RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780382|ref|YP_003064795.1| ATP dependent RNA helicase
protein [Candidatus Liberibacter asiaticus str. psy62]
(465 letters)
>gnl|CDD|183308 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 344 bits (884), Expect = 4e-95
Identities = 155/385 (40%), Positives = 227/385 (58%), Gaps = 18/385 (4%)
Query: 1 MDFADLGLSPKVVCAVLDA-GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPM 59
F+ L L P ++ A L+ GY + TPIQ +++P +L DV A+TG+GKTA+F L +
Sbjct: 4 TAFSTLPLPPALL-ANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGL 62
Query: 60 LTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKN-YNLTVALLIGGIPFEAQNKK 118
L L+ R RV+ L+L PTRELA QVA + + N+ V L GG+P Q
Sbjct: 63 LQKLDVKRFRVQ---ALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDS 119
Query: 119 LERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTR 178
LE GA +++ TPGRILDH +G L ++ + LV+DEADRMLDMGF I I P R
Sbjct: 120 LEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARR 179
Query: 179 QTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQL 238
QTLLFSAT + + +S+ F ++P ++V + IE F ++ LQ+L
Sbjct: 180 QTLLFSATYPEGIAAISQRFQRDPVEVKVESTHD-LPAIEQRFYEV--SPDERLPALQRL 236
Query: 239 L---QSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGT 295
L Q + ++FCN KK + +L QGFS A+HG+++QR R ++L F +
Sbjct: 237 LLHHQPESC----VVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRS 292
Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355
++VA+D+AARGLDI + V N+++ E ++HRIGRTGRAG G A +LVA E+++
Sbjct: 293 CSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQ 352
Query: 356 HIDAIEKLIEKKVDWLNGDLSSLNP 380
+AIE + +K++W L SL+P
Sbjct: 353 RANAIEDYLGRKLNW--EPLPSLSP 375
>gnl|CDD|182572 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 332 bits (854), Expect = 9e-92
Identities = 168/377 (44%), Positives = 234/377 (62%), Gaps = 18/377 (4%)
Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
M F LGLSP ++ AV + GY +PTPIQ + IP VL+ D+ AQTGTGKTA F LP+L
Sbjct: 1 MSFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLL 60
Query: 61 TILE------KGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEA 114
L KGR R R LIL PTRELAAQ+ +N Y K N+ ++ GG+
Sbjct: 61 QHLITRQPHAKGR---RPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINP 117
Query: 115 QNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLV 174
Q KL G DVL+ TPGR+LD ++ + ++ +EILV+DEADRMLDMGFI I+ + + +
Sbjct: 118 QMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKL 177
Query: 175 PFTRQTLLFSATMTDELQKVSENFLQNPKRIEV---NTPSSTAETIEHCFVATYAQYSKK 231
P RQ LLFSAT +D+++ ++E L NP IEV NT S H FV +K
Sbjct: 178 PAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVH-FV----DKKRK 232
Query: 232 CALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNF 291
LL Q++ + + ++F K +L L K G AIHGN Q +R + L++F
Sbjct: 233 RELLSQMI-GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADF 291
Query: 292 KEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAK 351
K G I+++VA+D+AARGLDI ++ HV N+++PN E+Y+HRIGRTGRA G+A +LV
Sbjct: 292 KSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCV 351
Query: 352 EDIKHIDAIEKLIEKKV 368
++ K + IEKL++K++
Sbjct: 352 DEHKLLRDIEKLLKKEI 368
>gnl|CDD|183029 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 314 bits (808), Expect = 2e-86
Identities = 146/381 (38%), Positives = 211/381 (55%), Gaps = 24/381 (6%)
Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
F++L L ++ A+ D GY +PT IQ + IP L DV G A TGTGKTA+F+LP L
Sbjct: 1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60
Query: 61 -TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKL 119
+L+ R + PR LIL PTRELA QVAD + K+ +L +A + GG+ + +
Sbjct: 61 QHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF 120
Query: 120 ERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179
D+++ TPGR+L + +E L++DEADRMLDMGF I+ I + + +Q
Sbjct: 121 SENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQ 180
Query: 180 TLLFSATMTDE-LQKVSENFLQNPKRIEVNTPSST----------AETIEHCFVATYAQY 228
TLLFSAT+ + +Q +E L +P +E A+ +EH
Sbjct: 181 TLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEH--------- 231
Query: 229 SKKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKIL 288
K ALL LL+ Q + I+F ++ V L L K G + C + G + Q R + +
Sbjct: 232 --KTALLCHLLK-QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAI 288
Query: 289 SNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTL 348
+G + ++VA+D+AARG+DI DV HV NFD+P A+ Y+HRIGRTGRAGR G A +L
Sbjct: 289 KRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISL 348
Query: 349 VAKEDIKHIDAIEKLIEKKVD 369
V D + IE+ IE+ +
Sbjct: 349 VEAHDHLLLGKIERYIEEPLK 369
>gnl|CDD|183247 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 294 bits (755), Expect = 3e-80
Identities = 142/379 (37%), Positives = 232/379 (61%), Gaps = 10/379 (2%)
Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
FADLGL ++ A+ D GY KP+PIQ + IP +L DV G+AQTG+GKTA+F LP+L
Sbjct: 6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLL 65
Query: 61 TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKN-YNLTVALLIGGIPFEAQNKKL 119
L+ ++ P+ L+L PTRELA QVA+ + K+ + V L GG ++ Q + L
Sbjct: 66 HNLD---PELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL 122
Query: 120 ERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179
+G +++ TPGR+LDH RG L ++ + LV+DEAD ML MGFI ++ I + +P Q
Sbjct: 123 RQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQ 182
