---------HHHHHHHHhhhcC-Cc-eeEEEEEee--CccC----CcchHhHHhhhceeEEE
Q 023062 145 RFSIAIDSVSEMVRHASI---------SSVAGILSNLRSH-DQ-VSSIFWLLH--SDLH----EIKFTSVLEYLSSMVAS 207 (288)
Q Consensus 145 ~~~VvIDSLs~LL~~~s~---------~~l~~~L~~L~~~-~~-v~SVv~llH--~DLh----~p~~l~aL~~LAttvit 207 (288)
+-+|||||++.+.+.... ..+...++.|+.. .+ =..+|.+-| .+.. .|.--..++|+++++|.
T Consensus 104 ~~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~t~q~~~~~~~~~~~p~~g~~~~~~~d~~i~ 183 (218)
T cd01394 104 VDLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVRPLGGHTLEHWSKVILR 183 (218)
T ss_pred CcEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHHHHHHhCCEEEEecCCEEcCCCCcccccCCcchhcceeEEEE
Confidence 458999999999642111 2345555555542 11 122333333 2332 12111368999999999
Q ss_pred EeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCce
Q 023062 208 VEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGI 262 (288)
Q Consensus 208 v~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~ 262 (288)
++-.. ++.+..+ .||+++......-.|.|.+.|+
T Consensus 184 l~~~~--------------------~~~r~~~-~~~~~~~~~~~~~~f~It~~Gi 217 (218)
T cd01394 184 LEKLR--------------------VGTRRAV-LEKHRFRPEGSSVYFRITDKGI 217 (218)
T ss_pred EEEcC--------------------CCeEEEE-EeeCCCCCCCceEEEEEeCCcc
Confidence 98321 1112223 3344444455556799988775
No 25
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=96.16 E-value=0.29 Score=49.25 Aligned_cols=147 Identities=19% Similarity=0.132 Sum_probs=83.7
Q ss_pred ccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHH
Q 023062 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (288)
Q Consensus 54 q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (288)
+++.|.++.+|-+++.+..-.++.|++. +++.+++. . +++.+...+
T Consensus 121 ~g~kvlYvs~EEs~~qi~~ra~rlg~~~----~~l~~~~e----~--------------------------~~~~I~~~i 166 (454)
T TIGR00416 121 NQMKVLYVSGEESLQQIKMRAIRLGLPE----PNLYVLSE----T--------------------------NWEQICANI 166 (454)
T ss_pred cCCcEEEEECcCCHHHHHHHHHHcCCCh----HHeEEcCC----C--------------------------CHHHHHHHH
Confidence 3568999999999988877666667662 34555431 0 112222222
Q ss_pred HHhhcccCCCCcEEEEEechhHHHhhC------ChHHHHHHHHhhhc---CCceeEEEEEeeCccCC--cchHhHHhhhc
Q 023062 134 IEQGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSIFWLLHSDLHE--IKFTSVLEYLS 202 (288)
Q Consensus 134 ~~~~~~~~~~~~~~VvIDSLs~LL~~~------s~~~l~~~L~~L~~---~~~v~SVv~llH~DLh~--p~~l~aL~~LA 202 (288)
.+ .++-+|||||++.+.... +..++-.++..|.+ ... ..++.+-|..-.+ .++ ..++|++
T Consensus 167 ~~-------~~~~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~g-iTvllt~hvtkeg~~aG~-~~le~lv 237 (454)
T TIGR00416 167 EE-------ENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRG-IAIFIVGHVTKEGSIAGP-KVLEHMV 237 (454)
T ss_pred Hh-------cCCcEEEEecchhhcccccccCCCCHHHHHHHHHHHHHHHHHhC-CEEEEEeccccCCccCCc-ccEeeec
Confidence 21 234579999999985421 12334344444443 222 2344444654332 133 5689999
Q ss_pred eeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceE
Q 023062 203 SMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIK 263 (288)
Q Consensus 203 ttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~ 263 (288)
++++.++-.... ....+.+ .|.|.|. ..+.-.|.|..+|+.
T Consensus 238 D~VI~Le~~~~~------------------~~R~L~v-~K~R~g~-~~e~~~f~it~~Gl~ 278 (454)
T TIGR00416 238 DTVLYFEGDRDS------------------RFRILRS-VKNRFGA-TNEIGIFEMTEQGLR 278 (454)
T ss_pred eEEEEEeccCCC------------------cEEEEEE-ecCCCCC-CCcEEEEEEecCCce
Confidence 999999842111 2233333 4445664 457778999999986
No 26
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=96.00 E-value=0.47 Score=45.53 Aligned_cols=40 Identities=18% Similarity=0.222 Sum_probs=31.1
Q ss_pred cCcEEEEEecCC--hHHHHHHHHhcCCCcCCCCCeEEEEecc
Q 023062 55 SRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 55 ~~~V~vlafe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
+..++++..|-+ |+.+.+.++++|+|.+..-+++.+.++|
T Consensus 130 ~~~vvYIdtE~~f~~eRi~~~a~~~g~d~~~~l~~i~~~~~~ 171 (313)
T TIGR02238 130 NGKVAYIDTEGTFRPDRIRAIAERFGVDPDAVLDNILYARAY 171 (313)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHcCCChHHhcCcEEEecCC
Confidence 568999999995 9999999999998876544567665554
No 27
>KOG4723 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.83 E-value=0.19 Score=46.40 Aligned_cols=185 Identities=15% Similarity=0.181 Sum_probs=102.5
Q ss_pred CCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCC--CCCeEEEEec
Q 023062 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC 93 (288)
Q Consensus 16 ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ 93 (288)
.|+--+.+++|+..+| |.-+|-|++ +-..+| .+.+.+++|.++-+.|--.+++-|.+-.. .+.+++++|+
T Consensus 16 ~EqgkltLl~d~~eT~-gsFl~H~~l---~~~Lka----n~~~cFlaf~k~fshy~i~~rKlG~~l~t~k~rgqlvF~dg 87 (248)
T KOG4723|consen 16 PEQGKLTLLLDTRETP-GSFLFHYYL---YHALKA----NESTCFLAFSKTFSHYAISMRKLGMDLKTKKNRGQLVFIDG 87 (248)
T ss_pred CCCccEEEEeecccCC-ceeeHHHHH---HHHHhc----CCcEEEEEeecchhHHHHHHHHhCCceeecccCCcEEEEhh
Confidence 4566789999999999 556666663 222222 27999999999999999999999999776 2334999999
Q ss_pred cc---CCCCCcccccCcccccccccccccc-ccccchhhHHHHHHHhh--cccCCCCcEEEEEechhHHHhhC---ChHH
Q 023062 94 YT---DPLGWKNWLIDKDISQEASSLSSFC-QDVRNLDKLYSLIIEQG--LIGQGKDRFSIAIDSVSEMVRHA---SISS 164 (288)
Q Consensus 94 fs---DPlgW~~~~~~~~~~~~~s~~~~~~-~~v~~L~sl~~~i~~~~--~~~~~~~~~~VvIDSLs~LL~~~---s~~~ 164 (288)
++ ||.-...+-+ ..-.|.- .-+.+ ..++.+.+..-.+.+-- +..-.....++++|+.+-+..-. -...
T Consensus 88 l~~~~~~i~~q~~kq--~~~t~~~-~~a~~~~ni~~v~e~~rE~~~~v~~~e~i~~~~~t~~vDd~sil~~~~~g~~~~~ 164 (248)
T KOG4723|consen 88 LSMLFAPISKQSKKQ--APETKNH-IKAVFAPNIQCVEENDREFENSVIIIEDIDILQSTHAVDDTSILQAILEGRCFSR 164 (248)
T ss_pred hhhhhCccchhhhhc--CchhHHH-HHhhcCcchhHHHHHHHHHhhheeeeeeeecccceEEEchHHHHHHHHcccchHH
Confidence 87 4444432211 0000000 00111 12333343322222222 22222345689999999885411 2344
Q ss_pred HHHHHHhhhcCCce--eEEEEEeeCccC----CcchHhHHhhhce-eEEEEeec
Q 023062 165 VAGILSNLRSHDQV--SSIFWLLHSDLH----EIKFTSVLEYLSS-MVASVEPF 211 (288)
Q Consensus 165 l~~~L~~L~~~~~v--~SVv~llH~DLh----~p~~l~aL~~LAt-tvitv~p~ 211 (288)
+..+++.=-.-++- -+.+.+.|.|.- .|-.+.....++. .++.-+|.
T Consensus 165 Vldfvhycatl~~e~~~~~vIlvH~~~~a~~erp~~ll~~~~~~~~l~l~aepl 218 (248)
T KOG4723|consen 165 VLDFVHYCATLPQEKSLGSVILVHMATRAISERPLTLLSARRITGFLRLSAEPL 218 (248)
T ss_pred HhhhhhhccccchhhcCCeEEEEecccchhccCchhhhhhhhhcceEEEecccc
Confidence 55555442111111 225667788765 2333333333333 66666664
No 28
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=95.66 E-value=0.84 Score=43.25 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=30.4
Q ss_pred CcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecc
Q 023062 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 56 ~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
..++++.+|. +|+.+.+.+++.|++.+..-+++++++++
T Consensus 137 ~~~~yi~te~~f~~~rl~~~~~~~g~~~~~~l~~i~~~~~~ 177 (317)
T PRK04301 137 GKAVYIDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAY 177 (317)
T ss_pred ceEEEEeCCCCcCHHHHHHHHHHcCCChHhhhccEEEEeCC
Confidence 5899999999 69999999988888765434567777654
No 29
>PTZ00035 Rad51 protein; Provisional
Probab=95.47 E-value=1.1 Score=43.33 Aligned_cols=156 Identities=14% Similarity=0.130 Sum_probs=85.6
Q ss_pred cCcEEEEEecCC--hHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHH
Q 023062 55 SRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (288)
Q Consensus 55 ~~~V~vlafe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (288)
+..++++..|.+ |+.+.+..++.|++....-+++.+..+|+- +.++..
T Consensus 152 ~g~vvyIdtE~~f~~eri~~ia~~~g~~~~~~l~nI~~~~~~~~------------------------------e~~~~~ 201 (337)
T PTZ00035 152 EGKVLYIDTEGTFRPERIVQIAERFGLDPEDVLDNIAYARAYNH------------------------------EHQMQL 201 (337)
T ss_pred CceEEEEEccCCCCHHHHHHHHHHhCCChHhHhhceEEEccCCH------------------------------HHHHHH
Confidence 457888999874 888888888888876544455665554421 111111
Q ss_pred HHHhh-cccCCCCcEEEEEechhHHHhhC-C--------hHHHHHHHHhhhcC---Cce-----eEEEEE------eeCc
Q 023062 133 IIEQG-LIGQGKDRFSIAIDSVSEMVRHA-S--------ISSVAGILSNLRSH---DQV-----SSIFWL------LHSD 188 (288)
Q Consensus 133 i~~~~-~~~~~~~~~~VvIDSLs~LL~~~-s--------~~~l~~~L~~L~~~---~~v-----~SVv~l------lH~D 188 (288)
+.++. ...+. ..-+|||||++.+.+.. . ...+.++++.|++. -.+ .++..- ++.|
T Consensus 202 l~~~~~~l~~~-~~~lvVIDSital~r~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~vavvvtNqv~~~~~~~~~~~~~ 280 (337)
T PTZ00035 202 LSQAAAKMAEE-RFALLIVDSATALFRVDYSGRGELAERQQHLGKFLRALQKLADEFNVAVVITNQVMADVDGASMFVAD 280 (337)
T ss_pred HHHHHHHhhcc-CccEEEEECcHHhhhhhccCcccHHHHHHHHHHHHHHHHHHHHHcCcEEEEecceEEecCCccccCCC
Confidence 12211 11222 33589999999997741 1 12356677777651 111 112211 1111
Q ss_pred cCCcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceE
Q 023062 189 LHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIK 263 (288)
Q Consensus 189 Lh~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~ 263 (288)
-..|--=..+.|.+++.+.+.-... ..-.++|. |.|+...-. -.|.|..+|+.
T Consensus 281 ~~~p~gG~~~~h~~~~Rl~l~k~~~-------------------~~R~~~i~-ksp~~p~~~--~~f~It~~Gi~ 333 (337)
T PTZ00035 281 PKKPIGGHIIAHASTTRLSLRKGRG-------------------EQRICKIY-DSPNLPESE--AVFAISEGGII 333 (337)
T ss_pred CccCCchHHHHhheeEEEEEEecCC-------------------CeeEEEEE-ECCCCCCee--EEEEEeCCccc
Confidence 1112122578999999998874221 12344444 555554333 47999998875
No 30
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=95.46 E-value=1.3 Score=43.12 Aligned_cols=155 Identities=11% Similarity=0.126 Sum_probs=87.0
Q ss_pred CcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHH
Q 023062 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (288)
Q Consensus 56 ~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (288)
..++++.+|. +|+-+.+..++.|++.+..-+++++.++| +.+.++..+
T Consensus 158 g~vlyIdtE~~f~~eRl~qia~~~~~~~~~~l~~i~~~~~~------------------------------~~e~~~~ll 207 (342)
T PLN03186 158 GKAMYIDTEGTFRPQRLIQIAERFGLNGADVLENVAYARAY------------------------------NTDHQSELL 207 (342)
T ss_pred ceEEEEECCCCccHHHHHHHHHHcCCChhhhccceEEEecC------------------------------CHHHHHHHH
Confidence 3799999999 69889999998888865433556655543 111222222
Q ss_pred HHhh-cccCCCCcEEEEEechhHHHhhC--C-------hHHHHHHHHhhhc----CCceeEEEEEeeCccCC------cc
Q 023062 134 IEQG-LIGQGKDRFSIAIDSVSEMVRHA--S-------ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE------IK 193 (288)
Q Consensus 134 ~~~~-~~~~~~~~~~VvIDSLs~LL~~~--s-------~~~l~~~L~~L~~----~~~v~SVv~llH~DLh~------p~ 193 (288)
..+. ..... ..-+|||||++.+.+.. + ...+.++++.|++ +...+-+.--+.++... |.
T Consensus 208 ~~~~~~~~~~-~~~LIVIDSI~alfr~~~~~~g~l~~r~~~L~~~l~~L~~lA~~~~vaVviTNqv~~~~~~~~~~~~~~ 286 (342)
T PLN03186 208 LEAASMMAET-RFALMIVDSATALYRTEFSGRGELSARQMHLGKFLRSLQRLADEFGVAVVITNQVVAQVDGSAFFAGPQ 286 (342)
T ss_pred HHHHHHhhcc-CCCEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCEEEccCCccccCCCc
Confidence 2222 11222 34589999999997631 1 1235677777775 11111112222223321 21
Q ss_pred ----hHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceE
Q 023062 194 ----FTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIK 263 (288)
Q Consensus 194 ----~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~ 263 (288)
-=..++|.+++.|.++-.. +..+.--..|-|.+.... -.|.|..+|+.
