Query 013117
Match_columns 449
No_of_seqs 201 out of 513
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 00:34:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013117.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013117hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05625 PAXNEB: PAXNEB protei 100.0 9.4E-85 2E-89 667.4 19.8 343 95-449 1-363 (363)
2 KOG3949 RNA polymerase II elon 100.0 7.8E-73 1.7E-77 557.5 22.2 342 94-449 1-360 (360)
3 PF06745 KaiC: KaiC; InterPro 99.9 3.6E-23 7.8E-28 198.3 16.5 219 122-416 1-222 (226)
4 PRK04328 hypothetical protein; 99.9 8.8E-22 1.9E-26 192.6 21.2 232 120-418 3-235 (249)
5 TIGR03877 thermo_KaiC_1 KaiC d 99.9 1.4E-21 3.1E-26 189.5 20.7 231 121-418 2-233 (237)
6 PRK06067 flagellar accessory p 99.9 6E-20 1.3E-24 177.2 20.6 226 120-421 5-231 (234)
7 TIGR02655 circ_KaiC circadian 99.8 6E-20 1.3E-24 195.6 19.5 218 119-417 242-462 (484)
8 COG0467 RAD55 RecA-superfamily 99.8 1.4E-18 3E-23 170.5 18.6 232 120-418 3-234 (260)
9 TIGR02655 circ_KaiC circadian 99.8 1E-18 2.2E-23 186.2 18.7 227 121-419 2-231 (484)
10 TIGR03881 KaiC_arch_4 KaiC dom 99.8 2.3E-18 4.9E-23 165.3 19.3 226 121-417 1-228 (229)
11 PRK09302 circadian clock prote 99.8 3.2E-18 7E-23 183.3 20.0 225 119-428 252-479 (509)
12 PRK09302 circadian clock prote 99.8 4.6E-18 9.9E-23 182.1 20.9 230 117-418 8-240 (509)
13 COG2874 FlaH Predicted ATPases 99.8 5.4E-18 1.2E-22 160.3 17.5 226 121-421 9-234 (235)
14 TIGR03878 thermo_KaiC_2 KaiC d 99.8 7.7E-18 1.7E-22 165.8 19.2 226 121-411 3-249 (259)
15 TIGR03880 KaiC_arch_3 KaiC dom 99.7 3E-16 6.5E-21 150.4 18.6 217 125-418 1-219 (224)
16 PRK08533 flagellar accessory p 99.7 2.2E-15 4.8E-20 145.9 19.8 223 120-418 4-226 (230)
17 PRK09361 radB DNA repair and r 99.6 1.9E-14 4.1E-19 137.9 18.9 174 120-361 3-190 (225)
18 cd01394 radB RadB. The archaea 99.6 4.6E-15 1E-19 141.3 14.5 175 122-363 1-188 (218)
19 TIGR00416 sms DNA repair prote 99.6 1.5E-14 3.3E-19 153.1 18.2 202 118-415 72-278 (454)
20 cd01121 Sms Sms (bacterial rad 99.6 7.6E-14 1.6E-18 144.2 19.4 203 117-415 59-266 (372)
21 PRK11823 DNA repair protein Ra 99.6 7.8E-14 1.7E-18 147.4 19.1 202 118-415 58-264 (446)
22 cd01393 recA_like RecA is a b 99.5 6.2E-13 1.3E-17 127.0 16.3 193 122-389 1-217 (226)
23 TIGR02237 recomb_radB DNA repa 99.5 5.7E-13 1.2E-17 126.0 14.7 167 129-362 1-179 (209)
24 PLN03187 meiotic recombination 99.5 8.4E-13 1.8E-17 135.0 15.4 195 119-391 105-325 (344)
25 cd01123 Rad51_DMC1_radA Rad51_ 99.4 8.8E-13 1.9E-17 126.7 12.9 177 122-361 1-204 (235)
26 TIGR02238 recomb_DMC1 meiotic 99.4 1.9E-12 4.2E-17 131.0 15.1 180 119-362 75-281 (313)
27 PRK04301 radA DNA repair and r 99.4 3.5E-12 7.6E-17 129.1 17.0 195 119-390 81-299 (317)
28 PRK09354 recA recombinase A; P 99.4 3.1E-12 6.6E-17 130.8 15.5 170 119-362 38-229 (349)
29 cd01122 GP4d_helicase GP4d_hel 99.4 4.3E-12 9.2E-17 124.7 15.3 217 121-388 12-247 (271)
30 TIGR02012 tigrfam_recA protein 99.4 3.1E-12 6.8E-17 129.6 13.5 171 119-362 33-224 (321)
31 cd00983 recA RecA is a bacter 99.4 1E-11 2.2E-16 125.9 16.9 171 119-363 33-225 (325)
32 TIGR02236 recomb_radA DNA repa 99.3 4.5E-11 9.8E-16 120.4 16.5 197 118-391 73-294 (310)
33 PTZ00035 Rad51 protein; Provis 99.3 3.9E-11 8.5E-16 122.7 16.0 180 119-362 97-303 (337)
34 PLN03186 DNA repair protein RA 99.3 8E-11 1.7E-15 120.5 15.3 196 118-391 101-323 (342)
35 TIGR02239 recomb_RAD51 DNA rep 99.3 7.7E-11 1.7E-15 119.5 14.3 195 119-391 75-297 (316)
36 PRK09519 recA DNA recombinatio 99.2 3.3E-10 7.2E-15 126.0 15.3 170 118-361 37-228 (790)
37 cd00984 DnaB_C DnaB helicase C 99.2 3.6E-10 7.8E-15 109.0 13.8 193 128-363 2-209 (242)
38 COG1066 Sms Predicted ATP-depe 99.1 1.1E-09 2.4E-14 112.7 14.4 168 118-361 71-243 (456)
39 PRK05973 replicative DNA helic 99.1 9.5E-10 2.1E-14 107.2 12.4 141 129-340 54-194 (237)
40 cd01124 KaiC KaiC is a circadi 98.9 3.2E-08 7E-13 91.2 15.2 47 142-189 1-47 (187)
41 PF08423 Rad51: Rad51; InterP 98.9 3.1E-08 6.8E-13 97.7 14.8 195 119-391 17-238 (256)
42 TIGR00665 DnaB replicative DNA 98.9 1.8E-08 3.9E-13 106.1 14.0 200 119-361 175-389 (434)
43 PF09807 DUF2348: Uncharacteri 98.8 3.3E-07 7.2E-12 90.2 18.6 230 127-409 3-248 (249)
44 PRK05748 replicative DNA helic 98.8 1E-07 2.2E-12 101.1 14.2 199 119-361 183-399 (448)
45 PF00154 RecA: recA bacterial 98.6 1.6E-06 3.5E-11 88.2 17.9 172 117-362 29-222 (322)
46 PRK09165 replicative DNA helic 98.5 1.4E-06 3.1E-11 93.6 13.1 198 119-361 197-427 (497)
47 PHA02542 41 41 helicase; Provi 98.4 1.6E-06 3.5E-11 92.6 11.9 201 119-361 169-386 (473)
48 TIGR03600 phage_DnaB phage rep 98.4 4.1E-06 8.8E-11 88.1 14.6 201 119-361 174-388 (421)
49 PF03796 DnaB_C: DnaB-like hel 98.4 7.9E-06 1.7E-10 80.2 14.8 199 122-362 2-215 (259)
50 PRK08760 replicative DNA helic 98.2 2.1E-05 4.6E-10 84.3 15.1 197 120-361 210-423 (476)
51 PRK08506 replicative DNA helic 98.2 1E-05 2.3E-10 86.5 12.5 198 120-361 173-386 (472)
52 PRK07773 replicative DNA helic 98.2 3.7E-06 7.9E-11 96.4 9.6 175 119-339 197-377 (886)
53 PRK06321 replicative DNA helic 98.2 1E-05 2.2E-10 86.6 12.0 196 120-361 207-423 (472)
54 PF13481 AAA_25: AAA domain; P 98.1 6.7E-06 1.5E-10 76.3 6.4 166 120-338 12-188 (193)
55 COG0468 RecA RecA/RadA recombi 98.1 5.7E-05 1.2E-09 75.5 13.4 172 119-362 39-228 (279)
56 PRK05595 replicative DNA helic 98.0 3.1E-05 6.7E-10 82.2 11.6 197 120-361 182-395 (444)
57 PRK07004 replicative DNA helic 97.9 0.00015 3.3E-09 77.4 13.9 198 120-361 194-408 (460)
58 PRK05636 replicative DNA helic 97.7 0.00019 4.1E-09 77.5 10.8 197 120-361 246-459 (505)
59 PRK08006 replicative DNA helic 97.7 0.00049 1.1E-08 73.8 12.6 199 120-361 205-420 (471)
60 PRK06904 replicative DNA helic 97.5 0.00098 2.1E-08 71.5 11.8 199 120-361 202-418 (472)
61 cd01120 RecA-like_NTPases RecA 97.3 0.006 1.3E-07 53.7 13.0 71 290-360 84-164 (165)
62 PRK08840 replicative DNA helic 97.2 0.003 6.6E-08 67.6 12.5 200 119-361 197-413 (464)
63 cd01125 repA Hexameric Replica 97.1 0.0088 1.9E-07 58.0 13.1 77 290-366 110-195 (239)
64 PF10483 Elong_Iki1: Elongator 96.6 0.11 2.3E-06 52.2 16.6 69 291-365 88-163 (280)
65 PRK06749 replicative DNA helic 96.6 0.0043 9.2E-08 65.9 6.6 67 120-188 167-233 (428)
66 KOG1564 DNA repair protein RHP 96.3 0.028 6.1E-07 56.3 10.2 65 115-179 77-146 (351)
67 PF07088 GvpD: GvpD gas vesicl 95.9 0.0089 1.9E-07 62.3 4.8 75 114-188 232-309 (484)
68 PF07088 GvpD: GvpD gas vesicl 95.5 0.22 4.8E-06 52.2 12.7 203 139-418 9-215 (484)
69 KOG1433 DNA repair protein RAD 93.6 0.12 2.7E-06 52.8 5.8 59 117-177 88-147 (326)
70 COG0305 DnaB Replicative DNA h 93.4 1 2.3E-05 47.9 12.4 194 119-361 176-390 (435)
71 PRK04296 thymidine kinase; Pro 93.0 3.7 8E-05 38.5 14.4 36 139-175 1-36 (190)
72 COG3598 RepA RecA-family ATPas 89.6 1.8 4E-05 44.5 8.9 50 291-340 194-243 (402)
73 KOG1434 Meiotic recombination 88.8 0.17 3.6E-06 50.3 0.8 36 117-152 92-127 (335)
74 PF14417 MEDS: MEDS: MEthanoge 78.9 56 0.0012 30.5 13.5 154 136-345 15-170 (191)
75 PF05763 DUF835: Protein of un 78.1 6.4 0.00014 35.4 6.2 67 267-343 59-125 (136)
76 PF09818 ABC_ATPase: Predicted 77.5 42 0.00092 36.0 12.9 45 314-365 373-417 (448)
77 TIGR02710 CRISPR-associated pr 41.1 14 0.00031 38.8 1.5 22 72-93 76-97 (380)
78 PF13245 AAA_19: Part of AAA d 37.9 80 0.0017 25.1 5.1 40 140-180 10-53 (76)
79 COG4544 Uncharacterized conser 36.3 31 0.00066 34.0 2.8 58 119-177 32-92 (260)
80 PF09670 Cas_Cas02710: CRISPR- 33.6 19 0.00042 37.7 1.1 24 71-94 74-97 (379)
81 PRK06851 hypothetical protein; 32.6 90 0.0019 32.8 5.8 51 122-176 198-249 (367)
82 PF13173 AAA_14: AAA domain 29.2 99 0.0021 26.6 4.7 37 140-178 2-38 (128)
83 cd00544 CobU Adenosylcobinamid 29.0 82 0.0018 29.1 4.3 33 142-178 1-33 (169)
84 cd01133 F1-ATPase_beta F1 ATP 25.4 1.2E+02 0.0026 30.5 5.1 67 119-188 50-120 (274)
85 KOG0734 AAA+-type ATPase conta 25.3 85 0.0018 34.9 4.1 48 132-186 331-379 (752)
86 PRK12724 flagellar biosynthesi 23.6 1.4E+02 0.0031 32.0 5.4 43 136-179 219-262 (432)
87 cd01132 F1_ATPase_alpha F1 ATP 23.6 1.1E+02 0.0023 30.9 4.3 67 119-188 50-119 (274)
88 PF00047 ig: Immunoglobulin do 23.5 57 0.0012 23.8 1.8 24 61-84 5-33 (64)
89 PHA00520 packaging NTPase P4 21.6 2.2E+02 0.0047 29.3 5.9 52 292-343 184-241 (330)
90 PRK13343 F0F1 ATP synthase sub 20.3 1.2E+02 0.0026 33.2 4.2 66 120-188 144-212 (502)
91 PF04604 L_biotic_typeA: Type- 20.2 55 0.0012 24.6 1.1 11 126-136 17-27 (51)
No 1
>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=100.00 E-value=9.4e-85 Score=667.36 Aligned_cols=343 Identities=33% Similarity=0.588 Sum_probs=196.6
Q ss_pred cceeccCCC-CCCCCCCCcccCC-CCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcE
Q 013117 95 SSFSRNLSA-VSSSQTPGVKCGP-NGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPL 172 (449)
Q Consensus 95 sSF~r~~~~-~~~~~~~GtRpsp-~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~v 172 (449)
|||+||... ...+++||||||+ |||++|||||++||+|||||||+||++|||||++++|+++|+|||+||||++||++
T Consensus 1 ~SF~kr~~~~~~~~~~pGtrpS~~~~~~~~STG~~sLD~lLGGGlPlGs~llIeEd~~t~ya~~LlkyF~AEGi~~~h~v 80 (363)
T PF05625_consen 1 MSFRKRNASQAASPPIPGTRPSPHNGQPLTSTGIPSLDDLLGGGLPLGSILLIEEDGTTDYASVLLKYFAAEGIVHGHHV 80 (363)
T ss_dssp -------------TTBTTEEE-TTTSSEEE--S-HHHHHHTTSSEETT-EEEEEE-SS--THHHHHHHHHHHHHHH-EEE
T ss_pred CccccccccccccCCCCccccCCCCCCEEEecCChhHHHHhcCCcccccEEEEecCCcCHHHHHHHHHHHHhccccCCeE
Confidence 699999986 5556899999998 99999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCChhhHhhcCCCCCCcccccccc-----cchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccc
Q 013117 173 LYASPSKDPRGFLGTLPSPASLKHDKSRD-----RESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPL 247 (449)
Q Consensus 173 l~vs~~e~p~~il~~LP~~~~~~~~k~~~-----~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l 247 (449)
++++. +++|+++||+++.+++.+... +...++++|||||||+++.+.+.. ...+ ..+.|||+|||||+|
T Consensus 81 ~v~~~---~~~~~~~LP~~~~~~~~~~~~~~~~~~~~~~~~~mKIAWRY~~~~~~~~~-~~~~--~~~~fcH~FDLsk~~ 154 (363)
T PF05625_consen 81 LVASP---PEAWLRELPGPVSESEKKEKKSKIAEESSESDEDMKIAWRYEKLPKFQSS-VGSS--SYPNFCHQFDLSKRM 154 (363)
T ss_dssp EEE-S----GGGGGG-EEE------------------------------------------------TTSS--EETTSE-
T ss_pred EEEeC---ChHHHhhCCCccCcchhccccccccccCCCCccCCeeEeecccCcccccc-ccCC--ccccccccccccccc
Confidence 99997 999999999998664433222 235568899999999998744321 1111 146899999999999
Q ss_pred cccccccceeeeeeccC----CcchHHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCCC--HHHHHHHHHHH
Q 013117 248 ERHYFTRQRVNCVGIQH----SKNLAALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSNM--DWEMLSFIKSL 321 (449)
Q Consensus 248 ~~~~~~~~~i~~~~~~~----~~~~~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~--~~~ll~FL~~L 321 (449)
+++.+.+....+..... ...|..+++.|.++|++.... .+.+|+||+|+||++|.|+.... .+++++|||+|
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~i~~~i~~~~~~--~~~~v~RI~I~sl~SP~w~~~~~~~~~~ll~FL~~L 232 (363)
T PF05625_consen 155 DPEPLSAEIIFIPPDQPPSSSSSPYRSLLQQIQQIISKSGFS--PPSKVLRIVIPSLGSPLWYPPSASQPSELLRFLHSL 232 (363)
T ss_dssp SS---TTTEEEE-TTS--------HHHHHHHHHHHHHH------TTTSEEEEEETTTT-TTTS-GGGGBHHHHHHHHHHH
T ss_pred ChhhccccceEecCCCCcchhHHHHHHHHHHHHHHHHhhccC--CCCceEEEEEcCCCCcccCCcccccHHHHHHHHHHH
Confidence 98877766655543322 235888888888888854322 45789999999999999987652 44699999999
Q ss_pred HHhhh--hcCcEEEEeeCCCCCC--cchhhhhhhhcceEEEEEeeCCC-cHHHhhhccCCCCcceeEEEeeecccccCCc
Q 013117 322 KGMVR--SSNAVVVITFPPSLLS--LSSTKRWQHMADTLLSVAAIPDE-DKELAKLLSGYQDMVGLLNVHKVARLNTQVP 396 (449)
Q Consensus 322 R~llR--~s~~taliT~p~~l~~--~~~~~~le~laDgVI~L~~f~~~-~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~ 396 (449)
|+++| .+++||+||+|+++|+ +.+..+|+|+||+||+|++|+++ ++++++. |++|||||||+|||++|++++
T Consensus 233 R~LlR~~~s~~v~~iTlP~~L~~~~~~~~~~l~~l~D~vi~Le~F~~~~~~~~~~~---~~~~~Gll~v~KLp~~~sl~~ 309 (363)
T PF05625_consen 233 RALLRKYSSNAVAMITLPSHLYPRSPSLVRRLEHLADGVIELESFAGSMEKETNPP---FKDYHGLLHVHKLPRLNSLGP 309 (363)
T ss_dssp HHHHHHTTTTEEEEEEEEGTTS---HHHHHHHHHHSSEEEEEEE--HHHHHTTT-G---GG---EEEEEEE-TTHHHHT-
T ss_pred HHHHhccCCCEEEEEEECHHHhccChHHHHHHHHhCCEEEEeecCCCccccccCCc---CcCCcEEEEEEEeccccccCC
Confidence 99999 8999999999999995 45678999999999999999986 5666655 888999999999999999999
Q ss_pred ccccCceeeEEEcceeceEEeeccCCCCCCCCCCccCC--CCcccCCCCCCCCCC
Q 013117 397 LILEATTFSIKLQKRRFLVLECLNQAPVDGSSGSSYGT--SGSCSGSSKAGTLDF 449 (449)
Q Consensus 397 ~~~~~~~lAFKl~rrr~~vIE~lhLpP~d~~~~~~~~~--~~~c~~~~~~~~lDF 449 (449)
+.++..|||||++||| |+||+|||||||++.++.... ...|++.+++++|||
T Consensus 310 ~~~~~~~laFKl~Rkk-f~IE~lhLPPe~~~~~~~~~~~~~~~~~~~~~~~~ldF 363 (363)
T PF05625_consen 310 MTPDSSDLAFKLKRKK-FVIEPLHLPPEDGETESRSQSSASGSCSSSSTKKSLDF 363 (363)
T ss_dssp ---EEEEEEEEE-SS--EEEEE---------------------------------
T ss_pred CCCCccceEEEeeeee-EEEEEecCCcccCCCccccCCCCcccccCCCCCCCCCC
Confidence 9999999999998765 999999999998875544432 356777778999999
No 2
>KOG3949 consensus RNA polymerase II elongator complex, subunit ELP4 [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=7.8e-73 Score=557.49 Aligned_cols=342 Identities=34% Similarity=0.535 Sum_probs=280.5
Q ss_pred ccceeccCCCCCCCCCCCcccCC-CCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcE
Q 013117 94 LSSFSRNLSAVSSSQTPGVKCGP-NGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPL 172 (449)
Q Consensus 94 msSF~r~~~~~~~~~~~GtRpsp-~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~v 172 (449)
|+||+||.+. +.+.+.|+|||+ ++|..+|||+++||.+||||||+||++|||||..+.|+++|+|||+|||+++||.+
T Consensus 1 ~tsf~r~s~~-~~p~~~gvr~S~~~~q~~tSSG~~~lD~iLGgGLp~gs~vLIeEd~~~~~~s~LlK~FlAEGlv~~~~~ 79 (360)
T KOG3949|consen 1 MTSFQRKSNV-SGPSIAGVRPSPKNGQLITSSGIADLDQILGGGLPLGSSVLIEEDRSMIYHSVLLKYFLAEGLVNNHTL 79 (360)
T ss_pred Cccccccccc-cCCcccccccCCCCCceEeccCchhHHHHhcCCcccCcEEEEeecccchhHHHHHHHHHHhhhccCceE
Confidence 7999999544 333688999996 89999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCChhhHhhcCCCCCCccccccc----c---cchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccc
Q 013117 173 LYASPSKDPRGFLGTLPSPASLKHDKSR----D---RESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRK 245 (449)
Q Consensus 173 l~vs~~e~p~~il~~LP~~~~~~~~k~~----~---~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk 245 (449)
++++..++|++|.++||++..+++.+.+ . ...++...|||||||+++.+.+. . .....++|.||+.+
T Consensus 80 ~~as~~~dp~~~~~~LP~~~~~~~~~~~~~~~~~~~~~~en~~~mkIAWRY~~l~~~~~-~-----~~~~~~g~~~n~d~ 153 (360)
T KOG3949|consen 80 LLASPKKDPKMFLRELPGPLTSKDKKEKSDEDAPNSKTAENNNKMKIAWRYQDLSKVKK-P-----LASARLGYYFNFDK 153 (360)
T ss_pred EeeccccchHHHHhhCCCCcCCccccccchhhccCCccccCccceeeeeecchhhhccc-c-----ccccCCCCccchhh
Confidence 9999999999999999999987654433 1 11444558999999999864322 1 22446777777776
Q ss_pred cccccccccceeee------eeccCCcchHHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCC---CHHHHHH
Q 013117 246 PLERHYFTRQRVNC------VGIQHSKNLAALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSN---MDWEMLS 316 (449)
Q Consensus 246 ~l~~~~~~~~~i~~------~~~~~~~~~~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~---~~~~ll~ 316 (449)
++....+....++. .++.....|+.+.+.+.++.+...+...+.++++||+|+||++|.|+++. ....+++
T Consensus 154 ~k~~~~ve~~~~d~~~p~~~ss~~~~~~~~~~~~~~~e~~s~~k~gs~~~~~llRivi~sl~sp~~~~~~c~~~~~~~ik 233 (360)
T KOG3949|consen 154 RKPQYLVENSNWDGFLPIPISSLSLSAPYEPLLDILQEIESTTKRGSNPIKNLLRIVIQSLGSPAWEDSICCAENLGLIK 233 (360)
T ss_pred hcchhhcccccccccccceecccccCCCchHHHHHHHHHHhhcCCCChhhhhhHhhhhhhcCCcccccchhhhhhccHHH
Confidence 66533233222222 22234566888887777777766554444578999999999999998742 1234889
Q ss_pred HHHHHHHhhhhcCcEEEEeeCCCCCCc-chhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCC
Q 013117 317 FIKSLKGMVRSSNAVVVITFPPSLLSL-SSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQV 395 (449)
Q Consensus 317 FL~~LR~llR~s~~taliT~p~~l~~~-~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~ 395 (449)
||+.||+++|.++.+|+||+|+++++. +...++++++|.||.|++|++.++|++++ |++|||||||||||++|+++
T Consensus 234 fL~~Lrslvr~~~~vciit~p~~l~~~~~~~~~l~~laD~vi~Le~f~~~e~e~~~~---~k~~~Gllhi~Klp~~~~~~ 310 (360)
T KOG3949|consen 234 FLYLLRSLVRSSYSVCIITAPSSLIPKPSLIARLENLADTVIGLEPFPGNEKETNPL---YKDYHGLLHIHKLPRLNTLG 310 (360)
T ss_pred HHHHHHHHHhhcceEEEEeechhhccchhHHHHHHHHHHHHhcccccCCcccccccc---cccccceeeeeecccccccc
Confidence 999999999999999999999999987 56789999999999999999999998766 99999999999999999999
Q ss_pred cccccCceeeEEEcceeceEEeeccCCCCCCCCCCccCCCCcccCCCCCCCCCC
Q 013117 396 PLILEATTFSIKLQKRRFLVLECLNQAPVDGSSGSSYGTSGSCSGSSKAGTLDF 449 (449)
Q Consensus 396 ~~~~~~~~lAFKl~rrr~~vIE~lhLpP~d~~~~~~~~~~~~c~~~~~~~~lDF 449 (449)
++.++..|||||++ ||+|+||+|||||+|++....+.+ +.|++ .+++|||
T Consensus 311 ~~~~e~~dlafklk-Rk~F~IE~~~lPP~d~e~~~~~~s-g~~~~--~~~sLDF 360 (360)
T KOG3949|consen 311 THTLEAKDLAFKLK-RKKFTIEKWHLPPEDAEPSAKPWS-GPAKI--PKKSLDF 360 (360)
T ss_pred cccccccceeeeee-cceeEEEeccCCCcccCCCCCCCC-CCCCC--CcccCCC
Confidence 99999999999998 567999999999999988876663 24543 6789999
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=99.90 E-value=3.6e-23 Score=198.33 Aligned_cols=219 Identities=20% Similarity=0.301 Sum_probs=149.1
Q ss_pred eecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCccccccc
Q 013117 122 VSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLKHDKSR 200 (449)
Q Consensus 122 iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~ 200 (449)
|+|||++||++|+||||.||++||++++++| +++|+.||+++|+.+ |++|+|+++++.++++++++.+.
T Consensus 1 V~TGI~~LD~~l~GGip~gs~~li~G~~GsG-KT~l~~q~l~~~~~~~ge~vlyvs~ee~~~~l~~~~~s~--------- 70 (226)
T PF06745_consen 1 VPTGIPGLDELLGGGIPKGSVVLISGPPGSG-KTTLALQFLYNGLKNFGEKVLYVSFEEPPEELIENMKSF--------- 70 (226)
T ss_dssp E--SSTTHHHHTTTSEETTSEEEEEESTTSS-HHHHHHHHHHHHHHHHT--EEEEESSS-HHHHHHHHHTT---------
T ss_pred CCCCchhHHHhhcCCCCCCcEEEEEeCCCCC-cHHHHHHHHHHhhhhcCCcEEEEEecCCHHHHHHHHHHc---------
Confidence 6899999999999999999999999999888 578889999999999 99999999999999999986433
Q ss_pred ccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHH
Q 013117 201 DRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLA 280 (449)
Q Consensus 201 ~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~ 280 (449)
.|+...+.+.++ .+.+|........ ...+...+...+.+.++
T Consensus 71 ------------g~d~~~~~~~g~-------------l~~~d~~~~~~~~-------------~~~~~~~l~~~i~~~i~ 112 (226)
T PF06745_consen 71 ------------GWDLEEYEDSGK-------------LKIIDAFPERIGW-------------SPNDLEELLSKIREAIE 112 (226)
T ss_dssp ------------TS-HHHHHHTTS-------------EEEEESSGGGST--------------TSCCHHHHHHHHHHHHH
T ss_pred ------------CCcHHHHhhcCC-------------EEEEecccccccc-------------cccCHHHHHHHHHHHHH
Confidence 244433321111 1122221110000 01235566666666666
Q ss_pred HhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CCcchhhhhhh-hcceEEE
Q 013117 281 QHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LSLSSTKRWQH-MADTLLS 358 (449)
Q Consensus 281 ~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~~~~~~~le~-laDgVI~ 358 (449)
.. +..|||||||... +.. ..+..+.+|++.|...+|+.++|+++|..... ........+++ +||+||.
T Consensus 113 ~~--------~~~~vVIDsls~l-~~~-~~~~~~r~~l~~l~~~l~~~~~t~llt~~~~~~~~~~~~~~i~~~l~D~vI~ 182 (226)
T PF06745_consen 113 EL--------KPDRVVIDSLSAL-LLY-DDPEELRRFLRALIKFLKSRGVTTLLTSEMPSGSEDDGTFGIEHYLADGVIE 182 (226)
T ss_dssp HH--------TSSEEEEETHHHH-TTS-SSGGGHHHHHHHHHHHHHHTTEEEEEEEEESSSSSSSSSTSHHHHHSSEEEE
T ss_pred hc--------CCCEEEEECHHHH-hhc-CCHHHHHHHHHHHHHHHHHCCCEEEEEEccccCcccccccchhhhcccEEEE
Confidence 43 3489999999877 322 23667899999999999999999999998433 23333467777 9999999
Q ss_pred EEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEE
Q 013117 359 VAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVL 416 (449)
Q Consensus 359 L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vI 416 (449)
|+...... .....|+|.|+-..+ ++...+-|.+.. +++.|
T Consensus 183 L~~~~~~~-----------~~~R~l~I~K~Rg~~------~~~~~~~f~I~~-~Gi~i 222 (226)
T PF06745_consen 183 LRYEEEGG-----------RIRRRLRIVKMRGSR------HSTGIHPFEITP-GGIEI 222 (226)
T ss_dssp EEEEEETT-----------EEEEEEEEEEETTS----------BEEEEEEET-TEEEE
T ss_pred EEEEeeCC-----------EEEEEEEEEEcCCCC------CCCcEEEEEEEC-CeEEE
Confidence 99854321 346889999993332 345567888875 56554
No 4
>PRK04328 hypothetical protein; Provisional
Probab=99.89 E-value=8.8e-22 Score=192.63 Aligned_cols=232 Identities=17% Similarity=0.206 Sum_probs=156.3
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
.+++|||++||++|+||+|.|+++||.+++++| +++|+.+|+++|+.+|++++|++++++|+++++++-..+.+-
T Consensus 3 ~rv~tGi~~LD~lL~GGip~gs~ili~G~pGsG-KT~l~~~fl~~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~---- 77 (249)
T PRK04328 3 KRVKTGIPGMDEILYGGIPERNVVLLSGGPGTG-KSIFSQQFLWNGLQMGEPGVYVALEEHPVQVRRNMRQFGWDV---- 77 (249)
T ss_pred ceecCCchhHHHHhcCCCcCCcEEEEEcCCCCC-HHHHHHHHHHHHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCH----
Confidence 479999999999999999999999999998887 468889999999999999999999999999998864444321
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
.+..+++.+.|.+.|....+... . ...++ +.+..+++.+.+.+.+.+
T Consensus 78 --~~~~~~~~l~iid~~~~~~~~~~---------------------~---------~~~~~-~~~~~~~~~~~~~i~~~i 124 (249)
T PRK04328 78 --RKYEEEGKFAIVDAFTGGIGSAA---------------------K---------REKYV-VKDPDDVRELIDVLRQAI 124 (249)
T ss_pred --HHHhhcCCEEEEecccccccccc---------------------c---------ccccc-ccCcccHHHHHHHHHHHH
Confidence 11122334666555543221000 0 00000 011123344554444444
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcch-hhhhhhhcceEEE
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSS-TKRWQHMADTLLS 358 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~-~~~le~laDgVI~ 358 (449)
+. .++.||||||+....... +....++++.|...+++.|+|+++|.+........ ...++++||+||.