Query: 180 TLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLL 239
T LFSATM + +++++ F++ P+ + + + +T I + + +K L + L
Sbjct: 183 TALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGM--RKNEALVRFL 240
Query: 240 QSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLM 299
+++D IIF K + + +LE+ G++ A++G+++Q R + L K+G + ++
Sbjct: 241 EAED-FDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDIL 299
Query: 300 VASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED---IKH 356
+A+D+AARGLD+ + V N+D+P +E+Y+HRIGRTGRAGR G+A V + +++
Sbjct: 300 IATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRN 359
Query: 357 IDAIEKLIEKKVDWLNGDL 375
I+ KL +V+ N +L
Sbjct: 360 IERTMKLTIPEVELPNAEL 378
>gnl|CDD|179884 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 289 bits (743), Expect = 8e-79
Identities = 149/406 (36%), Positives = 223/406 (54%), Gaps = 15/406 (3%)
Query: 3 FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLP---- 58
F+D L P+VV A+ G+ TPIQ +PL L DV G AQTGTGKT +F+
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 59 MLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKK 118
+L+ +V PR LI+ PTRELA Q+ + E + L + L GG ++ Q K
Sbjct: 70 LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129
Query: 119 LERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFT- 177
LE G D+LI T GR++D+ + + + I+++V+DEADRM D+GFI I+ + +P
Sbjct: 130 LESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPAN 189
Query: 178 -RQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETI-EHCFVATYAQYSKKCALL 235
R +LFSAT++ +++++ + NP+ +EV T I E F Y +K LL
Sbjct: 190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELF---YPSNEEKMRLL 246
Query: 236 QQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGT 295
Q L++ ++ IIF N K + L G V + G++ Q+ R++IL F G
Sbjct: 247 QTLIE-EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGD 305
Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355
+ ++VA+D+AARGL IP V HVFN+D+P+ E+Y+HRIGRTGRAG G + +L +E
Sbjct: 306 LDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYAL 365
Query: 356 HIDAIEKLIEKKVDWLNGD----LSSLNPPLEKIDIAQHNHARKNN 397
++ AIE I + D L+ L PL N R++
Sbjct: 366 NLPAIETYIGHSIPVSKYDSDALLTDLPKPLRLTRPRTGNGPRRSG 411
>gnl|CDD|179276 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 283 bits (726), Expect = 6e-77
Identities = 144/375 (38%), Positives = 224/375 (59%), Gaps = 12/375 (3%)
Query: 3 FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
F D L+P+++ A+ D G+ TPIQ + + L HD G AQTGTGKTA+F++ ++
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 63 L-----EKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNK 117
L K R PR LI+ PTREL Q+A + K L V +GG+ F+ Q K
Sbjct: 149 LLQTPPPKERYMGE-PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLK 207
Query: 118 KLE-RGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176
+LE R D+L+ TPGR+LD RG++ ++ +E++V+DEADRMLDMGFIP ++ I P
Sbjct: 208 QLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPR 267
Query: 177 T--RQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCAL 234
RQTLLFSAT TD++ +++ + +P +E+ + ++T+E A S K L
Sbjct: 268 KEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAG--SDKYKL 325
Query: 235 LQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEG 294
L L+ +Q+ + ++F N+K V + L K G + + G++ Q R+K L F+EG
Sbjct: 326 LYNLV-TQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREG 384
Query: 295 TIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI 354
I+++VA+D+A RG+ I + HV NF +P ++Y+HRIGRTGRAG G + + ++D
Sbjct: 385 KIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDA 444
Query: 355 KHIDAIEKLIEKKVD 369
+ IE+L+ +K+
Sbjct: 445 FQLPEIEELLGRKIS 459
>gnl|CDD|185453 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 266 bits (682), Expect = 8e-72
Identities = 147/423 (34%), Positives = 230/423 (54%), Gaps = 27/423 (6%)
Query: 12 VVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLP-MLTILEKGRARV 70
++ ++ +AG+ +PTPIQ++ P+ L D+ GIA+TG+GKT +F+LP ++ I + R
Sbjct: 141 ILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRY 200
Query: 71 -RMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICT 129
P L+L PTRELA Q+ + K+G + + + GG+P Q L RG ++LI
Sbjct: 201 GDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIAC 260
Query: 130 PGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTD 189
PGR++D + + LV+DEADRMLDMGF P I+ I S + RQTL++SAT
Sbjct: 261 PGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPK 320
Query: 190 ELQKVSENFL-QNPKRIEVNTPSSTA-ETIEHCFVATYAQYSKKCAL---LQQLLQSQDT 244
E+Q ++ + + P + V + TA I+ V ++ K+ L LQ++++ D
Sbjct: 321 EVQSLARDLCKEEPVHVNVGSLDLTACHNIKQ-EVFVVEEHEKRGKLKMLLQRIMRDGDK 379
Query: 245 MKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDL 304
+ +IF KK L L G+ IHG+ Q R +L+ FK G +M+A+D+
Sbjct: 380 I---LIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDV 436
Query: 305 AARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLI 364
A+RGLD+ DV +V NFD PN+ E+Y+HRIGRTGRAG G ++T + + +L
Sbjct: 437 ASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKY-------RLA 489
Query: 365 EKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDRRKKNYSSQKSHIPLKE 424
V L + P LEK+ ++ R N ++ G+ R N ++ IPL
Sbjct: 490 RDLVKVLREAKQPVPPELEKL-----SNERSNGTERRRWGGYGRFSNNVNN----IPLGG 540
Query: 425 SEK 427
S +
Sbjct: 541 SNR 543
>gnl|CDD|179861 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 259 bits (663), Expect = 1e-69