T Consensus 287 ~~P~gG~~~~h~~~tRl~L~k~~--------------------~~~R~~~v~ksp~~p~~e--~~F~I~~~Gi~ 338 (342)
T PLN03186 287 LKPIGGNIMAHASTTRLALRKGR--------------------GENRICKVISSPCLPEAE--ARFSISSEGVT 338 (342)
T ss_pred cccchhHHHHhhccEEEEEEecC--------------------CCeEEEEEEECCCCCCeE--EEEEEECCcee
Confidence 1138999999999998321 112222333445554333 77999998875
No 31
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=95.31 E-value=0.93 Score=44.26 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=30.8
Q ss_pred CcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecc
Q 023062 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 56 ~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
..+.++.+|. +|+-+.+..++.|++.+..-++|.+.++|
T Consensus 161 ~~vvyIdTE~tF~peRl~~ia~~~g~d~~~~l~~I~~~~~~ 201 (344)
T PLN03187 161 GKVAYIDTEGTFRPDRIVPIAERFGMDADAVLDNIIYARAY 201 (344)
T ss_pred ceEEEEEcCCCCCHHHHHHHHHHcCCChhhhcCeEEEecCC
Confidence 5899999999 69999999999999875544567665554
No 32
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=95.13 E-value=2.5 Score=40.54 Aligned_cols=155 Identities=12% Similarity=0.098 Sum_probs=83.7
Q ss_pred CcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHH
Q 023062 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (288)
Q Consensus 56 ~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (288)
..++++..|. +|+-+.+..++.|++....-+++.+.++|+ .+.++..+
T Consensus 131 ~~vvyIdtE~~f~~~Rl~~ia~~~~~~~~~~l~~i~~~~~~~------------------------------~~~~~~~l 180 (316)
T TIGR02239 131 GKALYIDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAYN------------------------------TDHQLQLL 180 (316)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHcCCChHHhhccEEEEecCC------------------------------hHHHHHHH
Confidence 4678898988 688888888888877654344565555431 11111222
Q ss_pred HHhh-cccCCCCcEEEEEechhHHHhhCC---------hHHHHHHHHhhhcC----CceeEEEEEeeCccC---------
Q 023062 134 IEQG-LIGQGKDRFSIAIDSVSEMVRHAS---------ISSVAGILSNLRSH----DQVSSIFWLLHSDLH--------- 190 (288)
Q Consensus 134 ~~~~-~~~~~~~~~~VvIDSLs~LL~~~s---------~~~l~~~L~~L~~~----~~v~SVv~llH~DLh--------- 190 (288)
.++. +.... ..-+|||||++.+.+..- ...+.++++.|++. ....=+..-+.+|.-
T Consensus 181 ~~~~~~~~~~-~~~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~vavv~tNqv~~~~~~~~~~~~g~ 259 (316)
T TIGR02239 181 QQAAAMMSES-RFALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLADEFGVAVVITNQVVAQVDGAGSMFAGD 259 (316)
T ss_pred HHHHHhhccC-CccEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEEECceEEecCCccccccCC
Confidence 2222 22222 345899999999976321 12345666666651 111111122222222
Q ss_pred --CcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceE
Q 023062 191 --EIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIK 263 (288)
Q Consensus 191 --~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~ 263 (288)
.|--=..++|.+++.|.++-... ..+.--..|-|.+... .-.|.|...|+.
T Consensus 260 ~~~p~gG~~~~h~~~~ri~l~k~~~--------------------~~R~~~v~ksp~~p~~--~~~f~i~~~Gi~ 312 (316)
T TIGR02239 260 PKKPIGGNIMAHASTTRLSLRKGRG--------------------EQRICKIYDSPCLPES--EAMFAIYEDGIG 312 (316)
T ss_pred CCcCCchHHHHhhccEEEEEEecCC--------------------CeEEEEEEECCCCCCe--EEEEEEeCCcee
Confidence 12123578999999999983211 1222223344555433 377889888875
No 33
>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
Probab=95.06 E-value=0.26 Score=43.40 Aligned_cols=126 Identities=14% Similarity=0.101 Sum_probs=69.1
Q ss_pred CcEEEEEecCC--hHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHH
Q 023062 56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI 133 (288)
Q Consensus 56 ~~V~vlafe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i 133 (288)
..+.++..|.+ ++.+.+..+..+.+.....+++.++++++ +. ++...+..+
T Consensus 54 ~~v~yi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~~-~~--------------------------~~~~~l~~~ 106 (226)
T cd01393 54 GKVVYIDTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYN-GE--------------------------QQLEIVEEL 106 (226)
T ss_pred ceEEEEecCCCCCHHHHHHHHHHhccchhhhhccEEEEeCCC-HH--------------------------HHHHHHHHH
Confidence 68899999986 66677766766666443345677777642 11 111111111
Q ss_pred HHhhcccCCCCcEEEEEechhHHHhhC--Ch-------HHHHHHHHhhhcCC-c-eeEEEEEeeCc--cC-----CcchH
Q 023062 134 IEQGLIGQGKDRFSIAIDSVSEMVRHA--SI-------SSVAGILSNLRSHD-Q-VSSIFWLLHSD--LH-----EIKFT 195 (288)
Q Consensus 134 ~~~~~~~~~~~~~~VvIDSLs~LL~~~--s~-------~~l~~~L~~L~~~~-~-v~SVv~llH~D--Lh-----~p~~l 195 (288)
.+ + ....+.-+||||||+.+.... .. ..+.++++.|++.. . =..||.+-|.. .- ...+.
T Consensus 107 ~~--~-~~~~~~~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~tnq~~~~~~~~~~~~~~p~ 183 (226)
T cd01393 107 ER--I-MSSGRVDLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGDPETPA 183 (226)
T ss_pred HH--H-hhcCCeeEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHHHHHHhCcEEEEEEEEeeecccccCCCcccc
Confidence 11 1 112344589999999986532 11 23445555555421 1 12344444432 21 12233
Q ss_pred --hHHhhhceeEEEEeec
Q 023062 196 --SVLEYLSSMVASVEPF 211 (288)
Q Consensus 196 --~aL~~LAttvitv~p~ 211 (288)
.+++|.+++.+.++..
T Consensus 184 ~G~~~~~~~~~ri~l~~~ 201 (226)
T cd01393 184 GGNALAHASTTRLDLRKG 201 (226)
T ss_pred CchhhhCcccEEEEEEec
Confidence 6999999999999853
No 34
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=94.94 E-value=0.069 Score=47.60 Aligned_cols=146 Identities=12% Similarity=0.041 Sum_probs=69.8
Q ss_pred cCcEEEEEecCChHHHHHHH--HhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccc-cccccchhhHHH
Q 023062 55 SRGLVVVAYSRSPSFYVDLL--KRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSF-CQDVRNLDKLYS 131 (288)
Q Consensus 55 ~~~V~vlafe~spe~y~~~l--k~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~-~~~v~~L~sl~~ 131 (288)
+..|.++.+|-+++++..-+ ...|++. .+ +.+.--+...|..-....+.... ..+.+ ...--.++.+..
T Consensus 42 g~~vly~s~E~~~~~~~~r~~~~~~~~~~----~~--~~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~l~~ 113 (242)
T cd00984 42 GKPVLFFSLEMSKEQLLQRLLASESGISL----SK--LRTGSLSDEDWERLAEAIGELKE--LPIYIDDSSSLTVSDIRS 113 (242)
T ss_pred CCceEEEeCCCCHHHHHHHHHHHhcCCCH----HH--HhcCCCCHHHHHHHHHHHHHHhc--CCEEEeCCCCCCHHHHHH
Confidence 78999999999999999865 3345542 11 11111111122110000000000 00111 111113344433
Q ss_pred HHHHhhcccCCCCcEEEEEechhHHHhhC----ChHHHHHHHHhhhcC-CceeE-EEEEeeCc-----c--CCc-----c
Q 023062 132 LIIEQGLIGQGKDRFSIAIDSVSEMVRHA----SISSVAGILSNLRSH-DQVSS-IFWLLHSD-----L--HEI-----K 193 (288)
Q Consensus 132 ~i~~~~~~~~~~~~~~VvIDSLs~LL~~~----s~~~l~~~L~~L~~~-~~v~S-Vv~llH~D-----L--h~p-----~ 193 (288)
.|..+. .+. ++-+||||+|+.+-... ....+..++..|+.. .+... ++.+.|.. - ..| .
T Consensus 114 ~i~~~~--~~~-~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q~~r~~~~~~~~~~~~~~~~ 190 (242)
T cd00984 114 RARRLK--KEH-GLGLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQLSRGVESRADKRPMLSDLR 190 (242)
T ss_pred HHHHHH--Hhc-CCCEEEEcCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhhhccCCCCCCHHHHh
Confidence 344322 233 34489999999764332 123455666666652 22333 44444421 1 111 2
Q ss_pred hHhHHhhhceeEEEEeec
Q 023062 194 FTSVLEYLSSMVASVEPF 211 (288)
Q Consensus 194 ~l~aL~~LAttvitv~p~ 211 (288)
-.+++++.|++++.++..
T Consensus 191 gS~~i~~~aD~vi~l~~~ 208 (242)
T cd00984 191 ESGSIEQDADVVMFLYRD 208 (242)
T ss_pred hhcccccCCCEEEEEecc
Confidence 236789999999999864
No 35
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=94.88 E-value=1.4 Score=41.33 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=29.4
Q ss_pred CcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecc
Q 023062 56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 56 ~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
..++++.+|- +|+.+.+.++..|++.....+++.++.++
T Consensus 130 ~~~~yi~te~~f~~~rl~~~~~~~gl~~~~~~~~i~i~~~~ 170 (310)
T TIGR02236 130 GKAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAY 170 (310)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHcCCCHHHHhhceEEEecC
Confidence 4899999999 79999999988888754334566666653
No 36
>PRK05973 replicative DNA helicase; Provisional
Probab=94.31 E-value=0.42 Score=44.32 Aligned_cols=62 Identities=13% Similarity=-0.025 Sum_probs=41.1
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCC
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS 83 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~ 83 (288)
.|=.++.+++---=...|=+.+..+++. .++.+++.++++.||-+++++.+-++..|++...
T Consensus 59 GGl~~Gsl~LIaG~PG~GKT~lalqfa~-------~~a~~Ge~vlyfSlEes~~~i~~R~~s~g~d~~~ 120 (237)
T PRK05973 59 SQLKPGDLVLLGARPGHGKTLLGLELAV-------EAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ 120 (237)
T ss_pred CCCCCCCEEEEEeCCCCCHHHHHHHHHH-------HHHhcCCeEEEEEEeCCHHHHHHHHHHcCCChHH
Confidence 4555555554333334444444444422 2334588999999999999999999999988654
No 37
>PF05625 PAXNEB: PAXNEB protein; InterPro: IPR008728 The RNA polymerase II elongator complex is a major histone acetyltransferase component of the RNA polymerase II (RNAPII) holoenzyme and is involved in transcriptional elongation [, ]. It may also play some role in wobble uridine tRNA modification []. This entry represents the ELP4 subunit. ELP4 is not required for the association of the complex with nascent RNA transcript, but is required for complex integrity and histone acetyltransferase activity. It is also required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA in yeast species.; GO: 0006357 regulation of transcription from RNA polymerase II promoter, 0033588 Elongator holoenzyme complex; PDB: 4EJS_A 4A8J_A.
Probab=94.19 E-value=0.13 Score=50.32 Aligned_cols=69 Identities=23% Similarity=0.227 Sum_probs=49.4
Q ss_pred EEEEEechhHHHhhC----ChHHHHHHHHhhhc----CCceeEEEEEeeCccC--CcchHhHHhhhceeEEEEeecCcc
Q 023062 146 FSIAIDSVSEMVRHA----SISSVAGILSNLRS----HDQVSSIFWLLHSDLH--EIKFTSVLEYLSSMVASVEPFNQA 214 (288)
Q Consensus 146 ~~VvIDSLs~LL~~~----s~~~l~~~L~~L~~----~~~v~SVv~llH~DLh--~p~~l~aL~~LAttvitv~p~~~~ 214 (288)
.=|+|-||-..+... ....+++||++||. +.....++..+=.++- .++.+..|+|+++++|.|+|.+..
T Consensus 202 ~RI~I~sl~SP~w~~~~~~~~~~ll~FL~~LR~LlR~~~s~~v~~iTlP~~L~~~~~~~~~~l~~l~D~vi~Le~F~~~ 280 (363)
T PF05625_consen 202 LRIVIPSLGSPLWYPPSASQPSELLRFLHSLRALLRKYSSNAVAMITLPSHLYPRSPSLVRRLEHLADGVIELESFAGS 280 (363)
T ss_dssp EEEEETTTT-TTTS-GGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEEGTTS---HHHHHHHHHHSSEEEEEEE--HH
T ss_pred EEEEEcCCCCcccCCcccccHHHHHHHHHHHHHHHhccCCCEEEEEEECHHHhccChHHHHHHHHhCCEEEEeecCCCc
Confidence 447788776655422 23348999999988 3445567777788887 789999999999999999998765
No 38
>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51. It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....
Probab=93.36 E-value=3.4 Score=38.30 Aligned_cols=156 Identities=16% Similarity=0.167 Sum_probs=83.6
Q ss_pred cCcEEEEEecC--ChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHH
Q 023062 55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (288)
Q Consensus 55 ~~~V~vlafe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (288)
+..++++..|. +++-+.+.+++++++.+..-+++++..+|+ .+.++..
T Consensus 72 ~~~vvyidTe~~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~~------------------------------~~~l~~~ 121 (256)
T PF08423_consen 72 GGKVVYIDTEGTFSPERLQQIAERFGLDPEEILDNIFVIRVFD------------------------------LEELLEL 121 (256)
T ss_dssp SSEEEEEESSSSS-HHHHHHHHHHTTS-HHHHHHTEEEEE-SS------------------------------HHHHHHH
T ss_pred CCceEEEeCCCCCCHHHHHHHhhccccccchhhhceeeeecCC------------------------------HHHHHHH
Confidence 34699999887 688888888888877544445677666543 1222222
Q ss_pred HHHhh-cccCCCCcEEEEEechhHHHhhC-----C----hHHHHHHHHhhhc----CCc----eeEEEEEeeC------c
Q 023062 133 IIEQG-LIGQGKDRFSIAIDSVSEMVRHA-----S----ISSVAGILSNLRS----HDQ----VSSIFWLLHS------D 188 (288)
Q Consensus 133 i~~~~-~~~~~~~~~~VvIDSLs~LL~~~-----s----~~~l~~~L~~L~~----~~~----v~SVv~llH~------D 188 (288)
+..+. ...+.+- -+|||||++.+.+.. . ...+.++++.|++ +.- +.++..-... |
T Consensus 122 L~~l~~~l~~~~i-kLIVIDSIaalfr~e~~~~~~~~~R~~~L~~~~~~L~~lA~~~~iaVvvTNqv~~~~~~~~~~~~~ 200 (256)
T PF08423_consen 122 LEQLPKLLSESKI-KLIVIDSIAALFRSEFSGRGDLAERQRMLARLARILKRLARKYNIAVVVTNQVTTKIDSNSLFDGD 200 (256)
T ss_dssp HHHHHHHHHHSCE-EEEEEETSSHHHHHHSGSTTTHHHHHHHHHHHHHHHHHHHHHTT-EEEEEEEECSSTT----SSTT
T ss_pred HHHHHhhccccce-EEEEecchHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHHhCCceEEeeceeeecCCcccccccc
Confidence 22222 1123334 499999999998732 1 2334455555555 111 1222211111 1
Q ss_pred cCCcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcCceE
Q 023062 189 LHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELAGIK 263 (288)
Q Consensus 189 Lh~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~ 263 (288)
...|--=..+.|..++-+.++-.. ++-+.-...|-|+-. .. .-.|.|.++|++
T Consensus 201 ~~~PalG~~w~h~~~~Rl~l~k~~--------------------~~~R~~~i~ksp~~p-~~-~~~f~It~~Gi~ 253 (256)
T PF08423_consen 201 RLKPALGHSWSHAVTTRLFLSKGR--------------------GSERVATIVKSPSLP-EG-SASFQITEDGIR 253 (256)
T ss_dssp SEEETTHHHHHHHSSEEEEEEECS--------------------TTEEEEEEEECSSSS-SE-EEEEEEETTEEE
T ss_pred cceecCcchhhhhccEEEEEEeCC--------------------CCeEEEEEeECCCCC-Cc-eEEEEEeCCCcc
Confidence 122333346899999999998421 122333334444432 22 345999999875
No 39
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=93.32 E-value=2 Score=34.55 Aligned_cols=67 Identities=15% Similarity=0.124 Sum_probs=44.5
Q ss_pred CCcEEEEEechhHHHhhC------ChHHHHHHHHhhhcC-C-ceeEEEEEeeCccCCcc------hHhHHhhhceeEEEE
Q 023062 143 KDRFSIAIDSVSEMVRHA------SISSVAGILSNLRSH-D-QVSSIFWLLHSDLHEIK------FTSVLEYLSSMVASV 208 (288)
Q Consensus 143 ~~~~~VvIDSLs~LL~~~------s~~~l~~~L~~L~~~-~-~v~SVv~llH~DLh~p~------~l~aL~~LAttvitv 208 (288)
..+-++|||++..++... ....+.+.|.+|... . .=..+|.+.|.+--+.. ...+++|++++++.+
T Consensus 84 ~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~l 163 (165)
T cd01120 84 GGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVL 163 (165)
T ss_pred CCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccccCcccccCccceeeecceEEEE
Confidence 355689999999987642 234556667766652 2 23457778887644321 346899999999877
Q ss_pred e
Q 023062 209 E 209 (288)
Q Consensus 209 ~ 209 (288)
.