T Consensus 125 ~~--------~~~~~vVIDSlt~l~~~~---~~~~r~~~~~l~~~lk~~g~t~llt~e~~~~~~~~~~~~~~~~~D~vI~ 193 (249)
T PRK04328 125 KD--------IGAKRVVIDSVSTLYLTK---PAMARSIVMQLKRVLSGLGCTAIFVSQVSVGERGFGGPGVEHAVDGIIR 193 (249)
T ss_pred Hh--------hCCCEEEEeChhHhhcCC---hHHHHHHHHHHHHHHHhCCCEEEEEECccccccccCCCCcEEEEEEEEE
Confidence 42 356899999999764422 34456888889999999999999998776432222 2457899999999
Q ss_pred EEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 359 VAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 359 L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
|+..... ......+.|.|+ +-. .+....+-|.+.. +++.|.+
T Consensus 194 L~~~~~~-----------~~~~R~l~I~K~-Rg~-----~~~~~~~~~~It~-~Gi~v~~ 235 (249)
T PRK04328 194 LDLDEID-----------GELKRSLIVWKM-RGT-----KHSMRRHPFEITD-KGIVVYP 235 (249)
T ss_pred EEEEecC-----------CcEEEEEEEEEc-cCC-----CCCCceEEEEEcC-CCEEEEe
Confidence 9986431 123577889998 222 1344456788864 5666654
No 5
>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=99.88 E-value=1.4e-21 Score=189.48 Aligned_cols=231 Identities=18% Similarity=0.228 Sum_probs=154.5
Q ss_pred EeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccccccc
Q 013117 121 FVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSR 200 (449)
Q Consensus 121 ~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~ 200 (449)
+++|||++||++|+||+|.|+++||.+++++| +++|..+|+++|+.+|++++|++++++++++++++-....+-
T Consensus 2 ri~tGi~~LD~~l~GG~~~gs~~lI~G~pGsG-KT~la~~~l~~~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~----- 75 (237)
T TIGR03877 2 RVKTGIPGMDEILHGGIPERNVVLLSGGPGTG-KSIFSQQFLWNGLQMGEPGIYVALEEHPVQVRRNMAQFGWDV----- 75 (237)
T ss_pred ccccCcHhHHHHhcCCCcCCeEEEEEcCCCCC-HHHHHHHHHHHHHHcCCcEEEEEeeCCHHHHHHHHHHhCCCH-----
Confidence 68999999999999999999999999999888 578889999999999999999999999999999864333221
Q ss_pred ccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHH
Q 013117 201 DRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLA 280 (449)
Q Consensus 201 ~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~ 280 (449)
.+..+++.+.|.+.|...... ... ...++ +.+..+++++.+.+.+.++
T Consensus 76 -~~~~~~g~l~~~d~~~~~~~~-----------------------~~~-------~~~~~-~~~~~~~~~~~~~i~~~i~ 123 (237)
T TIGR03877 76 -RKYEEEGKFAIVDAFTGGIGE-----------------------AAE-------REKYV-VKDPTDVRELIDVLRQAIR 123 (237)
T ss_pred -HHHhhcCCEEEEecccccccc-----------------------ccc-------ccccc-ccCcccHHHHHHHHHHHHH
Confidence 011122344443333221100 000 00000 1111234555555544444
Q ss_pred HhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcch-hhhhhhhcceEEEE
Q 013117 281 QHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSS-TKRWQHMADTLLSV 359 (449)
Q Consensus 281 ~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~-~~~le~laDgVI~L 359 (449)
. .+..|||||||....... +....++++.|..++++.|+|+++|.+.+...... ...+++++|+||.|
T Consensus 124 ~--------~~~~~vVIDSls~l~~~~---~~~~r~~l~~l~~~lk~~~~t~llt~~~~~~~~~~~~~~~~~~~D~vI~L 192 (237)
T TIGR03877 124 D--------INAKRVVIDSVTTLYITK---PAMARSIVMQLKRVLSGLGCTSIFVSQVSVGERGFGGPGVEHAVDGIIRL 192 (237)
T ss_pred H--------hCCCEEEEcChhHhhcCC---hHHHHHHHHHHHHHHHhCCCEEEEEECcccccccccccceEEEEeEEEEE
Confidence 2 246799999999764422 34456888999999999999999998765432211 24578999999999
Q ss_pred EeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 360 AAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 360 ~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
+..... ......+.|.|+ +-+. +....+-|++.. +++.|.+
T Consensus 193 ~~~~~~-----------~~~~R~l~i~K~-Rg~~-----~~~~~~~~~It~-~Gi~v~~ 233 (237)
T TIGR03877 193 DLDEID-----------GELKRSLIVWKM-RGTK-----HSMRRHPFEITD-KGIIVYP 233 (237)
T ss_pred EEEeeC-----------CceEEEEEEEEC-CCCC-----CCCceEEEEEcC-CCEEEEe
Confidence 986532 123577889998 2222 344557799874 5666654
No 6
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=99.85 E-value=6e-20 Score=177.22 Aligned_cols=226 Identities=20% Similarity=0.271 Sum_probs=150.5
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
.+++|||++||++|+||+|.|++++|.++.++| +++|+.+|+++|+.+|++|+|+++++.++++++++-.
T Consensus 5 ~~~~tGi~~LD~~l~gG~~~g~~~~i~G~~GsG-Kt~l~~~~~~~~~~~g~~~~y~~~e~~~~~~~~~~~~--------- 74 (234)
T PRK06067 5 EIISTGNEELDRKLGGGIPFPSLILIEGDHGTG-KSVLSQQFVYGALKQGKKVYVITTENTSKSYLKQMES--------- 74 (234)
T ss_pred eEEecCCHHHHHhhCCCCcCCcEEEEECCCCCC-hHHHHHHHHHHHHhCCCEEEEEEcCCCHHHHHHHHHH---------
Confidence 579999999999999999999999999988887 5788899999999999999999999999999998522
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
+.|....+...+. ...+|+.. ..+.+ .......+.+.+.+.+
T Consensus 75 ------------~g~~~~~~~~~g~-------------l~i~~~~~---------~~~~~----~~~~~~~ll~~l~~~i 116 (234)
T PRK06067 75 ------------VKIDISDFFLWGY-------------LRIFPLNT---------EGFEW----NSTLANKLLELIIEFI 116 (234)
T ss_pred ------------CCCChhHHHhCCC-------------ceEEeccc---------ccccc----CcchHHHHHHHHHHHH
Confidence 2233333211110 01111100 00000 0012234444444444
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcchhhhhhhhcceEEEE
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSSTKRWQHMADTLLSV 359 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~~~~le~laDgVI~L 359 (449)
++ .+..||+|||+....... ....+.+|++.|+.+.+ .++++++|.....+......++++++|+||.|
T Consensus 117 ~~--------~~~~~iviDs~t~~~~~~--~~~~~~~~l~~l~~l~~-~g~tvllt~~~~~~~~~~~~~~~~l~DgvI~L 185 (234)
T PRK06067 117 KS--------KREDVIIIDSLTIFATYA--EEDDILNFLTEAKNLVD-LGKTILITLHPYAFSEELLSRIRSICDVYLKL 185 (234)
T ss_pred Hh--------cCCCEEEEecHHHHHhcC--CHHHHHHHHHHHHHHHh-CCCEEEEEecCCcCCHHHHHHHHhheEEEEEE
Confidence 32 246799999998653322 24568899888876555 57888888876554444456789999999999
Q ss_pred EeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccC-ceeeEEEcceeceEEeeccC
Q 013117 360 AAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEA-TTFSIKLQKRRFLVLECLNQ 421 (449)
Q Consensus 360 ~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~-~~lAFKl~rrr~~vIE~lhL 421 (449)
+..... ..+...|.|.|+-..+ +.. ..+.|.+...+++.|.+.-+
T Consensus 186 ~~~~~~-----------~~~~r~l~i~K~Rg~~------~~~~~~~~~~I~~~~Gi~v~~~~~ 231 (234)
T PRK06067 186 RAEQIG-----------GRYVKVLEVVKLRGAR------KTTGNIISFDVDPAFGIKIIPLSL 231 (234)
T ss_pred EeeccC-----------CEEeEEEEEEhhcCCC------CCCCCEEEEEEcCCCCeEEEEeec
Confidence 974321 1345778899982222 233 45678886546788887443
No 7
>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=99.84 E-value=6e-20 Score=195.63 Aligned_cols=218 Identities=20% Similarity=0.211 Sum_probs=155.3
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
..+++|||++||++||||+|.||++||.+++++| +++|+.||+++|+.+|++|+|++++|+++++++++-+.+.+-
T Consensus 242 ~~~~~tGi~~lD~~lgGG~~~gs~~li~G~~G~G-Kt~l~~~f~~~~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~--- 317 (484)
T TIGR02655 242 NVRVSSGVVRLDEMCGGGFFKDSIILATGATGTG-KTLLVSKFLENACANKERAILFAYEESRAQLLRNAYSWGIDF--- 317 (484)
T ss_pred ccccCCChHhHHHHhcCCccCCcEEEEECCCCCC-HHHHHHHHHHHHHHCCCeEEEEEeeCCHHHHHHHHHHcCCCh---
Confidence 4589999999999999999999999999999888 578899999999999999999999999999999864443321
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASF 278 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~ 278 (449)
++...++.++|-|.|... .+..++++.+.+.
T Consensus 318 ---~~~~~~g~l~~~~~~p~~----------------------------------------------~~~~~~~~~i~~~ 348 (484)
T TIGR02655 318 ---EEMEQQGLLKIICAYPES----------------------------------------------AGLEDHLQIIKSE 348 (484)
T ss_pred ---HHHhhCCcEEEEEccccc----------------------------------------------CChHHHHHHHHHH
Confidence 111223345554443210 0112333333333
Q ss_pred HHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC-C-cch-hhhhhhhcce
Q 013117 279 LAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL-S-LSS-TKRWQHMADT 355 (449)
Q Consensus 279 L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~-~-~~~-~~~le~laDg 355 (449)
++ . .++.||||||+....... ....+..+++.|...+++.++|+++|...+.+ . ... ...+++++|+
T Consensus 349 i~---~-----~~~~~vvIDsi~~~~~~~--~~~~~r~~~~~l~~~lk~~~it~~~t~~~~~~~~~~~~~~~~~s~l~D~ 418 (484)
T TIGR02655 349 IA---D-----FKPARIAIDSLSALARGV--SNNAFRQFVIGVTGYAKQEEITGFFTNTSDQFMGSHSITDSHISTITDT 418 (484)
T ss_pred HH---H-----cCCCEEEEcCHHHHHHhc--CHHHHHHHHHHHHHHHhhCCCeEEEeecccccccCCccCCCCeeEeeeE
Confidence 33 2 356899999998764432 23456889999999999999999999887653 2 122 2467899999
Q ss_pred EEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEe
Q 013117 356 LLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLE 417 (449)
Q Consensus 356 VI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE 417 (449)
||.|+.+... .+.+..+.|.|+ +-+. ++..-+-|.+. .+++.|.
T Consensus 419 ii~l~~~e~~-----------g~~~r~i~V~K~-R~~~-----~~~~~~~~~It-~~Gi~v~ 462 (484)
T TIGR02655 419 ILMLQYVEIR-----------GEMSRAINVFKM-RGSW-----HDKGIREFMIS-DKGPEIK 462 (484)
T ss_pred EEEEEEEecC-----------CEEEEEEEEEEc-cCCC-----CCCceEEEEEc-CCcEEEc
Confidence 9999997652 134677888998 3222 45555678887 4576664
No 8
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=99.80 E-value=1.4e-18 Score=170.51 Aligned_cols=232 Identities=17% Similarity=0.250 Sum_probs=154.2
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
.+++|||++||++|+||||.|+++||.|.+++| +++|..||+.+|+.+|++|+|++++++++++++++.
T Consensus 3 ~~~~TGI~glD~~l~GG~p~g~~~lI~G~pGsG-KT~f~~qfl~~~~~~ge~vlyvs~~e~~~~l~~~~~---------- 71 (260)
T COG0467 3 ERIPTGIPGLDEILGGGLPRGSVVLITGPPGTG-KTIFALQFLYEGAREGEPVLYVSTEESPEELLENAR---------- 71 (260)
T ss_pred ccccCCCcchHHHhcCCCcCCcEEEEEcCCCCc-HHHHHHHHHHHHHhcCCcEEEEEecCCHHHHHHHHH----------
Confidence 578999999999999999999999999999888 578889999999999999999999999999999852
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
.+.|.++.+.++++. ...|........ ... ...+..++..+.+.|.+++
T Consensus 72 -----------~~g~d~~~~~~~g~l-------------~i~d~~~~~~~~------~~~-~~~~~~~~~~l~~~I~~~~ 120 (260)
T COG0467 72 -----------SFGWDLEVYIEKGKL-------------AILDAFLSEKGL------VSI-VVGDPLDLEELLDRIREIV 120 (260)
T ss_pred -----------HcCCCHHHHhhcCCE-------------EEEEcccccccc------ccc-cccCCccHHHHHHHHHHHH
Confidence 266777655433321 112211111000 000 0011123455666555555
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcchhhhhhhhcceEEEE
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSSTKRWQHMADTLLSV 359 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~~~~le~laDgVI~L 359 (449)
+. .+..|++|||++....+.. .+....+++..|+..++..++|++++.....+........++++||||.|
T Consensus 121 ~~--------~~~~~~ViDsi~~~~~~~~-~~~~~r~~~~~l~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~vdgvI~l 191 (260)
T COG0467 121 EK--------EGADRVVIDSITELTLYLN-DPALVRRILLLLKRFLKKLGVTSLLTTEAPVEERGESGVEEYIVDGVIRL 191 (260)
T ss_pred HH--------hCCCEEEEeCCchHhhhcC-chHHHHHHHHHHHHHHHhCCCEEEEEecccccCCCccceEEEEEEEEEEE
Confidence 52 2368999999996544332 23444899999999999988999999876554432112345699999999
Q ss_pred EeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 360 AAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 360 ~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
...... +.-..+.+.|.|+-... +...-+-|.+...+++++.+
T Consensus 192 ~~~~~~----------~~~~r~~~~i~k~r~~~------~~~~~~~~~i~~g~gi~i~~ 234 (260)
T COG0467 192 DLKEIE----------GGGDRRYLRILKMRGTP------HSLKVIPFEITDGEGIVVYP 234 (260)
T ss_pred eeeccc----------CceEEEEEEEEeccccc------cCCceeceEEecCCcEEEec
Confidence 884321 22233488899982211 22334556665434555544
No 9
>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=99.80 E-value=1e-18 Score=186.24 Aligned_cols=227 Identities=17% Similarity=0.218 Sum_probs=145.2
Q ss_pred EeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 121 FVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 121 ~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
+++|||++||++|+||||.|+++||.+++++| +++|..||+++|+.+ |++++|++++|+++++++++-.
T Consensus 2 r~~TGI~gLD~il~GGlp~g~~~Li~G~pGsG-KT~la~qfl~~g~~~~ge~~lyvs~eE~~~~l~~~~~~--------- 71 (484)
T TIGR02655 2 KIRTMIEGFDDISHGGLPIGRSTLVSGTSGTG-KTLFSIQFLYNGIIHFDEPGVFVTFEESPQDIIKNARS--------- 71 (484)
T ss_pred cCCCCchhHHHhcCCCCCCCeEEEEEcCCCCC-HHHHHHHHHHHHHHhCCCCEEEEEEecCHHHHHHHHHH---------
Confidence 68999999999999999999999999999888 578889999999998 9999999999999999998533
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
+.|.++.+..+++ -+..|...... .... .+..++..+.+.+.+.+
T Consensus 72 ------------~G~~~~~~~~~g~-------------l~~~~~~~~~~-------~~~~---~~~~~l~~~l~~i~~~l 116 (484)
T TIGR02655 72 ------------FGWDLQKLVDEGK-------------LFILDASPDPE-------GQDV---VGGFDLSALIERINYAI 116 (484)
T ss_pred ------------cCCCHHHHhhcCc-------------eEEEecCchhc-------cccc---cccCCHHHHHHHHHHHH
Confidence 4555554432211 01111110000 0000 00012334443333333
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCC-CCCcchhhhh-hhhcceEE
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPS-LLSLSSTKRW-QHMADTLL 357 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~-l~~~~~~~~l-e~laDgVI 357 (449)
+ . .+..||+|||+..+.... +......+++..|-..++..++|+++|.+.. .+.......+ +++||+||
T Consensus 117 s---~-----g~~qRVvIDSl~aL~~~~-~~~~~~r~~l~~Li~~L~~~g~TvLLtsh~~~~~~~~~~~~~~e~laDgVI 187 (484)
T TIGR02655 117 R---K-----YKAKRVSIDSVTAVFQQY-DAVSVVRREIFRLVARLKQIGVTTVMTTERIEEYGPIARYGVEEFVSDNVV 187 (484)
T ss_pred H---H-----hCCcEEEEeehhHhhhhc-CchHHHHHHHHHHHHHHHHCCCEEEEEecCcccccccccCCceeEeeeeEE
Confidence 3 1 345799999998764322 2222344455555555567899999998643 2222112334 88999999
Q ss_pred EEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEeec
Q 013117 358 SVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLECL 419 (449)
Q Consensus 358 ~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~l 419 (449)
.|+...... .....|.|.|+ +-. .++...+.|.+.. +++.|.+.
T Consensus 188 ~L~~~~~~~-----------~~~R~l~I~K~-Rgs-----~~~~~~~~~~It~-~Gi~v~p~ 231 (484)
T TIGR02655 188 ILRNVLEGE-----------RRRRTLEILKL-RGT-----SHMKGEYPFTITD-HGINIFPL 231 (484)
T ss_pred EEEEEecCC-----------EEEEEEEEEEC-CCC-----CcCCceEEEEEcC-CcEEEEec
Confidence 999764321 23578999998 322 2445567899974 57777653
No 10
>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=99.80 E-value=2.3e-18 Score=165.31 Aligned_cols=226 Identities=19% Similarity=0.263 Sum_probs=149.6
Q ss_pred EeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccccccc
Q 013117 121 FVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSR 200 (449)
Q Consensus 121 ~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~ 200 (449)
+++|||++||++|+||+|.|++++|.+++++| +++|+.+|+.+|+.+|++++|++.++.++++.+.+
T Consensus 1 ri~tGi~~LD~~l~GGi~~G~~~~i~G~~G~G-KT~l~~~~~~~~~~~g~~~~~is~e~~~~~i~~~~------------ 67 (229)
T TIGR03881 1 RLSTGVEGLDKLLEGGIPRGFFVAVTGEPGTG-KTIFCLHFAYKGLRDGDPVIYVTTEESRESIIRQA------------ 67 (229)
T ss_pred CcCCChhhHHHhhcCCCcCCeEEEEECCCCCC-hHHHHHHHHHHHHhcCCeEEEEEccCCHHHHHHHH------------
Confidence 47999999999999999999999999998887 57888999999999999999999999988887753
Q ss_pred ccchhhccccEEEeeccccccCCCCCCCCCCCCCCCcccccc-ccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 201 DRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFD-FRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 201 ~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FD-Lsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
..+.|.++++..++.. ...| ++.. ....+.. ...+.+++...+.+.+
T Consensus 68 ---------~~~g~~~~~~~~~~~l-------------~i~d~~~~~---------~~~~~~~-~~~~~~~~~~~i~~~~ 115 (229)
T TIGR03881 68 ---------AQFGMDFEKAIEEGKL-------------VIIDALMKE---------KEDEWSL-RELSIEELLNKVIEAK 115 (229)
T ss_pred ---------HHhCCCHHHHhhcCCE-------------EEEEccccc---------ccccccc-ccCCHHHHHHHHHHHH
Confidence 1233444433211110 0011 0000 0000000 0123455655555554
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCC-cchhhhhhhhcceEEE
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLS-LSSTKRWQHMADTLLS 358 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~-~~~~~~le~laDgVI~ 358 (449)
+++. .+..|++|||+..... . .+.....|++.|+.++++.++|+++|.+..... ......++++||+||.
T Consensus 116 ~~~~------~~~~~vvIDsl~~l~~-~--~~~~~r~~~~~l~~~l~~~~~tvil~~~~~~~~~~~~~~~~~~l~D~vI~ 186 (229)
T TIGR03881 116 KYLG------YGHARLVIDSMSAFWL-D--KPAMARKYSYYLKRVLNRWNFTILLTSQYAITTSQAFGFGIEHVADGIIR 186 (229)
T ss_pred Hhhc------cCceEEEecCchhhhc-c--ChHHHHHHHHHHHHHHHhCCCEEEEEecccccCCCCcccceEEEEeEEEE
Confidence 4321 2357999999987633 2 233457788899999999999999998743322 1222457899999999
Q ss_pred EEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEe
Q 013117 359 VAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLE 417 (449)
Q Consensus 359 L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE 417 (449)
|+.+... ......+.|.|+ +-. .++...+-|.+...+++++|
T Consensus 187 L~~~~~~-----------~~~~R~i~i~K~-R~~-----~~~~~~~~~~I~~~~Gi~v~ 228 (229)
T TIGR03881 187 FRKVVVD-----------GELRRYLIVEKM-RQT-----NHDKRAWEIDIVPGKGLVLK 228 (229)
T ss_pred EEEeccC-----------CcEEEEEEEEec-cCC-----CCCCceeEEEEcCCCceEEe
Confidence 9986532 134677999998 222 24455677888644677765
No 11
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=99.79 E-value=3.2e-18 Score=183.28 Aligned_cols=225 Identities=18% Similarity=0.169 Sum_probs=155.3
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
..+++|||++||++|+||+|.|++++|.++.++| +++|+.+|+++|+.+|++++|+++++.++++++++.
T Consensus 252 ~~~~~tGi~~lD~~l~GG~~~g~~~li~G~~G~G-KT~l~~~~~~~~~~~g~~~~yis~e~~~~~i~~~~~--------- 321 (509)
T PRK09302 252 NERISSGVPDLDEMLGGGFFRGSIILVSGATGTG-KTLLASKFAEAACRRGERCLLFAFEESRAQLIRNAR--------- 321 (509)
T ss_pred cccccCCcHHHHHhhcCCCCCCcEEEEEcCCCCC-HHHHHHHHHHHHHhCCCcEEEEEecCCHHHHHHHHH---------
Confidence 4589999999999999999999999999988887 478889999999999999999999999999988742
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASF 278 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~ 278 (449)
.+.|.+..+..++.. +..+. .+ ...+++.+...+.+.
T Consensus 322 ------------~~g~~~~~~~~~g~l-------------~i~~~----~~--------------~~~~~~~~~~~i~~~ 358 (509)
T PRK09302 322 ------------SWGIDLEKMEEKGLL-------------KIICA----RP--------------ESYGLEDHLIIIKRE 358 (509)
T ss_pred ------------HcCCChHHHhhcCCc-------------eeecC----Cc--------------ccCCHHHHHHHHHHH
Confidence 245666554322211 00000 00 001123343333343
Q ss_pred HHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC---Ccchhhhhhhhcce
Q 013117 279 LAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL---SLSSTKRWQHMADT 355 (449)
Q Consensus 279 L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~---~~~~~~~le~laDg 355 (449)
++. .++.|||||||....... ....+.+|++.|...+++.|+|+++|...+.. .......+++++|+
T Consensus 359 i~~--------~~~~~vVIDslt~l~~~~--~~~~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g~~~~~~~~~~~l~D~ 428 (509)
T PRK09302 359 IEE--------FKPSRVAIDPLSALARGG--SLNEFRQFVIRLTDYLKSEEITGLFTNLTPDFMGSHSITESHISSLTDT 428 (509)
T ss_pred HHH--------cCCCEEEEcCHHHHHHhC--CHHHHHHHHHHHHHHHHhCCCeEEEEeccccccCCCCCCcCceEEeeeE
Confidence 331 356799999998764422 24568899999999999999999999876542 22223467899999
Q ss_pred EEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEeeccCCCCCCCC
Q 013117 356 LLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLECLNQAPVDGSS 428 (449)
Q Consensus 356 VI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~lhLpP~d~~~ 428 (449)
||.|+.+... ......+.|.|+-..+ ++..-+-|.+. ..++.|. +|.++.+
T Consensus 429 vI~L~~~~~~-----------~~~~R~l~I~K~Rg~~------~~~~~~~f~It-~~Gi~v~----~~~~~~~ 479 (509)
T PRK09302 429 WILLQYVEIN-----------GEMNRALYVLKMRGSW------HSNQIREFVIT-DKGIHIK----DPFRGFE 479 (509)
T ss_pred EEEEEEeecC-----------CeeEEEEEEEEcCCCC------CCCceEEEEEe-CCcEEEc----ccccCCC
Confidence 9999986532 1235778999982221 34445678886 4576664 4554443
No 12
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=99.79 E-value=4.6e-18 Score=182.12 Aligned_cols=230 Identities=15% Similarity=0.198 Sum_probs=152.5
Q ss_pred CCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCcc
Q 013117 117 NGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLK 195 (449)
Q Consensus 117 ~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~ 195 (449)
|...+++|||++||++|+||+|.|+++||.+++++| +++|+.+|+++|+.+ |++|+|++++++++++++++-+
T Consensus 8 ~~~~ri~TGI~~LD~~l~GG~p~Gs~~li~G~pGsG-KT~l~~qf~~~~~~~~ge~~lyis~ee~~~~i~~~~~~----- 81 (509)
T PRK09302 8 PGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTG-KTLFALQFLVNGIKRFDEPGVFVTFEESPEDIIRNVAS----- 81 (509)
T ss_pred CCCccccCCchhHHHhhcCCCCCCcEEEEEeCCCCC-HHHHHHHHHHHHHHhcCCCEEEEEccCCHHHHHHHHHH-----
Confidence 356699999999999999999999999999999888 578889999999999 9999999999999999998633
Q ss_pred cccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHH
Q 013117 196 HDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHC 275 (449)
Q Consensus 196 ~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i 275 (449)
+.|.+..+..++. -..+|+..... +.. .. ...+++.+.+.+
T Consensus 82 ----------------~g~d~~~~~~~g~-------------l~~~~~~~~~~-------~~~--~~-~~~~~~~l~~~l 122 (509)
T PRK09302 82 ----------------FGWDLQKLIDEGK-------------LFILDASPDPS-------EQE--EA-GEYDLEALFIRI 122 (509)
T ss_pred ----------------cCCCHHHHhhCCe-------------EEEEecCcccc-------ccc--cc-ccccHHHHHHHH
Confidence 3444444321111 01111110000 000 00 011234555555
Q ss_pred HHHHHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CCcchhhh-hhhhc
Q 013117 276 ASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LSLSSTKR-WQHMA 353 (449)
Q Consensus 276 ~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~~~~~~~-le~la 353 (449)
.+.+++ .+..||+|||+.++.... +....+.+++..|...++..++|+++|.+... +....... .+++|
T Consensus 123 ~~~i~~--------~~~~~vVIDSls~l~~~~-d~~~~~r~~l~~L~~~Lk~~g~TvLlt~~~~~~~~~~~~~~~~~~la 193 (509)
T PRK09302 123 EYAIDK--------IGAKRVVLDSIEALFSGF-SNEAVVRRELRRLFAWLKQKGVTAVITGERGDEYGPLTRYGVEEFVS 193 (509)
T ss_pred HHHHHh--------hCCCEEEECCHHHHHhhc-cCHHHHHHHHHHHHHHHHhCCCEEEEEECCccCcCCccccCceEEEe
Confidence 454442 346799999999874432 22445677777777778888999999986432 12111122 37899
Q ss_pred ceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 354 DTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 354 DgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
|+||.|+..... ...+..|.|.|+-..+ +....+.|.+. .++++|.+
T Consensus 194 DgVI~L~~~~~~-----------~~~~R~l~I~K~Rg~~------~~~~~~~f~I~-~~Gi~v~p 240 (509)
T PRK09302 194 DCVIILRNRLEG-----------EKRTRTLRILKYRGTT------HGKNEYPFTIT-EDGISVLP 240 (509)
T ss_pred eEEEEEeEEccC-----------CeEEEEEEEEECCCCC------cCCccEEEEEC-CCcEEEEe
Confidence 999999875321 1246889999983222 34446889995 45777765
No 13
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.78 E-value=5.4e-18 Score=160.26 Aligned_cols=226 Identities=21% Similarity=0.259 Sum_probs=167.2
Q ss_pred EeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccccccc
Q 013117 121 FVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSR 200 (449)
Q Consensus 121 ~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~ 200 (449)
.+++|..+||.-||||+|.||++|||+|.+|| +++|+++|++.++.+|+++.|++++..-.+++++|.+...+-
T Consensus 9 ii~~gndelDkrLGGGiP~GsL~lIEGd~~tG-KSvLsqr~~YG~L~~g~~v~yvsTe~T~refi~qm~sl~ydv----- 82 (235)
T COG2874 9 IIKSGNDELDKRLGGGIPVGSLILIEGDNGTG-KSVLSQRFAYGFLMNGYRVTYVSTELTVREFIKQMESLSYDV----- 82 (235)
T ss_pred hccCCcHHHHhhccCCCccCeEEEEECCCCcc-HHHHHHHHHHHHHhCCceEEEEEechhHHHHHHHHHhcCCCc-----
Confidence 58999999999999999999999999999998 588999999999999999999999999999999986655431
Q ss_pred ccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHH
Q 013117 201 DRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLA 280 (449)
Q Consensus 201 ~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~ 280 (449)
.-.+.|.|-.++.-+. + .+++ +...-+.+++.+.++++
T Consensus 83 --------~~~~l~G~l~~~~~~~---~-----------~~~~--------------------~~~~~~~~L~~l~~~~k 120 (235)
T COG2874 83 --------SDFLLSGRLLFFPVNL---E-----------PVNW--------------------GRRSARKLLDLLLEFIK 120 (235)
T ss_pred --------hHHHhcceeEEEEecc---c-----------cccc--------------------ChHHHHHHHHHHHhhHH
Confidence 1124455544331100 0 0000 11122455555556655
Q ss_pred HhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcchhhhhhhhcceEEEEE
Q 013117 281 QHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSSTKRWQHMADTLLSVA 360 (449)
Q Consensus 281 ~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~~~~le~laDgVI~L~ 360 (449)
.. .-.-|+||||.....++ .+.+++.|+..+|.+.. .|-+.++|++.+.++.++..+++.+||..+.|+
T Consensus 121 ~~--------~~dViIIDSls~~~~~~--~~~~vl~fm~~~r~l~d-~gKvIilTvhp~~l~e~~~~rirs~~d~~l~L~ 189 (235)
T COG2874 121 RW--------EKDVIIIDSLSAFATYD--SEDAVLNFMTFLRKLSD-LGKVIILTVHPSALDEDVLTRIRSACDVYLRLR 189 (235)
T ss_pred hh--------cCCEEEEecccHHhhcc--cHHHHHHHHHHHHHHHh-CCCEEEEEeChhhcCHHHHHHHHHhhheeEEEE
Confidence 32 23589999999876654 36789999999998765 589999999999999999999999999999998
Q ss_pred eeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEeeccC
Q 013117 361 AIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLECLNQ 421 (449)
Q Consensus 361 ~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~lhL 421 (449)
...-. .++.-++.|.|++-.-. .-.+...|....+.+++||+..+
T Consensus 190 ~~~~G-----------g~~~~~~~i~K~~ga~~-----s~~~~I~F~V~P~~Glkvep~Sv 234 (235)
T COG2874 190 LEELG-----------GDLIKVLEIVKYRGARK-----SFQNIISFRVEPGFGLKVEPASV 234 (235)
T ss_pred hhhhC-----------CeeeEEEEEeeecCchh-----hcCCceeEEecCCCceEEEEeec
Confidence 74321 13456777778732221 12345789999999999998653
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=99.78 E-value=7.7e-18 Score=165.80 Aligned_cols=226 Identities=15% Similarity=0.190 Sum_probs=139.2
Q ss_pred EeecCchhHHHHh--------------cCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhh
Q 013117 121 FVSSGIADLDKIL--------------GGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLG 186 (449)
Q Consensus 121 ~iSTGIp~LD~lL--------------GGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~ 186 (449)
-++|||++||++| +||||.|++++|.+++++| +++|+.||+++|+.+|++++|+++++.++.+..
T Consensus 3 ~~~tGi~glD~~l~~~~~~~~~~~~~~~GGip~gs~~lI~G~pGtG-KT~l~~qf~~~~a~~Ge~vlyis~Ee~~~~~~~ 81 (259)
T TIGR03878 3 GVPTGVEGLDELFFKVEIEEGKIVRKPLGGIPAYSVINITGVSDTG-KSLMVEQFAVTQASRGNPVLFVTVESPANFVYT 81 (259)
T ss_pred CccCCchhHHHhhccccccccccccccCCCeECCcEEEEEcCCCCC-HHHHHHHHHHHHHhCCCcEEEEEecCCchHHHH
Confidence 3789999999999 5999999999999998887 578889999999999999999999866654444
Q ss_pred cCCCCCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCc
Q 013117 187 TLPSPASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSK 266 (449)
Q Consensus 187 ~LP~~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~ 266 (449)
++- .....+.|..+.+.+ + ...+|.....+ . ..