Identities = 138/375 (36%), Positives = 224/375 (59%), Gaps = 10/375 (2%)
Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
+ F+ L P ++ + AG+ + TPIQ T+P+ L DV G AQTGTGKT +F++ ++
Sbjct: 9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVM 68
Query: 61 TILEKGRARVRM----PRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQN 116
L A PR LIL PTRELA Q+ + K+G + L AL+ GG+ ++ Q
Sbjct: 69 NRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQR 128
Query: 117 KKLERGADVLICTPGRILDHFNRGKLL-MNNIEILVIDEADRMLDMGFIPYIQNITSLVP 175
+ L++G DV+I TPGR++D+ + K++ ++ EI V+DEADRM D+GFI I+ + +P
Sbjct: 129 ELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMP 188
Query: 176 --FTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCA 233
TRQTLLFSAT++ + +++ + P+++ V T + TA + + +K
Sbjct: 189 ERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIY--FPADEEKQT 246
Query: 234 LLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKE 293
LL LL + + ++F N K V + +LE+ G+ V + G++ Q+ R +L+ F++
Sbjct: 247 LLLGLLSRSEGART-MVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQK 305
Query: 294 GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED 353
G ++++VA+D+AARGL I V +V+N+D+P AE+Y+HRIGRT R G G A + +
Sbjct: 306 GQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERY 365
Query: 354 IKHIDAIEKLIEKKV 368
+ IE IE+K+
Sbjct: 366 AMSLPDIEAYIEQKI 380
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 245 bits (626), Expect = 2e-65
Identities = 125/367 (34%), Positives = 207/367 (56%), Gaps = 5/367 (1%)
Query: 3 FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
F L L+ ++ + G+ KP+ IQ + I +L +D G AQ+GTGKTA+FV+ L +
Sbjct: 30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89
Query: 63 LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG 122
++ + + LIL PTRELA Q+ G + +GG KL+ G
Sbjct: 90 ID---YDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAG 146
Query: 123 ADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLL 182
+++ TPGR+ D ++ L ++++++ ++DEAD ML GF I ++ +P Q L
Sbjct: 147 VHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVAL 206
Query: 183 FSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQ 242
FSATM +E+ +++ F+++PKRI V T E I +VA + K L L ++
Sbjct: 207 FSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKE-EWKFDTLCDLYETL 265
Query: 243 DTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVAS 302
T+ II+CN ++ V L + ++ F+V +HG++DQ+ R I+ F+ G+ ++++ +
Sbjct: 266 -TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITT 324
Query: 303 DLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEK 362
DL ARG+D+ V V N+D+P ENYIHRIGR+GR GR G A V +DI+ + IE+
Sbjct: 325 DLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384
Query: 363 LIEKKVD 369
+++
Sbjct: 385 HYNTQIE 391
>gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 207 bits (528), Expect = 5e-54
Identities = 112/358 (31%), Positives = 191/358 (53%), Gaps = 7/358 (1%)
Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
+ F+ GL PK++ + AGY PTPIQ++ IP L + A TG+GKTASF++P++
Sbjct: 121 LSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPII 180
Query: 61 ----TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQN 116
TI + R P ++L PTREL QV D + GK AL++GG Q
Sbjct: 181 SRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL 240
Query: 117 KKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176
++++G ++++ TPGR++D ++ + ++N+ +LV+DE D ML+ GF + I +
Sbjct: 241 YRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS- 299
Query: 177 TRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQ 236
Q LLFSAT++ E++K + + ++ I + P+ + ++ + + KK L
Sbjct: 300 QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETK-QKKQKLFD 358
Query: 237 QLLQSQDTMKNGIIFCNQKKNVVNLCHSLEK-QGFSVCAIHGNIDQRSRMKILSNFKEGT 295
L Q ++F + + L +++ G +IHG + R +++ +F G
Sbjct: 359 ILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418
Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED 353
+ ++VA+ + RG+D+ V V FD+PN + YIH+IGR R G G A V +ED
Sbjct: 419 VPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEED 476
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 174 bits (444), Expect = 3e-44
Identities = 75/206 (36%), Positives = 115/206 (55%), Gaps = 8/206 (3%)
Query: 16 VLDAGYVKPTPIQIKTIPLVLQR-HDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPR 74
+ G+ P Q + I +L DV A TG+GKT + +LP L L++G+ R
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG----KR 56
Query: 75 TLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG-ADVLICTPGRI 133
L+L PTRELA Q A+ +K G + L V L GG Q +KLE G D+L+ TPGR+
Sbjct: 57 VLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL 116
Query: 134 LDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQK 193
LD L ++N++++++DEA R+LD GF ++ + L+P Q LL SAT +E++
Sbjct: 117 LDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176
Query: 194 VSENFLQNPKRIEVNTPSSTAETIEH 219
+ E FL +P + ++ + E IE
Sbjct: 177 LLELFLNDP--VFIDVGPTPLEPIEQ 200
>gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 99 bits (250), Expect = 1e-21
Identities = 36/80 (45%), Positives = 50/80 (62%)
Query: 261 LCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNF 320
L L++ G V +HG + Q R +IL F G I+++VA+D+A RGLD+P V V +
Sbjct: 3 LAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIY 62
Query: 321 DVPNRAENYIHRIGRTGRAG 340
D+P +YI RIGR GRAG
Sbjct: 63 DLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ.
