RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1604
(693 letters)
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 262 bits (671), Expect = 1e-83
Identities = 97/200 (48%), Positives = 134/200 (67%), Gaps = 10/200 (5%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
FE GL L++ + + KPTPIQ AIP L GRD++G AQTGSGKTAAFLIPI+
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 260 LLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNR 319
L SP + P+ +I APTREL +QI EVA K + LK+ + YGG S R
Sbjct: 61 LDPSPKK------DGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIR 114
Query: 320 QLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 379
+L++G +I+VAT GRL D+L+RG++ L+ V+++VLDEADRMLDMGF I+ +++ +P
Sbjct: 115 KLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKL--LP 172
Query: 380 DVANRQTLMFSATFPETIQK 399
+RQTL+FSAT P+ ++
Sbjct: 173 K--DRQTLLFSATMPKEVRD 190
Score = 117 bits (297), Expect = 3e-30
Identities = 41/91 (45%), Positives = 63/91 (69%), Gaps = 11/91 (12%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
K+G +I+VAT GRL D+L+RG++ L+ V+++VLDEADRMLDMGF I+ +++ +P
Sbjct: 117 KRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKL--LPK- 173
Query: 459 ANRQTLMFSATFPETIQK-------NYIFIA 482
+RQTL+FSAT P+ ++ N + I
Sbjct: 174 -DRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 260 bits (666), Expect = 7e-79
Identities = 109/252 (43%), Positives = 161/252 (63%), Gaps = 14/252 (5%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
K+G +I+VAT GRL D++ RG++ L+ V +VLDEADRMLDMGF+ DI+ ++ +P
Sbjct: 148 KRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKIL--KALP-- 203
Query: 459 ANRQTLMFSATFPETIQ-------KNYIFIAVGIIGGAST--DVVQTILEVPKQQKKKKL 509
+RQTL+FSAT P+ I+ + + I V + T + Q LEV +++K +L
Sbjct: 204 PDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLEL 263
Query: 510 LE-LLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKK 568
L LL+++DE VIVFV T R + +A L + ++HG Q +R++A+ FK +
Sbjct: 264 LLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGE 323
Query: 569 MKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDG 628
++VLVAT VA+RGLDI + HVINYDLP + ++YVHRIGRTGR G KG A SF +++
Sbjct: 324 LRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEV 383
Query: 629 AIAKDLVRILEQ 640
K + + LE+
Sbjct: 384 KKLKRIEKRLER 395
Score = 239 bits (611), Expect = 7e-71
Identities = 90/212 (42%), Positives = 128/212 (60%), Gaps = 11/212 (5%)
Query: 189 SGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGK 248
+ F S GL L++ LK + +PTPIQ AIP L GRD++G AQTG+GK
Sbjct: 20 LSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGK 79
Query: 249 TAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICL 307
TAAFL+P++ +L+S +I APTREL +QI E K L++ +
Sbjct: 80 TAAFLLPLLQKILKSVER------KYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAV 133
Query: 308 HYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLG 367
YGG S L++G +I+VAT GRL D++ RG++ L+ V +VLDEADRMLDMGF+
Sbjct: 134 VYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFID 193
Query: 368 DIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
DI+ ++ +P +RQTL+FSAT P+ I++
Sbjct: 194 DIEKIL--KALP--PDRQTLLFSATMPDDIRE 221
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 228 bits (582), Expect = 2e-66
Identities = 115/287 (40%), Positives = 170/287 (59%), Gaps = 26/287 (9%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
++G IL+A GRL D L+ +L V ++VLDEADRMLDMGF I+ ++ PD
Sbjct: 251 RRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQ-IRPD- 308
Query: 459 ANRQTLMFSATFPETIQK--------NYIFIAVGIIG-GASTDVVQTILEVPKQQKKKKL 509
RQTLM+SAT+P+ +Q + + VG + A ++ Q + V + +K+ KL
Sbjct: 309 --RQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKL 366
Query: 510 LELLRE--KDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTK 567
LL+ +D D +++FV T + ADF+ L IHG + Q +R +++FKT
Sbjct: 367 KMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTG 426
Query: 568 KMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQD 627
K +++AT VASRGLD+K +++VIN+D P +I++YVHRIGRTGR G KG + +F PD+
Sbjct: 427 KSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKY 486
Query: 628 GAIAKDLVRILEQAGQPV-PEFLKFG---GGG------GGYGRGGDA 664
+A+DLV++L +A QPV PE K G GGYGR +