T Consensus 164 ~ 164 (165)
T cd01120 164 S 164 (165)
T ss_pred e
Confidence 5
No 40
>cd01125 repA Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
Probab=92.79 E-value=2.2 Score=38.43 Aligned_cols=140 Identities=14% Similarity=0.092 Sum_probs=71.9
Q ss_pred ccCcEEEEEecCChHHHHHHHHhcCCCc--CCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHH
Q 023062 54 QSRGLVVVAYSRSPSFYVDLLKRRGIDI--ASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS 131 (288)
Q Consensus 54 q~~~V~vlafe~spe~y~~~lk~~G~d~--~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~ 131 (288)
+...|++++.|.+++++.+-++..+..- +....++++.+....|+.+..... . .....++.+
T Consensus 40 ~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~g~~~~l~~~~~~~-----------~---~~~~~~~~l-- 103 (239)
T cd01125 40 EPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDSGRIQPISIAREGR-----------I---IVVPEFERI-- 103 (239)
T ss_pred CCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEeccCCCceecccCCc-----------c---cccHHHHHH--
Confidence 4568999999999998887776654421 011245555433222222211000 0 011222332
Q ss_pred HHHHhhcccCCCCcEEEEEechhHHH--hhCChHHHHHHHHhhhcC-CceeEEEEEeeCccCC----------cchHhHH
Q 023062 132 LIIEQGLIGQGKDRFSIAIDSVSEMV--RHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHE----------IKFTSVL 198 (288)
Q Consensus 132 ~i~~~~~~~~~~~~~~VvIDSLs~LL--~~~s~~~l~~~L~~L~~~-~~v~SVv~llH~DLh~----------p~~l~aL 198 (288)
.+. + . ..++-+|+||+++.+- ...+....-.++..|+.. ......+.++|.+-.. ..=.++|
T Consensus 104 --~~~-~-~-~~~~~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~~~~~~~~~~~rGssal 178 (239)
T cd01125 104 --IEQ-L-L-IRRIDLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGSAKDGDTQEAARGASAL 178 (239)
T ss_pred --HHH-H-H-hcCCCEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCcccccCcccccccCcHHHH
Confidence 221 1 1 2345699999998761 122344444455555441 1223333444444432 2336778
Q ss_pred hhhceeEEEEeecCcc
Q 023062 199 EYLSSMVASVEPFNQA 214 (288)
Q Consensus 199 ~~LAttvitv~p~~~~ 214 (288)
...+..++.+.++...
T Consensus 179 ~~~~r~~~~l~~~~~~ 194 (239)
T cd01125 179 VDGARWVRALTRMTSE 194 (239)
T ss_pred hcccceEEEEeeCCHH
Confidence 8888899999887665
No 41
>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding
Probab=91.55 E-value=13 Score=37.87 Aligned_cols=195 Identities=14% Similarity=0.168 Sum_probs=109.2
Q ss_pred CCCCCeeEeecCC---CCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEe
Q 023062 16 GEHAPALTIKDSK---ASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILD 92 (288)
Q Consensus 16 ge~ap~l~i~dsl---~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D 92 (288)
++.--+|+|+..= .+.|...+++-+ ....+|.++.--++++...+..- .+-.+ -++..|+|
T Consensus 7 ~~~G~TLLIKG~PGTGKTtfaLelL~~l------------~~~~~v~YISTRVd~d~vy~~y~---~~~~~-i~~~~vlD 70 (484)
T PF07088_consen 7 QEPGQTLLIKGEPGTGKTTFALELLNSL------------KDHGNVMYISTRVDQDTVYEMYP---WIEES-IDPTNVLD 70 (484)
T ss_pred CCCCcEEEEecCCCCCceeeehhhHHHH------------hccCCeEEEEeccCHHHHHHhhh---hhccc-cChhhhhh
Confidence 3334456666532 445555555444 44568999999999886654221 01111 23456789
Q ss_pred cccCCCCCcccccCccccccccccccccccccchhhHHHHHHHhhcccCCCCcEEEEEec----hhHHH-hhCChHHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDS----VSEMV-RHASISSVAG 167 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDS----Ls~LL-~~~s~~~l~~ 167 (288)
+..||+.-..... +|.---++++++..+++. .+..++.+||+|| ++-+= +|..++++-.
T Consensus 71 atQd~~~~~~~~~-------------vp~~~l~~ds~~~f~~~i---~~~~k~~iI~~DSWdaiieyla~~~~~~ed~e~ 134 (484)
T PF07088_consen 71 ATQDPFELPLDKD-------------VPFERLDIDSFRDFVDKI---NEAGKKPIIAFDSWDAIIEYLAEEHDEPEDIET 134 (484)
T ss_pred hccchhhcccccc-------------CcccccCHHHHHHHHHHh---hhcccCcEEEEecHHHHHHHhhhhhcCcHHHHH
Confidence 9999986644211 222122356654444432 2234556999999 44332 2666676666
Q ss_pred HHHhhhc---CCceeEEEEEeeCccCCcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEec-
Q 023062 168 ILSNLRS---HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKR- 243 (288)
Q Consensus 168 ~L~~L~~---~~~v~SVv~llH~DLh~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kR- 243 (288)
++++|-. ...+.-|+.+ |-.-...|+|+++.||+++....+ .+.-.=.++.+|
T Consensus 135 l~~dLv~lard~g~~LIlVs------Esa~~~~LdYivDGVVTL~v~~de-----------------rGR~~R~L~LeKL 191 (484)
T PF07088_consen 135 LTNDLVELARDMGINLILVS------ESAENEPLDYIVDGVVTLQVKNDE-----------------RGRTRRYLRLEKL 191 (484)
T ss_pred HHHHHHHHHhhcCceEEEEE------ecCCCCcchheeeeEEEEEecccc-----------------CCceEEEEEehhh
Confidence 6666532 2223333332 445567799999999999643331 033344555556
Q ss_pred CCCCeeeeEeEEEEEcCceEEE
Q 023062 244 RNGRVRVMCEEILVELAGIKFT 265 (288)
Q Consensus 244 r~GRV~~~~E~f~i~~~~~~f~ 265 (288)
|.=|+.+...-|+..++..++.
T Consensus 192 RGV~I~q~~Y~fTL~nGrF~~f 213 (484)
T PF07088_consen 192 RGVRIKQRLYPFTLANGRFRSF 213 (484)
T ss_pred cCcccCCccceEEeeCCEEEEe
Confidence 5555666666677776665533
No 42
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=90.02 E-value=4 Score=40.15 Aligned_cols=222 Identities=12% Similarity=0.040 Sum_probs=103.2
Q ss_pred CCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEeccc
Q 023062 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (288)
Q Consensus 16 ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fs 95 (288)
|=+++-+.+----...|=+.+..+++ ..++ ..++.+|.++.+|-+++++.+-+-..+.+.+. .++ ..+.-
T Consensus 191 G~~~G~l~vi~g~pg~GKT~~~l~~a----~~~a--~~~g~~vl~~SlEm~~~~i~~R~~~~~~~v~~--~~~--~~g~l 260 (434)
T TIGR00665 191 GLQPSDLIILAARPSMGKTAFALNIA----ENAA--IKEGKPVAFFSLEMSAEQLAMRMLSSESRVDS--QKL--RTGKL 260 (434)
T ss_pred CCCCCeEEEEEeCCCCChHHHHHHHH----HHHH--HhCCCeEEEEeCcCCHHHHHHHHHHHhcCCCH--HHh--ccCCC
Confidence 44555455443334444444444442 2222 12467999999999999998766544222211 122 12222
Q ss_pred CCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhC----ChHHHHHHHH
Q 023062 96 DPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHA----SISSVAGILS 170 (288)
Q Consensus 96 DPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~----s~~~l~~~L~ 170 (288)
++..|.+-....+...+ ..+-+... --+++.+...+.. +..+.+ .-+||||+|..+-... ....+....+
T Consensus 261 ~~~~~~~~~~a~~~l~~--~~l~i~d~~~~~~~~i~~~i~~--~~~~~~-~~~vvID~l~~i~~~~~~~~r~~~i~~i~~ 335 (434)
T TIGR00665 261 SDEDWEKLTSAAGKLSE--APLYIDDTPGLTITELRAKARR--LKREHG-LGLIVIDYLQLMSGSGRSENRQQEVSEISR 335 (434)
T ss_pred CHHHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHH--HHHhcC-CCEEEEcchHhcCCCCCCCCHHHHHHHHHH
Confidence 23345321000000000 01111100 0123333333332 223333 3489999998763211 1133555556
Q ss_pred hhhcCC-ce-eEEEEEee--CccC-----Cc-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhccccee
Q 023062 171 NLRSHD-QV-SSIFWLLH--SDLH-----EI-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGK 236 (288)
Q Consensus 171 ~L~~~~-~v-~SVv~llH--~DLh-----~p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~ 236 (288)
.|+... .. ..|+++.| .+.. .| .-.+++++.|++++.++.... |... +..++.
T Consensus 336 ~Lk~lA~e~~i~vi~lsqlnr~~~~r~~~~p~lsdlr~Sg~ieq~aD~vi~l~r~~~---~~~~----------~~~~~~ 402 (434)
T TIGR00665 336 SLKALAKELNVPVIALSQLSRSVEQREDKRPQLSDLRESGSIEQDADIVMFLYRDEY---YNPD----------SEDKGI 402 (434)
T ss_pred HHHHHHHHhCCeEEEEeccCcchhccCCCCCChHHHhhccchhhcCCEEEEeccccc---cCCC----------cCCCCc
Confidence 666522 22 22444444 2221 12 334899999999999985321 2111 001233
Q ss_pred EEEEEec-CCCCeeeeEeEEEEEcCceEEEeC
Q 023062 237 FHVRFKR-RNGRVRVMCEEILVELAGIKFTPV 267 (288)
Q Consensus 237 ~~Vr~kR-r~GRV~~~~E~f~i~~~~~~f~~~ 267 (288)
..+...| |+|..-. =.+.+.+...+|...
T Consensus 403 ~~l~v~KnR~G~~g~--~~l~~~~~~~~f~~~ 432 (434)
T TIGR00665 403 AEIIIAKQRNGPTGT--VKLAFQGEYTRFENL 432 (434)
T ss_pred eEEEEecCCCCCCCe--EEEEEecCCCcccCC
Confidence 4443333 7887553 267777777888653
No 43
>PF05763 DUF835: Protein of unknown function (DUF835); InterPro: IPR008553 The members of this archaebacterial protein entry are around 250-300 amino acid residues in length. The function of these proteins is not known.
Probab=90.01 E-value=1.4 Score=37.50 Aligned_cols=73 Identities=16% Similarity=0.312 Sum_probs=47.2
Q ss_pred chhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhcCCce--eEEEEEeeCccCCcchHhHHhh
Q 023062 125 NLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQV--SSIFWLLHSDLHEIKFTSVLEY 200 (288)
Q Consensus 125 ~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~~~~v--~SVv~llH~DLh~p~~l~aL~~ 200 (288)
+|..+...|.+ +..+.+.. +|+||++--|+.+++..++..||..|+-+.-. ..++..+-.+.-+++..+.|+.
T Consensus 59 ~L~~l~~~i~~--fl~~~~~~-vViiD~lEYL~l~NgF~~v~KFL~~LkD~~~~~~~~lIl~~~~~al~ere~~lL~r 133 (136)
T PF05763_consen 59 NLHKLLDTIVR--FLKENGNG-VVIIDGLEYLILENGFESVLKFLASLKDYALLNNGTLILVVDPEALDEREWALLRR 133 (136)
T ss_pred hhHHHHHHHHH--HHHhCCCc-EEEEecHHHHHHHcCHHHHHHHHHHhHHHeeccCCEEEEEEChhhcCHHHHHHHHH
Confidence 34444333333 33443333 99999999999999999999999999964322 2355555555556665555543
No 44
>PHA02542 41 41 helicase; Provisional
Probab=84.17 E-value=52 Score=33.54 Aligned_cols=217 Identities=13% Similarity=0.044 Sum_probs=105.5
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHH--HhcCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLL--KRRGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~l--k~~G~d~~~~~~~v~i~D 92 (288)
.|-+++-+.|--.-..-|=+.+..++ +..++ .++++|.+|.+|-+++++..-+ ...|++. +++. .
T Consensus 185 gGl~~G~LiiIaarPgmGKTtfalni----A~~~a---~~g~~Vl~fSLEM~~~ql~~Rl~a~~~~i~~----~~l~--~ 251 (473)
T PHA02542 185 GGAERKTLNVLLAGVNVGKSLGLCSL----AADYL---QQGYNVLYISMEMAEEVIAKRIDANLLDVSL----DDID--D 251 (473)
T ss_pred CCCCCCcEEEEEcCCCccHHHHHHHH----HHHHH---hcCCcEEEEeccCCHHHHHHHHHHHHcCCCH----HHHh--h
Confidence 45666666665544555455544444 33222 3477999999999999988855 3344553 2221 1
Q ss_pred cccCCCCCcccccCcccccccccccccc---c---cccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhh-------
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFC---Q---DVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRH------- 159 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~---~---~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~------- 159 (288)
+ +.-.|.+......... ...+.+. . .+.++++ .+..+.. ..+.+.-+||||.|..|-..