Length = 591
Score = 85.9 bits (213), Expect = 2e-17
Identities = 88/353 (24%), Positives = 140/353 (39%), Gaps = 47/353 (13%)
Query: 20 GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILE 79
GY P Q + I VL DV + TG GK+ + +P L L KG T+++
Sbjct: 10 GYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL--LLKGL-------TVVIS 60
Query: 80 PTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGA----DVLICTPGRIL- 134
P L D G A L + + Q + +L P R+
Sbjct: 61 PLISLMKDQVDQLRAAGVA----AAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQ 116
Query: 135 DHFNRGKLLMNNIEILVIDEADRMLDMG--FIPYIQNITSLV---PFTRQTLLFSATMTD 189
D+F L I ++ +DEA + G F P Q + SL P + +AT
Sbjct: 117 DYF-LNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFP-QVPRIALTATADA 174
Query: 190 ELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYA------QYSKKCALLQQLLQ--S 241
E ++ L+ + F+ ++ KK + LL
Sbjct: 175 ETRQDIRELLRLAD--------------ANEFITSFDRPNLRFSVVKKNNKQKFLLDYLK 220
Query: 242 QDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVA 301
+ ++GII+ + +K V L LE QG S A H + + R + +F +++MVA
Sbjct: 221 KHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVA 280
Query: 302 SDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI 354
++ G+D P+V V ++D+P E+Y GR GR G +A L + DI
Sbjct: 281 TNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADI 333
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 69.4 bits (170), Expect = 2e-12
Identities = 39/112 (34%), Positives = 59/112 (52%), Gaps = 7/112 (6%)
Query: 235 LQQL---LQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNF 291
L QL +Q Q K+GII+CN + V + L+ +G S A H +D R + F
Sbjct: 224 LDQLMRYVQEQRG-KSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAF 282
Query: 292 KEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHG 343
+ +Q++VA+ G++ P+V V +FD+P E+Y TGRAGR G
Sbjct: 283 QRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQ---ETGRAGRDG 331
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University).
Length = 470
Score = 66.3 bits (162), Expect = 1e-11
Identities = 36/134 (26%), Positives = 65/134 (48%), Gaps = 2/134 (1%)
Query: 235 LQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEG 294
L + ++ + K+GII+C +K + SL+ G + A H ++ +R + F+
Sbjct: 216 LLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRD 275
Query: 295 TIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI 354
IQ++VA+ G++ PDV V ++ +P E+Y GR GR G + A DI
Sbjct: 276 EIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADI 335
Query: 355 KHIDAIEKLIEKKV 368
+ + L+E+
Sbjct: 336 NRLRRL--LMEEPD 347
Score = 27.0 bits (60), Expect = 9.3
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 20 GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
G P+Q++ I VL D + TG GK+ + LP L
Sbjct: 8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48
>gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 60.7 bits (148), Expect = 7e-10
Identities = 72/346 (20%), Positives = 135/346 (39%), Gaps = 80/346 (23%)
Query: 23 KPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPM-LTILEKGRARVRMPRTLILEPT 81
KP +Q +L IA TG GKT +F L M L + +KG+ ++ I+ PT
Sbjct: 80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKT-TFGLVMSLYLAKKGK------KSYIIFPT 132
Query: 82 RELAAQVADNFEKYGKNYNLTVALLI--GGIPFEAQNKKLER----GADVLICTPGRILD 135
R L QV + EK+G+ V +L + + + + LER D+L+ T +
Sbjct: 133 RLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSK 192
Query: 136 HFNRGKLLMNNIEI--LVIDEAD----------RMLDM-GFIP-YIQNITSLVPFTRQTL 181
+F+ + + + +D+ D ++L + GF I+ L+ R+
Sbjct: 193 NFD----ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKY- 247
Query: 182 LFSATMTDELQKVSENFLQ---------------NPK--RI---------EVNTPSSTAE 215
+ ++++++ E + P+ R+ EV +P
Sbjct: 248 ---EEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFEVGSPVFYLR 304
Query: 216 TIEHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQ---KKNVVNLCHSLEKQGFSV 272
I ++ K L+++L G+IF K+ L LE G +
Sbjct: 305 NIVDSYIVDEDSVEKLVELVKRL------GDGGLIFVPSDKGKEYAEELAEYLEDLGINA 358
Query: 273 CAIHGNIDQRSRMKILSNFKEGTIQLMV--AS--DLAARGLDIPDV 314
+++ F+EG + ++V AS + RG+D+P+
Sbjct: 359 ELAISGFERK-----FEKFEEGEVDVLVGVASYYGVLVRGIDLPER 399
>gnl|CDD|162177 TIGR01054, rgy, reverse gyrase. Generally, these gyrases are
encoded as a single polypeptide. An exception was found
in Methanopyrus kandleri, where enzyme is split within
the topoisomerase domain, yielding a heterodimer of gene
products designated RgyB and RgyA.