T Consensus 82 ~l~-----------------~~a~~~g~d~~~~~~-~--------------l~~id~~~~~~-------------~--~~ 114 (259)
T TIGR03878 82 SLK-----------------ERAKAMGVDFDKIEE-N--------------IILIDAASSTE-------------L--RE 114 (259)
T ss_pred HHH-----------------HHHHHcCCCHHHHhC-C--------------EEEEECCCchh-------------h--hh
Confidence 320 001123344332210 0 01111110000 0 01
Q ss_pred chHHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCC----
Q 013117 267 NLAALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLS---- 342 (449)
Q Consensus 267 ~~~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~---- 342 (449)
+.+.+...+.+.++ + .++.||||||+...... ......++++.|..+++..++|+++|.+.....
T Consensus 115 ~~~~l~~~l~~~i~----~----~~~~~vVIDSls~l~~~---~~~~~r~~~~~L~~~lk~~~~t~ll~~e~~~~~~~~~ 183 (259)
T TIGR03878 115 NVPNLLATLAYAIK----E----YKVKNTVIDSITGLYEA---KEMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEELS 183 (259)
T ss_pred hHHHHHHHHHHHHH----h----hCCCEEEEcCchHhccc---chHHHHHHHHHHHHHHHHcCCeEEEEeccccCccccc
Confidence 22334433333333 1 45789999999875321 234567888999999999999999998643211
Q ss_pred --cchhhhhhhhcceEEEEEeeCCCcHHHhhhc-cCCCCcceeEEEeeecccccCCcccccCceeeEEEcce
Q 013117 343 --LSSTKRWQHMADTLLSVAAIPDEDKELAKLL-SGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKR 411 (449)
Q Consensus 343 --~~~~~~le~laDgVI~L~~f~~~~~e~~~~~-~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rr 411 (449)
......+++++|+||.|+......+....+. .........|.|.|+ +-. .++...+-|.+..+
T Consensus 184 ~~~~~~~~~~~l~D~vI~L~~~~~~~~~~~~~~~~~~~~~~R~l~I~Km-Rg~-----~h~~~~~~~~It~~ 249 (259)
T TIGR03878 184 AEAAGGYAVSHIVDGTIVLAKQLIMSRFDASLYKKPIGEIVRLFRIDGC-RMC-----GHDTKTHVLEIDET 249 (259)
T ss_pred ccccCCcceeEeeccEEEEeeeeccchhhhhhccccccceEEEEEEEEc-cCC-----CCCCceeEEEEcCC
Confidence 1112357999999999997543221111110 001235677888998 222 14555677888643
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=99.72 E-value=3e-16 Score=150.37 Aligned_cols=217 Identities=18% Similarity=0.286 Sum_probs=135.2
Q ss_pred CchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccccccch
Q 013117 125 GIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSRDRES 204 (449)
Q Consensus 125 GIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~~~~~ 204 (449)
||++||++||||+|.|++++|.+++++| +++|+.+|+++|+.+|++|+|+++++.++++++.+-
T Consensus 1 Gi~~LD~~l~gGi~~g~~~li~G~~G~G-Kt~~~~~~~~~~~~~g~~~~y~s~e~~~~~l~~~~~--------------- 64 (224)
T TIGR03880 1 GIPGLDEMLGGGFPEGHVIVVIGEYGTG-KTTFSLQFLYQGLKNGEKAMYISLEEREERILGYAK--------------- 64 (224)
T ss_pred CchhhHHHhcCCCCCCeEEEEECCCCCC-HHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHH---------------
Confidence 8999999999999999999999887776 468889999999999999999999999999998752
Q ss_pred hhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHHHhhh
Q 013117 205 EQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQHQR 284 (449)
Q Consensus 205 ~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~~~~ 284 (449)
.+.|.+..+.++ . ...+|+... +. ....+.+.+.+..++++
T Consensus 65 ------~~~~~~~~~~~~-~-------------l~~~~~~~~---------~~-------~~~~~~l~~~~~~~i~~--- 105 (224)
T TIGR03880 65 ------SKGWDLEDYIDK-S-------------LYIVRLDPS---------DF-------KTSLNRIKNELPILIKE--- 105 (224)
T ss_pred ------HcCCChHHHHhC-C-------------eEEEecCHH---------HH-------HhhHHHHHHHHHHHHHH---
Confidence 234554433211 0 011111100 00 00122333333333331
Q ss_pred ccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcc--hhhhhhhhcceEEEEEee
Q 013117 285 NDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLS--STKRWQHMADTLLSVAAI 362 (449)
Q Consensus 285 ~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~--~~~~le~laDgVI~L~~f 362 (449)
.++.||+|||+........ ...+....++.|-..++..++|++++.......+. ....++++||+||.|+..
T Consensus 106 -----~~~~~vVIDsls~l~~~~~-~~~~~r~~l~~l~~~lk~~~~tvll~s~~~~~~~~~~~~~~~~~l~D~vI~L~~~ 179 (224)
T TIGR03880 106 -----LGASRVVIDPISLLETLFD-DDAERRTELFRFYSSLRETGVTTILTSEADKTNVFASKYGLIEYLADGVIILKYV 179 (224)
T ss_pred -----hCCCEEEEcChHHHhhhcC-CHHHHHHHHHHHHHHHHhCCCEEEEEEcccCCCCCccCCCceEEEEeEEEEEeee
Confidence 3467999999987632111 23334444444444455789999999875432211 123368999999999764
Q ss_pred CCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 363 PDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 363 ~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
.... ......-|.|.|+ +-+. ++...+.|.+. ..++.+-+
T Consensus 180 ~~~~---------~~~~~r~l~v~K~-Rg~~-----~~~~~~~~~i~-~~Gi~v~~ 219 (224)
T TIGR03880 180 RNSD---------LRDVRLAVEVVKM-RRSK-----HSREIKPYEIT-DSGITVYS 219 (224)
T ss_pred eccc---------CcceEEEEEEEEc-cCCC-----CCCceEEEEEc-CCcEEEec
Confidence 3211 1123446889998 3222 45556788886 45665543
No 16
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=99.68 E-value=2.2e-15 Score=145.92 Aligned_cols=223 Identities=17% Similarity=0.187 Sum_probs=141.3
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
..+-+|+.+||++||||+|.|++++|.|+.++| +++|+.+|+++++.+|++++|+++++.++++++++-.
T Consensus 4 ~~~~~~~~~ld~~l~ggi~~g~~~~i~G~~G~G-KTtl~~~~~~~~~~~g~~~~yi~~e~~~~~~~~~~~~--------- 73 (230)
T PRK08533 4 AKIELSRDELHKRLGGGIPAGSLILIEGDESTG-KSILSQRLAYGFLQNGYSVSYVSTQLTTTEFIKQMMS--------- 73 (230)
T ss_pred EEEEEEEeeeehhhCCCCCCCcEEEEECCCCCC-HHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHH---------
Confidence 357899999999999999999999999998887 4677799999999999999999999999999998522
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
+.|..+.+...+. + ...++...+ .........+..++
T Consensus 74 ------------~g~~~~~~~~~~~------------l-~~~~~~~~~------------------~~~~~~~~~l~~il 110 (230)
T PRK08533 74 ------------LGYDINKKLISGK------------L-LYIPVYPLL------------------SGNSEKRKFLKKLM 110 (230)
T ss_pred ------------hCCchHHHhhcCc------------E-EEEEecccc------------------cChHHHHHHHHHHH
Confidence 3333322211000 0 000100000 00001111122333
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcchhhhhhhhcceEEEE
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSSTKRWQHMADTLLSV 359 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~~~~le~laDgVI~L 359 (449)
+.... .+..|++||++++...... ++.....++..|+.+. ..+.|+++|.....+.......++++||+||.|
T Consensus 111 ~~~~~-----~~~~~lVIDe~t~~l~~~~-d~~~~~~l~~~l~~l~-~~g~tvi~t~~~~~~~~~~~~~~~~~~DgvI~L 183 (230)
T PRK08533 111 NTRRF-----YEKDVIIIDSLSSLISNDA-SEVAVNDLMAFFKRIS-SLNKVIILTANPKELDESVLTILRTAATMLIRL 183 (230)
T ss_pred HHHHh-----cCCCEEEEECccHHhcCCc-chHHHHHHHHHHHHHH-hCCCEEEEEecccccccccceeEEEeeeEEEEE
Confidence 32211 3467999999998643221 2232333444444333 347788888876654433234579999999999
Q ss_pred EeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 360 AAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 360 ~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
+..... ..+...+.|.|+=. ....-.+.+.|+.....++++|-
T Consensus 184 ~~~~~~-----------~~~~R~i~V~KmR~-----~~~~~~~~~~f~i~~~~g~~~~~ 226 (230)
T PRK08533 184 EVKVFG-----------GDLKNSAKIVKYNM-----AKGSFQKSIPFRVEPKIGLAVEI 226 (230)
T ss_pred EEeecC-----------CEEEEEEEEEEecC-----CccccCCEEEEEEcCCccEEEEE
Confidence 986442 13467888999922 11222447999998888999985
No 17
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=99.63 E-value=1.9e-14 Score=137.88 Aligned_cols=174 Identities=16% Similarity=0.236 Sum_probs=113.6
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCC-ChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSK-DPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e-~p~~il~~LP~~~~~~~~k 198 (449)
.+++||+++||++|+||+|.|++++|.+.+++| +++|+.+|+++++.+|++++|++++. .++.|.+-. .
T Consensus 3 ~~i~tGi~~lD~~l~GGi~~g~i~~i~G~~GsG-KT~l~~~la~~~~~~~~~v~yi~~e~~~~~r~~~~~-~-------- 72 (225)
T PRK09361 3 ERLPTGCKMLDELLGGGFERGTITQIYGPPGSG-KTNICLQLAVEAAKNGKKVIYIDTEGLSPERFKQIA-G-------- 72 (225)
T ss_pred ccccCCcHHHHHHhcCCCCCCeEEEEECCCCCC-HHHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHH-h--------
Confidence 479999999999999999999999999988887 56888999999999999999999872 223332211 0
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASF 278 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~ 278 (449)
. .+.+..+ ++.+.. ..++..+.+.+..+
T Consensus 73 --------~-------~~~~~~~----------------------------------~~~~~~---~~~~~~~~~~i~~~ 100 (225)
T PRK09361 73 --------E-------DFEELLS----------------------------------NIIIFE---PSSFEEQSEAIRKA 100 (225)
T ss_pred --------h-------ChHhHhh----------------------------------CeEEEe---CCCHHHHHHHHHHH
Confidence 0 0000000 000000 01122222222222
Q ss_pred HHHhhhccCCCCceeEEEEcCCCcccccC---CCC----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CC-----cch
Q 013117 279 LAQHQRNDGSSALAGRIAIQSLCAPQCEH---SNM----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LS-----LSS 345 (449)
Q Consensus 279 L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~---~~~----~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~-----~~~ 345 (449)
.+.+. .++.+|||||+.++.... ... ...+.+++..|+.++++.++++++|..... .. +..
T Consensus 101 ~~~~~------~~~~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~v~vi~tnq~~~~~~~~~~~~~g 174 (225)
T PRK09361 101 EKLAK------ENVGLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRPLG 174 (225)
T ss_pred HHHHH------hcccEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEccceecCCCCcccCCC
Confidence 22111 257899999998764321 111 245788888999999999999999987542 11 111
Q ss_pred hhhhhhhcceEEEEEe
Q 013117 346 TKRWQHMADTLLSVAA 361 (449)
Q Consensus 346 ~~~le~laDgVI~L~~ 361 (449)
...++|++|++|.|+.
T Consensus 175 g~~~~~~~d~ii~l~~ 190 (225)
T PRK09361 175 GHTLEHWSKTILRLEK 190 (225)
T ss_pred cchhhhhccEEEEEEE
Confidence 2468999999999988
No 18
>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=99.63 E-value=4.6e-15 Score=141.32 Aligned_cols=175 Identities=13% Similarity=0.129 Sum_probs=112.9
Q ss_pred eecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccccc
Q 013117 122 VSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSRD 201 (449)
Q Consensus 122 iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~~ 201 (449)
++|||++||++|+||||.|++++|.+.+++| +++|+.+|+++++.+|++++|++.++...+-++++-.
T Consensus 1 i~TGi~~LD~~l~GGi~~g~i~~i~G~~GsG-KT~l~~~~a~~~~~~g~~v~yi~~e~~~~~~~~~~~~----------- 68 (218)
T cd01394 1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTG-KTNIAIQLAVETAGQGKKVAYIDTEGLSSERFRQIAG----------- 68 (218)
T ss_pred CCcchhHHHHHhcCCccCCeEEEEECCCCCC-HHHHHHHHHHHHHhcCCeEEEEECCCCCHHHHHHHHh-----------
Confidence 5899999999999999999999999988887 5788899999999999999999886543322222100
Q ss_pred cchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHHH
Q 013117 202 RESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQ 281 (449)
Q Consensus 202 ~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~ 281 (449)
.. ...+. .++.++. ..++.++...+..+..
T Consensus 69 ------~~------~~~~~----------------------------------~~~~~~~---~~~~~~~~~~~~~~~~- 98 (218)
T cd01394 69 ------DR------PERAA----------------------------------SSIIVFE---PMDFNEQGRAIQETET- 98 (218)
T ss_pred ------HC------hHhhh----------------------------------cCEEEEe---CCCHHHHHHHHHHHHH-
Confidence 00 00000 0000000 0111222211111211
Q ss_pred hhhccCCCCceeEEEEcCCCcccccCCCC-------HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CC-----cchhhh
Q 013117 282 HQRNDGSSALAGRIAIQSLCAPQCEHSNM-------DWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LS-----LSSTKR 348 (449)
Q Consensus 282 ~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~-------~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~-----~~~~~~ 348 (449)
+.. .++.+|+|||+..+....... ...+.+++..|+.++++.++++++|....- .. +.....
T Consensus 99 ~~~-----~~~~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~t~q~~~~~~~~~~~p~~g~~ 173 (218)
T cd01394 99 FAD-----EKVDLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVRPLGGHT 173 (218)
T ss_pred HHh-----cCCcEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHHHHHHhCCEEEEecCCEEcCCCCcccccCCcc
Confidence 111 236899999998874321111 136788899999999999999999987542 11 111246
Q ss_pred hhhhcceEEEEEeeC
Q 013117 349 WQHMADTLLSVAAIP 363 (449)
Q Consensus 349 le~laDgVI~L~~f~ 363 (449)
|+|++|++|.|+...
T Consensus 174 ~~~~~d~~i~l~~~~ 188 (218)
T cd01394 174 LEHWSKVILRLEKLR 188 (218)
T ss_pred hhcceeEEEEEEEcC
Confidence 899999999999754
No 19
>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=99.61 E-value=1.5e-14 Score=153.08 Aligned_cols=202 Identities=17% Similarity=0.170 Sum_probs=136.5
Q ss_pred CCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 118 GTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 118 g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
...+++|||++||++||||+|.|+++||.+++++| +++|+.+|++++..+|++++|++.+|+.+++...+
T Consensus 72 ~~~ri~TGi~~LD~vLgGGi~~GsvilI~G~pGsG-KTTL~lq~a~~~a~~g~kvlYvs~EEs~~qi~~ra--------- 141 (454)
T TIGR00416 72 EVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIG-KSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRA--------- 141 (454)
T ss_pred ccCccccCcHHHHHHhcCCccCCeEEEEEcCCCCC-HHHHHHHHHHHHHhcCCcEEEEECcCCHHHHHHHH---------
Confidence 35789999999999999999999999999999888 57889999999999999999999998888776542
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
.++.|..+++. .+ . ..+++.+. +
T Consensus 142 ------------~rlg~~~~~l~--------------------------------------~~--~-e~~~~~I~----~ 164 (454)
T TIGR00416 142 ------------IRLGLPEPNLY--------------------------------------VL--S-ETNWEQIC----A 164 (454)
T ss_pred ------------HHcCCChHHeE--------------------------------------Ec--C-CCCHHHHH----H
Confidence 12223222110 00 0 01122222 2
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCcccccC----CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcc-hhhhhhhh
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCEH----SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLS-STKRWQHM 352 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~----~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~-~~~~le~l 352 (449)
.++ . .++.+|+|||+....... +.....+..++..|..+.+..++|+++|.+...-... -...++|+
T Consensus 165 ~i~---~-----~~~~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~giTvllt~hvtkeg~~aG~~~le~l 236 (454)
T TIGR00416 165 NIE---E-----ENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHM 236 (454)
T ss_pred HHH---h-----cCCcEEEEecchhhcccccccCCCCHHHHHHHHHHHHHHHHHhCCEEEEEeccccCCccCCcccEeee
Confidence 222 1 356899999998753211 1123467888999999999999999999754321100 02347999
Q ss_pred cceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceE
Q 013117 353 ADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLV 415 (449)
Q Consensus 353 aDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~v 415 (449)
+|+||.|+.... ...+.|++.|.. .+. ...-..|.+. .+++.
T Consensus 237 vD~VI~Le~~~~-------------~~~R~L~v~K~R-~g~------~~e~~~f~it-~~Gl~ 278 (454)
T TIGR00416 237 VDTVLYFEGDRD-------------SRFRILRSVKNR-FGA------TNEIGIFEMT-EQGLR 278 (454)
T ss_pred ceEEEEEeccCC-------------CcEEEEEEecCC-CCC------CCcEEEEEEe-cCCce
Confidence 999999986211 235789999983 221 1223468886 35654
No 20
>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=99.58 E-value=7.6e-14 Score=144.22 Aligned_cols=203 Identities=18% Similarity=0.201 Sum_probs=135.4
Q ss_pred CCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccc
Q 013117 117 NGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKH 196 (449)
Q Consensus 117 ~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~ 196 (449)
....+++|||++||++|||||+.|+++||.+++++| +++|+.+|+++...++++++|++.++.++++...+
T Consensus 59 ~~~~ri~TGi~eLD~vLgGGi~~GslvLI~G~pG~G-KStLllq~a~~~a~~g~~VlYvs~EEs~~qi~~Ra-------- 129 (372)
T cd01121 59 EEEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIG-KSTLLLQVAARLAKRGGKVLYVSGEESPEQIKLRA-------- 129 (372)
T ss_pred cccCccccCCHHHHHhhcCCccCCeEEEEEeCCCCC-HHHHHHHHHHHHHhcCCeEEEEECCcCHHHHHHHH--------
Confidence 346799999999999999999999999999999888 57889999999999999999999988887765531
Q ss_pred ccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHH
Q 013117 197 DKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCA 276 (449)
Q Consensus 197 ~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~ 276 (449)
.++.|..+++ ..+. ..+++.+.
T Consensus 130 -------------~rlg~~~~~l--------------------------------------~l~~---e~~le~I~---- 151 (372)
T cd01121 130 -------------DRLGISTENL--------------------------------------YLLA---ETNLEDIL---- 151 (372)
T ss_pred -------------HHcCCCcccE--------------------------------------EEEc---cCcHHHHH----
Confidence 1121211110 0000 01122222
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC----CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcc-hhhhhhh
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH----SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLS-STKRWQH 351 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~----~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~-~~~~le~ 351 (449)
+.++ . .++.+|+|||+....... +.....+..++..|+.+.+..+++++++.+...-... -...++|
T Consensus 152 ~~i~---~-----~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghvtk~g~~aG~~~leh 223 (372)
T cd01121 152 ASIE---E-----LKPDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAGPKVLEH 223 (372)
T ss_pred HHHH---h-----cCCcEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeeccCCCcccCcccchh
Confidence 2222 1 356899999997652211 1123567889999999999999999999764431111 1246799
Q ss_pred hcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceE
Q 013117 352 MADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLV 415 (449)
Q Consensus 352 laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~v 415 (449)
++|+||.|+.... .....|++.|. +.+. ...-..|.+. .+++.
T Consensus 224 ~vD~Vi~le~~~~-------------~~~R~Lri~Kn-R~g~------~~ei~~F~i~-~~Gl~ 266 (372)
T cd01121 224 MVDTVLYFEGDRH-------------SEYRILRSVKN-RFGS------TNELGVFEMR-ENGLR 266 (372)
T ss_pred hceEEEEEEcCCC-------------CcEEEEEEEeC-CCCC------CCCEEEEEEC-CCCeE
Confidence 9999998765211 13578899997 2221 1123468886 35665
No 21
>PRK11823 DNA repair protein RadA; Provisional
Probab=99.58 E-value=7.8e-14 Score=147.41 Aligned_cols=202 Identities=17% Similarity=0.205 Sum_probs=134.4
Q ss_pred CCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 118 GTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 118 g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
...+++||+++||++||||+|.|+++||.+++++| +++|+.+|++++..+|++++|++.+++++++...+
T Consensus 58 ~~~ri~TGi~~LD~~LgGGi~~Gs~~lI~G~pG~G-KTtL~lq~a~~~a~~g~~vlYvs~Ees~~qi~~ra--------- 127 (446)
T PRK11823 58 EEPRISTGIGELDRVLGGGLVPGSVVLIGGDPGIG-KSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRA--------- 127 (446)
T ss_pred cCCcccCCcHHHHHHhcCCccCCEEEEEECCCCCC-HHHHHHHHHHHHHhcCCeEEEEEccccHHHHHHHH---------
Confidence 35789999999999999999999999999998888 57889999999998999999999998888876542
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
.++.|..++. ... . ..++..+. +
T Consensus 128 ------------~rlg~~~~~l--------------------------------------~~~--~-e~~l~~i~----~ 150 (446)
T PRK11823 128 ------------ERLGLPSDNL--------------------------------------YLL--A-ETNLEAIL----A 150 (446)
T ss_pred ------------HHcCCChhcE--------------------------------------EEe--C-CCCHHHHH----H
Confidence 1122211110 000 0 01122222 2
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCcccccC----CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcc-hhhhhhhh
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCEH----SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLS-STKRWQHM 352 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~----~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~-~~~~le~l 352 (449)
.++ . .++.+|+|||+....... +.....+..++..|+.++++.+++++++.+...-... -...++|+
T Consensus 151 ~i~---~-----~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv~hvtk~~~~ag~~~lehl 222 (446)
T PRK11823 151 TIE---E-----EKPDLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGPRVLEHM 222 (446)
T ss_pred HHH---h-----hCCCEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeeccCCCCcCCcchhhhh
Confidence 222 1 356899999997653211 1123467888999999999999999999654321110 12458999
Q ss_pred cceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceE
Q 013117 353 ADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLV 415 (449)
Q Consensus 353 aDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~v 415 (449)
+|+||.|+. +. ......|+|.|.. ... ...-..|.+.. +++.
T Consensus 223 vD~Vi~le~---~~----------~~~~R~l~i~K~R-~g~------~~e~~~f~it~-~Gi~ 264 (446)
T PRK11823 223 VDTVLYFEG---DR----------HSRYRILRAVKNR-FGA------TNEIGVFEMTE-QGLR 264 (446)
T ss_pred CeEEEEEEc---CC----------CCceEEEEEccCC-CCC------CCceEEEEEcC-CCce
Confidence 999998763 11 1224778888873 221 11234588863 5654
No 22
>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=99.50 E-value=6.2e-13 Score=127.00 Aligned_cols=193 Identities=16% Similarity=0.171 Sum_probs=124.3
Q ss_pred eecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcC------CcEEEEcCCCC--hhhHhhcCCCCCC
Q 013117 122 VSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHG------QPLLYASPSKD--PRGFLGTLPSPAS 193 (449)
Q Consensus 122 iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g------~~vl~vs~~e~--p~~il~~LP~~~~ 193 (449)
++||+++||++|+||+|.|+++.|.++.++| +++|+.+++++.+.++ ..++|++.++. ++.+.+..-
T Consensus 1 i~tG~~~lD~~l~GG~~~g~v~~I~G~~GsG-KT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~~~~~---- 75 (226)
T cd01393 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSG-KTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLVQLAV---- 75 (226)
T ss_pred CCCCcHHHHHHhCCCCcCCcEEEEeCCCCCC-hhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHHHHHH----
Confidence 5899999999999999999999999988887 4678899999998888 89999998653 222322100
Q ss_pred cccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHH
Q 013117 194 LKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQE 273 (449)
Q Consensus 194 ~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~ 273 (449)
...+..+.+. .++.++.. .+..++..
T Consensus 76 -----------------~~~~~~~~~~----------------------------------~~i~~~~~---~~~~~~~~ 101 (226)
T cd01393 76 -----------------RFGLDPEEVL----------------------------------DNIYVARP---YNGEQQLE 101 (226)
T ss_pred -----------------Hhccchhhhh----------------------------------ccEEEEeC---CCHHHHHH
Confidence 0000000000 01111111 12233333
Q ss_pred HHHHHHHHhhhccCCCCceeEEEEcCCCcccccC-CCC------HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CC---
Q 013117 274 HCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH-SNM------DWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LS--- 342 (449)
Q Consensus 274 ~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~-~~~------~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~--- 342 (449)
.+.++++... ..++..|||||+..+.+.. ... ...+.+++..|+.+.+..++++++|....- ..
T Consensus 102 ~l~~~~~~~~-----~~~~~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~tnq~~~~~~~~~ 176 (226)
T cd01393 102 IVEELERIMS-----SGRVDLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMF 176 (226)
T ss_pred HHHHHHHHhh-----cCCeeEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHHHHHHhCcEEEEEEEEeeeccccc
Confidence 3333332111 2467899999999875432 111 145788999999999999999999986431 11
Q ss_pred -----cchhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeec
Q 013117 343 -----LSSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVA 389 (449)
Q Consensus 343 -----~~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp 389 (449)
+.....|.|++|.+|.|+...+.. .-...++|.|-|
T Consensus 177 ~~~~~p~~G~~~~~~~~~ri~l~~~~~~~-----------~~~r~~~~~k~~ 217 (226)
T cd01393 177 GDPETPAGGNALAHASTTRLDLRKGRGII-----------GERRIAKVVKSP 217 (226)
T ss_pred CCCccccCchhhhCcccEEEEEEecCCcc-----------CcEEEEEEEeCC
Confidence 122368899999999999754321 124678888875
No 23
>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=99.48 E-value=5.7e-13 Score=126.01 Aligned_cols=167 Identities=15% Similarity=0.190 Sum_probs=108.6
Q ss_pred HHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCC-ChhhHhhcCCCCCCcccccccccchhhc
Q 013117 129 LDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSK-DPRGFLGTLPSPASLKHDKSRDRESEQE 207 (449)
Q Consensus 129 LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e-~p~~il~~LP~~~~~~~~k~~~~~~~~~ 207 (449)
||++||||+|.|++++|.+++++| +++|+.+|+++++.+|++++|+++++ .++.+.+.+-.
T Consensus 1 lD~~l~GGi~~g~i~~i~G~~GsG-KT~l~~~~~~~~~~~g~~v~yi~~e~~~~~rl~~~~~~----------------- 62 (209)
T TIGR02237 1 IDELLGGGVERGTITQIYGPPGSG-KTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAED----------------- 62 (209)
T ss_pred ChhhhcCCCCCCeEEEEECCCCCC-HHHHHHHHHHHHHhCCCeEEEEECCCCCHHHHHHHHHh-----------------
Confidence 799999999999999999988887 56788999999999999999999986 55555553100
Q ss_pred cccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHHHhhhccC
Q 013117 208 KGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQHQRNDG 287 (449)
Q Consensus 208 ~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~~~~~~~ 287 (449)
| .+.+. + + .+.++ . .++.++.+.+..+.+.+..
T Consensus 63 ------~-~~~~~-~-~-------------i~~~~-------------------~---~~~~~~~~~~~~l~~~~~~--- 95 (209)
T TIGR02237 63 ------R-PERAL-S-N-------------FIVFE-------------------V---FDFDEQGVAIQKTSKFIDR--- 95 (209)
T ss_pred ------C-hHHHh-c-C-------------EEEEE-------------------C---CCHHHHHHHHHHHHHHHhh---
Confidence 0 01000 0 0 00111 0 0112222112222222211
Q ss_pred CCCceeEEEEcCCCcccccCCC-C----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CCc-----chhhhhhhhcceE
Q 013117 288 SSALAGRIAIQSLCAPQCEHSN-M----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LSL-----SSTKRWQHMADTL 356 (449)
Q Consensus 288 ~~~~v~RIvIdSL~Sp~~~~~~-~----~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~~-----~~~~~le~laDgV 356 (449)
.++.+|||||+.++.+.... . ...+.+++..|+.++++.++++++|.+..- .+. .....++|++|++
T Consensus 96 --~~~~lvVIDSis~l~~~~~~~~~~~~~~~l~~~~~~L~~~~~~~~v~vl~t~~~~~~~~~~~~~~~gg~~~~~~~d~v 173 (209)
T TIGR02237 96 --DSASLVVVDSFTALYRLELSDDRISRNRELARQLTLLLSLARKKNLAVVITNQVYTDVNNGTLRPLGGHLLEHWSKVI 173 (209)
T ss_pred --cCccEEEEeCcHHHhHHHhCCccHHHHHHHHHHHHHHHHHHHHcCCEEEEEcccEEecCCCCCcCCCcchhheeeeEE
Confidence 25789999999987442211 1 236788888999999999999999987532 111 1123579999999
Q ss_pred EEEEee
Q 013117 357 LSVAAI 362 (449)
Q Consensus 357 I~L~~f 362 (449)
|.|+.+
T Consensus 174 i~l~~~ 179 (209)
T TIGR02237 174 LRLEKF 179 (209)
T ss_pred EEEEec
Confidence 999875
No 24
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=99.47 E-value=8.4e-13 Score=134.99 Aligned_cols=195 Identities=11% Similarity=0.111 Sum_probs=126.1
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh------cCCcEEEEcCCC--ChhhHhhcCCC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV------HGQPLLYASPSK--DPRGFLGTLPS 190 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~------~g~~vl~vs~~e--~p~~il~~LP~ 190 (449)
..++|||+++||++||||||.|+++.|-++.++| ++.|+.+|+..... -+.+++|+++++ .|+.+.+.+-+
T Consensus 105 ~~~isTG~~~LD~lLgGGi~~G~ItEI~G~~GsG-KTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~ 183 (344)
T PLN03187 105 VVRITTGSQALDELLGGGIETRCITEAFGEFRSG-KTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAER 183 (344)
T ss_pred CceecCCcHhHHhhcCCCCCCCeEEEEecCCCCC-hhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence 5689999999999999999999999999998887 56788999876653 136899999988 57777765311
Q ss_pred CCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHH
Q 013117 191 PASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAA 270 (449)
Q Consensus 191 ~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~ 270 (449)
+.|..+.+. .++.+.. ..+.+.
T Consensus 184 ---------------------~g~d~~~~l----------------------------------~~I~~~~---~~~~e~ 205 (344)
T PLN03187 184 ---------------------FGMDADAVL----------------------------------DNIIYAR---AYTYEH 205 (344)
T ss_pred ---------------------cCCChhhhc----------------------------------CeEEEec---CCCHHH
Confidence 122211110 0011100 112223
Q ss_pred HHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCC------C-HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC---
Q 013117 271 LQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSN------M-DWEMLSFIKSLKGMVRSSNAVVVITFPPSL--- 340 (449)
Q Consensus 271 l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~------~-~~~ll~FL~~LR~llR~s~~taliT~p~~l--- 340 (449)
+...+..+...+.. .++.+|||||+.++...... . ...+.+|++.|+.+.+..|+++++|.....