T Consensus 252 -l-~~~~~~~~~~~~~~~~--~~~l~I~~~d~~~lt~~~ir~---~~rrlk~-~~g~~~dlVvIDYLqL~~~~~~~~~~~ 323 (473)
T PHA02542 252 -L-SKAEYKAKMEKLRSKT--QGKLIIKQYPTGGAHAGHFRA---LLNELKL-KKNFKPDVIIVDYLGICASSRLRVSSE 323 (473)
T ss_pred -c-CHHHHHHHHHHHHHHh--CCCceeecCCCCCCCHHHHHH---HHHHHHH-hcCCCCCEEEEechhhccCCcccCCCC
Confidence 1 2234543111000000 0011000 1 1222332 2222211 12223458999999765311
Q ss_pred CChHHHHHHHHhhhc----CCceeEEEEEeeCccCC---c-----chHhHHhhhceeEEEEeecCccccccccchhhhhh
Q 023062 160 ASISSVAGILSNLRS----HDQVSSIFWLLHSDLHE---I-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSM 227 (288)
Q Consensus 160 ~s~~~l~~~L~~L~~----~~~v~SVv~llH~DLh~---p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~ 227 (288)
.....+...-+.|+. ...+.=+++-++.++.. | .-.+++|+.|+.++.++-... |
T Consensus 324 nr~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~dP~lsDLreSG~IEqdAD~vl~l~r~~~---~---------- 390 (473)
T PHA02542 324 NSYTYVKAIAEELRGLAVEHDVVVWTAAQTTRSGWDSSDVDMSDTAESAGLPATADFMLAVIETEE---L---------- 390 (473)
T ss_pred ChHHHHHHHHHHHHHHHHHhCCeEEEEEeeCccccccCCCcchhcccccchHhhcCEEEEEecCcc---c----------
Confidence 112234444444444 22234455555655543 2 556899999999999974221 1
Q ss_pred hhhcccceeEEEEEecCCCCeee-eEeEEEEEcCceEEEeCC
Q 023062 228 LEQNFRKGKFHVRFKRRNGRVRV-MCEEILVELAGIKFTPVL 268 (288)
Q Consensus 228 ~~~n~~~~~~~Vr~kRr~GRV~~-~~E~f~i~~~~~~f~~~~ 268 (288)
.+.+.+.+.| -|-|+|..-. -.=++.+.+.-.+|...+
T Consensus 391 --~~~~~~eliv-~KnR~G~~g~~g~v~l~f~~~~~~F~~~~ 429 (473)
T PHA02542 391 --AQMGQQLVKQ-LKSRYGDKNKFNKFLMGVDKGNQRWYDVD 429 (473)
T ss_pred --ccCCeEEEEE-ecCCCCCCCCceEEEEEEECCcCcccccc
Confidence 0012233333 3558888642 122445566667776543
No 45
>PF03192 DUF257: Pyrococcus protein of unknown function, DUF257; InterPro: IPR005489 This family of proteins is of unknown function.; PDB: 2EKD_C.
Probab=81.76 E-value=15 Score=33.45 Aligned_cols=152 Identities=17% Similarity=0.266 Sum_probs=88.7
Q ss_pred eeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEE---------
Q 023062 21 ALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHIL--------- 91 (288)
Q Consensus 21 ~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~--------- 91 (288)
+++||-+-.++ +.++ +...+...+.++-+|.+.-+=.+-..|..-||..|+|.+.+ +++-++
T Consensus 13 ~VLVEy~S~~~--~el~------~~~li~~~~~~~~~vlI~DilDtl~i~~~~l~~~Gi~~~~l-~~~~VIKiGG~~~~G 83 (210)
T PF03192_consen 13 TVLVEYSSSSP--PELL------FYELIKWAREKGYPVLIDDILDTLHIYKKHLELMGIDTDIL-DNIKVIKIGGRIEVG 83 (210)
T ss_dssp EEEEEE-TTS---THHH------HHHHHH---T-SS-BEEEEETTHHHHHHHHHHHTT---HHH-HCSEEEEES-S---S
T ss_pred EEEEEeCCCCc--HHHH------HHHHHHHhhhcCCCEEEEEcCCCHHHHHHHHHHcCCCcccc-cCceEEEecCeeeee
Confidence 57788766333 2332 23345556666779999998888999999999999997541 223333
Q ss_pred ------ecccCCCCCcccccCccccccccccccccccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHH--hhCChH
Q 023062 92 ------DCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMV--RHASIS 163 (288)
Q Consensus 92 ------D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL--~~~s~~ 163 (288)
+..+||.-|. +-|..+.+- +.. ++++..++=-+.-++ ...++.
T Consensus 84 nVv~ri~~~~d~~~~~--------------------------k~Y~~~~~~-~~~--~~~~i~ivlGiekl~~~~~~~~~ 134 (210)
T PF03192_consen 84 NVVGRIPITSDPSVYL--------------------------KEYEEILEK-VLE--KEKVINIVLGIEKLFYFFENSPR 134 (210)
T ss_dssp EEEEEE-----BBTTB--------------------------HHHHHHHTT------S-SEEEEEE-HHHHH-HH-S-HH
T ss_pred eEEEEEecccChHHHH--------------------------HHHHHHHHH-Hhc--cCCeEEEEecHHHHHHHHhccHH
Confidence 2233333222 112111110 112 344677777788887 457899
Q ss_pred HHHHHHHhhhcCCc--eeEEEEEeeCccCCc---chHhHHhhhceeEEEEee
Q 023062 164 SVAGILSNLRSHDQ--VSSIFWLLHSDLHEI---KFTSVLEYLSSMVASVEP 210 (288)
Q Consensus 164 ~l~~~L~~L~~~~~--v~SVv~llH~DLh~p---~~l~aL~~LAttvitv~p 210 (288)
.+..++..+.+.-. -..-+..+..|+-+. .++..||-+||+|+.++.
T Consensus 135 e~~~~~~~i~~~lg~~~r~a~yfiN~dvl~~~~~~~l~~LEeiattVi~i~~ 186 (210)
T PF03192_consen 135 ELILFFNSISRFLGNERRIAFYFINRDVLEKISPEVLPLLEEIATTVIEIEK 186 (210)
T ss_dssp HHHHHHHHHHCCTT-TTEEEEEEEEHHHHHHHHHHHHHHHHHHSSEEEEEET
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEchHHhcccCchHHHHHHHHhhheEEEec
Confidence 99999999987422 234788999999976 889999999999999984
No 46
>PRK09165 replicative DNA helicase; Provisional
Probab=78.73 E-value=43 Score=34.16 Aligned_cols=239 Identities=11% Similarity=0.024 Sum_probs=112.2
Q ss_pred ccCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHH--------hhccccCcEEEEEecCChHHHHHHHH--hcCCCcCC
Q 023062 14 LEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYIL--------AGKSQSRGLVVVAYSRSPSFYVDLLK--RRGIDIAS 83 (288)
Q Consensus 14 ~~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~--------a~~~q~~~V~vlafe~spe~y~~~lk--~~G~d~~~ 83 (288)
+.|=+++-+.|----...|=+.+..+++...+.... ....+++.|.+|.+|-+++++.+-+- ..|++.
T Consensus 211 ~gG~~~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEMs~~ql~~R~la~~s~v~~-- 288 (497)
T PRK09165 211 LGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEMSAEQLATRILSEQSEISS-- 288 (497)
T ss_pred cCCCCCCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcCCHHHHHHHHHHHhcCCCH--
Confidence 345666666665555555555555555432221100 00124678999999999999988553 234442
Q ss_pred CCCeEEEEecccCCCCCcccccCcccccccccccccc-ccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhC--
Q 023062 84 SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFC-QDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHA-- 160 (288)
Q Consensus 84 ~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~-~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~-- 160 (288)
+++ .++.-+...|.+-........+. ++-+. ..--.++.+.+.+.. ++.+.+ .-+|+||.|..|-...
T Consensus 289 --~~i--~~~~l~~~e~~~l~~a~~~l~~~--~l~I~d~~~~ti~~i~~~ir~--l~~~~~-~~lvvIDyLqli~~~~~~ 359 (497)
T PRK09165 289 --SKI--RRGKISEEDFEKLVDASQELQKL--PLYIDDTPALSISQLRARARR--LKRQHG-LDLLVVDYLQLIRGSSKR 359 (497)
T ss_pred --HHH--hcCCCCHHHHHHHHHHHHHHhcC--CeEEeCCCCCCHHHHHHHHHH--HHHhcC-CCEEEEcchHhccCCCCC
Confidence 222 23322333443211000000000 01110 000123333333333 223333 3489999999653111
Q ss_pred --C--hHHHHHHHHhhhc----CCceeEEEEEeeCccCC-----c-----chHhHHhhhceeEEEEeecCccccccc-cc
Q 023062 161 --S--ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE-----I-----KFTSVLEYLSSMVASVEPFNQAAFGQR-VD 221 (288)
Q Consensus 161 --s--~~~l~~~L~~L~~----~~~v~SVv~llH~DLh~-----p-----~~l~aL~~LAttvitv~p~~~~~~~~~-~~ 221 (288)
. ...+....+.|+. ...+.-+++-+..++.. | .-.+++|.-|++++-++-.. .|.+ ..
T Consensus 360 ~~~~r~~ev~~is~~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLr~Sg~IEqdAD~v~~l~R~~---~y~~~~~ 436 (497)
T PRK09165 360 SSDNRVQEISEITQGLKALAKELNIPVIALSQLSRQVEQRDDKRPQLSDLRESGSIEQDADVVMFVYREE---YYLKRKE 436 (497)
T ss_pred CCCchHHHHHHHHHHHHHHHHHhCCeEEEeecccchhhccCCCCCchhhhhhccchhccCCEEEEEeehh---hhccccc
Confidence 1 1234444444444 23334455555655542 2 45678999999999997321 1110 00
Q ss_pred hhh------hhhhhhcccceeEEEE-EecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 222 LEN------LSMLEQNFRKGKFHVR-FKRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 222 ~~~------~~~~~~n~~~~~~~Vr-~kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
|+. ...-+.+..++...+. -|.|+|..-.- .+.+.+...+|...+
T Consensus 437 ~~~~~~~~~~~~~~~~~~~~~~e~ivaKnR~G~~g~~--~~~f~~~~~~f~~~~ 488 (497)
T PRK09165 437 PREGTPKHEEWQEKMEKVHNKAEVIIAKQRHGPTGTV--KLAFESEFTRFGDLA 488 (497)
T ss_pred cccccchhhhhhhhhcccCCceEEEEeccCCCCCeeE--EEEEecCCCcccCcc
Confidence 100 0000001112445554 44488877643 466677777887543
No 47
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=78.05 E-value=2.3 Score=36.34 Aligned_cols=39 Identities=15% Similarity=0.172 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhh-------ccccCcEEEEEecCChHHHHHHHHhc
Q 023062 39 YVLTQLSNYILAG-------KSQSRGLVVVAYSRSPSFYVDLLKRR 77 (288)
Q Consensus 39 h~~~~l~s~i~a~-------~~q~~~V~vlafe~spe~y~~~lk~~ 77 (288)
+++.+++..++.+ ..+...|.++.+|.+++++..-+++.
T Consensus 47 ~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~~~~~~rl~~~ 92 (193)
T PF13481_consen 47 TLALQLAAALATGRPFLGELPPRPGRVLYISLEDSESQIARRLRAL 92 (193)
T ss_dssp HHHHHHHHHHHT---TT---------EEEEESSS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCccCCcccccCceEEEEeccCCHHHHHHHHHHH
Confidence 3444445555542 12567999999999999998877755
No 48
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=77.55 E-value=8.4 Score=35.05 Aligned_cols=223 Identities=12% Similarity=0.047 Sum_probs=101.9
Q ss_pred CCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhc--CCCcCCCCCeEEEEec
Q 023062 16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRR--GIDIASSHDWIHILDC 93 (288)
Q Consensus 16 ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~--G~d~~~~~~~v~i~D~ 93 (288)
|=.++-|.|----...+=+.++.+++. .++. ..+.+|.++.+|-+++++..-+-.+ |++. +++ .+.
T Consensus 15 G~~~g~L~vi~a~pg~GKT~~~l~ia~----~~a~--~~~~~vly~SlEm~~~~l~~R~la~~s~v~~----~~i--~~g 82 (259)
T PF03796_consen 15 GLRPGELTVIAARPGVGKTAFALQIAL----NAAL--NGGYPVLYFSLEMSEEELAARLLARLSGVPY----NKI--RSG 82 (259)
T ss_dssp SB-TT-EEEEEESTTSSHHHHHHHHHH----HHHH--TTSSEEEEEESSS-HHHHHHHHHHHHHTSTH----HHH--HCC
T ss_pred CCCcCcEEEEEecccCCchHHHHHHHH----HHHH--hcCCeEEEEcCCCCHHHHHHHHHHHhhcchh----hhh--hcc
Confidence 445555555555555555555555522 2221 2247999999999999876633222 3321 111 111
Q ss_pred ccCCCCCcccccCccccccccccccc-cccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhh----CChHHHHHH
Q 023062 94 YTDPLGWKNWLIDKDISQEASSLSSF-CQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRH----ASISSVAGI 168 (288)
Q Consensus 94 fsDPlgW~~~~~~~~~~~~~s~~~~~-~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~----~s~~~l~~~ 168 (288)
--++..|..-........ ...+.+ +..--.++.+.+.|..+. ..+++.-+|+||.|.-|=.. .....+...
T Consensus 83 ~l~~~e~~~~~~~~~~l~--~~~l~i~~~~~~~~~~i~~~i~~~~--~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i 158 (259)
T PF03796_consen 83 DLSDEEFERLQAAAEKLS--DLPLYIEDTPSLTIDDIESKIRRLK--REGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEI 158 (259)
T ss_dssp GCHHHHHHHHHHHHHHHH--TSEEEEEESSS-BHHHHHHHHHHHH--HHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHHh--hCcEEEECCCCCCHHHHHHHHHHHH--hhccCCCEEEechHHHhcCCCCCCCHHHHHHHH
Confidence 111233332100000000 001111 111224444444444433 33345569999999865331 223444444
Q ss_pred HHhhhcCCc--eeEEEEEee--CccC-----Cc-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccc
Q 023062 169 LSNLRSHDQ--VSSIFWLLH--SDLH-----EI-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRK 234 (288)
Q Consensus 169 L~~L~~~~~--v~SVv~llH--~DLh-----~p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~ 234 (288)
.+.|+.-.. =..||++.| .+.. .| .-.+++++-|++++-++..... .+..+. .+.
T Consensus 159 ~~~Lk~lA~~~~i~vi~~sQlnr~~~~~~~~~p~l~dl~~sg~Ie~~AD~vl~l~r~~~~---~~~~~~--------~~~ 227 (259)
T PF03796_consen 159 SRELKALAKELNIPVIALSQLNREAEDREDKRPSLSDLRESGAIEQDADVVLFLHRDEKY---DEDRDD--------KGE 227 (259)
T ss_dssp HHHHHHHHHHHTSEEEEEEEBSGGGGGSSSCS--HHHHCSTSSHHHH-SEEEEEEEHCHC---HCCSSC--------TTE
T ss_pred HHHHHHHHHHcCCeEEEccccChhhhcccccccchhhhhhhHHHHHHHhhhhhhccchhh---ccccCC--------CCe
Confidence 444444111 123444444 4432 23 2247899999999999864332 110000 123
Q ss_pred eeEEEEEecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 235 GKFHVRFKRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 235 ~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
..++|. |-|+|..-.-. +.+.+...+|...+
T Consensus 228 ~~l~v~-KnR~G~~g~v~--~~f~~~~~~f~~~~ 258 (259)
T PF03796_consen 228 AELIVA-KNRNGPTGTVP--LRFNPETSRFTDLE 258 (259)
T ss_dssp EEEEEE-EESSS--EEEE--EEEETTTTEEEE--
T ss_pred EEEEEE-ecCCCCCceEE--EEEECCCCeEeecc
Confidence 444443 33688877433 88888888887653
No 49
>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange.
Probab=77.22 E-value=40 Score=32.86 Aligned_cols=139 Identities=16% Similarity=0.162 Sum_probs=71.8
Q ss_pred CCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCcc
Q 023062 29 ASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKD 108 (288)
Q Consensus 29 ~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~ 108 (288)
...+=+.+..|++.. ...+++.+.++.+|-+++. +.+++.|+|. +++++.. |....+-
T Consensus 64 ~GsGKTtLal~~~~~-------~~~~g~~~vyId~E~~~~~--~~a~~lGvd~----~~l~v~~----p~~~eq~----- 121 (325)
T cd00983 64 ESSGKTTLALHAIAE-------AQKLGGTVAFIDAEHALDP--VYAKKLGVDL----DNLLISQ----PDTGEQA----- 121 (325)
T ss_pred CCCCHHHHHHHHHHH-------HHHcCCCEEEECccccHHH--HHHHHcCCCH----HHheecC----CCCHHHH-----
Confidence 344445555555332 2234678999999988763 5566778773 4565433 3211110
Q ss_pred ccccccccccccccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCC-------------hHHHHHHHHhhhcC
Q 023062 109 ISQEASSLSSFCQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHAS-------------ISSVAGILSNLRSH 175 (288)
Q Consensus 109 ~~~~~s~~~~~~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s-------------~~~l~~~L~~L~~~ 175 (288)
+..++. +.+.+ ..-+|||||++.+..+.. ...+.++|+.|...