Length = 1171
Score = 55.2 bits (133), Expect = 3e-08
Identities = 68/318 (21%), Positives = 116/318 (36%), Gaps = 65/318 (20%)
Query: 44 IAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTV 103
IA TG GKT +F L M L K R I+ PT L QVA+ + +
Sbjct: 99 IAPTGVGKT-TFGLAMSLFLAKKGKRC-----YIILPTTLLVIQVAEKISSLAEKAGVGT 152
Query: 104 ALLI---GGIPFEAQNKKLER----GADVLICTPGRILDHFNRGKLLMNNIEILVIDEAD 156
+ +P + + + +ER D+LI T + +++ L + + +D+ D
Sbjct: 153 VNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE---LGPKFDFIFVDDVD 209
Query: 157 RMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAET 216
+L + + L+ F+ + + A L+ L KR+E+ +
Sbjct: 210 ALLKAS--KNVDKLLKLLGFSEELIE-KAWKLIRLRLKLYRALHAKKRLELLEAIPGKK- 265
Query: 217 IEHCFV---ATYAQYSKKCALLQQLL-----QSQDTMKN--------------------- 247
C + AT K+ L ++LL DT++N
Sbjct: 266 -RGCLIVSSATGRPRGKRAKLFRELLGFEVGGGSDTLRNVVDVYVEDEDLKETLLEIVKK 324
Query: 248 ----GIIFCNQ---KKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMV 300
GI++ + K+ + LE G A H + F EG I +++
Sbjct: 325 LGTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPKE----DYEKFAEGEIDVLI 380
Query: 301 --AS--DLAARGLDIPDV 314
AS RGLD+P+
Sbjct: 381 GVASYYGTLVRGLDLPER 398
>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 48.3 bits (116), Expect = 4e-06
Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 24/138 (17%)
Query: 231 KCALLQQLLQSQDTMKNG---IIFCNQK---KNVVNLCHSLEKQGFSVCAIHGNID---- 280
K L+++++ Q I+F + + +V+L LEK+G G
Sbjct: 348 KLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDL---LEKEGIKAVRFVGQASKDGD 404
Query: 281 ----QRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHV-FNFDVPN--RAENYIHRI 333
Q+ +++IL F+ G ++V++ +A GLDIP V V F VP+ R+ I R
Sbjct: 405 KGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS---IQRK 461
Query: 334 GRTGRAGRHGKAFTLVAK 351
GRTGR G+ L+AK
Sbjct: 462 GRTGR-QEEGRVVVLIAK 478
Score = 39.9 bits (94), Expect = 0.001
Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 6/111 (5%)
Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALL 106
TG GKTA +L + L K +V LIL PT+ L Q A+ F K+ + +
Sbjct: 38 TGLGKTAIALLVIAERLHKKGGKV-----LILAPTKPLVEQHAEFFRKFLNIPEEKIVVF 92
Query: 107 IGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADR 157
G + + +L A V++ TP I + G++ + ++ +L+ DEA R
Sbjct: 93 TGEVS-PEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHR 142
>gnl|CDD|161975 TIGR00643, recG, ATP-dependent DNA helicase RecG.
Length = 630
Score = 46.6 bits (111), Expect = 1e-05
Identities = 28/114 (24%), Positives = 49/114 (42%), Gaps = 15/114 (13%)
Query: 48 GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLI 107
G+GKT L ML +E G + ++ PT LA Q ++ + VALL
Sbjct: 266 GSGKTLVAALAMLAAIEAGY------QVALMAPTEILAEQHYNSLRNLLAPLGIEVALLT 319
Query: 108 GGIPFEAQNKKLER----GADVLICTPGRILDHFNRGKLLMNNIEILVIDEADR 157
G + + + + LE +++ T I + K+ + +++IDE R
Sbjct: 320 GSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHR 368
Score = 33.1 bits (76), Expect = 0.17
Identities = 26/104 (25%), Positives = 47/104 (45%), Gaps = 12/104 (11%)
Query: 256 KNVVNLCHSLEK--QGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPD 313
K L L+K ++V +HG + + ++ F+EG + ++VA+ + G+D+P+
Sbjct: 467 KAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526
Query: 314 VGHVFNFDVPNRAENY----IHRI-GRTGRAGRHGKAFTLVAKE 352
V AE + +H++ GR GR LV K
Sbjct: 527 A----TVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCL-LVYKN 565
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 43.0 bits (101), Expect = 2e-04
Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 20/131 (15%)
Query: 44 IAQTGTGKT-ASFVLPMLTILEKGRARVRMP------RTLILEPTRELAAQVADNF---- 92
IA TG+GKT A+F+ + + +G R R L + P + L V N
Sbjct: 2 IAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPL 61
Query: 93 -------EKYGK-NYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRI-LDHFNRGKLL 143
+ G+ NL V + G P + ++K D+LI TP + L +R +
Sbjct: 62 KGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARET 121
Query: 144 MNNIEILVIDE 154
+ +E ++IDE
Sbjct: 122 LRGVETVIIDE 132
Score = 37.2 bits (86), Expect = 0.008
Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 15/124 (12%)
Query: 276 HGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGR 335
HG++ + R K G ++ +VA+ G+D+ V V P + + RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
Query: 336 TGR--AGRHGKAFTLVAKEDIKHIDA---IEKLIEKKVDWLNGDLSSLNPPLEKIDI-AQ 389
G G F + D+ +D+ +E + G L +L PP +D+ AQ
Sbjct: 368 AGHQVGGVSKGLFFPRTRRDL--VDSAVIVECM-------FAGRLENLTPPHNPLDVLAQ 418
Query: 390 HNHA 393
A
Sbjct: 419 QTVA 422
>gnl|CDD|178682 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 42.2 bits (99), Expect = 3e-04
Identities = 25/94 (26%), Positives = 44/94 (46%)
Query: 248 GIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAAR 307
GII+C + + + L++ G HG++D R + + + I ++ A+
Sbjct: 683 GIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGM 742
Query: 308 GLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGR 341
G++ PDV V + +P E Y GR GR G+
Sbjct: 743 GINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQ 776
>gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transacribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families.