Sbjct: 487 -RLARDLVKVLREAKQPVPPELEKLSNERSNGTERRRWGGYGRFSNN 532
Score = 186 bits (474), Expect = 3e-51
Identities = 91/212 (42%), Positives = 129/212 (60%), Gaps = 7/212 (3%)
Query: 188 VSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSG 247
++G+N P+P+ SFE + ++K+LK + +T+PTPIQ P L GRD++G A+TGSG
Sbjct: 120 IAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSG 179
Query: 248 KTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICL 307
KT AFL+P + H+ P + Y P V++ APTREL QI E K+ SS ++ +
Sbjct: 180 KTLAFLLPAIVHINAQP---LLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTV 236
Query: 308 HYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLG 367
YGG L +G IL+A GRL D L+ +L V ++VLDEADRMLDMGF
Sbjct: 237 AYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEP 296
Query: 368 DIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
I+ ++ PD RQTLM+SAT+P+ +Q
Sbjct: 297 QIRKIVSQ-IRPD---RQTLMWSATWPKEVQS 324
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 213 bits (544), Expect = 3e-60
Identities = 139/427 (32%), Positives = 207/427 (48%), Gaps = 85/427 (19%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+F GL+ +++ L Y KP+PIQ IP L GRD++G AQTGSGKTAAF +P++H
Sbjct: 7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLH 66
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGASSMHF 317
+L P++++ APTREL +Q+ E ++ + + + YGG
Sbjct: 67 NLDPE--------LKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQ 118
Query: 318 NRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 377
R L +G I+V T GRL D L RG + L+ + +VLDEAD ML MGF+ D++ +M +
Sbjct: 119 LRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIM--AQ 176
Query: 378 MPDVANRQTLMFSATFPETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRM 437
+P QT +FSAT P EA R
Sbjct: 177 IP--EGHQTALFSATMP--------------------------------------EAIRR 196
Query: 438 LDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTI 497
+ F+ + Q V S++ T P D+ Q+
Sbjct: 197 ITRRFMKEPQEVRIQSSV------------TTRP--------------------DISQSY 224
Query: 498 LEVPKQQKKKKLLELLREKDEDGVIVFVSTIRNADF-IACYLCETEIATTSIHGSRLQSQ 556
V +K + L+ L +D D I+FV T +NA +A L + +++G Q+
Sbjct: 225 WTVWGMRKNEALVRFLEAEDFDAAIIFVRT-KNATLEVAEALERNGYNSAALNGDMNQAL 283
Query: 557 REQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKG 616
REQ + K ++ +L+AT VA+RGLD++ I V+NYD+P + + YVHRIGRTGR G G
Sbjct: 284 REQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAG 343
Query: 617 RATSFYD 623
RA F +
Sbjct: 344 RALLFVE 350
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 184 bits (469), Expect = 1e-54
Identities = 78/180 (43%), Positives = 108/180 (60%), Gaps = 14/180 (7%)
Query: 222 TPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICA 281
TPIQ AIPA L G+D++ A TGSGKT AFL+PI+ LL G P+ ++ A
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKG--------GPQALVLA 52
Query: 282 PTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKG-CNILVATMGRLKDILD 340
PTREL QI+E K L++ L GG S R+L+KG +ILV T GRL D+L
Sbjct: 53 PTRELAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLR 112
Query: 341 RGRISLAS-VRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
RG++ L ++ +VLDEA R+LDMGF D++ ++ +P +RQ L+ SAT P ++
Sbjct: 113 RGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSR--LPP--DRQILLLSATLPRNLED 168
Score = 86.2 bits (214), Expect = 1e-19
Identities = 33/81 (40%), Positives = 52/81 (64%), Gaps = 5/81 (6%)
Query: 397 IQKKGCNILVATMGRLKDILDRGRISLAS-VRFVVLDEADRMLDMGFLGDIQHVMQHSTM 455
++K +ILV T GRL D+L RG++ L ++ +VLDEA R+LDMGF D++ ++ +
Sbjct: 92 LKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSR--L 149
Query: 456 PDVANRQTLMFSATFPETIQK 476
P +RQ L+ SAT P ++
Sbjct: 150 PP--DRQILLLSATLPRNLED 168
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 192 bits (491), Expect = 3e-54
Identities = 91/253 (35%), Positives = 135/253 (53%), Gaps = 18/253 (7%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +I+V T GR+ D L +G + L ++ +VLDEADRMLDMGF I +++ P A
Sbjct: 123 GAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQ--AP--AR 178
Query: 461 RQTLMFSATFPETI-------QKNYIFIAVGIIGGASTDVVQTILEVPKQQKKKKLLELL 513
RQTL+FSAT+PE I Q++ + + V + Q EV ++ L LL
Sbjct: 179 RQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPA-IEQRFYEVSPDERLPALQRLL 237