T Consensus 122 --------------l~i~~~---------li~s~-~~~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~~~Lr~L~~~ 177 (325)
T cd00983 122 --------------LEIADS---------LVRSG-AVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGS 177 (325)
T ss_pred --------------HHHHHH---------HHhcc-CCCEEEEcchHhhcccccccccccccchHHHHHHHHHHHHHHHHH
Confidence 011111 12333 345899999999975321 11234555555541
Q ss_pred ---CceeE-EEEEeeCccC----Cc---chHhHHhhhceeEEEEeecCc
Q 023062 176 ---DQVSS-IFWLLHSDLH----EI---KFTSVLEYLSSMVASVEPFNQ 213 (288)
Q Consensus 176 ---~~v~S-Vv~llH~DLh----~p---~~l~aL~~LAttvitv~p~~~ 213 (288)
..+.. ++--++.+.- .| .-=.+|.|.|++.+.+.-...
T Consensus 178 ~~k~~~~vI~tNQvr~~ig~~~g~~e~~~GG~~L~~~ss~rl~lrk~~~ 226 (325)
T cd00983 178 INKSNTTVIFINQLREKIGVMFGNPETTTGGNALKFYSSVRLDIRRIET 226 (325)
T ss_pred HHhCCCEEEEEEccccccccccCCCccCCCchHHhhhcceEEEEEeecc
Confidence 11222 2222233331 12 112469999999999975543
No 50
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=73.45 E-value=63 Score=28.28 Aligned_cols=139 Identities=13% Similarity=0.099 Sum_probs=87.9
Q ss_pred HHHHHHHHHHHHhhccccCcEEEEEe-cCChHHHHHHHHhcCCCcCC--CCCeEEEEeccc--CCCCCcccccCcccccc
Q 023062 38 NYVLTQLSNYILAGKSQSRGLVVVAY-SRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYT--DPLGWKNWLIDKDISQE 112 (288)
Q Consensus 38 ~h~~~~l~s~i~a~~~q~~~V~vlaf-e~spe~y~~~lk~~G~d~~~--~~~~v~i~D~fs--DPlgW~~~~~~~~~~~~ 112 (288)
..++..+..+|+++..+++.+.+++= ....+...+.|++.|.|... -...+.++|... -+-|+.+...
T Consensus 30 ~e~~~~~~~Fi~~GL~~ge~~l~v~~~~~~~~~l~~~L~~~~~d~~~~~~~gqL~~~~~~~~Y~~~g~f~~~~------- 102 (191)
T PF14417_consen 30 EELLEVLVPFIREGLARGERCLYVAPDPRRVEELRDELRKAGPDVEQYLDSGQLELLDAEEWYLPDGRFDPAR------- 102 (191)
T ss_pred HHHHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHHHhcCCchhhcccCCCEEEecchhhhccCCCcCHHH-------
Confidence 56777889999999999999999998 78889999999988887544 234688888521 1222222101
Q ss_pred ccccccccccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCChHHHHHHHHhhhc--CCceeEEEEEeeCccC
Q 023062 113 ASSLSSFCQDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS--HDQVSSIFWLLHSDLH 190 (288)
Q Consensus 113 ~s~~~~~~~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~--~~~v~SVv~llH~DLh 190 (288)
.+..+.+. +.+ ....+-.++-++-| ..|.+.. ....+.++=..+-. .......++.|..+.-
T Consensus 103 ---------~i~~~~~~---~~~--a~~~G~~~lRv~ge-~~w~~~~-~~~~l~~yE~~ln~~~~~~~~~~lC~Yd~~~~ 166 (191)
T PF14417_consen 103 ---------MIAFWRAA---LEQ--ALAEGYRGLRVIGE-MTWALRS-GWEELLRYEALLNRLFAEHPFTALCAYDRRRF 166 (191)
T ss_pred ---------HHHHHHHH---HHH--HHhCCCCcEEEEEe-chhhccc-cHHHHHHHHHHHHHHhcCCCEEEEeccchHhC
Confidence 11111211 111 23455566777777 7788777 55555544333333 2335668899998888
Q ss_pred CcchHhHHh
Q 023062 191 EIKFTSVLE 199 (288)
Q Consensus 191 ~p~~l~aL~ 199 (288)
.+..+..+.
T Consensus 167 ~~~~~~~~~ 175 (191)
T PF14417_consen 167 SPEVLADAL 175 (191)
T ss_pred CHHHHHHHH
Confidence 887665543
No 51
>PRK09354 recA recombinase A; Provisional
Probab=72.51 E-value=29 Score=34.13 Aligned_cols=61 Identities=13% Similarity=0.095 Sum_probs=36.4
Q ss_pred CCCCCeeE-eecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEE
Q 023062 16 GEHAPALT-IKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHI 90 (288)
Q Consensus 16 ge~ap~l~-i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i 90 (288)
|=..+.++ |.. -...+=+.+..|++.+ ...+++.++++.+|-+++. +.+++.|+|. +++++
T Consensus 56 Gip~G~IteI~G-~~GsGKTtLal~~~~~-------~~~~G~~~~yId~E~s~~~--~~a~~lGvdl----d~lli 117 (349)
T PRK09354 56 GLPRGRIVEIYG-PESSGKTTLALHAIAE-------AQKAGGTAAFIDAEHALDP--VYAKKLGVDI----DNLLV 117 (349)
T ss_pred CCcCCeEEEEEC-CCCCCHHHHHHHHHHH-------HHHcCCcEEEECCccchHH--HHHHHcCCCH----HHeEE
Confidence 34444333 333 2444445566666332 2245789999999998874 5567778884 45654
No 52
>TIGR02012 tigrfam_recA protein RecA. This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.
Probab=71.88 E-value=26 Score=34.02 Aligned_cols=50 Identities=10% Similarity=0.059 Sum_probs=31.2
Q ss_pred CCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEE
Q 023062 29 ASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHIL 91 (288)
Q Consensus 29 ~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~ 91 (288)
...+=+.+..|++... ..+++.+.++.+|-+++. ..+++.|+|. +++++.
T Consensus 64 ~GsGKTtLaL~~~~~~-------~~~g~~v~yId~E~~~~~--~~a~~lGvd~----~~l~v~ 113 (321)
T TIGR02012 64 ESSGKTTLALHAIAEA-------QKAGGTAAFIDAEHALDP--VYARKLGVDI----DNLLVS 113 (321)
T ss_pred CCCCHHHHHHHHHHHH-------HHcCCcEEEEcccchhHH--HHHHHcCCCH----HHeEEe
Confidence 4444455566664322 235778899999988765 3466778884 456653
No 53
>PRK05748 replicative DNA helicase; Provisional
Probab=71.54 E-value=57 Score=32.50 Aligned_cols=223 Identities=13% Similarity=0.089 Sum_probs=104.1
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHH-h-cCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK-R-RGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk-~-~G~d~~~~~~~v~i~D 92 (288)
.|=+++.+.|----...|=+.+..+++.. ++ ..++++|.+|.+|-+++++.+-+- . .+++. .++. .
T Consensus 198 ~G~~~G~livIaarpg~GKT~~al~ia~~----~a--~~~g~~v~~fSlEms~~~l~~R~l~~~~~v~~----~~i~--~ 265 (448)
T PRK05748 198 SGLQPNDLIIVAARPSVGKTAFALNIAQN----VA--TKTDKNVAIFSLEMGAESLVMRMLCAEGNIDA----QRLR--T 265 (448)
T ss_pred CCCCCCceEEEEeCCCCCchHHHHHHHHH----HH--HhCCCeEEEEeCCCCHHHHHHHHHHHhcCCCH----HHhh--c
Confidence 45566656555444444445544444322 11 134779999999999999887552 2 12221 1111 1
Q ss_pred cccCCCCCcccccCcccccccccccccc-ccccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhCC-----hHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFC-QDVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHAS-----ISSVA 166 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~-~~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~s-----~~~l~ 166 (288)
+--....|..-..-.....+ .++-+. ..--.++.+.+.+.. +..+.++.-+||||.|.-+=.... ...+.
T Consensus 266 ~~l~~~e~~~~~~a~~~l~~--~~~~i~d~~~~ti~~i~~~~r~--~~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~ 341 (448)
T PRK05748 266 GQLTDDDWPKLTIAMGSLSD--APIYIDDTPGIKVTEIRARCRR--LAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVS 341 (448)
T ss_pred CCCCHHHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHH--HHHhcCCCCEEEEccchhcCCCCCCCcCHHHHHH
Confidence 11112334321000000000 011110 000122233333333 223322344899999996621111 13455
Q ss_pred HHHHhhhc----CCceeEEEEEeeCccCC---cch-------HhHHhhhceeEEEEeecCccccccccchhhhhhhhhcc
Q 023062 167 GILSNLRS----HDQVSSIFWLLHSDLHE---IKF-------TSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNF 232 (288)
Q Consensus 167 ~~L~~L~~----~~~v~SVv~llH~DLh~---p~~-------l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~ 232 (288)
...+.|+. ...+.-+++-+..+... ..| .+++++-|++++.++... .|.++ .+
T Consensus 342 ~i~~~LK~lAke~~i~vi~lsQlnr~~~~r~~k~p~lsdlr~Sg~Ieq~AD~v~~l~r~~---~~~~~-~~--------- 408 (448)
T PRK05748 342 EISRSLKALAKELKVPVIALSQLSRGVEQRQDKRPVMSDIRESGSIEQDADIVAFLYRDD---YYDEE-TE--------- 408 (448)
T ss_pred HHHHHHHHHHHHhCCeEEEecccChhHhhcCCCCCChHHHHhhcchhcCCCEEEEEeccc---ccCcc-cc---------
Confidence 55566654 22233344444443321 122 488999999999998432 12111 00
Q ss_pred cceeEEEE-EecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 233 RKGKFHVR-FKRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 233 ~~~~~~Vr-~kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
.++...+. -|.|+|.+-.- .|.+.+...+|...+
T Consensus 409 ~~~~~e~~v~K~R~G~~g~~--~~~~~~~~~~f~~~~ 443 (448)
T PRK05748 409 NKNTIEIIIAKQRNGPVGTV--ELAFQKEYNKFVNLA 443 (448)
T ss_pred CCCceEEEEeccCCCCCceE--EEEEeCCCCcccccc
Confidence 12333333 34478876653 555667777776543
No 54
>PRK08760 replicative DNA helicase; Provisional
Probab=70.59 E-value=91 Score=31.71 Aligned_cols=224 Identities=14% Similarity=0.062 Sum_probs=106.1
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecc
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
.|=+.+-++|----.+.|=+.+..+++. .++ ..++.+|.++.+|-+++++..-+-..+-..+. .++ -.+.
T Consensus 224 ~G~~~G~LivIaarPg~GKTafal~iA~----~~a--~~~g~~V~~fSlEMs~~ql~~Rl~a~~s~i~~--~~i--~~g~ 293 (476)
T PRK08760 224 AGLQPTDLIILAARPAMGKTTFALNIAE----YAA--IKSKKGVAVFSMEMSASQLAMRLISSNGRINA--QRL--RTGA 293 (476)
T ss_pred cCCCCCceEEEEeCCCCChhHHHHHHHH----HHH--HhcCCceEEEeccCCHHHHHHHHHHhhCCCcH--HHH--hcCC
Confidence 4555565666544455545554444422 211 12367899999999999988866544322211 222 1222
Q ss_pred cCCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhh----CChHHHHHHH
Q 023062 95 TDPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRH----ASISSVAGIL 169 (288)
Q Consensus 95 sDPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~----~s~~~l~~~L 169 (288)
-.+..|.+-..-.+...+ .++-+... --.++.+.+.+.. +..+.+ .-+||||.|..|-.. .....+....
T Consensus 294 l~~~e~~~~~~a~~~l~~--~~l~I~d~~~~t~~~I~~~~r~--l~~~~~-~~lVvIDyLql~~~~~~~~~r~~ei~~Is 368 (476)
T PRK08760 294 LEDEDWARVTGAIKMLKE--TKIFIDDTPGVSPEVLRSKCRR--LKREHD-LGLIVIDYLQLMSVPGNSENRATEISEIS 368 (476)
T ss_pred CCHHHHHHHHHHHHHHhc--CCEEEeCCCCCCHHHHHHHHHH--HHHhcC-CCEEEEecHHhcCCCCCCcccHHHHHHHH
Confidence 233345321000000000 01111100 0112233222322 223333 348999999855211 1123355555
Q ss_pred Hhhhc----CCceeEEEEEeeCccCC-----c-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccce
Q 023062 170 SNLRS----HDQVSSIFWLLHSDLHE-----I-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKG 235 (288)
Q Consensus 170 ~~L~~----~~~v~SVv~llH~DLh~-----p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~ 235 (288)
+.|+. ...+.=+++-+..++.. | .-.+++++-|++++-++... .|.++..+ .++
T Consensus 369 r~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSg~IeqdAD~vl~l~R~~---~y~~~~~~---------~~~ 436 (476)
T PRK08760 369 RSLKGLAKELNVPVIALSQLNRSLETRTDKRPVMADLRESGAIEQDADMIVFIYRDD---YYNKENSP---------DKG 436 (476)
T ss_pred HHHHHHHHHhCCEEEEeeccCccccccCCCCCCHHHHhhccchhcCCCEEEEEechh---hccccccc---------CCC
Confidence 55555 22233344445444431 2 45678899999999997421 12111001 123
Q ss_pred eEEE-EEecCCCCeeeeEeEEEEEcCceEEEeC
Q 023062 236 KFHV-RFKRRNGRVRVMCEEILVELAGIKFTPV 267 (288)
Q Consensus 236 ~~~V-r~kRr~GRV~~~~E~f~i~~~~~~f~~~ 267 (288)
...+ .-|-|+|.+-.- .+.+.+.-.+|...
T Consensus 437 ~~eliiaKnR~G~~g~~--~l~f~~~~~~f~~~ 467 (476)
T PRK08760 437 LAEIIIGKHRGGPTGSC--KLKFFGEYTRFDNL 467 (476)
T ss_pred ceEEEEEccCCCCCceE--EEEEecCCCceecc
Confidence 3444 445588876643 45556666777654
No 55
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=67.57 E-value=18 Score=35.54 Aligned_cols=181 Identities=11% Similarity=0.075 Sum_probs=82.8
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHH--hcCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK--RRGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk--~~G~d~~~~~~~v~i~D 92 (288)
.|=+++-++|----...|=+.+..+++ .+++ ..++.+|.++.+|-++++...-+- ..|++. .++. +
T Consensus 189 ~G~~~g~liviag~pg~GKT~~al~ia----~~~a--~~~g~~v~~fSlEm~~~~l~~Rl~~~~~~v~~----~~~~--~ 256 (421)
T TIGR03600 189 NGLVKGDLIVIGARPSMGKTTLALNIA----ENVA--LREGKPVLFFSLEMSAEQLGERLLASKSGINT----GNIR--T 256 (421)
T ss_pred cCCCCCceEEEEeCCCCCHHHHHHHHH----HHHH--HhCCCcEEEEECCCCHHHHHHHHHHHHcCCCH----HHHh--c
Confidence 355555555544444444444444432 2221 134779999999999998877532 234442 1111 1
Q ss_pred cccCCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhh---CChHHHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRH---ASISSVAGI 168 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~---~s~~~l~~~ 168 (288)
+--++-.|.+-....+...+ .++.++.. --.++.+.+.+.. +..+.++.-+||||+|..|-.. .....+...