Length = 926
Score = 41.6 bits (98), Expect = 5e-04
Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 9/98 (9%)
Query: 271 SVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENY- 329
+ HG + + +++ F +G Q++V + + G+DIP+ N + RA+ +
Sbjct: 688 RIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNA----NTIIIERADKFG 743
Query: 330 ---IHRI-GRTGRAGRHGKAFTLVAKEDIKHIDAIEKL 363
++++ GR GR+ + A+ L + DA ++L
Sbjct: 744 LAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRL 781
Score = 31.6 bits (72), Expect = 0.42
Identities = 45/157 (28%), Positives = 67/157 (42%), Gaps = 47/157 (29%)
Query: 24 PTPIQIKTI---------PLVLQRHDVCGIAQTGTGKT-----ASFVLPMLTILEKGRAR 69
TP Q+K I P + R VCG G GKT A+F +A
Sbjct: 452 ETPDQLKAIEEIKADMESPRPMDRL-VCG--DVGFGKTEVAMRAAF-----------KAV 497
Query: 70 VRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGA----DV 125
+ + +L PT LA Q + F++ N+ +T+ LL + QN+ L+ A D+
Sbjct: 498 LDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDI 557
Query: 126 LICTPGRILDHFNRGKLLMNNIE-----ILVIDEADR 157
LI T H KLL +++ +L+IDE R
Sbjct: 558 LIGT------H----KLLQKDVKFKDLGLLIIDEEQR 584
>gnl|CDD|161969 TIGR00631, uvrb, excinuclease ABC, B subunit. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 655
Score = 39.2 bits (92), Expect = 0.002
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 6/96 (6%)
Query: 255 KKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDV 314
KK +L L++ G V +H ID R++I+ + + G ++V +L GLD+P+V
Sbjct: 452 KKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEV 511
Query: 315 GHVFNFDVPN----RAE-NYIHRIGRTGRAGRHGKA 345
V D R+E + I IGR R +GK
Sbjct: 512 SLVAILDADKEGFLRSERSLIQTIGRAAR-NVNGKV 546
Score = 28.0 bits (63), Expect = 5.0
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 9/46 (19%)
Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNF 92
TG+GKT + M ++ A+V P TL++ + LAAQ+ + F
Sbjct: 38 TGSGKTFT----MANVI----AQVNRP-TLVIAHNKTLAAQLYNEF 74
>gnl|CDD|163529 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood
widely spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 35.1 bits (81), Expect = 0.040
Identities = 30/80 (37%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 10 PKVVCAVLDAGYVKPTPIQIKTIPLVLQ-RHDVCGIAQTGT--GKTASFVLPMLTILEKG 66
P VV A+ AG +P Q + L RH V +A TGT GK+ ++ LP+L+ L
Sbjct: 23 PDVVAALEAAGIHRPWQHQARAAELAHAGRHVV--VA-TGTASGKSLAYQLPVLSAL--- 76
Query: 67 RARVRMPRTLILEPTRELAA 86
A L L PT+ LAA
Sbjct: 77 -ADDPRATALYLAPTKALAA 95
>gnl|CDD|182836 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 34.0 bits (79), Expect = 0.077
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 48 GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLI 107
G+GKT L L +E G + ++ PT LA Q +N +K + + VALL
Sbjct: 292 GSGKTVVAALAALAAIEAGY------QAALMAPTEILAEQHYENLKKLLEPLGIRVALLT 345
Query: 108 GGIPFEAQNKKLER----GADVLICT 129
G + + + + LE AD++I T
Sbjct: 346 GSLKGKERREILEAIASGEADIVIGT 371
Score = 30.1 bits (69), Expect = 1.3
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 14/54 (25%)
Query: 256 KNVVNLCHSLEKQ--GFSVCAIHGNIDQRSRMK------ILSNFKEGTIQLMVA 301
++ L++ V +HG RMK +++ FK G I ++VA
Sbjct: 490 QSAEETYEELQEAFPELRVGLLHG------RMKPAEKDAVMAAFKAGEIDILVA 537
>gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 32.6 bits (75), Expect = 0.20
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 21 YVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKT-ASF--VLPMLTILEK 65
+ TP Q IPL+ + +V + TG+GKT A+F ++ L L +
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGR 77
>gnl|CDD|148966 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 31.2 bits (71), Expect = 0.57
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 48 GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVAD 90
G GKT VLP L + R+ RTL+L PTR + A++ +
Sbjct: 12 GAGKTRK-VLPELV---RECIDRRL-RTLVLAPTRVVLAEMEE 49
>gnl|CDD|171470 PRK12400, PRK12400, D-amino acid aminotransferase; Reviewed.
Length = 290
Score = 31.1 bits (70), Expect = 0.67
Identities = 26/92 (28%), Positives = 36/92 (39%), Gaps = 24/92 (26%)
Query: 289 SNFKE-GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFT 347
+NF E GTI L V+ + AR H F++DVP YI + R +G
Sbjct: 86 NNFHEDGTIYLQVSRGVQART-------HTFSYDVPPTIYAYITKKERPALWIEYG---- 134
Query: 348 LVAKEDIKHIDAIEKLIEKKVDWLNGDLSSLN 379
+ + E WL D+ SLN
Sbjct: 135 ------------VRAISEPDTRWLRCDIKSLN 154
>gnl|CDD|148463 pfam06862, DUF1253, Protein of unknown function (DUF1253). This
family represents the C-terminal portion (approximately
500 residues) of several hypothetical eukaryotic
proteins of unknown function.