Query: 514 REKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLV 573
+ +VF +T + +A L + ++HG Q R+Q + F + VLV
Sbjct: 238 LHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLV 297
Query: 574 ATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAIAKD 633
AT VA+RGLDIK + VINY+L ++ + +VHRIGRTGR G+KG A S P++
Sbjct: 298 ATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRAN-- 355
Query: 634 LVRILEQA-GQPV 645
+E G+ +
Sbjct: 356 ---AIEDYLGRKL 365
Score = 168 bits (429), Expect = 1e-45
Identities = 84/208 (40%), Positives = 115/208 (55%), Gaps = 25/208 (12%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+F + L L+ NL + YT+ TPIQ ++PA L G+D++ A+TGSGKTAAF + ++
Sbjct: 5 AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQ 64
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQ----IHEVACKYAYSSVLKICLHYGGASS 314
L V + Q V+ C PTREL Q I +A VL +C GG
Sbjct: 65 KLD------VKRFRVQALVL-C-PTRELADQVAKEIRRLARFIPNIKVLTLC---GGVP- 112
Query: 315 MHFNRQ---LEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQH 371
Q LE G +I+V T GR+ D L +G + L ++ +VLDEADRMLDMGF I
Sbjct: 113 --MGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDA 170
Query: 372 VMQHSTMPDVANRQTLMFSATFPETIQK 399
+++ P A RQTL+FSAT+PE I
Sbjct: 171 IIRQ--AP--ARRQTLLFSATYPEGIAA 194
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 185 bits (471), Expect = 1e-51
Identities = 110/313 (35%), Positives = 168/313 (53%), Gaps = 28/313 (8%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G ++LVAT GRL D+ + + L V +VLDEADRMLDMGF+ DI+ V+ + +P A
Sbjct: 125 GVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVL--AKLP--AK 180
Query: 461 RQTLMFSATFPETIQ-------KNYIFIAVGIIGGASTDVVQTILEVPKQQKKKKLLELL 513
RQ L+FSATF + I+ N + I V AS V Q + V K++K++ L +++
Sbjct: 181 RQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMI 240
Query: 514 REKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLV 573
+ + V+VF T A+ +A L + I + +IHG++ Q R +A+ DFK+ ++VLV
Sbjct: 241 GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLV 300
Query: 574 ATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAIAKD 633
AT +A+RGLDI+ + HV+NY+LP ++YVHRIGRTGR G A S D+ + +D
Sbjct: 301 ATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHK-LLRD 359
Query: 634 LVRILEQ----------------AGQPVPEFLKFGGGGGGYGRGGDAFGARDIRHDPDAA 677
+ ++L++ +P+ + GGGG GG R A
Sbjct: 360 IEKLLKKEIPRIAIPGYEPDPSIKAEPIQNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGA 419
Query: 678 PVWGGSGATEPEE 690
A +P
Sbjct: 420 KSASAKPAEKPSR 432
Score = 161 bits (410), Expect = 3e-43
Identities = 89/204 (43%), Positives = 124/204 (60%), Gaps = 14/204 (6%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
SF+S GL +++ + + Y +PTPIQ+ AIPA LEGRDLM AQTG+GKTA F +P++
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 259 HLLESPGELVTGYCAQP-EVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHF 317
HL+ +P +I PTREL QI E Y+ ++ + +GG S
Sbjct: 62 HLITRQ---PHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVS---I 115
Query: 318 NRQLEK---GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQ 374
N Q+ K G ++LVAT GRL D+ + + L V +VLDEADRMLDMGF+ DI+ V+
Sbjct: 116 NPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVL- 174
Query: 375 HSTMPDVANRQTLMFSATFPETIQ 398
+ +P A RQ L+FSATF + I+
Sbjct: 175 -AKLP--AKRQNLLFSATFSDDIK 195
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 172 bits (438), Expect = 3e-47
Identities = 79/193 (40%), Positives = 110/193 (56%), Gaps = 8/193 (4%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
F L E L++ L+ YT+PT IQ AIP L+GRD++G A TG+GKTAAFL+P + H
Sbjct: 3 FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62
Query: 260 LLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNR 319
LL+ P P ++I PTREL MQ+ + A + A + L I GG + M+
Sbjct: 63 LLDFPRR----KSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAE 118
Query: 320 QLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 379
+ +I+VAT GRL + +V ++LDEADRMLDMGF DI+ + +
Sbjct: 119 VFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAET--- 175
Query: 380 DVANRQTLMFSAT 392
+QTL+FSAT
Sbjct: 176 -RWRKQTLLFSAT 187
Score = 168 bits (428), Expect = 1e-45
Identities = 83/242 (34%), Positives = 121/242 (50%), Gaps = 43/242 (17%)