T Consensus 206 ~~~~l~~l~~~i~~-----~~~~LvVIDSital~r~~~~~rg~l~~rq~~L~~~~~~L~~lA~~~~vavvvTNqv~~~~~ 280 (344)
T PLN03187 206 QYNLLLGLAAKMAE-----EPFRLLIVDSVIALFRVDFTGRGELAERQQKLAQMLSRLTKIAEEFNVAVYMTNQVIADPG 280 (344)
T ss_pred HHHHHHHHHHHHHh-----cCCCEEEEeCcHHhhhccccCccchHHHHHHHHHHHHHHHHHHHHcCCEEEEEecEEEcCC
Confidence 33222222222221 35889999999987432111 1 134889999999999999999999986421
Q ss_pred ----C-C---cchhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeeccc
Q 013117 341 ----L-S---LSSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARL 391 (449)
Q Consensus 341 ----~-~---~~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~l 391 (449)
+ + +.....|.|.++..|.|+-..+ -...++|.|-|.+
T Consensus 281 ~~~~~~~~~~pagG~~~~h~~~~Rl~l~k~~~--------------~~R~~~v~ksp~l 325 (344)
T PLN03187 281 GGMFISDPKKPAGGHVLAHAATIRLMLRKGKG--------------EQRVCKVFDAPNL 325 (344)
T ss_pred cccccCCCCCCCCchhhheeeeEEEEEEcCCC--------------CeEEEEEEECCCC
Confidence 1 1 1123568899999998875322 1367888888653
No 25
>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=99.44 E-value=8.8e-13 Score=126.65 Aligned_cols=177 Identities=16% Similarity=0.203 Sum_probs=111.2
Q ss_pred eecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcC------CcEEEEcCCCC--hhhHhhcCCCCCC
Q 013117 122 VSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHG------QPLLYASPSKD--PRGFLGTLPSPAS 193 (449)
Q Consensus 122 iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g------~~vl~vs~~e~--p~~il~~LP~~~~ 193 (449)
+||||++||++|+||+|.|.++.|.+++++| +++|+.++++.++..+ +.++|++.++. ++.+.+.+
T Consensus 1 ~~tG~~~lD~~l~GGi~~g~i~~i~G~~GsG-KT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~~~----- 74 (235)
T cd01123 1 LTTGSKALDELLGGGIETGSITEIFGEFGSG-KTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQIA----- 74 (235)
T ss_pred CCCCchhhHhhccCCCCCCeEEEEECCCCCC-HHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHHHH-----
Confidence 5899999999999999999999999998887 5788899999877664 89999998663 33333221
Q ss_pred cccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHH
Q 013117 194 LKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQE 273 (449)
Q Consensus 194 ~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~ 273 (449)
..+.|..+.+. .++.++.. .+...+.+
T Consensus 75 ----------------~~~~~~~~~~~----------------------------------~~i~~~~~---~~~~~l~~ 101 (235)
T cd01123 75 ----------------ERFGLDPEEVL----------------------------------DNIYVARA---YNSDHQLQ 101 (235)
T ss_pred ----------------HHhccChHhHh----------------------------------cCEEEEec---CCHHHHHH
Confidence 01222111110 01111111 11122222
Q ss_pred HHHHHHHHhhhccCCCCceeEEEEcCCCcccccC--CC-----CHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-CC---
Q 013117 274 HCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SN-----MDWEMLSFIKSLKGMVRSSNAVVVITFPPSL-LS--- 342 (449)
Q Consensus 274 ~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~-----~~~~ll~FL~~LR~llR~s~~taliT~p~~l-~~--- 342 (449)
.+..+...+.. ..++.+|||||+.++.+.. .+ ....+.+|+..|+.+.+..++++++|..... ..
T Consensus 102 ~l~~l~~~l~~----~~~~~liVIDSis~~~~~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~~avl~tn~~~~~~~~~~ 177 (235)
T cd01123 102 LLEELEAILIE----SSRIKLVIVDSVTALFRAEFDGRGELAERQQHLAKLLRTLKRLADEFNVAVVITNQVTARPDGAA 177 (235)
T ss_pred HHHHHHHHHhh----cCCeeEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEeccEeecCCccc
Confidence 22222222221 1278999999999875421 11 1246889999999999999999999976432 11
Q ss_pred ----c----chhhhhhhhcceEEEEEe
Q 013117 343 ----L----SSTKRWQHMADTLLSVAA 361 (449)
Q Consensus 343 ----~----~~~~~le~laDgVI~L~~ 361 (449)
. .....|.+.++..+.|+-
T Consensus 178 ~~~~~~~~p~lG~~w~~~v~~Rl~l~~ 204 (235)
T cd01123 178 MFGGDPKKPAGGNIWAHASTTRLYLRK 204 (235)
T ss_pred ccCCCCeeccCccHhhCCceEEEEEEE
Confidence 1 113566778888888765
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=99.43 E-value=1.9e-12 Score=130.99 Aligned_cols=180 Identities=13% Similarity=0.101 Sum_probs=117.5
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh------cCCcEEEEcCCCC--hhhHhhcCCC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV------HGQPLLYASPSKD--PRGFLGTLPS 190 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~------~g~~vl~vs~~e~--p~~il~~LP~ 190 (449)
..++|||+++||++||||+|.|+++.|.++.++| +++|+.+|++.... .+.+++|+++++. |+.+.+.+-.
T Consensus 75 ~~~isTG~~~LD~lLgGGi~~G~iteI~G~~GsG-KTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~ 153 (313)
T TIGR02238 75 VLKITTGSQALDGILGGGIESMSITEVFGEFRCG-KTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAER 153 (313)
T ss_pred CceeCCCCHHHHHHhCCCCcCCeEEEEECCCCCC-cCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHH
Confidence 4689999999999999999999999999998887 57888999876543 3579999999884 6766654211
Q ss_pred CCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHH
Q 013117 191 PASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAA 270 (449)
Q Consensus 191 ~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~ 270 (449)
+.|..+.+.+ ++.+. ...+.+.
T Consensus 154 ---------------------~g~d~~~~l~----------------------------------~i~~~---~~~~~e~ 175 (313)
T TIGR02238 154 ---------------------FGVDPDAVLD----------------------------------NILYA---RAYTSEH 175 (313)
T ss_pred ---------------------cCCChHHhcC----------------------------------cEEEe---cCCCHHH
Confidence 1222221110 01110 0011222
Q ss_pred HHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCC------CH-HHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--
Q 013117 271 LQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSN------MD-WEMLSFIKSLKGMVRSSNAVVVITFPPSLL-- 341 (449)
Q Consensus 271 l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~------~~-~~ll~FL~~LR~llR~s~~taliT~p~~l~-- 341 (449)
..+.+..+...+.. .++.+|||||+.++...... .+ ..+.+|++.|+.+.+..++++++|.....-
T Consensus 176 ~~~~l~~l~~~i~~-----~~~~LvVIDSisal~r~~~~~~g~~~~r~~~l~~~~~~L~~la~~~~vavvitNqv~~~~~ 250 (313)
T TIGR02238 176 QMELLDYLAAKFSE-----EPFRLLIVDSIMALFRVDFSGRGELSERQQKLAQMLSRLNKISEEFNVAVFVTNQVQADPG 250 (313)
T ss_pred HHHHHHHHHHHhhc-----cCCCEEEEEcchHhhhhhccCccchHHHHHHHHHHHHHHHHHHHHcCcEEEEECceEecCC
Confidence 33222232222221 36889999999987432111 01 247899999999999999999999864321
Q ss_pred -------Cc---chhhhhhhhcceEEEEEee
Q 013117 342 -------SL---SSTKRWQHMADTLLSVAAI 362 (449)
Q Consensus 342 -------~~---~~~~~le~laDgVI~L~~f 362 (449)
++ .....|.|.++..|.|+-.
T Consensus 251 ~~~~~~~~~~~p~gG~~~~h~~~~Rl~l~k~ 281 (313)
T TIGR02238 251 ATMTFIADPKKPIGGHVLAHASTTRILLRKG 281 (313)
T ss_pred cccccCCCCccCcchhhhhhheeEEEEEEec
Confidence 11 1135789999999999864
No 27
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=99.43 E-value=3.5e-12 Score=129.07 Aligned_cols=195 Identities=12% Similarity=0.135 Sum_probs=124.6
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc------CCcEEEEcCCC--ChhhHhhcCCC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH------GQPLLYASPSK--DPRGFLGTLPS 190 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~------g~~vl~vs~~e--~p~~il~~LP~ 190 (449)
...++||+++||++||||+|.|++++|.++.++| +++|+.+|+++.+.. +.+++|+++++ +++.+.+.+-+
T Consensus 81 ~~~~~Tg~~~lD~~l~GGi~~g~vtei~G~~GsG-KT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~~ 159 (317)
T PRK04301 81 VGKITTGSKELDELLGGGIETQSITEFYGEFGSG-KTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAEA 159 (317)
T ss_pred CCccCCCCHHHHHHhcCCccCCcEEEEECCCCCC-HhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHHH
Confidence 3568999999999999999999999999988887 578889999987654 24899999987 46666654211
Q ss_pred CCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHH
Q 013117 191 PASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAA 270 (449)
Q Consensus 191 ~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~ 270 (449)
+.|..+.+.+ ++.++...+......
T Consensus 160 ---------------------~g~~~~~~l~----------------------------------~i~~~~~~~~~~~~~ 184 (317)
T PRK04301 160 ---------------------LGLDPDEVLD----------------------------------NIHVARAYNSDHQML 184 (317)
T ss_pred ---------------------cCCChHhhhc----------------------------------cEEEEeCCCHHHHHH
Confidence 2222221110 011111000000112
Q ss_pred HHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccC-CC--C----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC---
Q 013117 271 LQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH-SN--M----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL--- 340 (449)
Q Consensus 271 l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~-~~--~----~~~ll~FL~~LR~llR~s~~taliT~p~~l--- 340 (449)
+.+.+..++.. ..++.+|||||+.++.+.. .. . ...+.+|++.|+.+++..++++++|.....
T Consensus 185 ~~~~l~~~i~~-------~~~~~lvVIDSisa~~~~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~vavl~tnqv~~~~~ 257 (317)
T PRK04301 185 LAEKAEELIKE-------GENIKLVIVDSLTAHFRAEYVGRGNLAERQQKLNKHLHDLLRLADLYNAAVVVTNQVMARPD 257 (317)
T ss_pred HHHHHHHHHhc-------cCceeEEEEECchHHhhhhccCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEeceEEeccc
Confidence 22222233321 1468899999999875431 11 1 234778999999999999999999986431
Q ss_pred --CCc----chhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeecc
Q 013117 341 --LSL----SSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVAR 390 (449)
Q Consensus 341 --~~~----~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~ 390 (449)
+.. .....|.|.++..|.|+-..+. ...++|.|=|.
T Consensus 258 ~~~~~~~~~~~G~~~~~~~~~rl~l~k~~~~--------------~R~~~v~k~~~ 299 (317)
T PRK04301 258 AFFGDPTQPIGGHILGHTATFRIYLRKSKGN--------------KRIARLVDSPH 299 (317)
T ss_pred cccCccccCCcchHhHhheeEEEEEEecCCC--------------ceEEEEEeCCC
Confidence 111 1124588999999999874331 35777777633
No 28
>PRK09354 recA recombinase A; Provisional
Probab=99.42 E-value=3.1e-12 Score=130.77 Aligned_cols=170 Identities=16% Similarity=0.213 Sum_probs=115.3
Q ss_pred CeEeecCchhHHHHhc-CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhh-HhhcCCCCCCccc
Q 013117 119 TMFVSSGIADLDKILG-GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRG-FLGTLPSPASLKH 196 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLG-GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~-il~~LP~~~~~~~ 196 (449)
..++|||+++||.+|| ||+|.|++++|.++.++| +++|+.+|++++...|..++|+++++.+.. +.+.
T Consensus 38 ~~~isTGi~~LD~~LG~GGip~G~IteI~G~~GsG-KTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a~~--------- 107 (349)
T PRK09354 38 VEVISTGSLALDIALGIGGLPRGRIVEIYGPESSG-KTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKK--------- 107 (349)
T ss_pred CceecCCcHHHHHHhcCCCCcCCeEEEEECCCCCC-HHHHHHHHHHHHHHcCCcEEEECCccchHHHHHHH---------
Confidence 5689999999999999 999999999999988777 578889999999999999999999776543 1111
Q ss_pred ccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHH
Q 013117 197 DKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCA 276 (449)
Q Consensus 197 ~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~ 276 (449)
+.|...++. .. ..++.+.....+.
T Consensus 108 ---------------lGvdld~ll--------------------------------------i~---qp~~~Eq~l~i~~ 131 (349)
T PRK09354 108 ---------------LGVDIDNLL--------------------------------------VS---QPDTGEQALEIAD 131 (349)
T ss_pred ---------------cCCCHHHeE--------------------------------------Ee---cCCCHHHHHHHHH
Confidence 222222211 00 0011223332222
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCccccc--CC----C-----CHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-----
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCE--HS----N-----MDWEMLSFIKSLKGMVRSSNAVVVITFPPSL----- 340 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~--~~----~-----~~~~ll~FL~~LR~llR~s~~taliT~p~~l----- 340 (449)
.+++ ...+.+|||||+.+.... .. + ....+-++|+.|..+++.+++++++|.....
T Consensus 132 ~li~--------s~~~~lIVIDSvaaL~~~~E~eg~~gd~~~~~qar~ms~~Lr~L~~~l~k~~itvI~tNQvr~~ig~~ 203 (349)
T PRK09354 132 TLVR--------SGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNISKSNTTVIFINQIREKIGVM 203 (349)
T ss_pred HHhh--------cCCCCEEEEeChhhhcchhhhcCCccccchhHHHHHHHHHHHHHHHHHHHcCcEEEEEEeeeeccccc
Confidence 2222 146889999999976421 00 0 0123557899999999999999999976432
Q ss_pred CC-cch---hhhhhhhcceEEEEEee
Q 013117 341 LS-LSS---TKRWQHMADTLLSVAAI 362 (449)
Q Consensus 341 ~~-~~~---~~~le~laDgVI~L~~f 362 (449)
|. +.. ...+.|++...+.|+-.
T Consensus 204 ~g~pe~~~GG~aL~~~ss~rl~lrr~ 229 (349)
T PRK09354 204 FGNPETTTGGNALKFYASVRLDIRRI 229 (349)
T ss_pred cCCCCcCCCchhhHhhheeeeEEecc
Confidence 22 222 24578888888888764
No 29
>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=99.41 E-value=4.3e-12 Score=124.73 Aligned_cols=217 Identities=12% Similarity=0.097 Sum_probs=130.1
Q ss_pred EeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 121 FVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 121 ~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
.++||+++||+++ ||++.|.+++|.+..++| +++|+.+|+++++.+ |++++|+++|+.++++.+.+-+...
T Consensus 12 ~~~tg~~~Ld~~~-gG~~~g~~~~i~g~~G~G-KT~l~~~~~~~~~~~~g~~vl~iS~E~~~~~~~~r~~~~~~------ 83 (271)
T cd01122 12 EVWWPFPVLNKLT-KGLRKGELIILTAGTGVG-KTTFLREYALDLITQHGVRVGTISLEEPVVRTARRLLGQYA------ 83 (271)
T ss_pred CCCCCcceeeeee-EEEcCCcEEEEEcCCCCC-HHHHHHHHHHHHHHhcCceEEEEEcccCHHHHHHHHHHHHh------
Confidence 7889999999999 799999999999887776 467889999999988 9999999999988888776421100
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFL 279 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L 279 (449)
.|++..... .... ....+...+| .+. ....+..+......+.+.+.+.+...+
T Consensus 84 -------------~~~~~~~~~--~~~~-----~~~~~~~~~~---~~~----~~~~l~i~d~~~~~~~~~i~~~i~~~~ 136 (271)
T cd01122 84 -------------GKRLHLPDT--VFIY-----TLEEFDAAFD---EFE----GTGRLFMYDSFGEYSMDSVLEKVRYMA 136 (271)
T ss_pred -------------CCCcccCCc--cccc-----cHHHHHHHHH---Hhc----CCCcEEEEcCCCccCHHHHHHHHHHHH
Confidence 011110000 0000 0000000000 000 000011100001113344444333332
Q ss_pred HHhhhccCCCCceeEEEEcCCCcccccC---CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCC----------cc--
Q 013117 280 AQHQRNDGSSALAGRIAIQSLCAPQCEH---SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLS----------LS-- 344 (449)
Q Consensus 280 ~~~~~~~~~~~~v~RIvIdSL~Sp~~~~---~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~----------~~-- 344 (449)
. . .++.+|+||++....... .+....+..++..|+.+.++.+++++++....-.. +.
T Consensus 137 ~----~----~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~~L~~la~~~~vtvll~sq~~~~~~~~~~~~~~~~~~~ 208 (271)
T cd01122 137 V----S----HGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSHLRRPDGDKTHEEGGEVSLS 208 (271)
T ss_pred h----c----CCceEEEECCHHHHhccCCCchhHHHHHHHHHHHHHHHHHHhCCEEEEEecccCccCCCccccCCCceEE
Confidence 2 1 367899999998764321 11234578899999999999999999998755321 11
Q ss_pred -h--hhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeee
Q 013117 345 -S--TKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKV 388 (449)
Q Consensus 345 -~--~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KL 388 (449)
+ ...+++.||+||.|+.....+ + .....-.|+|.|.
T Consensus 209 d~~gs~~i~~~aD~vi~l~r~~~~e-~-------~~~~~~~i~v~K~ 247 (271)
T cd01122 209 DFRGSAAIGQLADNVIALERNQQAE-L-------DERNTTYLRILKN 247 (271)
T ss_pred eccCcHhHhhhccEEEEEEecCccc-c-------ccCCcEEEEEEee
Confidence 1 246899999999999754321 0 1123467888887
No 30
>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=99.39 E-value=3.1e-12 Score=129.57 Aligned_cols=171 Identities=15% Similarity=0.209 Sum_probs=112.8
Q ss_pred CeEeecCchhHHHHhc-CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 119 TMFVSSGIADLDKILG-GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLG-GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
..++|||+++||.+|| ||+|.|++++|-++.++| +++|+.+|++++..+|.+|+|+++++.+.....+
T Consensus 33 ~~~i~TGi~~LD~~Lg~GGlp~G~iteI~G~~GsG-KTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~---------- 101 (321)
T TIGR02012 33 VETISTGSLSLDLALGVGGLPRGRIIEIYGPESSG-KTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAR---------- 101 (321)
T ss_pred CceecCCCHHHHHHhcCCCCcCCeEEEEECCCCCC-HHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHH----------
Confidence 4689999999999999 999999999999988777 5788899999999999999999987765442111
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
++.|...++. ... .++.+.....+..
T Consensus 102 -------------~lGvd~~~l~--------------------------------------v~~---p~~~eq~l~~~~~ 127 (321)
T TIGR02012 102 -------------KLGVDIDNLL--------------------------------------VSQ---PDTGEQALEIAET 127 (321)
T ss_pred -------------HcCCCHHHeE--------------------------------------Eec---CCCHHHHHHHHHH
Confidence 0122222111 000 0112233322222
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCcccccC--C-----C---C-HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-----C
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCEH--S-----N---M-DWEMLSFIKSLKGMVRSSNAVVVITFPPSL-----L 341 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~-----~---~-~~~ll~FL~~LR~llR~s~~taliT~p~~l-----~ 341 (449)
+++ ..++.+|||||+.+..... . + . ...+-+||+.|..+++..++++++|..... |
T Consensus 128 li~--------~~~~~lIVIDSv~al~~~~E~e~~~g~~~~~~~aR~m~~~lr~L~~~l~~~~~tvi~tNQvr~~~g~~~ 199 (321)
T TIGR02012 128 LVR--------SGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSKSNTTAIFINQIREKIGVMF 199 (321)
T ss_pred Hhh--------ccCCcEEEEcchhhhccchhhcccccccchhHHHHHHHHHHHHHHHHHHhCCCEEEEEecceeccCccc
Confidence 222 1468899999999764210 0 0 0 123458999999999999999999986432 2
Q ss_pred C-cch---hhhhhhhcceEEEEEee
Q 013117 342 S-LSS---TKRWQHMADTLLSVAAI 362 (449)
Q Consensus 342 ~-~~~---~~~le~laDgVI~L~~f 362 (449)
. +.. ...+.|++...+.|+-.
T Consensus 200 ~~~e~~~GG~aL~~~ss~r~~lrr~ 224 (321)
T TIGR02012 200 GNPETTTGGRALKFYASVRLDIRRI 224 (321)
T ss_pred CCCccCcCccHHHHHHhHhHhhhhh
Confidence 2 221 23467777777776543
No 31
>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=99.39 E-value=1e-11 Score=125.94 Aligned_cols=171 Identities=15% Similarity=0.228 Sum_probs=116.3
Q ss_pred CeEeecCchhHHHHhc-CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhh-HhhcCCCCCCccc
Q 013117 119 TMFVSSGIADLDKILG-GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRG-FLGTLPSPASLKH 196 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLG-GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~-il~~LP~~~~~~~ 196 (449)
..++|||+++||.+|| ||||.|++++|-++.++| +++|+.+|++++...|.+++|+++++.+.. +++.
T Consensus 33 ~~~isTGi~~LD~~Lg~GGlp~G~iteI~Gp~GsG-KTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~--------- 102 (325)
T cd00983 33 VEVIPTGSLSLDIALGIGGYPKGRIIEIYGPESSG-KTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKK--------- 102 (325)
T ss_pred CceecCCCHHHHHHhcCCCccCCeEEEEECCCCCC-HHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHH---------
Confidence 4689999999999999 999999999999988887 578889999999999999999998765432 2221
Q ss_pred ccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHH
Q 013117 197 DKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCA 276 (449)
Q Consensus 197 ~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~ 276 (449)
+.|...++. .. ...+.+.+.+.+.
T Consensus 103 ---------------lGvd~~~l~--------------------------------------v~---~p~~~eq~l~i~~ 126 (325)
T cd00983 103 ---------------LGVDLDNLL--------------------------------------IS---QPDTGEQALEIAD 126 (325)
T ss_pred ---------------cCCCHHHhe--------------------------------------ec---CCCCHHHHHHHHH
Confidence 122222111 00 0112233333332
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCccccc--CC-CC--------HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-----
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCE--HS-NM--------DWEMLSFIKSLKGMVRSSNAVVVITFPPSL----- 340 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~--~~-~~--------~~~ll~FL~~LR~llR~s~~taliT~p~~l----- 340 (449)
.+++ ...+.+|||||+.+..-. .. .. ...+.++|+.|..+++..++++++|.....
T Consensus 127 ~li~--------s~~~~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~~~Lr~L~~~~~k~~~~vI~tNQvr~~ig~~ 198 (325)
T cd00983 127 SLVR--------SGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSINKSNTTVIFINQLREKIGVM 198 (325)
T ss_pred HHHh--------ccCCCEEEEcchHhhcccccccccccccchHHHHHHHHHHHHHHHHHHHhCCCEEEEEEccccccccc
Confidence 3322 146889999999876321 00 00 124668999999999999999999987432
Q ss_pred C-Ccch---hhhhhhhcceEEEEEeeC
Q 013117 341 L-SLSS---TKRWQHMADTLLSVAAIP 363 (449)
Q Consensus 341 ~-~~~~---~~~le~laDgVI~L~~f~ 363 (449)
| ++.. ...|.|++...|.|+-..
T Consensus 199 ~g~~e~~~GG~~L~~~ss~rl~lrk~~ 225 (325)
T cd00983 199 FGNPETTTGGNALKFYSSVRLDIRRIE 225 (325)
T ss_pred cCCCccCCCchHHhhhcceEEEEEeec
Confidence 2 1222 245788899999888653
No 32
>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=99.32 E-value=4.5e-11 Score=120.35 Aligned_cols=197 Identities=13% Similarity=0.148 Sum_probs=123.6
Q ss_pred CCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhh-------hcCCcEEEEcCCC--ChhhHhhcC
Q 013117 118 GTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGL-------VHGQPLLYASPSK--DPRGFLGTL 188 (449)
Q Consensus 118 g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl-------~~g~~vl~vs~~e--~p~~il~~L 188 (449)
....++||+++||++||||||.|++++|-+++++| +++|+.+|+++.. .+| +++|+++++ +++.+.+.+
T Consensus 73 s~~~~~Tg~~~lD~~l~GGi~~g~i~ei~G~~g~G-KT~l~~~~~~~~~~~~~~g~~~~-~~~yi~te~~f~~~rl~~~~ 150 (310)
T TIGR02236 73 TIGKITTGSKELDELLGGGIETQAITEVFGEFGSG-KTQICHQLAVNVQLPEEKGGLGG-KAVYIDTENTFRPERIMQMA 150 (310)
T ss_pred cCCeecCCCHHHHHHhcCCCCCCeEEEEECCCCCC-HHHHHHHHHHHhcCCcccCCCcc-eEEEEECCCCCCHHHHHHHH
Confidence 35578999999999999999999999999998888 5788899998854 344 899999987 455555442
Q ss_pred CCCCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcch
Q 013117 189 PSPASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNL 268 (449)
Q Consensus 189 P~~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~ 268 (449)
-. +.|....+.+ ++.++..-.....
T Consensus 151 ~~---------------------~gl~~~~~~~----------------------------------~i~i~~~~~~~~~ 175 (310)
T TIGR02236 151 EA---------------------RGLDPDEVLK----------------------------------NIYVARAYNSNHQ 175 (310)
T ss_pred HH---------------------cCCCHHHHhh----------------------------------ceEEEecCCHHHH
Confidence 11 1111110000 0000000000000
Q ss_pred HHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccC-CCC------HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-
Q 013117 269 AALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH-SNM------DWEMLSFIKSLKGMVRSSNAVVVITFPPSL- 340 (449)
Q Consensus 269 ~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~-~~~------~~~ll~FL~~LR~llR~s~~taliT~p~~l- 340 (449)
..+.+.+.+++++.. ..+.+|+|||+.++.... ... ...+.++++.|+.+.+..++++++|.....
T Consensus 176 ~~lld~l~~~i~~~~------~~~~lVVIDSisa~~r~e~~~~~~~~~r~~~l~~~~~~L~~~a~~~~~~v~~tnqv~~~ 249 (310)
T TIGR02236 176 MLLVEKAEDLIKELN------NPVKLLIVDSLTSHFRAEYVGRGALAERQQKLNKHLHDLLRLADLYNAAVVVTNQVMAR 249 (310)
T ss_pred HHHHHHHHHHHHhcC------CCceEEEEecchHhhhHhhcCchhHHHHHHHHHHHHHHHHHHHHHhCcEEEEeceeeec
Confidence 122333334443211 247899999999874321 110 123678899999999999999999986421
Q ss_pred ----CCc----chhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeeccc
Q 013117 341 ----LSL----SSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARL 391 (449)
Q Consensus 341 ----~~~----~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~l 391 (449)
+.. .....|.|+++..|.|+-..+. ...++|.|=|.+
T Consensus 250 ~~~~~~~~~~~~~G~~~~h~~~~rl~l~~~~~~--------------~R~~~~~k~~~~ 294 (310)
T TIGR02236 250 PDAFFGDPTRPIGGHILGHAATFRVYLRKGKGD--------------KRIARLVDSPHL 294 (310)
T ss_pred CccccCccccCCcchhhhhheeEEEEEEecCCC--------------eEEEEEEECCCC
Confidence 111 1246789999999999874321 357788776443
No 33
>PTZ00035 Rad51 protein; Provisional
Probab=99.31 E-value=3.9e-11 Score=122.69 Aligned_cols=180 Identities=16% Similarity=0.177 Sum_probs=113.6
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh------cCCcEEEEcCCCC--hhhHhhcCCC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV------HGQPLLYASPSKD--PRGFLGTLPS 190 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~------~g~~vl~vs~~e~--p~~il~~LP~ 190 (449)
..++|||+++||++||||+|.|+++.|.++.++| +++|+.+|+..... .+..++|+++++. ++.+..-+-.
T Consensus 97 ~~~isTG~~~LD~lLgGGi~~G~iteI~G~~GsG-KT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri~~ia~~ 175 (337)
T PTZ00035 97 IIRITTGSTQLDKLLGGGIETGSITELFGEFRTG-KTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIAER 175 (337)
T ss_pred CccccCCcHHHHHHhCCCCCCCeEEEEECCCCCc-hhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHHHHHHHH
Confidence 4679999999999999999999999999988887 46788888876542 4668899998763 5544432100
Q ss_pred CCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHH
Q 013117 191 PASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAA 270 (449)
Q Consensus 191 ~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~ 270 (449)
+.|....+. .++.+.. ..+.+.
T Consensus 176 ---------------------~g~~~~~~l----------------------------------~nI~~~~---~~~~e~ 197 (337)
T PTZ00035 176 ---------------------FGLDPEDVL----------------------------------DNIAYAR---AYNHEH 197 (337)
T ss_pred ---------------------hCCChHhHh----------------------------------hceEEEc---cCCHHH
Confidence 111110000 0011110 112223
Q ss_pred HHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCC---C----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC---
Q 013117 271 LQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSN---M----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL--- 340 (449)
Q Consensus 271 l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~---~----~~~ll~FL~~LR~llR~s~~taliT~p~~l--- 340 (449)
+.+.+..+.+.+. ..++.+|||||+.++...... . ...+.+|++.|+.+.+..++++++|.....
T Consensus 198 ~~~~l~~~~~~l~-----~~~~~lvVIDSital~r~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~vavvvtNqv~~~~~ 272 (337)
T PTZ00035 198 QMQLLSQAAAKMA-----EERFALLIVDSATALFRVDYSGRGELAERQQHLGKFLRALQKLADEFNVAVVITNQVMADVD 272 (337)
T ss_pred HHHHHHHHHHHhh-----ccCccEEEEECcHHhhhhhccCcccHHHHHHHHHHHHHHHHHHHHHcCcEEEEecceEEecC
Confidence 3332222222222 146889999999986432111 0 234788999999999999999999985432
Q ss_pred ----C-Cc----chhhhhhhhcceEEEEEee
Q 013117 341 ----L-SL----SSTKRWQHMADTLLSVAAI 362 (449)
Q Consensus 341 ----~-~~----~~~~~le~laDgVI~L~~f 362 (449)
+ .. .....|.|.++..|.|+-.
T Consensus 273 ~~~~~~~~~~~p~gG~~~~h~~~~Rl~l~k~ 303 (337)
T PTZ00035 273 GASMFVADPKKPIGGHIIAHASTTRLSLRKG 303 (337)
T ss_pred CccccCCCCccCCchHHHHhheeEEEEEEec
Confidence 1 11 1135688999999999864
No 34
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=99.27 E-value=8e-11 Score=120.50 Aligned_cols=196 Identities=16% Similarity=0.150 Sum_probs=120.2
Q ss_pred CCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh------cCCcEEEEcCCC--ChhhHhhcCC
Q 013117 118 GTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV------HGQPLLYASPSK--DPRGFLGTLP 189 (449)
Q Consensus 118 g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~------~g~~vl~vs~~e--~p~~il~~LP 189 (449)
...+++||+++||++||||+|.|+++.|.+.+++| ++.|+.+++..-.. .+.+++|+++++ .|+.+.+-+-
T Consensus 101 ~~~~i~tG~~~LD~lL~GG~~~g~i~~i~G~~g~G-KT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~ 179 (342)
T PLN03186 101 EIIQITTGSRELDKILEGGIETGSITEIYGEFRTG-KTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAE 179 (342)
T ss_pred CcceeCCCCHHHHHhhcCCCcCceEEEEECCCCCC-ccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHHHH
Confidence 35689999999999999999999999999888777 45666666543221 124899999987 4665554320
Q ss_pred CCCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchH
Q 013117 190 SPASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLA 269 (449)
Q Consensus 190 ~~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~ 269 (449)
++.|..+.+.+ ++.+.. ..+.+
T Consensus 180 ---------------------~~~~~~~~~l~----------------------------------~i~~~~---~~~~e 201 (342)
T PLN03186 180 ---------------------RFGLNGADVLE----------------------------------NVAYAR---AYNTD 201 (342)
T ss_pred ---------------------HcCCChhhhcc----------------------------------ceEEEe---cCCHH
Confidence 11222221110 011100 01122
Q ss_pred HHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCC---C----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--
Q 013117 270 ALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSN---M----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL-- 340 (449)
Q Consensus 270 ~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~---~----~~~ll~FL~~LR~llR~s~~taliT~p~~l-- 340 (449)
.+...+......+. ..++.+|||||+.++...... . ...+.+|+..|+.+.+..++++++|.....