Length = 435
Score = 30.7 bits (70), Expect = 0.80
Identities = 42/239 (17%), Positives = 88/239 (36%), Gaps = 79/239 (33%)
Query: 123 ADVLICTP-G--RILDHFNRGKL---LMNNIEILVIDEADRMLDMGFIPYIQN------- 169
+D++I +P G I+++ + K +++IE+L++D+AD +L +QN
Sbjct: 126 SDIIIASPLGLRMIIENEDEKKRDYDFLSSIEVLIVDQADVIL-------MQNWEHVLTV 178
Query: 170 -----------------------ITSLVPFTRQTLLFSATMTDEL----QKVSENF---- 198
+ + RQT++FS+ +T E+ N+
Sbjct: 179 FKHLNKIPKKSHGADFSRVRMWYLDGQAKYYRQTIIFSSYITPEINSLFNSKCVNYRGKV 238
Query: 199 -LQNP-----------------KRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQ 240
L+ +R + ++ + F + +L QL +
Sbjct: 239 KLKPIYKSGVIGQVGLKVRQIFQRFDASSIVDDPDARFKFFTSN---------VLPQLRK 289
Query: 241 SQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLM 299
S +IF + V + + L+K+ S AI Q+ + + F G I+++
Sbjct: 290 S-SYDSGTLIFIPSYFDFVRIRNYLKKENVSFAAISEYTSQKKISRARTLFFSGRIKVL 347
>gnl|CDD|177392 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 30.7 bits (70), Expect = 0.83
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 9/52 (17%)
Query: 47 TGTGKTASFVLPMLT--ILEKGRARVRMPRTLILEPTRELAAQVADNFEKYG 96
T GK S + +L+ LE +V LI+ PT L Q+ D+F Y
Sbjct: 138 TSAGK--SLIQYLLSRYYLENYEGKV-----LIIVPTTSLVTQMIDDFVDYR 182
>gnl|CDD|180000 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 30.4 bits (70), Expect = 1.1
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 9/41 (21%)
Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQ 87
TG+GKT + M ++ R++ P TL+L + LAAQ
Sbjct: 41 TGSGKTFT----MANVIA----RLQRP-TLVLAHNKTLAAQ 72
>gnl|CDD|183477 PRK12367, PRK12367, short chain dehydrogenase; Provisional.
Length = 245
Score = 29.6 bits (67), Expect = 1.6
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 19/76 (25%)
Query: 332 RIGRTGRAGRHGKAFTLVAK---------------EDIKHIDAIEKLIEKKVDWLNGDLS 376
RIG TG +G GKA T + + ++ + I+ W G
Sbjct: 16 RIGITGASGALGKALTKAFRAKGAKVIGLTHSKINNSESNDESPNEWIK----WECGKEE 71
Query: 377 SLNPPLEKIDIAQHNH 392
SL+ L +D+ NH
Sbjct: 72 SLDKQLASLDVLILNH 87
>gnl|CDD|152563 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. There are two conserved sequence
motifs: GKT and YLP.
Length = 1192
Score = 29.6 bits (67), Expect = 1.9
Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 7/93 (7%)
Query: 352 EDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQ---KSTGFDR 408
DI+ I A +K I +++ L D L + QH H + +
Sbjct: 231 ADIQAIRAFQK-IRPEIEKLQEDFEQLLSLELR---LQHLHGELVADEERLAEEQEERKE 286
Query: 409 RKKNYSSQKSHIPLKESEKISKLQQDIQENDAD 441
K Q + + E +L Q+I +AD
Sbjct: 287 AKNELRFQLRTLDDEWKEARDELNQEISAANAD 319
>gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 29.4 bits (67), Expect = 1.9
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 27/77 (35%)
Query: 286 KILSNFKEGTIQLMVASDLAARGLDIPDV---------GHVFNFDVPNRA-ENYIHRIGR 335
++L+ F G +++ + + A+G D P+V +F+ D RA E R
Sbjct: 471 QLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDF--RASE-------R 521
Query: 336 T--------GRAGRHGK 344
T GRAGR K
Sbjct: 522 TFQLLTQVAGRAGRAEK 538
>gnl|CDD|185024 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 29.1 bits (66), Expect = 2.8
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 131 GRILDHFNRGKLLMNNIEILVIDEADRMLDM 161
GR+L F GKL+M +LV+DE +DM
Sbjct: 445 GRML--F--GKLMMQKPNVLVMDEPTNHMDM 471
>gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this
protein family are NifS, one of several related families
of cysteine desulfurase involved in iron-sulfur (FeS)
cluster biosynthesis. NifS is part of the NIF system,
usually associated with other nif genes involved in
nitrogenase expression and nitrogen fixation. The
protein family is given a fairly broad interpretation
here. It includes a clade nearly always found in
extended nitrogen fixation genomic regions, plus a
second clade more closely related to the first than to
IscS and also part of NifS-like/NifU-like systems. This
model does not extend to a more distantly clade found in
the epsilon proteobacteria such as Helicobacter pylori,
also named NifS in the literature, built instead in
TIGR03403.
Length = 379
Score = 28.7 bits (65), Expect = 3.6
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 15/48 (31%)
Query: 248 GIIFCNQKKN-----------VVNLCHSLEKQGFSVCAI----HGNID 280
+ +K V++LC LEKQG+ V + G +D
Sbjct: 78 SALAAQPEKRHIITTAVEHPAVLSLCQHLEKQGYKVTYLPVDEEGRLD 125
>gnl|CDD|161952 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University).