T Consensus 257 ~~l~~~~~~~~~~~~~~l~~--~~l~i~d~~~~t~~~i~~~~r~--~~~~~~~~~lvvIDyLql~~~~~~~~~~~~~~~i 332 (421)
T TIGR03600 257 GRFNDSDFNRLLNAVDRLSE--KDLYIDDTGGLTVAQIRSIARR--IKRKKGGLDLIVVDYIQLMAPTRGRDRNEELGGI 332 (421)
T ss_pred CCCCHHHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHH--HHHhcCCCCEEEEecccccCCCCCCCHHHHHHHH
Confidence 11112224321000000000 01111111 1123333333333 2233323458999999877421 112233344
Q ss_pred HHhhhcC-Cce-eEEEEEee--CccCC-----c-----chHhHHhhhceeEEEEeec
Q 023062 169 LSNLRSH-DQV-SSIFWLLH--SDLHE-----I-----KFTSVLEYLSSMVASVEPF 211 (288)
Q Consensus 169 L~~L~~~-~~v-~SVv~llH--~DLh~-----p-----~~l~aL~~LAttvitv~p~ 211 (288)
.+.|+.- ... ..|+++-| .+... | .-.+++++-|++++-++..
T Consensus 333 ~~~Lk~lAke~~i~Vi~lsQlnr~~~~r~~krp~lsdlr~Sg~Ieq~AD~v~~l~R~ 389 (421)
T TIGR03600 333 SRGLKALAKELDVPVVLLAQLNRGSEKRTDKRPIMSDLRDSGAIEQDADVIGLIHRE 389 (421)
T ss_pred HHHHHHHHHHhCCcEEEecccCcchhhcCCCCCChHHHhhcCCccccCcEEEEeccc
Confidence 4444441 111 22444544 33431 2 3446889999999999854
No 56
>PRK06321 replicative DNA helicase; Provisional
Probab=66.10 E-value=1.6e+02 Score=30.03 Aligned_cols=221 Identities=10% Similarity=0.018 Sum_probs=107.2
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHh--cCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKR--RGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~--~G~d~~~~~~~v~i~D 92 (288)
.|=+++-+.|----.+-|-+.+..++ +.+++ ..++.+|.++.+|-+++++.+-+-. .|++ .+++. +
T Consensus 221 ~Gl~~G~LiiiaarPgmGKTafal~i----a~~~a--~~~g~~v~~fSLEMs~~ql~~Rlla~~s~v~----~~~i~--~ 288 (472)
T PRK06321 221 NGFSPSNLMILAARPAMGKTALALNI----AENFC--FQNRLPVGIFSLEMTVDQLIHRIICSRSEVE----SKKIS--V 288 (472)
T ss_pred cCCCCCcEEEEEeCCCCChHHHHHHH----HHHHH--HhcCCeEEEEeccCCHHHHHHHHHHhhcCCC----HHHhh--c
Confidence 35556656555444444444444433 22222 1346799999999999999886542 2333 23343 2
Q ss_pred cccCCCCCcccccCccccccccccccccc-cccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhh-------CChHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQ-DVRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRH-------ASISS 164 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~-~v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~-------~s~~~ 164 (288)
+.-++..|.+-........+. .+-+.. .--.+..+.+.+.. +..+.+- -+||||.|..|-.. .....
T Consensus 289 ~~l~~~e~~~~~~a~~~l~~~--~~~idd~~~~ti~~i~~~~r~--~~~~~~~-~lvvIDyLql~~~~~~~~~~~~r~~e 363 (472)
T PRK06321 289 GDLSGRDFQRIVSVVNEMQEH--TLLIDDQPGLKITDLRARARR--MKESYDI-QFLIIDYLQLLSGSGNLRNSESRQTE 363 (472)
T ss_pred CCCCHHHHHHHHHHHHHHHcC--CEEEeCCCCCCHHHHHHHHHH--HHHhcCC-CEEEEcchHHcCCCCccCCcchHHHH
Confidence 222334464311100000000 111110 00022233333332 2233333 39999999776311 01234
Q ss_pred HHHHHHhhhc----CCceeEEEEEeeCccCC-----c-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhh
Q 023062 165 VAGILSNLRS----HDQVSSIFWLLHSDLHE-----I-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQ 230 (288)
Q Consensus 165 l~~~L~~L~~----~~~v~SVv~llH~DLh~-----p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~ 230 (288)
+...-+.|+. ...+.-+++-+..++.. | .-.+++|.-|+.++-++-.. .|. +++
T Consensus 364 i~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~~krP~lsDLReSG~IEqdAD~v~~l~R~~---~y~---~~~------ 431 (472)
T PRK06321 364 ISEISRMLKNLARELNIPILCLSQLSRKVEDRANHRPMMSDLRESGSIEQDSDLVMFLLRRE---YYD---PND------ 431 (472)
T ss_pred HHHHHHHHHHHHHHhCCcEEEEeecChhhhccCCCCCCHHHHhhcccccccCCEEEEEechh---hcC---CcC------
Confidence 5566666664 22233344455555542 2 44578999999999998421 121 111
Q ss_pred cccceeEEEE-EecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 231 NFRKGKFHVR-FKRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 231 n~~~~~~~Vr-~kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
..+...+. -|.|+|..-. =.+.+.+.-.+|...+
T Consensus 432 --~~~~~elivaKnR~G~~G~--v~l~f~~~~~~f~~~~ 466 (472)
T PRK06321 432 --KPGTAELIVAKNRHGSIGS--VPLVFEKEFARFRNYA 466 (472)
T ss_pred --CCCceEEEEEecCCCCCce--EEEEEecCCCcccCcc
Confidence 12334443 3447887743 2556667777776543
No 57
>PRK08506 replicative DNA helicase; Provisional
Probab=64.36 E-value=1.7e+02 Score=29.70 Aligned_cols=180 Identities=13% Similarity=0.051 Sum_probs=88.5
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHh--cCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKR--RGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~--~G~d~~~~~~~v~i~D 92 (288)
.|=+++-+.|----..-|=+.+..+++. .++ .++..|.++.+|-++++..+-+-. .|++. +++. .
T Consensus 187 ~G~~~G~LivIaarpg~GKT~fal~ia~----~~~---~~g~~V~~fSlEMs~~ql~~Rlla~~s~v~~----~~i~--~ 253 (472)
T PRK08506 187 KGFNKGDLIIIAARPSMGKTTLCLNMAL----KAL---NQDKGVAFFSLEMPAEQLMLRMLSAKTSIPL----QNLR--T 253 (472)
T ss_pred CCCCCCceEEEEcCCCCChHHHHHHHHH----HHH---hcCCcEEEEeCcCCHHHHHHHHHHHhcCCCH----HHHh--c
Confidence 4566666666544445545554444432 221 356799999999999999875533 44442 2332 2
Q ss_pred cccCCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhC----ChHHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHA----SISSVAG 167 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~----s~~~l~~ 167 (288)
+.-++..|..-....+.... ..+-+... --++..+.+.+.. +..+.++--+||||.|.-|-... ....+..
T Consensus 254 ~~l~~~e~~~~~~a~~~l~~--~~l~I~d~~~~ti~~I~~~~r~--l~~~~~~~~lvvIDyLql~~~~~~~~~r~~ev~~ 329 (472)
T PRK08506 254 GDLDDDEWERLSDACDELSK--KKLFVYDSGYVNIHQVRAQLRK--LKSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISE 329 (472)
T ss_pred CCCCHHHHHHHHHHHHHHHc--CCeEEECCCCCCHHHHHHHHHH--HHHhCCCCCEEEEcChhhccCCCCCCCHHHHHHH
Confidence 22234456421000000000 01111111 1123333333333 22333334589999998442111 1223444
Q ss_pred HHHhhhc----CCceeEEEEEeeCccC-----Cc-----chHhHHhhhceeEEEEeec
Q 023062 168 ILSNLRS----HDQVSSIFWLLHSDLH-----EI-----KFTSVLEYLSSMVASVEPF 211 (288)
Q Consensus 168 ~L~~L~~----~~~v~SVv~llH~DLh-----~p-----~~l~aL~~LAttvitv~p~ 211 (288)
.-+.|+. ...+.-+++-+..+.. .| +-.+++++-|++++.++..
T Consensus 330 isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSg~IeqdAD~vl~l~R~ 387 (472)
T PRK08506 330 ISRGLKLLARELDIPIIALSQLNRSLESRADKRPMLSDLRESGAIEQDADIILFVYRD 387 (472)
T ss_pred HHHHHHHHHHHhCCcEEEEeecCcchhhccCCCCChHHhhcchhhhhcCCEEEEEecc
Confidence 4444443 2223334555555553 23 4467899999999999853
No 58
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=60.04 E-value=1.1e+02 Score=33.60 Aligned_cols=156 Identities=14% Similarity=0.104 Sum_probs=81.3
Q ss_pred cccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHH
Q 023062 53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL 132 (288)
Q Consensus 53 ~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~ 132 (288)
.+++.+.++.+|-+++ .+-+++.|+|. +++.+.. |.. . +..+..
T Consensus 86 ~~G~~v~yId~E~t~~--~~~A~~lGvDl----~~llv~~----~~~-----------------------~---E~~l~~ 129 (790)
T PRK09519 86 AAGGVAAFIDAEHALD--PDYAKKLGVDT----DSLLVSQ----PDT-----------------------G---EQALEI 129 (790)
T ss_pred HcCCcEEEECCccchh--HHHHHHcCCCh----hHeEEec----CCC-----------------------H---HHHHHH
Confidence 4577899999988877 24556668885 3343222 210 0 001111
Q ss_pred HHHhhcccCCCCcEEEEEechhHHHhh------CC-------hHHHHHHHHhhhcC---CceeE-EEEEeeCcc------
Q 023062 133 IIEQGLIGQGKDRFSIAIDSVSEMVRH------AS-------ISSVAGILSNLRSH---DQVSS-IFWLLHSDL------ 189 (288)
Q Consensus 133 i~~~~~~~~~~~~~~VvIDSLs~LL~~------~s-------~~~l~~~L~~L~~~---~~v~S-Vv~llH~DL------ 189 (288)
+.+ +..++ ++-+|||||++.|..+ .+ ...+.++|+.|... ..+.. +.-.++.+.
T Consensus 130 i~~--lv~~~-~~~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~q~L~~L~~~l~~~nvtvi~TNQv~~~~g~~fg~ 206 (790)
T PRK09519 130 ADM--LIRSG-ALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGVMFGS 206 (790)
T ss_pred HHH--HhhcC-CCeEEEEcchhhhcchhhccCCCCcccHHHHHHHHHHHHHHHHHHHHhCCCEEEEEecceecCCCcCCC
Confidence 111 22232 3558999999999841 11 11124566666652 22222 222333333
Q ss_pred -CCcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEEEecCCCCeeeeEeEEEEEcC
Q 023062 190 -HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMCEEILVELA 260 (288)
Q Consensus 190 -h~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~kRr~GRV~~~~E~f~i~~~ 260 (288)
+.|.-=.+|.|-|++-|.|.-...+..+ ++ ..|.-.+..--+|+.+......|.+..+
T Consensus 207 p~~~~GG~~l~h~ss~Ri~lrk~~~ik~~-~~------------~~G~~~~~kv~ks~cLpe~e~v~~i~tG 265 (790)
T PRK09519 207 PETTTGGKALKFYASVRMDVRRVETLKDG-TN------------AVGNRTRVKVVKNKCLAEGTRIFDPVTG 265 (790)
T ss_pred CCcCCCCcccceeccEEEEeeeccccccC-cc------------ccceEEEEEEEECCCCCCceEEEEecCC
Confidence 1233345799999999999854443211 11 2233333333477777766666666533
No 59
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=53.03 E-value=39 Score=32.99 Aligned_cols=66 Identities=26% Similarity=0.177 Sum_probs=51.9
Q ss_pred eEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChH---HHHHHHHhcCCCcCCCCCeEEEEecccCCC
Q 023062 22 LTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPS---FYVDLLKRRGIDIASSHDWIHILDCYTDPL 98 (288)
Q Consensus 22 l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe---~y~~~lk~~G~d~~~~~~~v~i~D~fsDPl 98 (288)
-.|-|--+.||| |+.-.+...+.++..|+|+|+++. -..+-++|-|+. |-.++..|.-+.|.
T Consensus 158 e~VlD~cAAPGG-----------KTthla~~~~~~~~iV~A~D~~~~Rl~~l~~nl~RlG~~----nv~~~~~d~~~~~~ 222 (355)
T COG0144 158 ERVLDLCAAPGG-----------KTTHLAELMENEGAIVVAVDVSPKRLKRLRENLKRLGVR----NVIVVNKDARRLAE 222 (355)
T ss_pred CEEEEECCCCCC-----------HHHHHHHhcCCCCceEEEEcCCHHHHHHHHHHHHHcCCC----ceEEEecccccccc
Confidence 567888899998 666666667777888999999986 677889999988 45688889877776
Q ss_pred CCcc
Q 023062 99 GWKN 102 (288)
Q Consensus 99 gW~~ 102 (288)
.|..
T Consensus 223 ~~~~ 226 (355)
T COG0144 223 LLPG 226 (355)
T ss_pred cccc
Confidence 6643
No 60
>PRK05595 replicative DNA helicase; Provisional
Probab=52.83 E-value=2.5e+02 Score=28.01 Aligned_cols=221 Identities=12% Similarity=0.001 Sum_probs=104.0
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHh--cCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKR--RGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~--~G~d~~~~~~~v~i~D 92 (288)
.|=.++.+.|----..-|=+.+..+++. +++ ..++..|.++.+|-+++++..-+-. .|++. .++. .
T Consensus 196 ~G~~~g~liviaarpg~GKT~~al~ia~----~~a--~~~g~~vl~fSlEms~~~l~~R~~a~~~~v~~----~~~~--~ 263 (444)
T PRK05595 196 SGFQKGDMILIAARPSMGKTTFALNIAE----YAA--LREGKSVAIFSLEMSKEQLAYKLLCSEANVDM----LRLR--T 263 (444)
T ss_pred CCCCCCcEEEEEecCCCChHHHHHHHHH----HHH--HHcCCcEEEEecCCCHHHHHHHHHHHhcCCCH----HHHh--c
Confidence 3555665665444444444554444432 221 2357899999999999998885332 23332 2221 1
Q ss_pred cccCCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhC----ChHHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHA----SISSVAG 167 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~----s~~~l~~ 167 (288)
.--+-..|..-....+...+ ..+.+... --.++.+.+.+.. +..+. +.-+||||.|.-|-... ....+..
T Consensus 264 ~~l~~~e~~~~~~~~~~l~~--~~l~i~d~~~~t~~~i~~~~r~--~~~~~-~~~~vvIDylql~~~~~~~~~r~~~v~~ 338 (444)
T PRK05595 264 GNLEDKDWENIARASGPLAA--AKIFIDDTAGVSVMEMRSKCRR--LKIEH-GIDMILIDYLQLMSGGKGSESRQQEVSE 338 (444)
T ss_pred CCCCHHHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHH--HHHhc-CCCEEEEeHHHhccCCCCCccHHHHHHH
Confidence 10011224221000000000 01111100 1122333333333 22332 34489999998653111 1133444
Q ss_pred HHHhhhc----CCceeEEEEEeeCccC-----Cc-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhccc
Q 023062 168 ILSNLRS----HDQVSSIFWLLHSDLH-----EI-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFR 233 (288)
Q Consensus 168 ~L~~L~~----~~~v~SVv~llH~DLh-----~p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~ 233 (288)
.-+.|+. ...+.-+++-+..+.. -| .-.+++++-|++++-++.... |.++- ..