T Consensus 202 ~~~~ll~~~~~~~~-----~~~~~LIVIDSI~alfr~~~~~~g~l~~r~~~L~~~l~~L~~lA~~~~vaVviTNqv~~~~ 276 (342)
T PLN03186 202 HQSELLLEAASMMA-----ETRFALMIVDSATALYRTEFSGRGELSARQMHLGKFLRSLQRLADEFGVAVVITNQVVAQV 276 (342)
T ss_pred HHHHHHHHHHHHhh-----ccCCCEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHcCCEEEEEcCEEEcc
Confidence 22222211111111 146889999999987442111 0 124789999999999999999999986521
Q ss_pred -----CC-----cchhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeeccc
Q 013117 341 -----LS-----LSSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARL 391 (449)
Q Consensus 341 -----~~-----~~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~l 391 (449)
+. +.....|.|.++..|.|+-..+ -...++|.|=|.+
T Consensus 277 ~~~~~~~~~~~~P~gG~~~~h~~~tRl~L~k~~~--------------~~R~~~v~ksp~~ 323 (342)
T PLN03186 277 DGSAFFAGPQLKPIGGNIMAHASTTRLALRKGRG--------------ENRICKVISSPCL 323 (342)
T ss_pred CCccccCCCccccchhHHHHhhccEEEEEEecCC--------------CeEEEEEEECCCC
Confidence 11 1123578999999999985322 1366777776444
No 35
>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=99.25 E-value=7.7e-11 Score=119.54 Aligned_cols=195 Identities=17% Similarity=0.196 Sum_probs=119.4
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh---c---CCcEEEEcCCCC--hhhHhhcCCC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV---H---GQPLLYASPSKD--PRGFLGTLPS 190 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~---~---g~~vl~vs~~e~--p~~il~~LP~ 190 (449)
..+++||+++||++||||+|.|+++.|.+..++| +++|+.+++..-.. + ++.++|++.++. ++.+...+-
T Consensus 75 ~~~~~tg~~~lD~ll~gGi~~g~i~~i~G~~g~G-KT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl~~ia~- 152 (316)
T TIGR02239 75 VIQLTTGSKELDKLLGGGIETGSITEIFGEFRTG-KTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERLLAIAE- 152 (316)
T ss_pred cceeCCCCHHHHHHhcCCCCCCeEEEEECCCCCC-cCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHHHHHHH-
Confidence 5689999999999999999999999999988887 56777877763221 2 258899998763 444333210
Q ss_pred CCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHH
Q 013117 191 PASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAA 270 (449)
Q Consensus 191 ~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~ 270 (449)
++.|...++. .++.+.. ..+...
T Consensus 153 --------------------~~~~~~~~~l----------------------------------~~i~~~~---~~~~~~ 175 (316)
T TIGR02239 153 --------------------RYGLNPEDVL----------------------------------DNVAYAR---AYNTDH 175 (316)
T ss_pred --------------------HcCCChHHhh----------------------------------ccEEEEe---cCChHH
Confidence 0111111100 0011100 011222
Q ss_pred HHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCC---C----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC---
Q 013117 271 LQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSN---M----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL--- 340 (449)
Q Consensus 271 l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~---~----~~~ll~FL~~LR~llR~s~~taliT~p~~l--- 340 (449)
+...+..+...+. ..++.+|||||+.++...... . ...+.+|+..|+.+.++.++++++|.....
T Consensus 176 ~~~~l~~~~~~~~-----~~~~~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~vavv~tNqv~~~~~ 250 (316)
T TIGR02239 176 QLQLLQQAAAMMS-----ESRFALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLADEFGVAVVITNQVVAQVD 250 (316)
T ss_pred HHHHHHHHHHhhc-----cCCccEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEEECceEEecC
Confidence 2222222212111 146889999999987432211 1 124679999999999999999999986541
Q ss_pred -----C-C----cchhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeeccc
Q 013117 341 -----L-S----LSSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARL 391 (449)
Q Consensus 341 -----~-~----~~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~l 391 (449)
+ . +.....|+|.++..|.|+-..+. ...++|.|=|.+
T Consensus 251 ~~~~~~~g~~~~p~gG~~~~h~~~~ri~l~k~~~~--------------~R~~~v~ksp~~ 297 (316)
T TIGR02239 251 GAGSMFAGDPKKPIGGNIMAHASTTRLSLRKGRGE--------------QRICKIYDSPCL 297 (316)
T ss_pred CccccccCCCCcCCchHHHHhhccEEEEEEecCCC--------------eEEEEEEECCCC
Confidence 1 0 11246789999999999864321 256777776443
No 36
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=99.17 E-value=3.3e-10 Score=125.96 Aligned_cols=170 Identities=13% Similarity=0.173 Sum_probs=114.1
Q ss_pred CCeEeecCchhHHHHhc-CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChh-hHhhcCCCCCCcc
Q 013117 118 GTMFVSSGIADLDKILG-GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPR-GFLGTLPSPASLK 195 (449)
Q Consensus 118 g~~~iSTGIp~LD~lLG-GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~-~il~~LP~~~~~~ 195 (449)
...++|||+++||.+|| ||+|.|++++|.+..++| +++|+.+|++++...|++|+|+++++... ...+.
T Consensus 37 ~v~~isTGi~~LD~lLg~GGip~GsiteI~G~~GsG-KTtLal~~~~~a~~~G~~v~yId~E~t~~~~~A~~-------- 107 (790)
T PRK09519 37 PISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSG-KTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKK-------- 107 (790)
T ss_pred CCceecCCcHHHHHhhcCCCccCCeEEEEECCCCCC-HHHHHHHHHHHHHHcCCcEEEECCccchhHHHHHH--------
Confidence 35699999999999999 999999999999988887 57888999999999999999999876654 22222
Q ss_pred cccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHH
Q 013117 196 HDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHC 275 (449)
Q Consensus 196 ~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i 275 (449)
+.|...++. +. + ..+.+.+...+
T Consensus 108 ----------------lGvDl~~ll--------------------------------------v~--~-~~~~E~~l~~i 130 (790)
T PRK09519 108 ----------------LGVDTDSLL--------------------------------------VS--Q-PDTGEQALEIA 130 (790)
T ss_pred ----------------cCCChhHeE--------------------------------------Ee--c-CCCHHHHHHHH
Confidence 111111100 00 0 01112222222
Q ss_pred HHHHHHhhhccCCCCceeEEEEcCCCccccc--C----CCC-----HHHHHHHHHHHHHhhhhcCcEEEEeeCCCC----
Q 013117 276 ASFLAQHQRNDGSSALAGRIAIQSLCAPQCE--H----SNM-----DWEMLSFIKSLKGMVRSSNAVVVITFPPSL---- 340 (449)
Q Consensus 276 ~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~--~----~~~-----~~~ll~FL~~LR~llR~s~~taliT~p~~l---- 340 (449)
..+++ ..++..|||||+.+..-. . .+. ...+.+||+.|..+++..|+++++|.....
T Consensus 131 ~~lv~--------~~~~~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~q~L~~L~~~l~~~nvtvi~TNQv~~~~g~ 202 (790)
T PRK09519 131 DMLIR--------SGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGV 202 (790)
T ss_pred HHHhh--------cCCCeEEEEcchhhhcchhhccCCCCcccHHHHHHHHHHHHHHHHHHHHhCCCEEEEEecceecCCC
Confidence 22222 146789999999976420 0 001 122458999999999999999999986542
Q ss_pred -CCc-ch---hhhhhhhcceEEEEEe
Q 013117 341 -LSL-SS---TKRWQHMADTLLSVAA 361 (449)
Q Consensus 341 -~~~-~~---~~~le~laDgVI~L~~ 361 (449)
|.+ .. ...|.|.+-.-|.|+-
T Consensus 203 ~fg~p~~~~GG~~l~h~ss~Ri~lrk 228 (790)
T PRK09519 203 MFGSPETTTGGKALKFYASVRMDVRR 228 (790)
T ss_pred cCCCCCcCCCCcccceeccEEEEeee
Confidence 222 11 2557888888888875
No 37
>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=99.17 E-value=3.6e-10 Score=109.03 Aligned_cols=193 Identities=17% Similarity=0.149 Sum_probs=118.8
Q ss_pred hHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCcccccccccchhh
Q 013117 128 DLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLKHDKSRDRESEQ 206 (449)
Q Consensus 128 ~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~~~~~~~ 206 (449)
+||++++ ||+.|++++|.+.+++| +++|+.+|+++++.+ |++++|+++|+.++++++.+-+..
T Consensus 2 ~LD~~~~-Gl~~G~l~lI~G~~G~G-KT~~~~~~~~~~~~~~g~~vly~s~E~~~~~~~~r~~~~~-------------- 65 (242)
T cd00984 2 DLDNLTG-GLQPGDLIIIAARPSMG-KTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQRLLASE-------------- 65 (242)
T ss_pred chhhhhc-CCCCCeEEEEEeCCCCC-HHHHHHHHHHHHHHhCCCceEEEeCCCCHHHHHHHHHHHh--------------
Confidence 7999997 99999999999888777 578889999999998 999999999999999888752211
Q ss_pred ccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHHHhhhcc
Q 013117 207 EKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQHQRND 286 (449)
Q Consensus 207 ~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~~~~~~ 286 (449)
..|.+.... ++.... . ....+....+ .+. ...+... .....+++.+.+.|..+.+ +
T Consensus 66 -----~~~~~~~~~-~~~~~~--~--~~~~~~~~~~---~~~-----~~~~~i~-~~~~~~~~~l~~~i~~~~~----~- 121 (242)
T cd00984 66 -----SGISLSKLR-TGSLSD--E--DWERLAEAIG---ELK-----ELPIYID-DSSSLTVSDIRSRARRLKK----E- 121 (242)
T ss_pred -----cCCCHHHHh-cCCCCH--H--HHHHHHHHHH---HHh-----cCCEEEe-CCCCCCHHHHHHHHHHHHH----h-
Confidence 112221110 000000 0 0000000000 000 0011110 0111234555544444333 1
Q ss_pred CCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc---h--hhhhhhh
Q 013117 287 GSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS---S--TKRWQHM 352 (449)
Q Consensus 287 ~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~---~--~~~le~l 352 (449)
.++.+|+||++....... .+...++..++..|+.+.+..+++++++.+..-- . +. + ...+++.
T Consensus 122 ---~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q~~r~~~~~~~~~~~~~~~~gS~~i~~~ 198 (242)
T cd00984 122 ---HGLGLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQLSRGVESRADKRPMLSDLRESGSIEQD 198 (242)
T ss_pred ---cCCCEEEEcCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhhhccCCCCCCHHHHhhhcccccC
Confidence 367899999998654322 1224578999999999999999999999865421 1 11 1 1346889
Q ss_pred cceEEEEEeeC
Q 013117 353 ADTLLSVAAIP 363 (449)
Q Consensus 353 aDgVI~L~~f~ 363 (449)
||+||.|+...
T Consensus 199 aD~vi~l~~~~ 209 (242)
T cd00984 199 ADVVMFLYRDE 209 (242)
T ss_pred CCEEEEEeccc
Confidence 99999998753
No 38
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.11 E-value=1.1e-09 Score=112.69 Aligned_cols=168 Identities=19% Similarity=0.238 Sum_probs=112.3
Q ss_pred CCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 118 GTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 118 g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
..++++||+.+||++||||+-.||.+||-+|++-| +++||.|-+++=..++ +++||+.||+++||.-..
T Consensus 71 ~~~Ri~tg~~EldRVLGGG~V~Gs~iLIgGdPGIG-KSTLLLQva~~lA~~~-~vLYVsGEES~~QiklRA--------- 139 (456)
T COG1066 71 EEPRISTGIEELDRVLGGGLVPGSVILIGGDPGIG-KSTLLLQVAARLAKRG-KVLYVSGEESLQQIKLRA--------- 139 (456)
T ss_pred ecccccCChHHHHhhhcCCcccccEEEEccCCCCC-HHHHHHHHHHHHHhcC-cEEEEeCCcCHHHHHHHH---------
Confidence 36899999999999999999999999999999887 5788888887755455 999999999999987642
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
-|++-.. .++..+ . -.+++.
T Consensus 140 ----------------~RL~~~~----------------------------------~~l~l~--a-Et~~e~------- 159 (456)
T COG1066 140 ----------------DRLGLPT----------------------------------NNLYLL--A-ETNLED------- 159 (456)
T ss_pred ----------------HHhCCCc----------------------------------cceEEe--h-hcCHHH-------
Confidence 1222100 000000 0 012222
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCccccc---CC-CCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcch-hhhhhhh
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCE---HS-NMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSS-TKRWQHM 352 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~---~~-~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~-~~~le~l 352 (449)
+++.+.. .+..=++|||+-..... .. -.-..+..=-..|..+.++.|.+.++.-+...-..-- ..-+||+
T Consensus 160 I~~~l~~-----~~p~lvVIDSIQT~~s~~~~SapGsVsQVRe~t~~L~~~AK~~~i~~fiVGHVTKeG~IAGPrvLEHm 234 (456)
T COG1066 160 IIAELEQ-----EKPDLVVIDSIQTLYSEEITSAPGSVSQVREVAAELMRLAKTKNIAIFIVGHVTKEGAIAGPRVLEHM 234 (456)
T ss_pred HHHHHHh-----cCCCEEEEeccceeecccccCCCCcHHHHHHHHHHHHHHHHHcCCeEEEEEEEcccccccCchheeee
Confidence 2333322 35678999998654211 11 1223567777788899999999999887654322111 2456999
Q ss_pred cceEEEEEe
Q 013117 353 ADTLLSVAA 361 (449)
Q Consensus 353 aDgVI~L~~ 361 (449)
+|+|+.++.
T Consensus 235 VDtVlyFEG 243 (456)
T COG1066 235 VDTVLYFEG 243 (456)
T ss_pred eeEEEEEec
Confidence 999998765
No 39
>PRK05973 replicative DNA helicase; Provisional
Probab=99.09 E-value=9.5e-10 Score=107.22 Aligned_cols=141 Identities=13% Similarity=0.121 Sum_probs=96.2
Q ss_pred HHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccccccchhhcc
Q 013117 129 LDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSRDRESEQEK 208 (449)
Q Consensus 129 LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~~~~~~~~~ 208 (449)
+|+ |.||+|.|+++||.+.+++| +++|..+|+.+|+.+|++++|+++|++++++.+.+-+.
T Consensus 54 ~~~-l~GGl~~Gsl~LIaG~PG~G-KT~lalqfa~~~a~~Ge~vlyfSlEes~~~i~~R~~s~----------------- 114 (237)
T PRK05973 54 AEE-LFSQLKPGDLVLLGARPGHG-KTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRAL----------------- 114 (237)
T ss_pred HHH-hcCCCCCCCEEEEEeCCCCC-HHHHHHHHHHHHHhcCCeEEEEEEeCCHHHHHHHHHHc-----------------
Confidence 788 55699999999999888787 56788999999999999999999999999999985222
Q ss_pred ccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHHHhhhccCC
Q 013117 209 GLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQHQRNDGS 288 (449)
Q Consensus 209 ~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~~~~~~~~ 288 (449)
.|....+.. . ..||.... ..... ++.++..+
T Consensus 115 ----g~d~~~~~~--~--------------~~~d~~d~-------------------~~~~~-------ii~~l~~~--- 145 (237)
T PRK05973 115 ----GADRAQFAD--L--------------FEFDTSDA-------------------ICADY-------IIARLASA--- 145 (237)
T ss_pred ----CCChHHhcc--c--------------eEeecCCC-------------------CCHHH-------HHHHHHHh---
Confidence 233222110 0 01111100 01111 12222211
Q ss_pred CCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC
Q 013117 289 SALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL 340 (449)
Q Consensus 289 ~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l 340 (449)
.++.|||||+|........ ..++..++..|+.+++..+++++++...+-
T Consensus 146 -~~~~lVVIDsLq~l~~~~~--~~el~~~~~~Lk~~Ak~~gitvIl~sQl~r 194 (237)
T PRK05973 146 -PRGTLVVIDYLQLLDQRRE--KPDLSVQVRALKSFARERGLIIVFISQIDR 194 (237)
T ss_pred -hCCCEEEEEcHHHHhhccc--chhHHHHHHHHHHHHHhCCCeEEEEecCcc
Confidence 2457999999987643221 235788899999999999999999987653
No 40
>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=98.92 E-value=3.2e-08 Score=91.23 Aligned_cols=47 Identities=17% Similarity=0.359 Sum_probs=41.5
Q ss_pred EEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCC
Q 013117 142 LVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLP 189 (449)
Q Consensus 142 ~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP 189 (449)
++||.|++++| +++|..+|+++|+.+|++++|++++++++++++.+-
T Consensus 1 ~~li~G~~G~G-KT~l~~~~~~~~~~~g~~v~~~s~e~~~~~~~~~~~ 47 (187)
T cd01124 1 STLLSGGPGTG-KTTFALQFLYAGLARGEPGLYVTLEESPEELIENAE 47 (187)
T ss_pred CEEEEcCCCCC-HHHHHHHHHHHHHHCCCcEEEEECCCCHHHHHHHHH
Confidence 47888888887 578889999999999999999999999999998753
No 41
>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=98.90 E-value=3.1e-08 Score=97.69 Aligned_cols=195 Identities=18% Similarity=0.229 Sum_probs=119.5
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh------cCCcEEEEcCCCC--hhhHhhcCCC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV------HGQPLLYASPSKD--PRGFLGTLPS 190 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~------~g~~vl~vs~~e~--p~~il~~LP~ 190 (449)
...+|||+++||++|+|||+.|.++=|-|..++| ++.|+.+.++.=.. .+..++|++++.. ++.+.+-+
T Consensus 17 ~~~i~Tg~~~lD~~L~GGi~~g~itEi~G~~gsG-KTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~-- 93 (256)
T PF08423_consen 17 WSRISTGCKSLDELLGGGIPTGSITEIVGESGSG-KTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQIA-- 93 (256)
T ss_dssp S-EE--SSHHHHHHTTSSEETTSEEEEEESTTSS-HHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHHHH--
T ss_pred CCeeCCCCHHHHHhhCCCCCCCcEEEEEEecccc-cchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHHHh--
Confidence 4689999999999999999999999999998888 46788888766443 2567999987653 22222210
Q ss_pred CCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHH
Q 013117 191 PASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAA 270 (449)
Q Consensus 191 ~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~ 270 (449)
=+|..-. ++.+ .++.+... .++..
T Consensus 94 -----------------------~~~~~~~----------------------------~~~l--~~I~v~~~---~~~~~ 117 (256)
T PF08423_consen 94 -----------------------ERFGLDP----------------------------EEIL--DNIFVIRV---FDLEE 117 (256)
T ss_dssp -----------------------HHTTS-H----------------------------HHHH--HTEEEEE----SSHHH
T ss_pred -----------------------hcccccc----------------------------chhh--hceeeeec---CCHHH
Confidence 0111000 0000 01222111 12334
Q ss_pred HHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCC----C---CHHHHHHHHHHHHHhhhhcCcEEEEeeCCC-CCC
Q 013117 271 LQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHS----N---MDWEMLSFIKSLKGMVRSSNAVVVITFPPS-LLS 342 (449)
Q Consensus 271 l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~----~---~~~~ll~FL~~LR~llR~s~~taliT~p~~-l~~ 342 (449)
+.+.+.++...+.. .++.=|||||+.++.+... + ....+.+++..|+.+.++.++++++|.... ..+
T Consensus 118 l~~~L~~l~~~l~~-----~~ikLIVIDSIaalfr~e~~~~~~~~~R~~~L~~~~~~L~~lA~~~~iaVvvTNqv~~~~~ 192 (256)
T PF08423_consen 118 LLELLEQLPKLLSE-----SKIKLIVIDSIAALFRSEFSGRGDLAERQRMLARLARILKRLARKYNIAVVVTNQVTTKID 192 (256)
T ss_dssp HHHHHHHHHHHHHH-----SCEEEEEEETSSHHHHHHSGSTTTHHHHHHHHHHHHHHHHHHHHHTT-EEEEEEEECSSTT
T ss_pred HHHHHHHHHhhccc-----cceEEEEecchHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHHhCCceEEeeceeeecCC
Confidence 44333333232322 4689999999999854211 1 124789999999999999999999988543 111
Q ss_pred -----------cchhhhhhhhcceEEEEEeeCCCcHHHhhhccCCCCcceeEEEeeeccc
Q 013117 343 -----------LSSTKRWQHMADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNVHKVARL 391 (449)
Q Consensus 343 -----------~~~~~~le~laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V~KLp~l 391 (449)
|.....|.|.++.-|.|+-..++ ...+.|.|=|.+
T Consensus 193 ~~~~~~~~~~~PalG~~w~h~~~~Rl~l~k~~~~--------------~R~~~i~ksp~~ 238 (256)
T PF08423_consen 193 SNSLFDGDRLKPALGHSWSHAVTTRLFLSKGRGS--------------ERVATIVKSPSL 238 (256)
T ss_dssp ----SSTTSEEETTHHHHHHHSSEEEEEEECSTT--------------EEEEEEEECSSS
T ss_pred cccccccccceecCcchhhhhccEEEEEEeCCCC--------------eEEEEEeECCCC
Confidence 12246789999999999864331 477888887544
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=98.89 E-value=1.8e-08 Score=106.08 Aligned_cols=200 Identities=16% Similarity=0.167 Sum_probs=120.1
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh-cCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV-HGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~-~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
...++||+++||+++| |++.|.+++|.+.++.| +++|+.+|+..++. +|++++|+|+|..+++++..+-+..+.-+-
T Consensus 175 ~~gi~tG~~~LD~~~~-G~~~G~l~vi~g~pg~G-KT~~~l~~a~~~a~~~g~~vl~~SlEm~~~~i~~R~~~~~~~v~~ 252 (434)
T TIGR00665 175 ITGVPTGFTDLDKLTS-GLQPSDLIILAARPSMG-KTAFALNIAENAAIKEGKPVAFFSLEMSAEQLAMRMLSSESRVDS 252 (434)
T ss_pred CCcccCCchhhHhhcC-CCCCCeEEEEEeCCCCC-hHHHHHHHHHHHHHhCCCeEEEEeCcCCHHHHHHHHHHHhcCCCH
Confidence 4568999999999995 99999999999888777 46788999999886 699999999999999988764221110000
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
-+| +.+.+..+ ....+....+ .+. ...+. +.-....+...+...+..
T Consensus 253 ------------~~~--~~g~l~~~----------~~~~~~~a~~---~l~-----~~~l~-i~d~~~~~~~~i~~~i~~ 299 (434)
T TIGR00665 253 ------------QKL--RTGKLSDE----------DWEKLTSAAG---KLS-----EAPLY-IDDTPGLTITELRAKARR 299 (434)
T ss_pred ------------HHh--ccCCCCHH----------HHHHHHHHHH---HHh-----cCCEE-EECCCCCCHHHHHHHHHH
Confidence 000 00000000 0000000000 000 00111 100111234455544433
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCcccccCC--CCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--C-----Ccc---h
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCEHS--NMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL--L-----SLS---S 345 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~--~~~~~ll~FL~~LR~llR~s~~taliT~p~~l--~-----~~~---~ 345 (449)
+.+ + .++.+|+||+|........ +...++..+...||.+.++.+++++++....- . .+. +
T Consensus 300 ~~~----~----~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i~vi~lsqlnr~~~~r~~~~p~lsdl 371 (434)
T TIGR00665 300 LKR----E----HGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNVPVIALSQLSRSVEQREDKRPQLSDL 371 (434)
T ss_pred HHH----h----cCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEeccCcchhccCCCCCChHHH
Confidence 332 2 3578999999975422111 12346888899999999999999999886432 1 111 1
Q ss_pred --hhhhhhhcceEEEEEe
Q 013117 346 --TKRWQHMADTLLSVAA 361 (449)
Q Consensus 346 --~~~le~laDgVI~L~~ 361 (449)
...++..||.||.|+.
T Consensus 372 r~Sg~ieq~aD~vi~l~r 389 (434)
T TIGR00665 372 RESGSIEQDADIVMFLYR 389 (434)
T ss_pred hhccchhhcCCEEEEecc
Confidence 2457899999999975
No 43
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=98.81 E-value=3.3e-07 Score=90.17 Aligned_cols=230 Identities=20% Similarity=0.217 Sum_probs=139.6
Q ss_pred hhHHHHhc---CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccccccc
Q 013117 127 ADLDKILG---GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSRDRE 203 (449)
Q Consensus 127 p~LD~lLG---GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~~~~ 203 (449)
++|+.+|. +..|.|.++||++. .++ ++-|+-+|+..=++.|.+++++++.++..+|-+-+
T Consensus 3 ~eln~ll~~~~~~~~~g~~ili~d~-~~d-gsFLlh~~L~~~Lk~~~~V~fv~~~q~~~HY~~v~--------------- 65 (249)
T PF09807_consen 3 PELNSLLNWSPDSVPPGKLILIEDC-ETD-GSFLLHHFLSQYLKAGCKVCFVAFSQSFSHYNNVA--------------- 65 (249)
T ss_pred hHHHHHhcCCCCCCCCCeEEEEEcC-CCC-chhHHHHHHHHHhcCCCcEEEEEccCCHHHHHHHH---------------
Confidence 57888886 68899999999888 565 78889999999999999999999988888877753
Q ss_pred hhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccc-----c-ccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 204 SEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPL-----E-RHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 204 ~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l-----~-~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
+|+.+....+.++++ -..+|.-+.. + +..-......++.-.....+..+++.|.+
T Consensus 66 ------~KLG~NL~~~~~~gq-------------l~fiD~l~~~~~~l~~~~~~~~~~~~~~l~~~~~~~L~~L~~~I~~ 126 (249)
T PF09807_consen 66 ------QKLGVNLSAAKEKGQ-------------LVFIDGLKSSLDLLFDEDSSDEPNPLKFLREDNASSLRSLYEFIQE 126 (249)
T ss_pred ------HhhEecchHhccCCc-------------EEEeehhhhhhhhhhccccccCCccccccccCCcchHHHHHHHHHH
Confidence 333333333221111 1122222100 0 00000011122211112345667666655
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhh-cCcEEEEeeCCCCC--Cc--c-hhhhhhh
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRS-SNAVVVITFPPSLL--SL--S-STKRWQH 351 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~-s~~taliT~p~~l~--~~--~-~~~~le~ 351 (449)
.++. .+ ..+..-|+||.+....|.-. ...+++.|+|.+|+.+.. .++..++.+..+.. ++ . +...+.|
T Consensus 127 ~l~~---~~--~~~~~~liIDdls~Ll~lG~-s~~~vldF~~ycra~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h 200 (249)
T PF09807_consen 127 ALSP---AD--SNGSVVLIIDDLSVLLSLGV-SSNDVLDFIHYCRATLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAH 200 (249)
T ss_pred HHhh---cc--CCCCeEEEEeCHHHHHHcCC-CHHHHHHHHHHHHHHhccccCCCEEEEEecCCCCccchHHHHHHHHHH
Confidence 5552 11 13347899999988776322 356899999999975554 33332222333222 22 2 4578899
Q ss_pred hcceEEEEEeeCCCcHHHhhhccCCCCcceeEEE-eeecccccCCcccccCceeeEEEc
Q 013117 352 MADTLLSVAAIPDEDKELAKLLSGYQDMVGLLNV-HKVARLNTQVPLILEATTFSIKLQ 409 (449)
Q Consensus 352 laDgVI~L~~f~~~~~e~~~~~~~yk~~hGLL~V-~KLp~lntl~~~~~~~~~lAFKl~ 409 (449)
+||-+|.+++++-.- .++.||-|.| +|-..-.+. ......+|=||++
T Consensus 201 ~a~l~i~v~~L~TG~---------s~DVhGqL~v~~r~~~~~~~--~~~~~~~~~yKv~ 248 (249)
T PF09807_consen 201 MADLVITVEPLPTGY---------SKDVHGQLTVLWRGNSSSGY--HRPKTKTYQYKVQ 248 (249)
T ss_pred HhcEEEEecCCCCcc---------cccceEEEEEEEccCCcccc--ccccceEEEEeec
Confidence 999999999986421 4789999999 454433322 2233447888874
No 44
>PRK05748 replicative DNA helicase; Provisional
Probab=98.76 E-value=1e-07 Score=101.08 Aligned_cols=199 Identities=14% Similarity=0.139 Sum_probs=120.3
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh-cCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV-HGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~-~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
...++||+++||++++ |+..|++++|.+.++.| +++|+.+|+.+++. +|++++|+|+|.++++++..+=+..+.-+.
T Consensus 183 ~~gi~TG~~~LD~~~~-G~~~G~livIaarpg~G-KT~~al~ia~~~a~~~g~~v~~fSlEms~~~l~~R~l~~~~~v~~ 260 (448)
T PRK05748 183 ITGIPTGFTDLDKMTS-GLQPNDLIIVAARPSVG-KTAFALNIAQNVATKTDKNVAIFSLEMGAESLVMRMLCAEGNIDA 260 (448)
T ss_pred CCCccCChHHHHHhcC-CCCCCceEEEEeCCCCC-chHHHHHHHHHHHHhCCCeEEEEeCCCCHHHHHHHHHHHhcCCCH
Confidence 4568999999999986 99999999999877776 46788999999875 599999999999999988775211110000
Q ss_pred cccccchhhccccE-EEe-eccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHH
Q 013117 198 KSRDRESEQEKGLR-IAW-QYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHC 275 (449)
Q Consensus 198 k~~~~~~~~~~~mK-IAW-RY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i 275 (449)
. ....+.+. ..| ++.+ ..+ .+. ...+ ++.-...-+...+...+
T Consensus 261 -~----~i~~~~l~~~e~~~~~~---------------------a~~---~l~-----~~~~-~i~d~~~~ti~~i~~~~ 305 (448)
T PRK05748 261 -Q----RLRTGQLTDDDWPKLTI---------------------AMG---SLS-----DAPI-YIDDTPGIKVTEIRARC 305 (448)
T ss_pred -H----HhhcCCCCHHHHHHHHH---------------------HHH---HHh-----cCCE-EEECCCCCCHHHHHHHH
Confidence 0 00000000 001 0110 000 000 0011 11000111334454434
Q ss_pred HHHHHHhhhccCCCCceeEEEEcCCCcccccCC---CCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc-
Q 013117 276 ASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHS---NMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS- 344 (449)
Q Consensus 276 ~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~---~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~- 344 (449)
..+.+ +. .++.+|+||.|........ +...++-.+...||.+.+..+++++++....-- . +.
T Consensus 306 r~~~~----~~---~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke~~i~vi~lsQlnr~~~~r~~k~p~l 378 (448)
T PRK05748 306 RRLAQ----EH---GGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKELKVPVIALSQLSRGVEQRQDKRPVM 378 (448)
T ss_pred HHHHH----hc---CCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhHhhcCCCCCCh
Confidence 33322 21 1578999999986532111 123578899999999999999999998876531 1 11
Q ss_pred --h--hhhhhhhcceEEEEEe
Q 013117 345 --S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 --~--~~~le~laDgVI~L~~ 361 (449)
+ ...++.-||.||.|+-
T Consensus 379 sdlr~Sg~Ieq~AD~v~~l~r 399 (448)
T PRK05748 379 SDIRESGSIEQDADIVAFLYR 399 (448)
T ss_pred HHHHhhcchhcCCCEEEEEec
Confidence 1 1456899999999975
No 45
>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=98.64 E-value=1.6e-06 Score=88.17 Aligned_cols=172 Identities=14% Similarity=0.207 Sum_probs=107.4
Q ss_pred CCCeEeecCchhHHHHhc-CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCCh-hhHhhcCCCCCCc
Q 013117 117 NGTMFVSSGIADLDKILG-GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDP-RGFLGTLPSPASL 194 (449)
Q Consensus 117 ~g~~~iSTGIp~LD~lLG-GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p-~~il~~LP~~~~~ 194 (449)
.....+|||++.||..|| ||+|.|.++-|-++..+| ..+|+.+++++-...|..|+|+..+... ..+++.| |+
T Consensus 29 ~~~~~i~TG~~~LD~aLg~GG~p~G~ivEi~G~~ssG-KttLaL~~ia~~q~~g~~~a~ID~e~~ld~~~a~~l-Gv--- 103 (322)
T PF00154_consen 29 QNIEVISTGSPALDYALGIGGLPRGRIVEIYGPESSG-KTTLALHAIAEAQKQGGICAFIDAEHALDPEYAESL-GV--- 103 (322)
T ss_dssp CSS-EE--S-HHHHHHTSSSSEETTSEEEEEESTTSS-HHHHHHHHHHHHHHTT-EEEEEESSS---HHHHHHT-T----
T ss_pred cccceEecCCcccchhhccCccccCceEEEeCCCCCc-hhhhHHHHHHhhhcccceeEEecCcccchhhHHHhc-Cc---
Confidence 345789999999999999 999999999999887776 5778899999988889999999874322 2344433 11
Q ss_pred ccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHH
Q 013117 195 KHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEH 274 (449)
Q Consensus 195 ~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~ 274 (449)
|+.+ +-++. +++.+..++.