Length = 732
Score = 28.6 bits (64), Expect = 3.7
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 275 IHGNIDQRSRMKILSNFK-EGTIQLMVASDLAARGLDIPD 313
I+G Q+ RM+IL NF+ + + S + +D+P+
Sbjct: 521 IYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPE 560
>gnl|CDD|162132 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
Length = 711
Score = 28.5 bits (64), Expect = 4.0
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 67 RARVRMPRTLIL-EPTRELAAQVADNFEKYGKNYNLTVALLI 107
RA VR PR LIL E T L A+ ++ + TV LLI
Sbjct: 630 RALVRKPRVLILDEATSALDAECEQLLQESRSRASRTV-LLI 670
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 28.6 bits (64), Expect = 4.1
Identities = 41/152 (26%), Positives = 62/152 (40%), Gaps = 37/152 (24%)
Query: 24 PTPIQIKTI---------PLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPR 74
TP Q + I PL + R VCG G GKT + +E + +
Sbjct: 601 TTPDQAQAINAVLSDMCQPLAMDRL-VCG--DVGFGKTEVAMRAAFLAVENHK------Q 651
Query: 75 TLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGA----DVLICTP 130
+L PT LA Q DNF N+ + + +L + Q + L A D+LI T
Sbjct: 652 VAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGT- 710
Query: 131 GRILDHFNRGKLLMNNIE-----ILVIDEADR 157
H KLL ++++ +L++DE R
Sbjct: 711 -----H----KLLQSDVKWKDLGLLIVDEEHR 733
Score = 27.8 bits (62), Expect = 5.6
Identities = 25/102 (24%), Positives = 51/102 (50%), Gaps = 18/102 (17%)
Query: 276 HGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENY----IH 331
HG + +R +++++F ++V + + G+DIP N + RA+++ +H
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA----NTIIIERADHFGLAQLH 897
Query: 332 RI-GRTGRAGR---------HGKAFTLVAKEDIKHIDAIEKL 363
++ GR GR+ H KA T A++ ++ I ++E L
Sbjct: 898 QLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDL 939
>gnl|CDD|180231 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 28.1 bits (64), Expect = 5.0
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 80 PTRELAAQVADNFEKYGKN--YNLTVALLIGGIPFEAQNKKLERGADVL 126
PT EL VA FEK G + + L L+ + + E+ D+L
Sbjct: 479 PTPELIEHVAKLFEKEGIDAWFELDAKELLP-----DEADEYEKETDIL 522
>gnl|CDD|148831 pfam07451, SpoVAD, Stage V sporulation protein AD (SpoVAD). This
family contains the bacterial stage V sporulation
protein AD (SpoVAD), which is approximately 340 residues
long. This is one of six proteins encoded by the spoVA
operon, which is transcribed exclusively in the
forespore at about the time of dipicolinic acid (DPA)
synthesis in the mother cell. The functions of the
proteins encoded by the spoVA operon are unknown, but it
has been suggested they are involved in DPA transport
during sporulation.
Length = 329
Score = 27.9 bits (63), Expect = 5.7
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 9/36 (25%)
Query: 289 SNFKEGTIQLMVASDL---------AARGLDIPDVG 315
+ K+ I ++A DL AAR L IP +G
Sbjct: 66 AGLKKDDIDYLLAGDLLNQIISSSFAARTLGIPFLG 101
>gnl|CDD|161946 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University).
Length = 505
Score = 27.7 bits (62), Expect = 5.7
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 13/70 (18%)
Query: 286 KILSNFKEGTIQLMVASDLAARGLDIPDVG-----------HVFNFDVPNRAENYIHRIG 334
+L+ F G +++ + + A+G P+V H +F R + ++
Sbjct: 303 ALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQV- 361
Query: 335 RTGRAGRHGK 344
GRAGR
Sbjct: 362 -AGRAGRAED 370
>gnl|CDD|178197 PLN02585, PLN02585, magnesium protoporphyrin IX methyltransferase.
Length = 315
Score = 27.5 bits (61), Expect = 7.5
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 9/38 (23%)
Query: 403 STGFDRRKKNYSSQKSHIPLKESEKISKLQQDIQENDA 440
+TGF+R +K Y E+++++K+Q DI+ A
Sbjct: 99 TTGFERWRKIYG---------ETDEVNKVQLDIRLGHA 127
>gnl|CDD|183820 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 27.3 bits (61), Expect = 8.3
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 12/65 (18%)
Query: 299 MVASDLAARGLDI---PDVG-----HVFNFDVPNRAENYIHR--IGRTGRAGRHGKAFTL 348
VA+++A RG DI P V HV + + + I R GR GR G G +
Sbjct: 525 TVATNMAGRGTDIKLEPGVAARGGLHVILTE-RHDSAR-IDRQLAGRCGRQGDPGSYEAI 582
Query: 349 VAKED 353
++ ED
Sbjct: 583 LSLED 587
>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli.
Length = 850
Score = 27.1 bits (60), Expect = 9.4
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 45 AQTGTGKTASFVLPMLTILEKGRARVRMPRTLILE 79
A TGTGKT ++LP L + V T +L+
Sbjct: 271 APTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQ 305
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.320 0.136 0.394
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,617,564
Number of extensions: 496974
Number of successful extensions: 1134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1083
Number of HSP's successfully gapped: 66
Length of query: 465
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 368
Effective length of database: 3,898,497
Effective search space: 1434646896
Effective search space used: 1434646896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.6 bits)