T Consensus 339 is~~LK~lAke~~i~vi~lsQLnR~~e~r~~~rP~lsdlr~Sg~Ieq~AD~vl~l~r~~~---~~~~~----------~~ 405 (444)
T PRK05595 339 ISRSIKALAKEMECPVIALSQLSRAPEQRADHRPMLSDLRESGSIEQDADVVMFLYRDEY---YNKET----------ED 405 (444)
T ss_pred HHHHHHHHHHHhCCeEEEeeccCcchhccCCCCCchhhhhhhcccccCCCEEEEEecccc---ccccc----------CC
Confidence 4455554 2223334445555443 12 445789999999999985321 21110 01
Q ss_pred ceeEEE-EEecCCCCeeeeEeEEEEEcCceEEEeC
Q 023062 234 KGKFHV-RFKRRNGRVRVMCEEILVELAGIKFTPV 267 (288)
Q Consensus 234 ~~~~~V-r~kRr~GRV~~~~E~f~i~~~~~~f~~~ 267 (288)
++...+ .-|.|+|..-. =.|.+.+...+|...
T Consensus 406 ~~~~e~iv~K~R~G~~g~--~~~~~~~~~~~f~~~ 438 (444)
T PRK05595 406 KNVAECIIAKQRNGPTGT--VKLAWLGQYSKFGNL 438 (444)
T ss_pred CCceEEEEEccCCCCCce--EEEEEecCCCccccc
Confidence 233343 34557887663 345556666777654
No 61
>PRK08840 replicative DNA helicase; Provisional
Probab=41.98 E-value=3.9e+02 Score=27.16 Aligned_cols=228 Identities=12% Similarity=0.034 Sum_probs=112.1
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHH--hcCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK--RRGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk--~~G~d~~~~~~~v~i~D 92 (288)
.|=+.+-+.|--.-.+-|=+.+...+ +.+++ ..++.+|.+|.+|-++++..+-+- ..|++. .++. +
T Consensus 212 ~G~~~g~LiviaarPg~GKTafalni----a~~~a--~~~~~~v~~fSlEMs~~ql~~Rlla~~s~v~~----~~i~--~ 279 (464)
T PRK08840 212 AGLQGSDLIIVAARPSMGKTTFAMNL----CENAA--MDQDKPVLIFSLEMPAEQLMMRMLASLSRVDQ----TKIR--T 279 (464)
T ss_pred cCCCCCceEEEEeCCCCchHHHHHHH----HHHHH--HhCCCeEEEEeccCCHHHHHHHHHHhhCCCCH----HHHh--c
Confidence 45566666665555555554444333 22222 134779999999999998876432 223332 2221 2
Q ss_pred cccCCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHh-h---CChHHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVR-H---ASISSVAG 167 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~-~---~s~~~l~~ 167 (288)
.--.+-.|.+-....+...+. .++-+... --.++.+.+.+.. +..+.++.-+||||-|.-|-. . .....+..
T Consensus 280 ~~l~~~e~~~~~~a~~~l~~~-~~l~I~d~~~~ti~~i~~~~r~--~~~~~~~~~lvvIDYLql~~~~~~~~~r~~ei~~ 356 (464)
T PRK08840 280 GQLDDEDWARISSTMGILMEK-KNMYIDDSSGLTPTEVRSRARR--IAREHGGLSMIMVDYLQLMRVPALSDNRTLEIAE 356 (464)
T ss_pred CCCCHHHHHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHH--HHHhcCCCCEEEEccHHhcCCCCCCCchHHHHHH
Confidence 211233454311000000000 01111110 0112233223333 223333334899999986521 1 11234555
Q ss_pred HHHhhhcC----CceeEEEEEeeCccCC-----c-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhccc
Q 023062 168 ILSNLRSH----DQVSSIFWLLHSDLHE-----I-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFR 233 (288)
Q Consensus 168 ~L~~L~~~----~~v~SVv~llH~DLh~-----p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~ 233 (288)
.-+.|+.- ..+.-+++-+..++.. | .-.+++|.-|+.++-++.... |.... ..
T Consensus 357 isr~LK~lAkel~ipVi~LsQLnR~~e~r~~krP~lsDLreSG~IEqdAD~v~~l~R~~~---y~~~~----------~~ 423 (464)
T PRK08840 357 ISRSLKALAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEV---YNPDS----------PL 423 (464)
T ss_pred HHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchHhhhhcccccccCCEEEEEecccc---cCCCc----------CC
Confidence 55566652 2234455555565542 2 345678999999999985322 21110 01
Q ss_pred ceeEEEE-EecCCCCeeeeEeEEEEEcCceEEEeCCCcch
Q 023062 234 KGKFHVR-FKRRNGRVRVMCEEILVELAGIKFTPVLSEDE 272 (288)
Q Consensus 234 ~~~~~Vr-~kRr~GRV~~~~E~f~i~~~~~~f~~~~~~~~ 272 (288)
++...+. -|-|||..-.- .+.+.+.-.+|...+.++.
T Consensus 424 ~~~~elivaKnR~G~~G~v--~l~f~~~~~~f~~~~~~~~ 461 (464)
T PRK08840 424 KGTAEIIIGKQRNGPIGSV--RLTFQGQYSRFDNYAGPAF 461 (464)
T ss_pred CCceEEEEecccCCCCceE--EEEEecCcccccCCCCCCC
Confidence 2344443 45588877553 5566777778877665543
No 62
>PRK08006 replicative DNA helicase; Provisional
Probab=38.60 E-value=4.4e+02 Score=26.82 Aligned_cols=223 Identities=13% Similarity=0.042 Sum_probs=109.5
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhc--CCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRR--GIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~--G~d~~~~~~~v~i~D 92 (288)
.|=+++-|.|----.+-|=+.+..++ +.+++ ..++.+|.+|.+|-++++..+-+-.. |++ ..++. +
T Consensus 219 ~Gl~~G~LiiIaarPgmGKTafalni----a~~~a--~~~g~~V~~fSlEM~~~ql~~Rlla~~~~v~----~~~i~--~ 286 (471)
T PRK08006 219 AGLQPSDLIIVAARPSMGKTTFAMNL----CENAA--MLQDKPVLIFSLEMPGEQIMMRMLASLSRVD----QTRIR--T 286 (471)
T ss_pred cCCCCCcEEEEEeCCCCCHHHHHHHH----HHHHH--HhcCCeEEEEeccCCHHHHHHHHHHHhcCCC----HHHhh--c
Confidence 45666666665555555555544444 22222 12577999999999999888744322 222 12221 2
Q ss_pred cccCCCCCcccccCcccc-cccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhh----CChHHHH
Q 023062 93 CYTDPLGWKNWLIDKDIS-QEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRH----ASISSVA 166 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~-~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~----~s~~~l~ 166 (288)
..-+...|.+-..-.+.. .+. ++-+... --.++.+.+.+.. +..+.++.-+||||-|.-+-.. .....+.
T Consensus 287 ~~l~~~e~~~~~~a~~~~~~~~--~l~I~d~~~~t~~~i~~~~r~--~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~ 362 (471)
T PRK08006 287 GQLDDEDWARISGTMGILLEKR--NMYIDDSSGLTPTEVRSRARR--IFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIA 362 (471)
T ss_pred CCCCHHHHHHHHHHHHHHHhcC--CEEEECCCCCCHHHHHHHHHH--HHHhcCCCCEEEEccHHHccCCCCCCCcHHHHH
Confidence 222334454311000000 000 1111100 0112232222322 2233333459999999854211 1233456
Q ss_pred HHHHhhhcC----CceeEEEEEeeCccCC-----c-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcc
Q 023062 167 GILSNLRSH----DQVSSIFWLLHSDLHE-----I-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNF 232 (288)
Q Consensus 167 ~~L~~L~~~----~~v~SVv~llH~DLh~-----p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~ 232 (288)
..-+.|+.. ..+.-+++-+..++.. | .-.+++|.-|+.++-++... .|.+.-+
T Consensus 363 ~isr~LK~lAkel~ipVi~LsQLnR~~e~r~dkrP~lsDLreSG~IEqdAD~v~~l~R~~---~y~~~~~---------- 429 (471)
T PRK08006 363 EISRSLKALAKELQVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDE---VYHENSD---------- 429 (471)
T ss_pred HHHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchhhhhhcCcccccCCEEEEEeccc---ccccccC----------
Confidence 666666652 2234455555666542 2 44577899999999998432 1221100
Q ss_pred cceeEEE-EEecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 233 RKGKFHV-RFKRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 233 ~~~~~~V-r~kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
.++...+ .-|-|+|..-.- .|.+.+.-.+|...+
T Consensus 430 ~~g~~elivaKnR~G~~G~v--~l~f~~~~~~f~~~~ 464 (471)
T PRK08006 430 LKGIAEIIIGKQRNGPIGTV--RLTFNGQWSRFDNYA 464 (471)
T ss_pred CCCceEEEEecccCCCCceE--EEEEccCcccccCCC
Confidence 1244444 345588876543 455566667776544
No 63
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=38.59 E-value=54 Score=31.45 Aligned_cols=61 Identities=20% Similarity=0.327 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHhhccccCcEEEEEecC----ChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCC
Q 023062 37 FNYVLTQLSNYILAGKSQSRGLVVVAYSR----SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGW 100 (288)
Q Consensus 37 ~~h~~~~l~s~i~a~~~q~~~V~vlafe~----spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW 100 (288)
.+.|..+++..+.+++..++.|.+|.... ..+...+.|++.|... ..++.+-|-|.||..-
T Consensus 65 ~d~f~~~~~~~lv~g~L~g~~V~vV~~p~a~~~~~~~v~~~L~~AGA~v---~g~i~lt~~~~d~~~~ 129 (308)
T PF11382_consen 65 ADQFIAAVAPRLVAGRLTGRSVAVVTLPGADDEDVDAVRELLEQAGATV---TGRITLTDKFLDPEQA 129 (308)
T ss_pred HHHHHHHHHHHHhcCccCCCEEEEEEcCCCChHHHHHHHHHHHHCCCeE---EEEEEEchhhcChhhH
Confidence 56778888888899999999999999643 3557788888898886 5689999999999864
No 64
>PRK07004 replicative DNA helicase; Provisional
Probab=38.41 E-value=4.4e+02 Score=26.68 Aligned_cols=223 Identities=14% Similarity=0.045 Sum_probs=107.9
Q ss_pred cCCCCCeeEeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHH--hcCCCcCCCCCeEEEEe
Q 023062 15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK--RRGIDIASSHDWIHILD 92 (288)
Q Consensus 15 ~ge~ap~l~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk--~~G~d~~~~~~~v~i~D 92 (288)
.|=+.+-+.|----.+.|-+.+...++. +++ ..++.+|.++.+|-++++..+-+= ..+++ ..++. +
T Consensus 208 ~G~~~g~liviaarpg~GKT~~al~ia~----~~a--~~~~~~v~~fSlEM~~~ql~~R~la~~~~v~----~~~i~--~ 275 (460)
T PRK07004 208 SGMHGGELIIVAGRPSMGKTAFSMNIGE----YVA--VEYGLPVAVFSMEMPGTQLAMRMLGSVGRLD----QHRMR--T 275 (460)
T ss_pred cCCCCCceEEEEeCCCCCccHHHHHHHH----HHH--HHcCCeEEEEeCCCCHHHHHHHHHHhhcCCC----HHHHh--c
Confidence 4666666666555555555554444422 221 235789999999999999877442 11222 12221 2
Q ss_pred cccCCCCCcccccCcccccccccccccccc-ccchhhHHHHHHHhhcccCCCCcEEEEEechhHHHhhC----ChHHHHH
Q 023062 93 CYTDPLGWKNWLIDKDISQEASSLSSFCQD-VRNLDKLYSLIIEQGLIGQGKDRFSIAIDSVSEMVRHA----SISSVAG 167 (288)
Q Consensus 93 ~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~-v~~L~sl~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~~----s~~~l~~ 167 (288)
+.-....|.+-....+.-.+ ..+-+... --++..+.+.+.. +..+.++.-+||||=|.-+-... ....+..
T Consensus 276 g~l~~~e~~~~~~a~~~l~~--~~l~I~d~~~~~~~~i~~~~r~--l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~ 351 (460)
T PRK07004 276 GRLTDEDWPKLTHAVQKMSE--AQLFIDETGGLNPMELRSRARR--LARQCGKLGLIIIDYLQLMSGSSQGENRATEISE 351 (460)
T ss_pred CCCCHHHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHH--HHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHH
Confidence 22233445421000000000 01111110 0012222222222 22333334599999997763211 1223555
Q ss_pred HHHhhhc----CCceeEEEEEeeCccCC-----c-----chHhHHhhhceeEEEEeecCccccccccchhhhhhhhhccc
Q 023062 168 ILSNLRS----HDQVSSIFWLLHSDLHE-----I-----KFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFR 233 (288)
Q Consensus 168 ~L~~L~~----~~~v~SVv~llH~DLh~-----p-----~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~ 233 (288)
.-+.|+. ...+.-+++-+..++.. | .-.+++|.-|+.++-++... .|.+.-+. .+
T Consensus 352 Isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDLreSg~IeqdAD~v~~l~R~~---~y~~~~~~--------~g 420 (460)
T PRK07004 352 ISRSLKSLAKELDVPVIALSQLNRGLEQRPNKRPVMSDLRESGAIEQDADVILFIYRDE---VYNPDSPD--------KG 420 (460)
T ss_pred HHHHHHHHHHHhCCeEEEEeccChhhhccCCCCCChHHHhcchhhhhcCCEEEEecccc---ccCCCcCC--------CC
Confidence 5555555 22334344445444431 2 45578899999999998432 22211111 12
Q ss_pred ceeEEEEEecCCCCeeeeEeEEEEEcCceEEEeC
Q 023062 234 KGKFHVRFKRRNGRVRVMCEEILVELAGIKFTPV 267 (288)
Q Consensus 234 ~~~~~Vr~kRr~GRV~~~~E~f~i~~~~~~f~~~ 267 (288)
.+.+ +.-|-|+|.+-.- ++.+.+.-.+|...