T Consensus 104 -----------------------------------------------dl~r-----------llv~~---P~~~E~al~~ 122 (322)
T PF00154_consen 104 -----------------------------------------------DLDR-----------LLVVQ---PDTGEQALWI 122 (322)
T ss_dssp ------------------------------------------------GGG-----------EEEEE----SSHHHHHHH
T ss_pred -----------------------------------------------cccc-----------eEEec---CCcHHHHHHH
Confidence 1100 00000 1122333333
Q ss_pred HHHHHHHhhhccCCCCceeEEEEcCCCccc--------ccCCC---CHHHHHHHHHHHHHhhhhcCcEEEEeeCCC----
Q 013117 275 CASFLAQHQRNDGSSALAGRIAIQSLCAPQ--------CEHSN---MDWEMLSFIKSLKGMVRSSNAVVVITFPPS---- 339 (449)
Q Consensus 275 i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~--------~~~~~---~~~~ll~FL~~LR~llR~s~~taliT~p~~---- 339 (449)
+.++++ . ..+.=|||||+.+.. +.+.. ....|-+||+.|...+..++++++++-...
T Consensus 123 ~e~lir----s----g~~~lVVvDSv~al~p~~E~e~~~~~~~~g~~Ar~ms~~lr~lt~~l~~~~~~~i~INQ~R~~ig 194 (322)
T PF00154_consen 123 AEQLIR----S----GAVDLVVVDSVAALVPKAELEGEIGDQQVGLQARLMSQALRKLTPLLSKSNTTLIFINQVRDKIG 194 (322)
T ss_dssp HHHHHH----T----TSESEEEEE-CTT-B-HHHHTTSTSSTSSSHHHHHHHHHHHHHHHHHHTTT-EEEEEEEESSSSS
T ss_pred HHHHhh----c----ccccEEEEecCcccCCHHHHhhccccccCcchHHHHHHHHHHHHHHHHhhceEEEEeehHHHHHh
Confidence 333333 2 346689999998762 11111 124689999999999999999999987532
Q ss_pred -CC-Ccch---hhhhhhhcceEEEEEee
Q 013117 340 -LL-SLSS---TKRWQHMADTLLSVAAI 362 (449)
Q Consensus 340 -l~-~~~~---~~~le~laDgVI~L~~f 362 (449)
.| .+.. ...|.|+++..|.+.--
T Consensus 195 ~~~g~~~~t~GG~alkfyas~rl~i~k~ 222 (322)
T PF00154_consen 195 VMFGNPETTPGGRALKFYASVRLEIRKK 222 (322)
T ss_dssp SSSSSSSCCTSHHHHHHHCSEEEEEEEE
T ss_pred hccCCCcCCCCCchhhhhhhhHHhhhcc
Confidence 34 3332 36789999999999764
No 46
>PRK09165 replicative DNA helicase; Provisional
Probab=98.47 E-value=1.4e-06 Score=93.63 Aligned_cols=198 Identities=17% Similarity=0.176 Sum_probs=117.4
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc---------------CCcEEEEcCCCChhh
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH---------------GQPLLYASPSKDPRG 183 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~---------------g~~vl~vs~~e~p~~ 183 (449)
...++||+++||+++| |+..|.+++|.+.++.| +++|+.+|+.+.+.+ |++++|+|+|.++++
T Consensus 197 ~~gi~TG~~~LD~~~g-G~~~g~livIaarpg~G-KT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEMs~~q 274 (497)
T PRK09165 197 LSGISTGLRDLDSKLG-GLHPSDLIILAGRPSMG-KTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEMSAEQ 274 (497)
T ss_pred CCcccCChHHHhhhcC-CCCCCceEEEEeCCCCC-hHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcCCHHH
Confidence 4568999999999995 89999999999877666 456778888887653 789999999999999
Q ss_pred HhhcCCCCCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeecc
Q 013117 184 FLGTLPSPASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQ 263 (449)
Q Consensus 184 il~~LP~~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~ 263 (449)
+...+-+..+. | .+.++. .+. . ....|-...+-.+.+.. ..+. +.
T Consensus 275 l~~R~la~~s~-----------------v--~~~~i~-~~~--l-----~~~e~~~l~~a~~~l~~-----~~l~---I~ 319 (497)
T PRK09165 275 LATRILSEQSE-----------------I--SSSKIR-RGK--I-----SEEDFEKLVDASQELQK-----LPLY---ID 319 (497)
T ss_pred HHHHHHHHhcC-----------------C--CHHHHh-cCC--C-----CHHHHHHHHHHHHHHhc-----CCeE---Ee
Confidence 88874221110 0 000000 000 0 00000001111111110 0111 11
Q ss_pred CC--cchHHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccC----CCCHHHHHHHHHHHHHhhhhcCcEEEEeeC
Q 013117 264 HS--KNLAALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH----SNMDWEMLSFIKSLKGMVRSSNAVVVITFP 337 (449)
Q Consensus 264 ~~--~~~~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~----~~~~~~ll~FL~~LR~llR~s~~taliT~p 337 (449)
+. -++..+...+.. +.++ .++..|+||.|.-..-.. .+...++-.+...||.+.+..++.+++...
T Consensus 320 d~~~~ti~~i~~~ir~----l~~~----~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~is~~LK~lAkel~ipVi~lsQ 391 (497)
T PRK09165 320 DTPALSISQLRARARR----LKRQ----HGLDLLVVDYLQLIRGSSKRSSDNRVQEISEITQGLKALAKELNIPVIALSQ 391 (497)
T ss_pred CCCCCCHHHHHHHHHH----HHHh----cCCCEEEEcchHhccCCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEeec
Confidence 11 134455443433 2222 457899999997432111 112347889999999999999998888886
Q ss_pred CCCC--C-----cc---h--hhhhhhhcceEEEEEe
Q 013117 338 PSLL--S-----LS---S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 338 ~~l~--~-----~~---~--~~~le~laDgVI~L~~ 361 (449)
.+-- . +. + ...||.-||.|+.|+-
T Consensus 392 LnR~~e~r~~krP~lsDLr~Sg~IEqdAD~v~~l~R 427 (497)
T PRK09165 392 LSRQVEQRDDKRPQLSDLRESGSIEQDADVVMFVYR 427 (497)
T ss_pred ccchhhccCCCCCchhhhhhccchhccCCEEEEEee
Confidence 4421 1 11 1 2467899999999963
No 47
>PHA02542 41 41 helicase; Provisional
Probab=98.42 E-value=1.6e-06 Score=92.61 Aligned_cols=201 Identities=14% Similarity=0.138 Sum_probs=117.5
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
...++||+++||++++||+..|++++|.+.++.| +++|+.+|+...+.+|++++|+|+|...+++...+-+....-+
T Consensus 169 ~~gi~TG~~~LD~~t~gGl~~G~LiiIaarPgmG-KTtfalniA~~~a~~g~~Vl~fSLEM~~~ql~~Rl~a~~~~i~-- 245 (473)
T PHA02542 169 ANKIPFKLEILNKITKGGAERKTLNVLLAGVNVG-KSLGLCSLAADYLQQGYNVLYISMEMAEEVIAKRIDANLLDVS-- 245 (473)
T ss_pred CCccCCCcHHHHHhccCCCCCCcEEEEEcCCCcc-HHHHHHHHHHHHHhcCCcEEEEeccCCHHHHHHHHHHHHcCCC--
Confidence 3458899999999999999999999999777666 4577899998888889999999999999988876522110000
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccC--CcchHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQH--SKNLAALQEHCA 276 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~--~~~~~~l~~~i~ 276 (449)
-..++ .+.. ..|-.. ...+.. +...++. +...+ ..+...+.
T Consensus 246 --------~~~l~---~l~~----------------~~~~~~---~~~~~~--~~~~~l~-I~~~d~~~lt~~~ir---- 288 (473)
T PHA02542 246 --------LDDID---DLSK----------------AEYKAK---MEKLRS--KTQGKLI-IKQYPTGGAHAGHFR---- 288 (473)
T ss_pred --------HHHHh---hcCH----------------HHHHHH---HHHHHH--HhCCCce-eecCCCCCCCHHHHH----
Confidence 00000 0000 000000 000000 0000110 00111 11233343
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCccccc-----CCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--CC---cc--
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCE-----HSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL--LS---LS-- 344 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~-----~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l--~~---~~-- 344 (449)
..+.++..+.+ .++.-|+||.|.-..-. ..+...++-.....||.+.+..++.+++....+- .. +.
T Consensus 289 ~~~rrlk~~~g--~~~dlVvIDYLqL~~~~~~~~~~~nr~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~dP~ls 366 (473)
T PHA02542 289 ALLNELKLKKN--FKPDVIIVDYLGICASSRLRVSSENSYTYVKAIAEELRGLAVEHDVVVWTAAQTTRSGWDSSDVDMS 366 (473)
T ss_pred HHHHHHHHhcC--CCCCEEEEechhhccCCcccCCCCChHHHHHHHHHHHHHHHHHhCCeEEEEEeeCccccccCCCcch
Confidence 34443332211 24678999998643211 0122457888999999999999987777664431 11 21
Q ss_pred -h--hhhhhhhcceEEEEEe
Q 013117 345 -S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 -~--~~~le~laDgVI~L~~ 361 (449)
+ ...+|.-||.|+.|.-
T Consensus 367 DLreSG~IEqdAD~vl~l~r 386 (473)
T PHA02542 367 DTAESAGLPATADFMLAVIE 386 (473)
T ss_pred hcccccchHhhcCEEEEEec
Confidence 1 2468999999999954
No 48
>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=98.42 E-value=4.1e-06 Score=88.12 Aligned_cols=201 Identities=15% Similarity=0.159 Sum_probs=117.7
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhh-hcCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGL-VHGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl-~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
..-++||+++||++++ |+..|.+++|.+.++.| ++.|+.+++...+ .+|++++|+|.|..+++++..+=+..+
T Consensus 174 ~~gi~tG~~~LD~~~~-G~~~g~liviag~pg~G-KT~~al~ia~~~a~~~g~~v~~fSlEm~~~~l~~Rl~~~~~---- 247 (421)
T TIGR03600 174 LTGLSTGLPKLDRLTN-GLVKGDLIVIGARPSMG-KTTLALNIAENVALREGKPVLFFSLEMSAEQLGERLLASKS---- 247 (421)
T ss_pred CcceeCCChhHHHHhc-CCCCCceEEEEeCCCCC-HHHHHHHHHHHHHHhCCCcEEEEECCCCHHHHHHHHHHHHc----
Confidence 3458999999999998 89999999999888776 4677788887765 579999999999999888876421110
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCAS 277 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~ 277 (449)
.+.|. ++. .+. ... .....+...++ .+. ..++ ++.-....+...+...+
T Consensus 248 -------------~v~~~--~~~-~~~--l~~--~~~~~~~~~~~---~l~-----~~~l-~i~d~~~~t~~~i~~~~-- 296 (421)
T TIGR03600 248 -------------GINTG--NIR-TGR--FND--SDFNRLLNAVD---RLS-----EKDL-YIDDTGGLTVAQIRSIA-- 296 (421)
T ss_pred -------------CCCHH--HHh-cCC--CCH--HHHHHHHHHHH---HHh-----cCCE-EEECCCCCCHHHHHHHH--
Confidence 01010 000 000 000 00000000111 110 0111 11101112344444333
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCccccc-CCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc---h-
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCE-HSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS---S- 345 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~-~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~---~- 345 (449)
+++..+. .++.-|+||.|...... ..+...++-.+...||.+.+..+++++++....-- . +. +
T Consensus 297 --r~~~~~~---~~~~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~~i~Vi~lsQlnr~~~~r~~krp~lsdlr 371 (421)
T TIGR03600 297 --RRIKRKK---GGLDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELDVPVVLLAQLNRGSEKRTDKRPIMSDLR 371 (421)
T ss_pred --HHHHHhc---CCCCEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEEEecccCcchhhcCCCCCChHHHh
Confidence 3332221 25789999999754321 11223468888999999999999998888875421 1 11 1
Q ss_pred -hhhhhhhcceEEEEEe
Q 013117 346 -TKRWQHMADTLLSVAA 361 (449)
Q Consensus 346 -~~~le~laDgVI~L~~ 361 (449)
...++.-||.|+.|+.
T Consensus 372 ~Sg~Ieq~AD~v~~l~R 388 (421)
T TIGR03600 372 DSGAIEQDADVIGLIHR 388 (421)
T ss_pred hcCCccccCcEEEEecc
Confidence 2457889999999975
No 49
>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=98.38 E-value=7.9e-06 Score=80.17 Aligned_cols=199 Identities=16% Similarity=0.176 Sum_probs=112.2
Q ss_pred eecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCccccccc
Q 013117 122 VSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLKHDKSR 200 (449)
Q Consensus 122 iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~ 200 (449)
++||++.||+++| |+-.|.+++|.+.++.| +++|+.+++..-+.+ |.+++|+|.|.+.+++...+=+..+.-+..
T Consensus 2 i~TG~~~LD~~lg-G~~~g~L~vi~a~pg~G-KT~~~l~ia~~~a~~~~~~vly~SlEm~~~~l~~R~la~~s~v~~~-- 77 (259)
T PF03796_consen 2 IPTGFPALDRLLG-GLRPGELTVIAARPGVG-KTAFALQIALNAALNGGYPVLYFSLEMSEEELAARLLARLSGVPYN-- 77 (259)
T ss_dssp B-SSTHHHHHHHS-SB-TT-EEEEEESTTSS-HHHHHHHHHHHHHHTTSSEEEEEESSS-HHHHHHHHHHHHHTSTHH--
T ss_pred CCCChHHHHHHhc-CCCcCcEEEEEecccCC-chHHHHHHHHHHHHhcCCeEEEEcCCCCHHHHHHHHHHHhhcchhh--
Confidence 6899999999997 78899999999877666 467778888887776 699999999988888776631111000000
Q ss_pred ccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHH
Q 013117 201 DRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLA 280 (449)
Q Consensus 201 ~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~ 280 (449)
....+.+. ...|+.+. +....+. ...+-... ....+...+.+.| .
T Consensus 78 ---~i~~g~l~-~~e~~~~~---------------------~~~~~l~-----~~~l~i~~-~~~~~~~~i~~~i----~ 122 (259)
T PF03796_consen 78 ---KIRSGDLS-DEEFERLQ---------------------AAAEKLS-----DLPLYIED-TPSLTIDDIESKI----R 122 (259)
T ss_dssp ---HHHCCGCH-HHHHHHHH---------------------HHHHHHH-----TSEEEEEE-SSS-BHHHHHHHH----H
T ss_pred ---hhhccccC-HHHHHHHH---------------------HHHHHHh-----hCcEEEEC-CCCCCHHHHHHHH----H
Confidence 00000000 00011100 0000110 00111111 1112344554433 3
Q ss_pred HhhhccCCCCceeEEEEcCCCccccc--CCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cch-----h
Q 013117 281 QHQRNDGSSALAGRIAIQSLCAPQCE--HSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LSS-----T 346 (449)
Q Consensus 281 ~~~~~~~~~~~v~RIvIdSL~Sp~~~--~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~~-----~ 346 (449)
.+.... .++.=|+||.|.-.... ..+...++-.....||.+.+..++.+++..+..-- . +.. .
T Consensus 123 ~~~~~~---~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i~vi~~sQlnr~~~~~~~~~p~l~dl~~s 199 (259)
T PF03796_consen 123 RLKREG---KKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNIPVIALSQLNREAEDREDKRPSLSDLRES 199 (259)
T ss_dssp HHHHHS---TTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTSEEEEEEEBSGGGGGSSSCS--HHHHCST
T ss_pred HHHhhc---cCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCCeEEEccccChhhhcccccccchhhhhhh
Confidence 332221 46788999999754331 12235678889999999999999988888865421 1 111 2
Q ss_pred hhhhhhcceEEEEEee
Q 013117 347 KRWQHMADTLLSVAAI 362 (449)
Q Consensus 347 ~~le~laDgVI~L~~f 362 (449)
..+++.||.|+.|+.-
T Consensus 200 g~Ie~~AD~vl~l~r~ 215 (259)
T PF03796_consen 200 GAIEQDADVVLFLHRD 215 (259)
T ss_dssp SSHHHH-SEEEEEEEH
T ss_pred HHHHHHHhhhhhhccc
Confidence 4679999999999863
No 50
>PRK08760 replicative DNA helicase; Provisional
Probab=98.23 E-value=2.1e-05 Score=84.27 Aligned_cols=197 Identities=15% Similarity=0.141 Sum_probs=117.0
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh-cCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV-HGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~-~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
.-++||+++||+++| |+..|++++|.+.++.| +++|+.+|++..+. +|++++|+|+|..+++++..+-+..+.-+
T Consensus 210 ~Gi~TG~~~LD~~t~-G~~~G~LivIaarPg~G-KTafal~iA~~~a~~~g~~V~~fSlEMs~~ql~~Rl~a~~s~i~-- 285 (476)
T PRK08760 210 TGLPTGYNDFDAMTA-GLQPTDLIILAARPAMG-KTTFALNIAEYAAIKSKKGVAVFSMEMSASQLAMRLISSNGRIN-- 285 (476)
T ss_pred CcccCCcHHHHHHhc-CCCCCceEEEEeCCCCC-hhHHHHHHHHHHHHhcCCceEEEeccCCHHHHHHHHHHhhCCCc--
Confidence 458899999999886 69999999999877776 46778999988764 58999999999999999887533211100
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCC--cchHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHS--KNLAALQEHCA 276 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~--~~~~~l~~~i~ 276 (449)
. .+ ++.+++..+ .+..+...++ .+. ...+. +.+. -+.+.+...+.
T Consensus 286 --------~--~~--i~~g~l~~~----------e~~~~~~a~~---~l~-----~~~l~---I~d~~~~t~~~I~~~~r 332 (476)
T PRK08760 286 --------A--QR--LRTGALEDE----------DWARVTGAIK---MLK-----ETKIF---IDDTPGVSPEVLRSKCR 332 (476)
T ss_pred --------H--HH--HhcCCCCHH----------HHHHHHHHHH---HHh-----cCCEE---EeCCCCCCHHHHHHHHH
Confidence 0 00 011100000 0000000111 000 00111 1111 12344443333
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC-------Ccc---
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL-------SLS--- 344 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~-------~~~--- 344 (449)
. +.+. .++.-|+||.|....... .+...++-.....||.+.+..++.+++....+-- .|.
T Consensus 333 ~----l~~~----~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsD 404 (476)
T PRK08760 333 R----LKRE----HDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELNVPVIALSQLNRSLETRTDKRPVMAD 404 (476)
T ss_pred H----HHHh----cCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhCCEEEEeeccCccccccCCCCCCHHH
Confidence 3 3222 357789999987442111 1223568888999999999999988888765421 111
Q ss_pred h--hhhhhhhcceEEEEEe
Q 013117 345 S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 ~--~~~le~laDgVI~L~~ 361 (449)
+ ...||.-||.|+.|+-
T Consensus 405 LreSg~IeqdAD~vl~l~R 423 (476)
T PRK08760 405 LRESGAIEQDADMIVFIYR 423 (476)
T ss_pred HhhccchhcCCCEEEEEec
Confidence 1 2467889999999964
No 51
>PRK08506 replicative DNA helicase; Provisional
Probab=98.22 E-value=1e-05 Score=86.51 Aligned_cols=198 Identities=14% Similarity=0.166 Sum_probs=116.2
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKS 199 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~ 199 (449)
.-++||+++||+++ ||+..|.+++|.+.++.| +++|+.+++.+.+.+|++++|+|+|.+.++++..+-+..+.
T Consensus 173 ~Gi~TG~~~LD~~~-~G~~~G~LivIaarpg~G-KT~fal~ia~~~~~~g~~V~~fSlEMs~~ql~~Rlla~~s~----- 245 (472)
T PRK08506 173 IGLDTGFVELNKMT-KGFNKGDLIIIAARPSMG-KTTLCLNMALKALNQDKGVAFFSLEMPAEQLMLRMLSAKTS----- 245 (472)
T ss_pred CcccCChHHHHhhc-CCCCCCceEEEEcCCCCC-hHHHHHHHHHHHHhcCCcEEEEeCcCCHHHHHHHHHHHhcC-----
Confidence 34889999999998 689999999999877666 46778999999888999999999999999988775221110
Q ss_pred cccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCC--cchHHHHHHHHH
Q 013117 200 RDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHS--KNLAALQEHCAS 277 (449)
Q Consensus 200 ~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~--~~~~~l~~~i~~ 277 (449)
.....+ +...+.. ..+..+...++ ++. ...+ + +.+. -++..+...+.
T Consensus 246 -----v~~~~i----~~~~l~~----------~e~~~~~~a~~---~l~-----~~~l-~--I~d~~~~ti~~I~~~~r- 294 (472)
T PRK08506 246 -----IPLQNL----RTGDLDD----------DEWERLSDACD---ELS-----KKKL-F--VYDSGYVNIHQVRAQLR- 294 (472)
T ss_pred -----CCHHHH----hcCCCCH----------HHHHHHHHHHH---HHH-----cCCe-E--EECCCCCCHHHHHHHHH-
Confidence 000000 0000000 00000000111 000 0011 1 1111 13444443333
Q ss_pred HHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC-------Ccc---h
Q 013117 278 FLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL-------SLS---S 345 (449)
Q Consensus 278 ~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~-------~~~---~ 345 (449)
++..+ ..++.=|+||.|.-..-.. .+...++......||.+.+..++.+++....+-- .+. +
T Consensus 295 ---~l~~~---~~~~~lvvIDyLql~~~~~~~~~r~~ev~~isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsDL 368 (472)
T PRK08506 295 ---KLKSQ---HPEIGLAVIDYLQLMSGSGNFKDRHLQISEISRGLKLLARELDIPIIALSQLNRSLESRADKRPMLSDL 368 (472)
T ss_pred ---HHHHh---CCCCCEEEEcChhhccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEeecCcchhhccCCCCChHHh
Confidence 23221 1247889999996432111 1224568888899999999999877777654311 111 1
Q ss_pred --hhhhhhhcceEEEEEe
Q 013117 346 --TKRWQHMADTLLSVAA 361 (449)
Q Consensus 346 --~~~le~laDgVI~L~~ 361 (449)
...|+.-||.|+.|+-
T Consensus 369 reSg~IeqdAD~vl~l~R 386 (472)
T PRK08506 369 RESGAIEQDADIILFVYR 386 (472)
T ss_pred hcchhhhhcCCEEEEEec
Confidence 2457899999999974
No 52
>PRK07773 replicative DNA helicase; Validated
Probab=98.22 E-value=3.7e-06 Score=96.38 Aligned_cols=175 Identities=14% Similarity=0.178 Sum_probs=107.4
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
..-++||+++||+++ ||+..|.+++|.+.++.| +++|+.+|+.+++.+ |++++|+|+|.++++++..+=+..+.
T Consensus 197 ~~Gi~TG~~~LD~l~-~Gl~~G~livIagrPg~G-KT~fal~ia~~~a~~~~~~V~~fSlEms~~ql~~R~~s~~~~--- 271 (886)
T PRK07773 197 ARGVPTGFTELDAMT-NGLHPGQLIIVAARPSMG-KTTFGLDFARNCAIRHRLAVAIFSLEMSKEQLVMRLLSAEAK--- 271 (886)
T ss_pred CCCccCChhHhcccc-CCCCCCcEEEEEeCCCCC-cHHHHHHHHHHHHHhcCCeEEEEecCCCHHHHHHHHHHHhcC---
Confidence 345889999999998 799999999999887776 467889999998765 89999999999999998875221111
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCcccccc-ccccccccccccceeeeeeccCC--cchHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFD-FRKPLERHYFTRQRVNCVGIQHS--KNLAALQEH 274 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FD-Lsk~l~~~~~~~~~i~~~~~~~~--~~~~~l~~~ 274 (449)
| .++++. .+. .. -..++ ++..+. .+...++. +.+. -++.++...
T Consensus 272 --------------i--~~~~i~-~g~--l~---------~~~~~~~~~a~~--~l~~~~i~---i~d~~~~~i~~i~~~ 318 (886)
T PRK07773 272 --------------I--KLSDMR-SGR--MS---------DDDWTRLARAMG--EISEAPIF---IDDTPNLTVMEIRAK 318 (886)
T ss_pred --------------C--CHHHHh-cCC--CC---------HHHHHHHHHHHH--HHhcCCEE---EECCCCCCHHHHHHH
Confidence 0 011110 000 00 00000 000000 00001111 1111 134455443
Q ss_pred HHHHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCC
Q 013117 275 CASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPS 339 (449)
Q Consensus 275 i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~ 339 (449)
+..+.+ + .++..|+||.|....-.. .+...++..+...||.+.++.+++++++...+
T Consensus 319 ~r~~~~----~----~~~~lvvIDyLql~~~~~~~~~r~~ei~~isr~LK~lAkel~vpvi~lsQLn 377 (886)
T PRK07773 319 ARRLRQ----E----ANLGLIVVDYLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVVALSQLS 377 (886)
T ss_pred HHHHHH----h----cCCCEEEEcchhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHCCcEEEecccC
Confidence 433332 2 357899999997543111 11235799999999999999999999888655
No 53
>PRK06321 replicative DNA helicase; Provisional
Probab=98.21 E-value=1e-05 Score=86.64 Aligned_cols=196 Identities=13% Similarity=0.124 Sum_probs=114.9
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhh--hcCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGL--VHGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl--~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
.-++||+++||++++ |+..|.+++|.+.++.| +++|+.+ +|.++ .+|++++|+|.|.+.++++..+-+..+.
T Consensus 207 ~Gi~tG~~~LD~~t~-Gl~~G~LiiiaarPgmG-KTafal~-ia~~~a~~~g~~v~~fSLEMs~~ql~~Rlla~~s~--- 280 (472)
T PRK06321 207 SGIPTHFIDLDKMIN-GFSPSNLMILAARPAMG-KTALALN-IAENFCFQNRLPVGIFSLEMTVDQLIHRIICSRSE--- 280 (472)
T ss_pred CccccCcHHHHHHhc-CCCCCcEEEEEeCCCCC-hHHHHHH-HHHHHHHhcCCeEEEEeccCCHHHHHHHHHHhhcC---
Confidence 347899999999997 89999999999777665 3456666 55555 4689999999999999998876331110
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCC--cchHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHS--KNLAALQEHC 275 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~--~~~~~l~~~i 275 (449)
.. ..+| +...+. ...|....+-...+.. ..+ .+.+. .+...+...+
T Consensus 281 -------v~--~~~i--~~~~l~-------------~~e~~~~~~a~~~l~~-----~~~---~idd~~~~ti~~i~~~~ 328 (472)
T PRK06321 281 -------VE--SKKI--SVGDLS-------------GRDFQRIVSVVNEMQE-----HTL---LIDDQPGLKITDLRARA 328 (472)
T ss_pred -------CC--HHHh--hcCCCC-------------HHHHHHHHHHHHHHHc-----CCE---EEeCCCCCCHHHHHHHH
Confidence 00 0011 111100 0001111010011110 111 11222 1344444433
Q ss_pred HHHHHHhhhccCCCCceeEEEEcCCCccccc-----CCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--CC-----c
Q 013117 276 ASFLAQHQRNDGSSALAGRIAIQSLCAPQCE-----HSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL--LS-----L 343 (449)
Q Consensus 276 ~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~-----~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l--~~-----~ 343 (449)
.. +.+. .++..|+||.|.-..-. ..+...++-.+...||.+.+..++.+++....+- -. +
T Consensus 329 r~----~~~~----~~~~lvvIDyLql~~~~~~~~~~~~r~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r~~krP 400 (472)
T PRK06321 329 RR----MKES----YDIQFLIIDYLQLLSGSGNLRNSESRQTEISEISRMLKNLARELNIPILCLSQLSRKVEDRANHRP 400 (472)
T ss_pred HH----HHHh----cCCCEEEEcchHHcCCCCccCCcchHHHHHHHHHHHHHHHHHHhCCcEEEEeecChhhhccCCCCC
Confidence 33 2222 45789999999653211 0112357888999999999999998888876531 11 1
Q ss_pred c---h--hhhhhhhcceEEEEEe
Q 013117 344 S---S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 344 ~---~--~~~le~laDgVI~L~~ 361 (449)
. + .-.+|.-||.|+.|+-
T Consensus 401 ~lsDLReSG~IEqdAD~v~~l~R 423 (472)
T PRK06321 401 MMSDLRESGSIEQDSDLVMFLLR 423 (472)
T ss_pred CHHHHhhcccccccCCEEEEEec
Confidence 1 1 2457889999999964
No 54
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=98.07 E-value=6.7e-06 Score=76.34 Aligned_cols=166 Identities=13% Similarity=0.121 Sum_probs=82.2
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh----------cCCcEEEEcCCCChhhHhhcCC
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV----------HGQPLLYASPSKDPRGFLGTLP 189 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~----------~g~~vl~vs~~e~p~~il~~LP 189 (449)
..++++.+.+|.+++|++|.|.+++|.+++++| +++++.+.++.-+. .+.+++|+++|.+..++.+.+-
T Consensus 12 ~~~~~~~~~~~~li~g~~~~g~l~~i~g~~g~G-KT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~~~~~~rl~ 90 (193)
T PF13481_consen 12 EDLDTGFPPLDWLIDGLLPRGELTLIAGPPGSG-KTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDSESQIARRLR 90 (193)
T ss_dssp -HHHS------EEETTEE-TTSEEEEEECSTSS-HHHHHHHHHHHHHT---TT---------EEEEESSS-HHHHHHHHH
T ss_pred hhccCCCCCcceeECCcccCCeEEEEEeCCCCC-HHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCCHHHHHHHHH
Confidence 347899999999999999999999999998887 46666777666554 4678999999888777776541
Q ss_pred CCCCcccccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccC-Ccch
Q 013117 190 SPASLKHDKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQH-SKNL 268 (449)
Q Consensus 190 ~~~~~~~~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~-~~~~ 268 (449)
.....- .. .....+ |. +... + .+..+.... ....
T Consensus 91 ~~~~~~------~~---~~~~~~-~~---------------------------~~~~-~-------~~~~~~~~~~~~~~ 125 (193)
T PF13481_consen 91 ALLQDY------DD---DANLFF-VD---------------------------LSNW-G-------CIRLFEPDSGGPLL 125 (193)
T ss_dssp HHHTTS-------H---HHHHHH-HH---------------------------H--E---------EE---TTS---TTS
T ss_pred HHhccc------CC---ccceEE-ee---------------------------cccc-c-------cceeeecccccccc
Confidence 111000 00 000000 00 0000 0 000000000 0001
Q ss_pred HHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCC
Q 013117 269 AALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPP 338 (449)
Q Consensus 269 ~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~ 338 (449)
....+.+.+.++ .. .++.=|+||++........+....+.+|+..|+.+.+..|++++++.++
T Consensus 126 ~~~~~~l~~~~~---~~----~~~~lvviD~l~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~vi~v~H~ 188 (193)
T PF13481_consen 126 DEDLEELEAALK---EL----YGPDLVVIDPLQSLHDGDENSNSAVAQLMQELKRLAKEYGVAVILVHHT 188 (193)
T ss_dssp HHHHHHHHHHHT---T--------SEEEEE-GGGG--S-TT-HHHHHHHHHHHHHHHHHH--EEEEEEEE
T ss_pred hHHHHHHHHHHh---hc----CCCcEEEEcCHHHHhcCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEECC
Confidence 222332333333 10 2478999999998765433444556899999999999999998888654
No 55
>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]
Probab=98.07 E-value=5.7e-05 Score=75.51 Aligned_cols=172 Identities=15% Similarity=0.184 Sum_probs=111.2
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCC--ChhhHhhcCCCCCCccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSK--DPRGFLGTLPSPASLKH 196 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e--~p~~il~~LP~~~~~~~ 196 (449)
...+|||...||.+||||||.|.++=|-+...+| +++|+.+-+++-...|..++|+.++. +|+.+..-.
T Consensus 39 ~~~i~TGs~~LD~~LGGGl~~g~ItEiyG~~gsG-KT~lal~~~~~aq~~g~~a~fIDtE~~l~p~r~~~l~-------- 109 (279)
T COG0468 39 IEAISTGSLALDEALGGGLPRGRITEIYGPESSG-KTTLALQLVANAQKPGGKAAFIDTEHALDPERAKQLG-------- 109 (279)
T ss_pred cccccccchhHHHHhcCCcccceEEEEecCCCcc-hhhHHHHHHHHhhcCCCeEEEEeCCCCCCHHHHHHHH--------
Confidence 6789999999999999999999999999888777 57888999999889999999998754 232222210
Q ss_pred ccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHH
Q 013117 197 DKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCA 276 (449)
Q Consensus 197 ~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~ 276 (449)
.+ . -.+ +-+ ....+.+.-..
T Consensus 110 --------~~--~------~d~--------------------------------------l~v---~~~~~~e~q~~--- 129 (279)
T COG0468 110 --------VD--L------LDN--------------------------------------LLV---SQPDTGEQQLE--- 129 (279)
T ss_pred --------Hh--h------hcc--------------------------------------eeE---ecCCCHHHHHH---
Confidence 00 0 000 000 00112222221
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC--CC-----CHHHHHHHHHHHHHhhhhcCcEEEEeeCCC-----CC-Cc
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SN-----MDWEMLSFIKSLKGMVRSSNAVVVITFPPS-----LL-SL 343 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~-----~~~~ll~FL~~LR~llR~s~~taliT~p~~-----l~-~~ 343 (449)
+++.+.+... .++.=|+|||+.++.-.. .+ ..+.+-+.++.|..+.+.+++++++|-... .+ ++
T Consensus 130 -i~~~~~~~~~--~~i~LvVVDSvaa~~r~~~~~d~~~~~~~r~ls~~l~~L~~~a~~~~~~vi~~NQv~~k~~~~f~~~ 206 (279)
T COG0468 130 -IAEKLARSGA--EKIDLLVVDSVAALVRAEEIEDGHLGLRARLLSKALRKLTRLANKYNTAVIFTNQVRAKIGVMFGDP 206 (279)
T ss_pred -HHHHHHHhcc--CCCCEEEEecCcccchhhhcCcchHHHHHHHHHHHHHHHHHHHHHcCcEEEEECceeeecCcccCCc
Confidence 2222222111 158899999999873211 11 124688999999999999999999998643 22 22
Q ss_pred ch---hhhhhhhcceEEEEEee
Q 013117 344 SS---TKRWQHMADTLLSVAAI 362 (449)
Q Consensus 344 ~~---~~~le~laDgVI~L~~f 362 (449)
.. ...+.|++-..+.|+-.
T Consensus 207 ~~~~GG~~L~~~as~rl~l~k~ 228 (279)
T COG0468 207 ETTTGGNALKFYASVRLDLRRI 228 (279)
T ss_pred ccCCCchHHHhhhheEEEEeec
Confidence 11 35567788777777764
No 56
>PRK05595 replicative DNA helicase; Provisional
Probab=98.04 E-value=3.1e-05 Score=82.21 Aligned_cols=197 Identities=14% Similarity=0.177 Sum_probs=115.6
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHh-hhhcCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQ-GLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAE-Gl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
.-++||+++||+++ ||+..|.+++|.+.++.| +++|+.+++.. ++.+|++|+|+|+|.+++++...+-+..+.
T Consensus 182 ~gi~tg~~~ld~~~-~G~~~g~liviaarpg~G-KT~~al~ia~~~a~~~g~~vl~fSlEms~~~l~~R~~a~~~~---- 255 (444)
T PRK05595 182 TGVASGFRELDAKT-SGFQKGDMILIAARPSMG-KTTFALNIAEYAALREGKSVAIFSLEMSKEQLAYKLLCSEAN---- 255 (444)
T ss_pred CcccCChHHHHHhc-CCCCCCcEEEEEecCCCC-hHHHHHHHHHHHHHHcCCcEEEEecCCCHHHHHHHHHHHhcC----
Confidence 45889999999998 599999999999777665 45677888876 456799999999999999988875322111
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCC--cchHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHS--KNLAALQEHCA 276 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~--~~~~~l~~~i~ 276 (449)
| .+.++. .+. .+. ..+..+...++ ++. ..++. +.+. -+...+...+.
T Consensus 256 -------------v--~~~~~~-~~~--l~~--~e~~~~~~~~~---~l~-----~~~l~---i~d~~~~t~~~i~~~~r 304 (444)
T PRK05595 256 -------------V--DMLRLR-TGN--LED--KDWENIARASG---PLA-----AAKIF---IDDTAGVSVMEMRSKCR 304 (444)
T ss_pred -------------C--CHHHHh-cCC--CCH--HHHHHHHHHHH---HHh-----cCCEE---EECCCCCCHHHHHHHHH
Confidence 0 000000 000 000 00000001100 110 01111 1111 23344444333
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc---
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS--- 344 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~--- 344 (449)
.+ ..+ .++.-|+||.|.-..-.. .+...++-.....||.+.++.++.+++....+-- . |.
T Consensus 305 ~~----~~~----~~~~~vvIDylql~~~~~~~~~r~~~v~~is~~LK~lAke~~i~vi~lsQLnR~~e~r~~~rP~lsd 376 (444)
T PRK05595 305 RL----KIE----HGIDMILIDYLQLMSGGKGSESRQQEVSEISRSIKALAKEMECPVIALSQLSRAPEQRADHRPMLSD 376 (444)
T ss_pred HH----HHh----cCCCEEEEeHHHhccCCCCCccHHHHHHHHHHHHHHHHHHhCCeEEEeeccCcchhccCCCCCchhh
Confidence 33 222 357789999987432111 1123468888899999999999988888765421 1 11
Q ss_pred h--hhhhhhhcceEEEEEe
Q 013117 345 S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 ~--~~~le~laDgVI~L~~ 361 (449)
+ ...++.-||.|+.|+-
T Consensus 377 lr~Sg~Ieq~AD~vl~l~r 395 (444)
T PRK05595 377 LRESGSIEQDADVVMFLYR 395 (444)
T ss_pred hhhhcccccCCCEEEEEec
Confidence 1 2457889999999974
No 57
>PRK07004 replicative DNA helicase; Provisional
Probab=97.91 E-value=0.00015 Score=77.42 Aligned_cols=198 Identities=16% Similarity=0.134 Sum_probs=115.5
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh-cCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV-HGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~-~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
.-++||+++||++++ |+..|.+++|.+-++.| +++|+.+|+..++. +|++++|+|+|..+++++..+-+..+.-+
T Consensus 194 ~gi~TG~~~LD~~t~-G~~~g~liviaarpg~G-KT~~al~ia~~~a~~~~~~v~~fSlEM~~~ql~~R~la~~~~v~-- 269 (460)
T PRK07004 194 TGTPTGFVDLDRMTS-GMHGGELIIVAGRPSMG-KTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQLAMRMLGSVGRLD-- 269 (460)
T ss_pred CCccCCcHHhccccc-CCCCCceEEEEeCCCCC-ccHHHHHHHHHHHHHcCCeEEEEeCCCCHHHHHHHHHHhhcCCC--
Confidence 467899999999986 89999999999877666 46777888888764 69999999999999998887522111000
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCc--chHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSK--NLAALQEHCA 276 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~--~~~~l~~~i~ 276 (449)
. .+| +-.++..+ .+..+.+.+ .++.. ..+ .+.+.+ +...+...+.
T Consensus 270 --------~--~~i--~~g~l~~~----------e~~~~~~a~---~~l~~-----~~l---~I~d~~~~~~~~i~~~~r 316 (460)
T PRK07004 270 --------Q--HRM--RTGRLTDE----------DWPKLTHAV---QKMSE-----AQL---FIDETGGLNPMELRSRAR 316 (460)
T ss_pred --------H--HHH--hcCCCCHH----------HHHHHHHHH---HHHhc-----CCE---EEECCCCCCHHHHHHHHH
Confidence 0 000 00000000 000001111 11110 011 111222 2334443333
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--C-----Ccc---
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL--L-----SLS--- 344 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l--~-----~~~--- 344 (449)
.+.+ .. .++.=|+||=|.-..-.. .+...++-.....||.+.+..++.+++....+- - .|.
T Consensus 317 ~l~~----~~---~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~lsD 389 (460)
T PRK07004 317 RLAR----QC---GKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELDVPVIALSQLNRGLEQRPNKRPVMSD 389 (460)
T ss_pred HHHH----hC---CCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEeccChhhhccCCCCCChHH
Confidence 3222 11 236678999886442111 122457889999999999999988887775431 1 111
Q ss_pred h--hhhhhhhcceEEEEEe
Q 013117 345 S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 ~--~~~le~laDgVI~L~~ 361 (449)
+ ...+|.-||.|+.|+-
T Consensus 390 LreSg~IeqdAD~v~~l~R 408 (460)
T PRK07004 390 LRESGAIEQDADVILFIYR 408 (460)
T ss_pred HhcchhhhhcCCEEEEecc
Confidence 1 2457889999999974
No 58
>PRK05636 replicative DNA helicase; Provisional
Probab=97.71 E-value=0.00019 Score=77.53 Aligned_cols=197 Identities=13% Similarity=0.153 Sum_probs=114.6
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhh-hcCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGL-VHGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl-~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
.-++||+++||+++ ||+..|.+++|.+.++.| +++|..+++...+ .+|++++|+|.|.+.++++..+=+..+.
T Consensus 246 ~Gi~TG~~~LD~~t-~Gl~~G~Liiiaarpg~G-KT~~al~~a~~~a~~~g~~v~~fSlEMs~~ql~~R~ls~~s~---- 319 (505)
T PRK05636 246 TGIPTGFKDLDDLT-NGLRGGQMIIVAARPGVG-KSTLALDFMRSASIKHNKASVIFSLEMSKSEIVMRLLSAEAE---- 319 (505)
T ss_pred CceecChHHHhhhc-CCCCCCceEEEEeCCCCC-HHHHHHHHHHHHHHhCCCeEEEEEeeCCHHHHHHHHHHHhcC----
Confidence 46889999999987 589999999999877666 4567788887765 4688999999999988888764211110
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCc--chHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSK--NLAALQEHCA 276 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~--~~~~l~~~i~ 276 (449)
| .+.++. .+. .+ ...|....+-...+.. ..+ .+.+.+ ++..+...+
T Consensus 320 -------------v--~~~~i~-~g~--l~-----~~e~~~~~~a~~~l~~-----~~l---~I~d~~~~ti~~I~~~~- 367 (505)
T PRK05636 320 -------------V--RLSDMR-GGK--MD-----EDAWEKLVQRLGKIAQ-----API---FIDDSANLTMMEIRSKA- 367 (505)
T ss_pred -------------C--CHHHHh-cCC--CC-----HHHHHHHHHHHHHHhc-----CCE---EEECCCCCCHHHHHHHH-
Confidence 0 001100 000 00 0000000000001110 011 112222 234444333
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--CC-----cc---
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL--LS-----LS--- 344 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l--~~-----~~--- 344 (449)
.++... .++.=|+||-|.-..-.. .+...++-.+...||.+.+..++.+++....+- .. +.
T Consensus 368 ---r~~~~~----~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~lsQLnR~~e~r~dkrP~lsD 440 (505)
T PRK05636 368 ---RRLKQK----HDLKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIAISQLNRGPESRTDKRPQLAD 440 (505)
T ss_pred ---HHHHHh----cCCCEEEEcchHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEeecCccccccCCCCCcHHH
Confidence 333222 357899999987432111 112357889999999999999988877775441 11 11
Q ss_pred h--hhhhhhhcceEEEEEe
Q 013117 345 S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 ~--~~~le~laDgVI~L~~ 361 (449)
+ .-.||.-||.|+.|+-
T Consensus 441 LreSG~IEqdAD~vl~l~R 459 (505)
T PRK05636 441 LRESGSLEQDADMVMLLYR 459 (505)
T ss_pred HhhcccccccCCEEEEEec
Confidence 1 2357889999999974
No 59
>PRK08006 replicative DNA helicase; Provisional
Probab=97.65 E-value=0.00049 Score=73.81 Aligned_cols=199 Identities=15% Similarity=0.167 Sum_probs=112.4
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhh-hcCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGL-VHGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl-~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
.-++||+++||+++ ||+-.|.+++|.+-++.| ++.|+.+++...+ .+|++++|+|.|-..++++..+=+..+.
T Consensus 205 ~Gi~TG~~~LD~~~-~Gl~~G~LiiIaarPgmG-KTafalnia~~~a~~~g~~V~~fSlEM~~~ql~~Rlla~~~~---- 278 (471)
T PRK08006 205 TGVNTGYDDLNKKT-AGLQPSDLIIVAARPSMG-KTTFAMNLCENAAMLQDKPVLIFSLEMPGEQIMMRMLASLSR---- 278 (471)
T ss_pred CcccCCCHHHHHhh-cCCCCCcEEEEEeCCCCC-HHHHHHHHHHHHHHhcCCeEEEEeccCCHHHHHHHHHHHhcC----
Confidence 34789999999998 589999999999776665 4566677777755 3689999999998888888764221110
Q ss_pred ccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCc--chHHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSK--NLAALQEHCA 276 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~--~~~~l~~~i~ 276 (449)
| .+.++. .+. ++.. .+......++ .+ +...++ .+.+.+ +...+...+.
T Consensus 279 -------------v--~~~~i~-~~~--l~~~--e~~~~~~a~~---~~----~~~~~l---~I~d~~~~t~~~i~~~~r 328 (471)
T PRK08006 279 -------------V--DQTRIR-TGQ--LDDE--DWARISGTMG---IL----LEKRNM---YIDDSSGLTPTEVRSRAR 328 (471)
T ss_pred -------------C--CHHHhh-cCC--CCHH--HHHHHHHHHH---HH----HhcCCE---EEECCCCCCHHHHHHHHH
Confidence 0 000000 000 0000 0000000000 00 000011 112221 2344443333
Q ss_pred HHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc---
Q 013117 277 SFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS--- 344 (449)
Q Consensus 277 ~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~--- 344 (449)
.+.. .. .++.=|+||-|.-..... .+...++-.....||.+.+..++.+++....+-- . |.
T Consensus 329 ~~~~----~~---~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~r~dkrP~lsD 401 (471)
T PRK08006 329 RIFR----EH---GGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKELQVPVVALSQLNRSLEQRADKRPVNSD 401 (471)
T ss_pred HHHH----hc---CCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchhh
Confidence 3222 11 247789999886432111 1224578999999999999999877777644321 0 11
Q ss_pred h--hhhhhhhcceEEEEEe
Q 013117 345 S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 ~--~~~le~laDgVI~L~~ 361 (449)
+ .-.||.-||.|+.|+-
T Consensus 402 LreSG~IEqdAD~v~~l~R 420 (471)
T PRK08006 402 LRESGSIEQDADLIMFIYR 420 (471)
T ss_pred hhhcCcccccCCEEEEEec
Confidence 1 2457889999999974
No 60
>PRK06904 replicative DNA helicase; Validated
Probab=97.46 E-value=0.00098 Score=71.51 Aligned_cols=199 Identities=15% Similarity=0.156 Sum_probs=112.0
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh-cCCcEEEEcCCCChhhHhhcCCCCCCccccc
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV-HGQPLLYASPSKDPRGFLGTLPSPASLKHDK 198 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~-~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k 198 (449)
.-++||+++||+++ ||+..|.+++|.+-++.| +++|+.+++...+. +|++++|+|.|-+.++++..+=+..+.-+
T Consensus 202 ~Gi~TG~~~LD~~t-~Gl~~G~LiiIaarPg~G-KTafalnia~~~a~~~g~~Vl~fSlEMs~~ql~~Rlla~~s~v~-- 277 (472)
T PRK06904 202 TGVTTGFTDLDKKT-AGLQPSDLIIVAARPSMG-KTTFAMNLCENAAMASEKPVLVFSLEMPAEQIMMRMLASLSRVD-- 277 (472)
T ss_pred CCccCChHHHHHHH-hccCCCcEEEEEeCCCCC-hHHHHHHHHHHHHHhcCCeEEEEeccCCHHHHHHHHHHhhCCCC--
Confidence 45789999999998 589999999999777665 45677777777664 58999999999888888876422111000
Q ss_pred ccccchhhccccEEEeecc-ccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCc--chHHHHHHH
Q 013117 199 SRDRESEQEKGLRIAWQYK-KYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSK--NLAALQEHC 275 (449)
Q Consensus 199 ~~~~~~~~~~~mKIAWRY~-~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~--~~~~l~~~i 275 (449)
..+| +.+ .+.++ .+..+...++ .+.. ..++ .+.+.+ +..++...+
T Consensus 278 ----------~~~i--~~g~~l~~~----------e~~~~~~a~~---~l~~----~~~l---~I~d~~~~t~~~i~~~~ 325 (472)
T PRK06904 278 ----------QTKI--RTGQNLDQQ----------DWAKISSTVG---MFKQ----KPNL---YIDDSSGLTPTELRSRA 325 (472)
T ss_pred ----------HHHh--ccCCCCCHH----------HHHHHHHHHH---HHhc----CCCE---EEECCCCCCHHHHHHHH
Confidence 0000 100 00000 0000000111 0000 0001 112221 233443333
Q ss_pred HHHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc--
Q 013117 276 ASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS-- 344 (449)
Q Consensus 276 ~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~-- 344 (449)
..+ .+.. .++.=|+||-|.-..... .+...++-.....||.+.+..++.+++....+-- . |.
T Consensus 326 r~~----~~~~---~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~lsQLnR~~e~r~~krP~ls 398 (472)
T PRK06904 326 RRV----YREN---GGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKELKVPVVALSQLNRTLENRGDKRPVNS 398 (472)
T ss_pred HHH----HHhC---CCCCEEEEecHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEEecCchhhccCCCCCchH
Confidence 222 2211 246679999886432111 1223578899999999999999877777654311 1 11
Q ss_pred -h--hhhhhhhcceEEEEEe
Q 013117 345 -S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 -~--~~~le~laDgVI~L~~ 361 (449)
+ .-.+|.-||.|+.|+-
T Consensus 399 DLreSG~IEqdAD~v~~l~R 418 (472)
T PRK06904 399 DLRESGSIEQDADLIMFIYR 418 (472)
T ss_pred HHhhcCccccCCcEEEEEec
Confidence 1 2357888999999964
No 61
>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=97.28 E-value=0.006 Score=53.70 Aligned_cols=71 Identities=14% Similarity=0.127 Sum_probs=49.8
Q ss_pred CceeEEEEcCCCcccccC----CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcc------hhhhhhhhcceEEEE
Q 013117 290 ALAGRIAIQSLCAPQCEH----SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLS------STKRWQHMADTLLSV 359 (449)
Q Consensus 290 ~~v~RIvIdSL~Sp~~~~----~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~------~~~~le~laDgVI~L 359 (449)
..+..|+||++....-.. ...+..+..++..|...+++.+++++++....-.... ....+++++|++|.|
T Consensus 84 ~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~l 163 (165)
T cd01120 84 GGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVL 163 (165)
T ss_pred CCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccccCcccccCccceeeecceEEEE
Confidence 457899999998642110 0113467899999999999889999998875532211 224679999999988
Q ss_pred E
Q 013117 360 A 360 (449)
Q Consensus 360 ~ 360 (449)
+
T Consensus 164 ~ 164 (165)
T cd01120 164 S 164 (165)
T ss_pred e
Confidence 5
No 62
>PRK08840 replicative DNA helicase; Provisional
Probab=97.24 E-value=0.003 Score=67.63 Aligned_cols=200 Identities=16% Similarity=0.153 Sum_probs=110.9
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh-cCCcEEEEcCCCChhhHhhcCCCCCCcccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV-HGQPLLYASPSKDPRGFLGTLPSPASLKHD 197 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~-~g~~vl~vs~~e~p~~il~~LP~~~~~~~~ 197 (449)
..-++||.++||.+++ |+-.|.+++|.+-++.| +++|+.+++...+. +|++++|+|+|-+.++++..+=+..+.
T Consensus 197 ~~gi~TG~~~LD~~~~-G~~~g~LiviaarPg~G-KTafalnia~~~a~~~~~~v~~fSlEMs~~ql~~Rlla~~s~--- 271 (464)
T PRK08840 197 VTGVDTGFTDLNKKTA-GLQGSDLIIVAARPSMG-KTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLMMRMLASLSR--- 271 (464)
T ss_pred CCCcCCCcHHHHHhhc-CCCCCceEEEEeCCCCc-hHHHHHHHHHHHHHhCCCeEEEEeccCCHHHHHHHHHHhhCC---
Confidence 3457899999999985 79999999999766555 34566677666553 589999999998888888764221110
Q ss_pred cccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCc--chHHHHHHH
Q 013117 198 KSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSK--NLAALQEHC 275 (449)
Q Consensus 198 k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~--~~~~l~~~i 275 (449)
.. ..+| +-..+. ...|-...+-...+. ....+ .+.+.+ +..++...+
T Consensus 272 -------v~--~~~i--~~~~l~-------------~~e~~~~~~a~~~l~----~~~~l---~I~d~~~~ti~~i~~~~ 320 (464)
T PRK08840 272 -------VD--QTKI--RTGQLD-------------DEDWARISSTMGILM----EKKNM---YIDDSSGLTPTEVRSRA 320 (464)
T ss_pred -------CC--HHHH--hcCCCC-------------HHHHHHHHHHHHHHH----hcCCE---EEECCCCCCHHHHHHHH
Confidence 00 0000 000000 000000000000000 00011 112222 233443333
Q ss_pred HHHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCC--C-----cc--
Q 013117 276 ASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLL--S-----LS-- 344 (449)
Q Consensus 276 ~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~--~-----~~-- 344 (449)
.++..+. .++.-|+||-|.-..... .+...++-.+...||.+.+..++.+++....+-- . |.
T Consensus 321 ----r~~~~~~---~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~r~~krP~ls 393 (464)
T PRK08840 321 ----RRIAREH---GGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSLEQRADKRPVNS 393 (464)
T ss_pred ----HHHHHhc---CCCCEEEEccHHhcCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccccCCCCCchH
Confidence 3232221 246789999886432111 1123578999999999999999877766654311 1 11
Q ss_pred -h--hhhhhhhcceEEEEEe
Q 013117 345 -S--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 345 -~--~~~le~laDgVI~L~~ 361 (449)
+ .-.+|.-||.|+.|+.
T Consensus 394 DLreSG~IEqdAD~v~~l~R 413 (464)
T PRK08840 394 DLRESGSIEQDADLIMFIYR 413 (464)
T ss_pred hhhhcccccccCCEEEEEec
Confidence 1 2457889999999975
No 63
>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=97.11 E-value=0.0088 Score=58.00 Aligned_cols=77 Identities=14% Similarity=0.124 Sum_probs=51.5
Q ss_pred CceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCc------ch---hhhhhhhcceEEEEE
Q 013117 290 ALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSL------SS---TKRWQHMADTLLSVA 360 (449)
Q Consensus 290 ~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~------~~---~~~le~laDgVI~L~ 360 (449)
.++..|+||++.+......++...+..|+..|+.+.+..+++++++.+...-.. .. ...+...+|.++.|.
T Consensus 110 ~~~~lvviDpl~~~~~~~~~d~~~~~~~~~~L~~~a~~~g~avl~v~H~~K~~~~~~~~~~~~rGssal~~~~r~~~~l~ 189 (239)
T cd01125 110 RRIDLVVIDPLVSFHGVSENDNGAMDAVIKALRRIAAQTGAAILLVHHVRKGSAKDGDTQEAARGASALVDGARWVRALT 189 (239)
T ss_pred cCCCEEEECChHHhCCCCcCCHHHHHHHHHHHHHHHHHhCCEEEEEeccCcccccCcccccccCcHHHHhcccceEEEEe
Confidence 357899999987652212234567788899999988888999999887653211 11 233445577888888
Q ss_pred eeCCCc
Q 013117 361 AIPDED 366 (449)
Q Consensus 361 ~f~~~~ 366 (449)
.....+
T Consensus 190 ~~~~~~ 195 (239)
T cd01125 190 RMTSEE 195 (239)
T ss_pred eCCHHH
Confidence 765543
No 64
>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=96.61 E-value=0.11 Score=52.24 Aligned_cols=69 Identities=22% Similarity=0.200 Sum_probs=43.1
Q ss_pred ceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC-------CCcchhhhhhhhcceEEEEEeeC
Q 013117 291 LAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL-------LSLSSTKRWQHMADTLLSVAAIP 363 (449)
Q Consensus 291 ~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l-------~~~~~~~~le~laDgVI~L~~f~ 363 (449)
.-.=|+||||....... ...+..||.+|++ ..+++++.+.+.++ +.+....-++|+|-.+|.++++.
T Consensus 88 ~~~lVvIDSLn~ll~~~---~~~l~~fLssl~~---~p~~svv~~~H~Dl~~~~~~~~~P~~l~lL~~LATtii~v~~~~ 161 (280)
T PF10483_consen 88 KKFLVVIDSLNYLLNHH---PCQLSQFLSSLLS---SPQSSVVGLYHTDLLPPSQNPYYPSPLSLLSYLATTIITVEPLS 161 (280)
T ss_dssp --EEEEES-GGGS-GG------GHHHHHHHH------TTEEEEEEEETTS---TTB-TS--HHHHHHHH-SEEEEEEE--
T ss_pred CCeEEEEEcchHHHHHH---HHHHHHHHHhccc---CCCcEEEEEEccCcCcccccccCcCHHHHHHHhceEEEEEcccC
Confidence 44679999998553322 2268888877773 34588888889998 66666778899999999999987
Q ss_pred CC
Q 013117 364 DE 365 (449)
Q Consensus 364 ~~ 365 (449)
..
T Consensus 162 ~~ 163 (280)
T PF10483_consen 162 HI 163 (280)
T ss_dssp -S
T ss_pred cc
Confidence 63
No 65
>PRK06749 replicative DNA helicase; Provisional
Probab=96.57 E-value=0.0043 Score=65.86 Aligned_cols=67 Identities=15% Similarity=0.178 Sum_probs=56.8
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcC
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTL 188 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~L 188 (449)
.-++||.++||++++ |+-.|.+++|.+-++.| ++.|+.+++...+.+|.+++|+|.|-+++++...+
T Consensus 167 ~Gi~TG~~~LD~~t~-Gl~~G~LiiIaarPgmG-KTafal~ia~~~a~~g~~v~~fSlEMs~~ql~~R~ 233 (428)
T PRK06749 167 TGIETGYTSLNKMTC-GLQEGDFVVLGARPSMG-KTAFALNVGLHAAKSGAAVGLFSLEMSSKQLLKRM 233 (428)
T ss_pred CCccCCcHHHHHHhC-CCCCCcEEEEEeCCCCC-chHHHHHHHHHHHhcCCCEEEEEeeCCHHHHHHHH
Confidence 457899999999875 79999999999776665 45777888888888899999999999999888764
No 66
>KOG1564 consensus DNA repair protein RHP57 [Replication, recombination and repair]
Probab=96.33 E-value=0.028 Score=56.26 Aligned_cols=65 Identities=20% Similarity=0.335 Sum_probs=43.5
Q ss_pred CCCCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-----CCcEEEEcCCC
Q 013117 115 GPNGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-----GQPLLYASPSK 179 (449)
Q Consensus 115 sp~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-----g~~vl~vs~~e 179 (449)
++.....++||++.||+.|+||+|.+.+.=|-+..++|...++++.-++=-+-. |-.++|+.+|.
T Consensus 77 s~~~~~~lttgc~~LD~~L~GGi~~~giTEi~GeSg~GKtQL~lQL~L~VQLp~~~GGL~~~~vYI~TE~ 146 (351)
T KOG1564|consen 77 SKTNRSKLTTGCVALDECLRGGIPTDGITEICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAVYICTES 146 (351)
T ss_pred ccCCchhcccccHHHHHHhcCCcccccHHHHhhccCCcHHHHHHHHHHHhhCchhhCCCCCceEEEEcCC
Confidence 333346799999999999999999999998887777774333333333221211 34567777643
No 67
>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=95.94 E-value=0.0089 Score=62.29 Aligned_cols=75 Identities=31% Similarity=0.382 Sum_probs=52.3
Q ss_pred cCCCCCeEeecCchhHHHHhcCCccCCcEEEEe--ecCCCChHHHHHHHHHHhhhhcCCcEEEEcCC-CChhhHhhcC
Q 013117 114 CGPNGTMFVSSGIADLDKILGGGFPLGSLVMVM--EDAEAPHHMLLLRNFMSQGLVHGQPLLYASPS-KDPRGFLGTL 188 (449)
Q Consensus 114 psp~g~~~iSTGIp~LD~lLGGGLPlGS~lLIe--Ed~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~-e~p~~il~~L 188 (449)
|-+|.....||||.+||.|+.||+-.||++++| +|-.-.|..+|...-++.-+.||..+.++-+- ..|..+-++|
T Consensus 232 P~~n~~~~~STGi~DlD~IlsGG~~~GS~v~Le~g~dv~~~~y~~Lt~~ai~Nfl~n~~gv~ivPp~~g~p~l~~n~l 309 (484)
T PF07088_consen 232 PIPNTKAHFSTGIRDLDEILSGGLNRGSCVLLELGHDVSKRYYQVLTAPAISNFLKNGMGVAIVPPREGSPGLLHNNL 309 (484)
T ss_pred cCCCCccccccCCCcHHHHhhccccCCcEEEEEecCCCCccceeeeeHHHHHHHHhcCCceEEeCCCCCCchhhhcch
Confidence 445667789999999999999999999999998 33332444555555566667777777776543 3444444444
No 68
>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=95.45 E-value=0.22 Score=52.24 Aligned_cols=203 Identities=12% Similarity=0.178 Sum_probs=110.2
Q ss_pred CCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChhhHhhcCCCCCCcccccccccchhhccccEEEeeccc
Q 013117 139 LGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPRGFLGTLPSPASLKHDKSRDRESEQEKGLRIAWQYKK 218 (449)
Q Consensus 139 lGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~~il~~LP~~~~~~~~k~~~~~~~~~~~mKIAWRY~~ 218 (449)
-|.++||-+.++|| +.+|..-++.. +...+.++|+|.--++..+.+.-|.....