T Consensus 421 ~~e~-ivaKnR~G~~G~v--~l~f~~~~~~F~~~ 451 (460)
T PRK07004 421 TAEI-IIGKQRNGPIGPV--RLTFLGQYTKFDNF 451 (460)
T ss_pred ceEE-EEEccCCCCCceE--EEEEecCCCcccCC
Confidence 2333 3445588876653 45556666777654
No 65
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=38.36 E-value=4.7e+02 Score=27.00 Aligned_cols=147 Identities=18% Similarity=0.165 Sum_probs=86.3
Q ss_pred cEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhHHHHHHHh
Q 023062 57 GLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQ 136 (288)
Q Consensus 57 ~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~~~ 136 (288)
.|++|.=|=|++..+---+|.|++. .++.++- + .+++.+.+.+.+
T Consensus 122 ~vLYVsGEES~~QiklRA~RL~~~~----~~l~l~a-------------E-----------------t~~e~I~~~l~~- 166 (456)
T COG1066 122 KVLYVSGEESLQQIKLRADRLGLPT----NNLYLLA-------------E-----------------TNLEDIIAELEQ- 166 (456)
T ss_pred cEEEEeCCcCHHHHHHHHHHhCCCc----cceEEeh-------------h-----------------cCHHHHHHHHHh-
Confidence 8999999999988887667776652 1222211 0 133333333332
Q ss_pred hcccCCCCcEEEEEechhHHHhh---CChHH------HHHHHHhhhcCCceeEEEEEeeCccCCc--chHhHHhhhceeE
Q 023062 137 GLIGQGKDRFSIAIDSVSEMVRH---ASISS------VAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEYLSSMV 205 (288)
Q Consensus 137 ~~~~~~~~~~~VvIDSLs~LL~~---~s~~~------l~~~L~~L~~~~~v~SVv~llH~DLh~p--~~l~aL~~LAttv 205 (288)
..|.++||||+-++-.. ..+.+ ....|-++-+... ..+|.+-|-.=.+. || ..||||=+|+
T Consensus 167 ------~~p~lvVIDSIQT~~s~~~~SapGsVsQVRe~t~~L~~~AK~~~-i~~fiVGHVTKeG~IAGP-rvLEHmVDtV 238 (456)
T COG1066 167 ------EKPDLVVIDSIQTLYSEEITSAPGSVSQVREVAAELMRLAKTKN-IAIFIVGHVTKEGAIAGP-RVLEHMVDTV 238 (456)
T ss_pred ------cCCCEEEEeccceeecccccCCCCcHHHHHHHHHHHHHHHHHcC-CeEEEEEEEcccccccCc-hheeeeeeEE
Confidence 46779999999998542 12222 2333333333233 34555666544431 22 4589999999
Q ss_pred EEEeecCccccccccchhhhhhhhhcccceeEEEEE--ecCCCCeeeeEeEEEEEcCceEEEeCC
Q 023062 206 ASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRF--KRRNGRVRVMCEEILVELAGIKFTPVL 268 (288)
Q Consensus 206 itv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr~--kRr~GRV~~~~E~f~i~~~~~~f~~~~ 268 (288)
+..|-+.+ ..+++.+ |-|=| .+.+.-.|....+|++=++=+
T Consensus 239 lyFEGd~~---------------------~~~RiLR~vKNRFG-~t~EiGvFeM~~~GL~eV~np 281 (456)
T COG1066 239 LYFEGDRH---------------------SRYRILRSVKNRFG-ATNELGVFEMTENGLREVSNP 281 (456)
T ss_pred EEEeccCC---------------------CceeeeehhcccCC-cccceeEEEEecCCeeEecCc
Confidence 99984322 4555555 55666 566777888888886544433
No 66
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=38.21 E-value=87 Score=24.25 Aligned_cols=57 Identities=21% Similarity=0.203 Sum_probs=45.1
Q ss_pred CCeeEeecCCCCCchhh------HHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHH
Q 023062 19 APALTIKDSKASPFGFD------VFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLK 75 (288)
Q Consensus 19 ap~l~i~dsl~~~~g~~------~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk 75 (288)
.|.+++-|.++.-++.. ....++..|.+.+.....+..++.+++....++..-..+.
T Consensus 58 ~~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~ 120 (132)
T PF00004_consen 58 KPCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALL 120 (132)
T ss_dssp TSEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHH
T ss_pred cceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHH
Confidence 58999999997766644 5677888888888877666667888888888888877776
No 67
>KOG3949 consensus RNA polymerase II elongator complex, subunit ELP4 [Chromatin structure and dynamics; Transcription]
Probab=34.73 E-value=77 Score=31.51 Aligned_cols=73 Identities=23% Similarity=0.128 Sum_probs=46.7
Q ss_pred HHHHHHhhhcCCc----eeEEEEEeeCccCCcchHhHHhhhceeEEEEeecCccccccccchhhhhhhhhcccceeEEEE
Q 023062 165 VAGILSNLRSHDQ----VSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVR 240 (288)
Q Consensus 165 l~~~L~~L~~~~~----v~SVv~llH~DLh~p~~l~aL~~LAttvitv~p~~~~~~~~~~~~~~~~~~~~n~~~~~~~Vr 240 (288)
+..||+-|++..+ +.-|-+-.|-+-+ |..+.-|+++|+++|.++|.+..... .+.+-+ .+.|.+|++
T Consensus 231 ~ikfL~~Lrslvr~~~~vciit~p~~l~~~-~~~~~~l~~laD~vi~Le~f~~~e~e-------~~~~~k-~~~Gllhi~ 301 (360)
T KOG3949|consen 231 LIKFLYLLRSLVRSSYSVCIITAPSSLIPK-PSLIARLENLADTVIGLEPFPGNEKE-------TNPLYK-DYHGLLHIH 301 (360)
T ss_pred HHHHHHHHHHHHhhcceEEEEeechhhccc-hhHHHHHHHHHHHHhcccccCCcccc-------cccccc-cccceeeee
Confidence 4468888877433 3334455566666 78999999999999999997654211 011111 146888888
Q ss_pred EecCCC
Q 023062 241 FKRRNG 246 (288)
Q Consensus 241 ~kRr~G 246 (288)
...|-+
T Consensus 302 Klp~~~ 307 (360)
T KOG3949|consen 302 KLPRLN 307 (360)
T ss_pred eccccc
Confidence 777543
No 68
>PF11633 SUD-M: Single-stranded poly(A) binding domain; InterPro: IPR024375 This domain identifies non-structural protein 3 (Nsp3). It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins [].; PDB: 2KQV_A 2W2G_A 2WCT_D 2JZE_A 2JZF_A 2RNK_A 2JZD_A.
Probab=32.89 E-value=16 Score=31.62 Aligned_cols=65 Identities=18% Similarity=0.226 Sum_probs=31.7
Q ss_pred ecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEeccc
Q 023062 25 KDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (288)
Q Consensus 25 ~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fs 95 (288)
..+.+.+..+.+...+.-.+...++-++. .+-+..++.|.++ +...|||+|++. ...++-+|+|.
T Consensus 6 ~~~~~~~~~~~ll~~v~~~~r~ml~~ak~-~g~~~pvc~D~~A--~~k~lkr~gv~~---~egl~t~~G~~ 70 (142)
T PF11633_consen 6 YNSAADNSKEELLGVVSWNFRAMLQHAKE-TGLLCPVCIDYPA--FCKTLKRKGVDP---KEGLQTVDGVQ 70 (142)
T ss_dssp ---S-------GGCEE---CHHHHHHHHH-HT-EEEEETT-HH--HHHHHHHTTS------SEEEES-SSE
T ss_pred ccCCCCCCCCceeeeeehhHHHHHHHHHh-cCcEEEEEeccHH--HHHHHhccCccc---ccceEEecceE
Confidence 33444444444444444444555554444 3567788888888 899999999996 66788877653
No 69
>PRK04296 thymidine kinase; Provisional
Probab=27.01 E-value=4.2e+02 Score=23.04 Aligned_cols=65 Identities=15% Similarity=0.106 Sum_probs=43.2
Q ss_pred CcEEEEEechhHHHhhCChHHHHHHHHhhhcCCceeEEEEEeeCccCC-c-chHhHHhhhceeEEEEeecCc
Q 023062 144 DRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHE-I-KFTSVLEYLSSMVASVEPFNQ 213 (288)
Q Consensus 144 ~~~~VvIDSLs~LL~~~s~~~l~~~L~~L~~~~~v~SVv~llH~DLh~-p-~~l~aL~~LAttvitv~p~~~ 213 (288)
..-+|+||.+.. .+..++..+++.++. ..+.-++.-+..|.-. + .....|..+|+.++.+....+
T Consensus 78 ~~dvviIDEaq~----l~~~~v~~l~~~l~~-~g~~vi~tgl~~~~~~~~f~~~~~L~~~aD~V~~l~~vC~ 144 (190)
T PRK04296 78 KIDCVLIDEAQF----LDKEQVVQLAEVLDD-LGIPVICYGLDTDFRGEPFEGSPYLLALADKVTELKAICV 144 (190)
T ss_pred CCCEEEEEcccc----CCHHHHHHHHHHHHH-cCCeEEEEecCcccccCcCchHHHHHHhcCeEEEeeEEcc
Confidence 345899999943 233446667777664 3455566666666554 3 466788899999999986543
No 70
>COG4544 Uncharacterized conserved protein [Function unknown]
Probab=26.35 E-value=1e+02 Score=29.31 Aligned_cols=53 Identities=11% Similarity=0.154 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEeccc
Q 023062 36 VFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYT 95 (288)
Q Consensus 36 ~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fs 95 (288)
.-.=++..|+...++.+..+.-||+...+ +-|.=-|+.+|++ ..|++++-|++
T Consensus 66 a~~GaAaAl~~~g~~~r~~gpVvWi~tr~---dlf~paL~~~Gl~----~~RlifVea~~ 118 (260)
T COG4544 66 AADGAAAALAVLGLAARRGGPVVWILTRE---DLFPPALAAFGLD----PERLIFVEARK 118 (260)
T ss_pred chhhHHHHHHHHhhhcccCCCEEEEEecc---cccchhHhhcCCC----hhhEEEEeCCc
Confidence 34446667777777776666678887743 3333338999999 57899999875
No 71
>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []. In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....
Probab=25.25 E-value=1e+02 Score=30.06 Aligned_cols=56 Identities=11% Similarity=0.114 Sum_probs=28.9
Q ss_pred EeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEe
Q 023062 23 TIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILD 92 (288)
Q Consensus 23 ~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D 92 (288)
-|.. -.+.+-+.++.|+++++ ..++.-+.++..|.+ ...+.+++.|+|. +++.++.
T Consensus 57 Ei~G-~~ssGKttLaL~~ia~~-------q~~g~~~a~ID~e~~--ld~~~a~~lGvdl----~rllv~~ 112 (322)
T PF00154_consen 57 EIYG-PESSGKTTLALHAIAEA-------QKQGGICAFIDAEHA--LDPEYAESLGVDL----DRLLVVQ 112 (322)
T ss_dssp EEEE-STTSSHHHHHHHHHHHH-------HHTT-EEEEEESSS-----HHHHHHTT--G----GGEEEEE
T ss_pred EEeC-CCCCchhhhHHHHHHhh-------hcccceeEEecCccc--chhhHHHhcCccc----cceEEec
Confidence 3443 35667778888885532 122445555555444 4556666779995 5676655
No 72
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=23.44 E-value=6.4e+02 Score=25.45 Aligned_cols=106 Identities=20% Similarity=0.226 Sum_probs=63.7
Q ss_pred CcEEEEEecCChHHHHHH----HHhcCCCcCCCCCeEEEEecccCCCCCcccccCccccccccccccccccccchhhH--
Q 023062 56 RGLVVVAYSRSPSFYVDL----LKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL-- 129 (288)
Q Consensus 56 ~~V~vlafe~spe~y~~~----lk~~G~d~~~~~~~v~i~D~fsDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl-- 129 (288)
+.|.+|.+|..+++.++- +++.|+.+.. +..+|. ||--| . +.+.++=.. ++
T Consensus 128 GkvlyvslEl~re~~L~Rl~~v~a~mgLsPad----vrn~dl-td~~G-----a------------a~~~d~l~p-kl~r 184 (402)
T COG3598 128 GKVLYVSLELYREDILERLEPVRARMGLSPAD----VRNMDL-TDVSG-----A------------ADESDVLSP-KLYR 184 (402)
T ss_pred CeEEEEEeccChHHHHHHHHHHHHHcCCChHh----hhheec-ccccc-----C------------CCccccccH-HHHH
Confidence 489999999999987764 4577888633 666675 44443 1 111121111 22
Q ss_pred -HHHHHHhhcccCCCCcEEEEEechhHHHhh--CChHHHHHHHHhhhc-CCcee-EEEEEeeCccC
Q 023062 130 -YSLIIEQGLIGQGKDRFSIAIDSVSEMVRH--ASISSVAGILSNLRS-HDQVS-SIFWLLHSDLH 190 (288)
Q Consensus 130 -~~~i~~~~~~~~~~~~~~VvIDSLs~LL~~--~s~~~l~~~L~~L~~-~~~v~-SVv~llH~DLh 190 (288)
+..++ ....|-+||||+.-.++-. .+-.++..|..++++ +..-. +|+.+-|+-.-
T Consensus 185 Rfek~~------~Q~rp~~vViDp~v~f~~G~s~s~vqv~~fi~~~rkla~~l~caIiy~hHtsks 244 (402)
T COG3598 185 RFEKIL------EQKRPDFVVIDPFVAFYEGKSISDVQVKEFIKKTRKLARNLECAIIYIHHTSKS 244 (402)
T ss_pred HHHHHH------HHhCCCeEEEcchhhhcCCccchhHHHHHHHHHHHHHHHhcCCeEEEEeccccc
Confidence 11222 2335678999999988773 344667888888887 22233 46666665544
No 73
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=23.06 E-value=81 Score=24.91 Aligned_cols=38 Identities=18% Similarity=0.270 Sum_probs=24.6
Q ss_pred hhccccCcEEEEEecCChHHHHHHHHhcCCCcCCCCCeEEEEecccCCC
Q 023062 50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPL 98 (288)
Q Consensus 50 a~~~q~~~V~vlafe~spe~y~~~lk~~G~d~~~~~~~v~i~D~fsDPl 98 (288)
+-.+.+-.+++|+++..+. ..+.++.++++ .+.|+||.
T Consensus 8 ~l~~~gv~lv~I~~g~~~~-~~~f~~~~~~p----------~~ly~D~~ 45 (115)
T PF13911_consen 8 ELEAAGVKLVVIGCGSPEG-IEKFCELTGFP----------FPLYVDPE 45 (115)
T ss_pred HHHHcCCeEEEEEcCCHHH-HHHHHhccCCC----------CcEEEeCc
Confidence 3333456799999887754 66666666666 24668884
No 74
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=20.67 E-value=1.7e+02 Score=25.16 Aligned_cols=39 Identities=21% Similarity=0.422 Sum_probs=26.1
Q ss_pred hhccccCcEEEEEecCChHHH----------------HHHHHhcCCCcCCCCCeEEEEecc
Q 023062 50 AGKSQSRGLVVVAYSRSPSFY----------------VDLLKRRGIDIASSHDWIHILDCY 94 (288)
Q Consensus 50 a~~~q~~~V~vlafe~spe~y----------------~~~lk~~G~d~~~~~~~v~i~D~f 94 (288)
.++.++-...++.|+.+|..+ .+.|++.|+| .++++|+-
T Consensus 31 ~a~~~~~~~~v~tF~~~P~~~~~~~~~~~~l~s~~ek~~~l~~~Gvd------~~~~~~F~ 85 (157)
T PF06574_consen 31 IAKEKGLKSVVLTFDPHPKEVLNPDKPPKLLTSLEEKLELLESLGVD------YVIVIPFT 85 (157)
T ss_dssp HHHHCT-EEEEEEESS-CHHHHSCTCCGGBSS-HHHHHHHHHHTTES------EEEEE-CC
T ss_pred hhhhcccceEEEEcccCHHHHhcCCCcccCCCCHHHHHHHHHHcCCC------EEEEecch
Confidence 344455578999999988655 4578888888 38888853
No 75
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=20.19 E-value=2.7e+02 Score=23.00 Aligned_cols=39 Identities=10% Similarity=0.146 Sum_probs=28.4
Q ss_pred EeecCCCCCchhhHHHHHHHHHHHHHHhhccccCcEEEEEecC
Q 023062 23 TIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSR 65 (288)
Q Consensus 23 ~i~dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~V~vlafe~ 65 (288)
..-|+-.|... ..+..|++++++..++. ...|+++.||.
T Consensus 3 vaiDtSGSis~-~~l~~fl~ev~~i~~~~---~~~v~vi~~D~ 41 (126)
T PF09967_consen 3 VAIDTSGSISD-EELRRFLSEVAGILRRF---PAEVHVIQFDA 41 (126)
T ss_pred EEEECCCCCCH-HHHHHHHHHHHHHHHhC---CCCEEEEEECC
Confidence 45677777766 67888888888755544 44699999993
Done!