T Consensus 9 ~G~TLLIKG~PGTG-KTtfaLelL~~-l~~~~~v~YISTRVd~d~vy~~y~~~~~~------------------------ 62 (484)
T PF07088_consen 9 PGQTLLIKGEPGTG-KTTFALELLNS-LKDHGNVMYISTRVDQDTVYEMYPWIEES------------------------ 62 (484)
T ss_pred CCcEEEEecCCCCC-ceeeehhhHHH-HhccCCeEEEEeccCHHHHHHhhhhhccc------------------------
Confidence 58999999888886 23444555554 66678899999755555555543221100
Q ss_pred cccCCCCCCCCCCCCCCCcccccccccc-ccccccccceeeeeeccCCcchHHHHHHHHHHHHHhhhccCCCCceeEEEE
Q 013117 219 YMGENQPNFDSHRDNKQDYCNEFDFRKP-LERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQHQRNDGSSALAGRIAI 297 (449)
Q Consensus 219 ~~~~~~~~~~~~~~~~~~f~h~FDLsk~-l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~~~~~~~~~~~v~RIvI 297 (449)
++ --|..|+++. +.-+. ..+ +++. ...+..+. ++++++... ..-.=|+|
T Consensus 63 --------i~--------~~~vlDatQd~~~~~~--~~~---vp~~-~l~~ds~~----~f~~~i~~~----~k~~iI~~ 112 (484)
T PF07088_consen 63 --------ID--------PTNVLDATQDPFELPL--DKD---VPFE-RLDIDSFR----DFVDKINEA----GKKPIIAF 112 (484)
T ss_pred --------cC--------hhhhhhhccchhhccc--ccc---Cccc-ccCHHHHH----HHHHHhhhc----ccCcEEEE
Confidence 00 0012222221 11000 000 0110 11234444 455554321 22357899
Q ss_pred cCCCccccc---CCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcchhhhhhhhcceEEEEEeeCCCcHHHhhhcc
Q 013117 298 QSLCAPQCE---HSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSSTKRWQHMADTLLSVAAIPDEDKELAKLLS 374 (449)
Q Consensus 298 dSL~Sp~~~---~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~~~~le~laDgVI~L~~f~~~~~e~~~~~~ 374 (449)
||.-...-+ .-+.+.++..|...|-.+.|..++=.++..+..- ...+++++||||.|+.- ..++-
T Consensus 113 DSWdaiieyla~~~~~~ed~e~l~~dLv~lard~g~~LIlVsEsa~-----~~~LdYivDGVVTL~v~-~derG------ 180 (484)
T PF07088_consen 113 DSWDAIIEYLAEEHDEPEDIETLTNDLVELARDMGINLILVSESAE-----NEPLDYIVDGVVTLQVK-NDERG------ 180 (484)
T ss_pred ecHHHHHHHhhhhhcCcHHHHHHHHHHHHHHhhcCceEEEEEecCC-----CCcchheeeeEEEEEec-cccCC------
Confidence 993322111 1112456888888888888988887777766543 24689999999999442 11111
Q ss_pred CCCCcceeEEEeeecccccCCcccccCceeeEEEcceeceEEee
Q 013117 375 GYQDMVGLLNVHKVARLNTQVPLILEATTFSIKLQKRRFLVLEC 418 (449)
Q Consensus 375 ~yk~~hGLL~V~KLp~lntl~~~~~~~~~lAFKl~rrr~~vIE~ 418 (449)
-+..-|.+.|| .+ .......|-|.|.-.||=.+++
T Consensus 181 ---R~~R~L~LeKL-----RG-V~I~q~~Y~fTL~nGrF~~f~p 215 (484)
T PF07088_consen 181 ---RTRRYLRLEKL-----RG-VRIKQRLYPFTLANGRFRSFTP 215 (484)
T ss_pred ---ceEEEEEehhh-----cC-cccCCccceEEeeCCEEEEecc
Confidence 12477888888 22 1123445778886666666666
No 69
>KOG1433 consensus DNA repair protein RAD51/RHP55 [Replication, recombination and repair]
Probab=93.60 E-value=0.12 Score=52.85 Aligned_cols=59 Identities=29% Similarity=0.423 Sum_probs=43.6
Q ss_pred CCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHh-hhhcCCcEEEEcC
Q 013117 117 NGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQ-GLVHGQPLLYASP 177 (449)
Q Consensus 117 ~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAE-Gl~~g~~vl~vs~ 177 (449)
.+.-.++||+.+||++|+||++.|++..|-+.+.+| ...|+..+..+ |-.. -.++|+..
T Consensus 88 ~~~~~l~Tg~~~lD~lL~gGi~~g~~TEi~G~p~~G-KtQlc~~~~v~~~gge-~~~l~IDs 147 (326)
T KOG1433|consen 88 SELGFLSTGSKALDKLLGGGIETGSLTELVGPPGSG-KTQLCHTLAVTCGGGE-GKVLYIDT 147 (326)
T ss_pred ccceeeccchhhhhHhhccCcccCceeEEecCCCcc-HHHHHHHHHHhccCCc-ceEEEEec
Confidence 345689999999999999999999999999888777 35666555554 2222 24556643
No 70
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=93.41 E-value=1 Score=47.93 Aligned_cols=194 Identities=16% Similarity=0.182 Sum_probs=107.0
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhh--cCCcEEEEcCCCChhhHhhcCCCCCCccc
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLV--HGQPLLYASPSKDPRGFLGTLPSPASLKH 196 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~--~g~~vl~vs~~e~p~~il~~LP~~~~~~~ 196 (449)
..=++||..+||.+.+| +-.|.+++|..-++- |++=+--.+|+.+. .+.++.++|.|=+.++|+..|=+..+.-
T Consensus 176 ~~Gi~tgf~~LD~~t~G-~~~~dLii~AaRP~m--GKTafalnia~n~a~~~~~~v~iFSLEM~~eql~~R~Ls~~s~v- 251 (435)
T COG0305 176 LIGVPTGFTDLDEITSG-FRPGDLIIVAARPGM--GKTALALNIALNAAADGRKPVAIFSLEMSEEQLVMRLLSSESGI- 251 (435)
T ss_pred CcccccCchhhHHHhcC-CccCCEEEEccCCCC--ChHHHHHHHHHHHHHhcCCCeEEEEccCCHHHHHHHhhcccccc-
Confidence 34578999999999997 999999999854433 34333333333333 4677899999888888888752221110
Q ss_pred ccccccchhhccccEEEeeccccccCCCCCCCCCCCCCCCcccccccc---ccccccccccceeeeeeccCCcc--hHHH
Q 013117 197 DKSRDRESEQEKGLRIAWQYKKYMGENQPNFDSHRDNKQDYCNEFDFR---KPLERHYFTRQRVNCVGIQHSKN--LAAL 271 (449)
Q Consensus 197 ~k~~~~~~~~~~~mKIAWRY~~~~~~~~~~~~~~~~~~~~f~h~FDLs---k~l~~~~~~~~~i~~~~~~~~~~--~~~l 271 (449)
. .-|| |-+. +..-||. +.+. .++... +-+.+.++ +.++
T Consensus 252 ---------~--~~ki--rtg~-------------------l~~~d~~~l~~a~~--~l~~~~---i~IdD~~~~si~ei 294 (435)
T COG0305 252 ---------E--SSKL--RTGR-------------------LSDDEWERLIKAAS--ELSEAP---IFIDDTPGLTITEI 294 (435)
T ss_pred ---------c--hhcc--cccc-------------------ccHHHHHHHHHHHH--HHhhCC---eeecCCCcCCHHHH
Confidence 0 0111 0000 1111111 1110 011111 11233332 3344
Q ss_pred HHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccC--CCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC--CCc----
Q 013117 272 QEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEH--SNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL--LSL---- 343 (449)
Q Consensus 272 ~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~--~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l--~~~---- 343 (449)
..++..+ .++ .++..|+||-|.-..-.. .+...++-..-.+|+++.|..++..+.....+. -++
T Consensus 295 r~~aRrl----k~~----~~l~~i~iDYLqLm~~~~~~~~r~qevs~iSr~LK~lAkEl~vpvialSQLsR~~E~R~dkr 366 (435)
T COG0305 295 RSKARRL----KLK----HNLGLIVIDYLQLMTGGKKSENRKQEVSEISRSLKGLAKELGVPVIALSQLNRSVEQRTDKR 366 (435)
T ss_pred HHHHHHH----HHh----cCccEEEEEEEEeecccccchhHHHHHHHHHHHHHHHHHhcCCcEEehhhhcccchhccccC
Confidence 3333222 222 459999999886432211 112458899999999999998887666554331 110
Q ss_pred ----ch--hhhhhhhcceEEEEEe
Q 013117 344 ----SS--TKRWQHMADTLLSVAA 361 (449)
Q Consensus 344 ----~~--~~~le~laDgVI~L~~ 361 (449)
.+ ...+|.=+|.|+.|..
T Consensus 367 P~lSDLRESGsIEQDAD~VmflyR 390 (435)
T COG0305 367 PMLSDLRESGALEQDADIVIFLHR 390 (435)
T ss_pred CccccCccCCchhhhCCEEEEEec
Confidence 11 2457888999999876
No 71
>PRK04296 thymidine kinase; Provisional
Probab=93.02 E-value=3.7 Score=38.50 Aligned_cols=36 Identities=11% Similarity=0.006 Sum_probs=30.5
Q ss_pred CCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEE
Q 013117 139 LGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYA 175 (449)
Q Consensus 139 lGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~v 175 (449)
.|++.||.++.++| +++++..++.+...+|++++++
T Consensus 1 ~g~i~litG~~GsG-KTT~~l~~~~~~~~~g~~v~i~ 36 (190)
T PRK04296 1 MAKLEFIYGAMNSG-KSTELLQRAYNYEERGMKVLVF 36 (190)
T ss_pred CcEEEEEECCCCCH-HHHHHHHHHHHHHHcCCeEEEE
Confidence 48899999887776 4568899999998899999988
No 72
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=89.58 E-value=1.8 Score=44.46 Aligned_cols=50 Identities=18% Similarity=0.183 Sum_probs=38.9
Q ss_pred ceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCC
Q 013117 291 LAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSL 340 (449)
Q Consensus 291 ~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l 340 (449)
...=|+||++-+..-........+..|+.++|.+.++..|.++..-.+..
T Consensus 194 rp~~vViDp~v~f~~G~s~s~vqv~~fi~~~rkla~~l~caIiy~hHtsk 243 (402)
T COG3598 194 RPDFVVIDPFVAFYEGKSISDVQVKEFIKKTRKLARNLECAIIYIHHTSK 243 (402)
T ss_pred CCCeEEEcchhhhcCCccchhHHHHHHHHHHHHHHHhcCCeEEEEecccc
Confidence 34679999998875554444567999999999999999988887776553
No 73
>KOG1434 consensus Meiotic recombination protein Dmc1 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=88.78 E-value=0.17 Score=50.28 Aligned_cols=36 Identities=28% Similarity=0.480 Sum_probs=29.7
Q ss_pred CCCeEeecCchhHHHHhcCCccCCcEEEEeecCCCC
Q 013117 117 NGTMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAP 152 (449)
Q Consensus 117 ~g~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~ 152 (449)
..+..|+||+.+||.+||||+|.=++.=|-+....|
T Consensus 92 ~~v~~ItTgs~~lD~ILGGGI~~m~iTEifGefr~G 127 (335)
T KOG1434|consen 92 KTVGSITTGSSALDDILGGGIPSMSITEIFGEFRCG 127 (335)
T ss_pred hccceeecchHHHhhhhcCCccchhhHHHcCCCCcC
Confidence 457899999999999999999998887776555443
No 74
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=78.92 E-value=56 Score=30.48 Aligned_cols=154 Identities=15% Similarity=0.167 Sum_probs=81.7
Q ss_pred CccCCc-EEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcC-CCChhhHhhcCCCCCCcccccccccchhhccccEEE
Q 013117 136 GFPLGS-LVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASP-SKDPRGFLGTLPSPASLKHDKSRDRESEQEKGLRIA 213 (449)
Q Consensus 136 GLPlGS-~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~-~e~p~~il~~LP~~~~~~~~k~~~~~~~~~~~mKIA 213 (449)
.+|.|. ++++=++. ..+ --.+--|+.+||.+|++|+|+.. ....+.+.+.|-....+- ......+.++|.
T Consensus 15 ~~~~g~H~c~~Y~~~-~e~-~~~~~~Fi~~GL~~ge~~l~v~~~~~~~~~l~~~L~~~~~d~------~~~~~~gqL~~~ 86 (191)
T PF14417_consen 15 DIPWGDHICAFYDDE-EEL-LEVLVPFIREGLARGERCLYVAPDPRRVEELRDELRKAGPDV------EQYLDSGQLELL 86 (191)
T ss_pred CCCCCceEEEEECCH-HHH-HHHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHHHhcCCch------hhcccCCCEEEe
Confidence 677755 44444332 333 23458899999999999999987 455556666552211100 001112233331
Q ss_pred eeccccccCCCCCCCCCCCCCCCccccccccccccccccccceeeeeeccCCcchHHHHHHHHHHHHHhhhccCCCCcee
Q 013117 214 WQYKKYMGENQPNFDSHRDNKQDYCNEFDFRKPLERHYFTRQRVNCVGIQHSKNLAALQEHCASFLAQHQRNDGSSALAG 293 (449)
Q Consensus 214 WRY~~~~~~~~~~~~~~~~~~~~f~h~FDLsk~l~~~~~~~~~i~~~~~~~~~~~~~l~~~i~~~L~~~~~~~~~~~~v~ 293 (449)
=-.+-|. .....+...+.+.+.+.+.+... ++ ..-.
T Consensus 87 ~~~~~Y~-----------------------------------------~~g~f~~~~~i~~~~~~~~~a~~-~G--~~~l 122 (191)
T PF14417_consen 87 DAEEWYL-----------------------------------------PDGRFDPARMIAFWRAALEQALA-EG--YRGL 122 (191)
T ss_pred cchhhhc-----------------------------------------cCCCcCHHHHHHHHHHHHHHHHh-CC--CCcE
Confidence 1100010 00011223444444443332221 12 2358
Q ss_pred EEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCcch
Q 013117 294 RIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSLSS 345 (449)
Q Consensus 294 RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~~~ 345 (449)
|++-+-- |.......++.+|=..|-.++....+++++..+...+++..
T Consensus 123 Rv~ge~~----w~~~~~~~~l~~yE~~ln~~~~~~~~~~lC~Yd~~~~~~~~ 170 (191)
T PF14417_consen 123 RVIGEMT----WALRSGWEELLRYEALLNRLFAEHPFTALCAYDRRRFSPEV 170 (191)
T ss_pred EEEEech----hhccccHHHHHHHHHHHHHHhcCCCEEEEeccchHhCCHHH
Confidence 9988732 32222345677877788888888899999998888777643
No 75
>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=78.11 E-value=6.4 Score=35.38 Aligned_cols=67 Identities=25% Similarity=0.294 Sum_probs=49.3
Q ss_pred chHHHHHHHHHHHHHhhhccCCCCceeEEEEcCCCcccccCCCCHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCc
Q 013117 267 NLAALQEHCASFLAQHQRNDGSSALAGRIAIQSLCAPQCEHSNMDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSL 343 (449)
Q Consensus 267 ~~~~l~~~i~~~L~~~~~~~~~~~~v~RIvIdSL~Sp~~~~~~~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~ 343 (449)
++..+.+.+.+++++ . +-.=|+||++-....+. .-..+++||..||..+-.+|++.++++..+.+++
T Consensus 59 ~L~~l~~~i~~fl~~----~----~~~vViiD~lEYL~l~N--gF~~v~KFL~~LkD~~~~~~~~lIl~~~~~al~e 125 (136)
T PF05763_consen 59 NLHKLLDTIVRFLKE----N----GNGVVIIDGLEYLILEN--GFESVLKFLASLKDYALLNNGTLILVVDPEALDE 125 (136)
T ss_pred hhHHHHHHHHHHHHh----C----CCcEEEEecHHHHHHHc--CHHHHHHHHHHhHHHeeccCCEEEEEEChhhcCH
Confidence 345566656666663 1 11378999998776543 3568999999999999888999999998877664
No 76
>PF09818 ABC_ATPase: Predicted ATPase of the ABC class; InterPro: IPR019195 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry consists of various predicted ABC transporter class ATPases.
Probab=77.46 E-value=42 Score=36.00 Aligned_cols=45 Identities=11% Similarity=0.259 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhhhcCcEEEEeeCCCCCCcchhhhhhhhcceEEEEEeeCCC
Q 013117 314 MLSFIKSLKGMVRSSNAVVVITFPPSLLSLSSTKRWQHMADTLLSVAAIPDE 365 (449)
Q Consensus 314 ll~FL~~LR~llR~s~~taliT~p~~l~~~~~~~~le~laDgVI~L~~f~~~ 365 (449)
+..|+..+|.+-+..++..++.+... -..-..+|.||.|+.+...
T Consensus 373 ITPfidrvr~l~~~~GvStIlV~Ggs-------gdy~~vAD~Vi~Md~Y~~~ 417 (448)
T PF09818_consen 373 ITPFIDRVRSLYEKLGVSTILVVGGS-------GDYFDVADRVIMMDEYRPK 417 (448)
T ss_pred cchHHHHHHHHHHHcCceEEEEeccc-------hhhHhhCCEEEEecCccch
Confidence 78999999999888898777776432 1234589999999866443
No 77
>TIGR02710 CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
Probab=41.08 E-value=14 Score=38.81 Aligned_cols=22 Identities=23% Similarity=0.137 Sum_probs=19.1
Q ss_pred eeecCCceecchhhhhhccCCc
Q 013117 72 WHFTGKTKLCSVDAAMATTKPR 93 (449)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~ 93 (449)
-.+|||||..|+++++||...+
T Consensus 76 vD~TGGTK~Msagl~laa~~~g 97 (380)
T TIGR02710 76 ADLTGGTKPMTAGLVLAAILYG 97 (380)
T ss_pred EECCCChHHHHHHHHHHHHhcC
Confidence 4689999999999999998743
No 78
>PF13245 AAA_19: Part of AAA domain
Probab=37.94 E-value=80 Score=25.14 Aligned_cols=40 Identities=18% Similarity=0.257 Sum_probs=26.9
Q ss_pred CcEEEEeecCCCChHHHHHHHHHHhhhhc----CCcEEEEcCCCC
Q 013117 140 GSLVMVMEDAEAPHHMLLLRNFMSQGLVH----GQPLLYASPSKD 180 (449)
Q Consensus 140 GS~lLIeEd~~t~~~~~LlkyFlAEGl~~----g~~vl~vs~~e~ 180 (449)
+.+++|.+.+++|. +.++...+++-+.+ +++++++++...
T Consensus 10 ~~~~vv~g~pGtGK-T~~~~~~i~~l~~~~~~~~~~vlv~a~t~~ 53 (76)
T PF13245_consen 10 SPLFVVQGPPGTGK-TTTLAARIAELLAARADPGKRVLVLAPTRA 53 (76)
T ss_pred CCeEEEECCCCCCH-HHHHHHHHHHHHHHhcCCCCeEEEECCCHH
Confidence 45677788887773 33556666665554 899999987543
No 79
>COG4544 Uncharacterized conserved protein [Function unknown]
Probab=36.26 E-value=31 Score=34.03 Aligned_cols=58 Identities=17% Similarity=0.295 Sum_probs=38.3
Q ss_pred CeEeecCchhHHHHhc-CCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCC--cEEEEcC
Q 013117 119 TMFVSSGIADLDKILG-GGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQ--PLLYASP 177 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLG-GGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~--~vl~vs~ 177 (449)
....+.|+|.+|..|- ||+++|-+-=+++-+... ..=+.--+.+-|+.+.+ +|+++..
T Consensus 32 ~~~LpfGvp~~Da~lpGGglalg~ihe~~ggg~ga-~~GaAaAl~~~g~~~r~~gpVvWi~t 92 (260)
T COG4544 32 AGILPFGVPPIDAALPGGGLALGEIHELEGGGAGA-ADGAAAALAVLGLAARRGGPVVWILT 92 (260)
T ss_pred ccccccCCCchhhhcCCcchhhhhhhhccCCCccc-hhhHHHHHHHHhhhcccCCCEEEEEe
Confidence 4568899999999885 577777766665332221 22233444455998877 8888864
No 80
>PF09670 Cas_Cas02710: CRISPR-associated protein (Cas_Cas02710)
Probab=33.60 E-value=19 Score=37.68 Aligned_cols=24 Identities=29% Similarity=0.267 Sum_probs=20.5
Q ss_pred EeeecCCceecchhhhhhccCCcc
Q 013117 71 SWHFTGKTKLCSVDAAMATTKPRL 94 (449)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~m 94 (449)
--.+|||||..|+++||||.-.+.
T Consensus 74 ~vDiTGGTK~Msaglalaa~~~~~ 97 (379)
T PF09670_consen 74 AVDITGGTKSMSAGLALAAIELGV 97 (379)
T ss_pred EEECCCCHHHHHHHHHHHHHHcCC
Confidence 347899999999999999988654
No 81
>PRK06851 hypothetical protein; Provisional
Probab=32.56 E-value=90 Score=32.76 Aligned_cols=51 Identities=10% Similarity=0.139 Sum_probs=40.2
Q ss_pred eecCchh-HHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEc
Q 013117 122 VSSGIAD-LDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYAS 176 (449)
Q Consensus 122 iSTGIp~-LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs 176 (449)
++-|.-+ +|.++.+ .-..++|.+++++| +++|++.++.+...+|..+.+.-
T Consensus 198 Tp~G~~s~~~~l~~~---~~~~~~i~G~pG~G-Kstl~~~i~~~a~~~G~~v~~~h 249 (367)
T PRK06851 198 TPKGAVDFVPSLTEG---VKNRYFLKGRPGTG-KSTMLKKIAKAAEERGFDVEVYH 249 (367)
T ss_pred CCCcHHhhHHhHhcc---cceEEEEeCCCCCc-HHHHHHHHHHHHHhCCCeEEEEe
Confidence 4455544 6788854 46789999988887 57899999999999999988763
No 82
>PF13173 AAA_14: AAA domain
Probab=29.23 E-value=99 Score=26.56 Aligned_cols=37 Identities=14% Similarity=0.234 Sum_probs=28.2
Q ss_pred CcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCC
Q 013117 140 GSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPS 178 (449)
Q Consensus 140 GS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~ 178 (449)
+-+++|.|....| +++|+++++.+=. ..+.++|++++
T Consensus 2 ~~~~~l~G~R~vG-KTtll~~~~~~~~-~~~~~~yi~~~ 38 (128)
T PF13173_consen 2 RKIIILTGPRGVG-KTTLLKQLAKDLL-PPENILYINFD 38 (128)
T ss_pred CCeEEEECCCCCC-HHHHHHHHHHHhc-ccccceeeccC
Confidence 4578999888887 5678889877644 67888888873
No 83
>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.
Probab=29.00 E-value=82 Score=29.08 Aligned_cols=33 Identities=15% Similarity=0.373 Sum_probs=24.8
Q ss_pred EEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCC
Q 013117 142 LVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPS 178 (449)
Q Consensus 142 ~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~ 178 (449)
++||.+...+| ++++..+|+++ .+++++|++..
T Consensus 1 ~~li~G~~~sG-KS~~a~~~~~~---~~~~~~y~at~ 33 (169)
T cd00544 1 IILVTGGARSG-KSRFAERLAAE---LGGPVTYIATA 33 (169)
T ss_pred CEEEECCCCCC-HHHHHHHHHHh---cCCCeEEEEcc
Confidence 36788777776 56788888876 77899998753
No 84
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=25.38 E-value=1.2e+02 Score=30.48 Aligned_cols=67 Identities=15% Similarity=0.255 Sum_probs=44.5
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhc-CCcEEEEcCCCChhh---HhhcC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVH-GQPLLYASPSKDPRG---FLGTL 188 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~-g~~vl~vs~~e~p~~---il~~L 188 (449)
...+.|||..+|-++- +..|.-++|-++.++| +++|+++.+.+=..+ ...++|+.-.|.+++ +++++
T Consensus 50 ~e~L~TGIr~ID~l~p--ig~GQr~~If~~~G~G-KTtLa~~i~~~i~~~~~~~~V~~~iGer~~Ev~e~~~~~ 120 (274)
T cd01133 50 TEILETGIKVIDLLAP--YAKGGKIGLFGGAGVG-KTVLIMELINNIAKAHGGYSVFAGVGERTREGNDLYHEM 120 (274)
T ss_pred CcccccCceeeeccCC--cccCCEEEEecCCCCC-hhHHHHHHHHHHHhcCCCEEEEEEeccCcHHHHHHHHHH
Confidence 3567899999999986 6689999999888776 345555555443222 334666665555544 55543
No 85
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.35 E-value=85 Score=34.88 Aligned_cols=48 Identities=35% Similarity=0.576 Sum_probs=31.7
Q ss_pred HhcCCccCCcEEEEeecCCCChHHHHH-HHHHHhhhhcCCcEEEEcCCCChhhHhh
Q 013117 132 ILGGGFPLGSLVMVMEDAEAPHHMLLL-RNFMSQGLVHGQPLLYASPSKDPRGFLG 186 (449)
Q Consensus 132 lLGGGLPlGS~lLIeEd~~t~~~~~Ll-kyFlAEGl~~g~~vl~vs~~e~p~~il~ 186 (449)
.|||=||+| +|+.++++|| ++|| |.-+.| .|=+.+|.+..|..+.++.
T Consensus 331 rLGGKLPKG--VLLvGPPGTG--KTlLARAvAGE---A~VPFF~~sGSEFdEm~VG 379 (752)
T KOG0734|consen 331 RLGGKLPKG--VLLVGPPGTG--KTLLARAVAGE---AGVPFFYASGSEFDEMFVG 379 (752)
T ss_pred hccCcCCCc--eEEeCCCCCc--hhHHHHHhhcc---cCCCeEeccccchhhhhhc
Confidence 368999999 5566777675 5554 655554 4567788877666555553
No 86
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=23.58 E-value=1.4e+02 Score=32.02 Aligned_cols=43 Identities=9% Similarity=0.121 Sum_probs=31.8
Q ss_pred CccCCcEEEEeecCCCChHHHHHHHHHHhh-hhcCCcEEEEcCCC
Q 013117 136 GFPLGSLVMVMEDAEAPHHMLLLRNFMSQG-LVHGQPLLYASPSK 179 (449)
Q Consensus 136 GLPlGS~lLIeEd~~t~~~~~LlkyFlAEG-l~~g~~vl~vs~~e 179 (449)
|...+.++++.+.+++| .++++..++++. ...|+++.+++.+.
T Consensus 219 g~~~~~vi~lvGptGvG-KTTtaaKLA~~~~~~~G~~V~Lit~Dt 262 (432)
T PRK12724 219 GKNQRKVVFFVGPTGSG-KTTSIAKLAAKYFLHMGKSVSLYTTDN 262 (432)
T ss_pred ccCCCeEEEEECCCCCC-HHHHHHHHHHHHHHhcCCeEEEecccc
Confidence 34467889999877777 456778888765 67799999998743
No 87
>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.
Probab=23.57 E-value=1.1e+02 Score=30.92 Aligned_cols=67 Identities=12% Similarity=0.179 Sum_probs=46.4
Q ss_pred CeEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChh---hHhhcC
Q 013117 119 TMFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPR---GFLGTL 188 (449)
Q Consensus 119 ~~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~---~il~~L 188 (449)
...+-|||..+|-++- +-.|.-++|-++.++|. ++|+...++.+...+-.|+|+...|.++ ++++++
T Consensus 50 ~e~L~TGI~~ID~l~p--igrGQr~~Ifg~~g~GK-t~L~l~~i~~~~~~~v~~V~~~iGer~~ev~e~~~~~ 119 (274)
T cd01132 50 NEPLQTGIKAIDAMIP--IGRGQRELIIGDRQTGK-TAIAIDTIINQKGKKVYCIYVAIGQKASTVAQVVKTL 119 (274)
T ss_pred ccccccCCEEeeccCC--cccCCEEEeeCCCCCCc-cHHHHHHHHHhcCCCeEEEEEecccchHHHHHHHHHH
Confidence 3567899999999886 66899999998887874 4554556666554454556666555544 455554
No 88
>PF00047 ig: Immunoglobulin domain The Prosite family only concerns antibodies and MHCs.; InterPro: IPR013151 Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.; PDB: 1B6U_A 3O4O_C 3VH8_H 1BIH_A 2C9A_A 2V5Y_A 1BQH_K 2ATP_A 3B9K_A 1NEZ_H ....
Probab=23.45 E-value=57 Score=23.80 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=18.8
Q ss_pred cceeee-----eeeEEeeecCCceecchh
Q 013117 61 SLSCRL-----STIYSWHFTGKTKLCSVD 84 (449)
Q Consensus 61 ~~~~~~-----~~~~~~~~~~~~~~~~~~ 84 (449)
.|.|++ ++.|+|++.|+.......
T Consensus 5 ~L~C~~~~~~~~~~~~W~~~~~~~~~~~~ 33 (64)
T PF00047_consen 5 TLTCSVSSGPPPTTVTWSKNGQSLPEGST 33 (64)
T ss_dssp EEEEEEEESSSTSEEEEEETTTTTSEEEE
T ss_pred EEEeecCCCCCCcEEEEEECCccccCcce
Confidence 367888 889999999988765543
No 89
>PHA00520 packaging NTPase P4
Probab=21.64 E-value=2.2e+02 Score=29.28 Aligned_cols=52 Identities=19% Similarity=0.195 Sum_probs=38.9
Q ss_pred eeEEEEcCCCcccccCC-C-----CHHHHHHHHHHHHHhhhhcCcEEEEeeCCCCCCc
Q 013117 292 AGRIAIQSLCAPQCEHS-N-----MDWEMLSFIKSLKGMVRSSNAVVVITFPPSLLSL 343 (449)
Q Consensus 292 v~RIvIdSL~Sp~~~~~-~-----~~~~ll~FL~~LR~llR~s~~taliT~p~~l~~~ 343 (449)
+.-|+||||-+...... + -...+..||..|-++.++.+|.+++++++.--++
T Consensus 184 v~VvvvDSlr~vl~~~~GnatsGGISr~~~~~LTdl~~iaas~gc~vV~~lNP~S~De 241 (330)
T PHA00520 184 VDVVVVDSLRNVLFELGGNATSGGISRGAYGLLTDLGNIAASRGCRVVATLNPMSDDE 241 (330)
T ss_pred ceEEEEechHHHHhhhccCCCCCcchHHHHHHHHHHHHHHHHcCcEEEEEcCCCCccH
Confidence 45699999976643211 0 1357999999999999999999999998754343
No 90
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=20.32 E-value=1.2e+02 Score=33.19 Aligned_cols=66 Identities=12% Similarity=0.170 Sum_probs=45.3
Q ss_pred eEeecCchhHHHHhcCCccCCcEEEEeecCCCChHHHHHHHHHHhhhhcCCcEEEEcCCCChh---hHhhcC
Q 013117 120 MFVSSGIADLDKILGGGFPLGSLVMVMEDAEAPHHMLLLRNFMSQGLVHGQPLLYASPSKDPR---GFLGTL 188 (449)
Q Consensus 120 ~~iSTGIp~LD~lLGGGLPlGS~lLIeEd~~t~~~~~LlkyFlAEGl~~g~~vl~vs~~e~p~---~il~~L 188 (449)
.-+.|||..+|.++- +..|.-++|-++.++|. ++|+...++.+...+-.|+|+.--+..+ ++++++
T Consensus 144 epl~TGIkaID~l~p--igrGQR~~I~g~~g~GK-t~Lal~~i~~~~~~dv~~V~~~IGer~rev~e~~~~l 212 (502)
T PRK13343 144 EPLQTGIKVVDALIP--IGRGQRELIIGDRQTGK-TAIAIDAIINQKDSDVICVYVAIGQKASAVARVIETL 212 (502)
T ss_pred cccccCCceeccccc--cccCCEEEeeCCCCCCc-cHHHHHHHHhhcCCCEEEEEEEeccChHHHHHHHHHH
Confidence 456799999999987 56899999999988874 5564555555543343457776555543 455554
No 91
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=20.18 E-value=55 Score=24.61 Aligned_cols=11 Identities=55% Similarity=0.933 Sum_probs=9.2
Q ss_pred chhHHHHhcCC
Q 013117 126 IADLDKILGGG 136 (449)
Q Consensus 126 Ip~LD~lLGGG 136 (449)
..+||.+|||+
T Consensus 17 ~eELd~ilGg~ 27 (51)
T PF04604_consen 17 DEELDQILGGA 27 (51)
T ss_pred HHHHHHHhCCC
Confidence 46899999985
Done!