Query: 404 ILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQT 463
I+VAT GRL + +V ++LDEADRMLDMGF DI+ + + +QT
Sbjct: 126 IVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAET----RWRKQT 181
Query: 464 LMFSAT--------FPETIQKNYIFIAVGIIGGASTDVVQTILEVPKQQKKK-------- 507
L+FSAT F E + + + + E ++++KK
Sbjct: 182 LLFSATLEGDAVQDFAERLLNDPVEVEA---------------EPSRRERKKIHQWYYRA 226
Query: 508 -------KLLE-LLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQ 559
LL LL++ + IVFV T +A +L + I + G +Q++R +
Sbjct: 227 DDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNE 286
Query: 560 AIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRAT 619
AI ++ VLVAT VA+RG+DI + HVIN+D+P+ D Y+HRIGRTGR G KG A
Sbjct: 287 AIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAI 346
Query: 620 SF 621
S
Sbjct: 347 SL 348
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 171 bits (435), Expect = 7e-47
Identities = 84/196 (42%), Positives = 112/196 (57%), Gaps = 9/196 (4%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
F L +V+ L+K + TPIQ A+P L GRD+ G AQTG+GKT AFL H+
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 260 LLESP---GELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMH 316
LL P V QP +I APTREL +QIH A A ++ LK+ L YGG
Sbjct: 70 LLSHPAPEDRKVN----QPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDK 125
Query: 317 FNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHS 376
+ LE G +IL+ T GRL D + I+L +++ VVLDEADRM D+GF+ DI+ + +
Sbjct: 126 QLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRR- 184
Query: 377 TMPDVANRQTLMFSAT 392
MP R ++FSAT
Sbjct: 185 -MPPANQRLNMLFSAT 199
Score = 152 bits (387), Expect = 2e-40
Identities = 80/232 (34%), Positives = 124/232 (53%), Gaps = 15/232 (6%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
G +IL+ T GRL D + I+L +++ VVLDEADRM D+GF+ DI+ + + MP
Sbjct: 132 SGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRR--MPPAN 189
Query: 460 NRQTLMFSATFPETIQK---------NYIFIAVGIIGGASTDVVQTILEVPKQQKKKKLL 510
R ++FSAT +++ Y+ + G ++ L P ++K +LL
Sbjct: 190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHR---IKEELFYPSNEEKMRLL 246
Query: 511 ELLREKD-EDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKM 569
+ L E++ D I+F +T + I +L + G Q +R + + +F +
Sbjct: 247 QTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDL 306
Query: 570 KVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSF 621
+LVAT VA+RGL I + HV NYDLP + ++YVHRIGRTGR G G + S
Sbjct: 307 DILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 171 bits (435), Expect = 1e-46
Identities = 91/238 (38%), Positives = 131/238 (55%), Gaps = 9/238 (3%)
Query: 395 ETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 454
+ ++ + C+ILVAT GRL D RG + L V +VLDEADRMLDMGF+ ++ +++ +
Sbjct: 207 KQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQT- 265
Query: 455 MPDVANRQTLMFSATFPETIQK-------NYIFIAVGIIGGASTDVVQTILEVPKQQKKK 507
P RQTL+FSATF + + + + + AS V Q + V K K
Sbjct: 266 -PRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYK 324
Query: 508 KLLELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTK 567
L L+ + + V+VF + I L + I + G Q +R + + F+
Sbjct: 325 LLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREG 384
Query: 568 KMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPD 625
K++VLVAT VA RG+ I GI HVIN+ LP++ D+YVHRIGRTGR G G + SF D
Sbjct: 385 KIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGED 442
Score = 150 bits (380), Expect = 5e-39
Identities = 84/202 (41%), Positives = 116/202 (57%), Gaps = 10/202 (4%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
F L L+ + + TPIQ + L G D +G AQTG+GKTAAFLI I++
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 260 LLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNR 319
LL++P Y +P +I APTRELV+QI + A + L + GG M F++
Sbjct: 149 LLQTPPP-KERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGG---MDFDK 204
Query: 320 QL----EKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQH 375
QL + C+ILVAT GRL D RG + L V +VLDEADRMLDMGF+ ++ +++
Sbjct: 205 QLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQ 264
Query: 376 STMPDVANRQTLMFSATFPETI 397
+ P RQTL+FSATF + +
Sbjct: 265 T--PRKEERQTLLFSATFTDDV 284
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 162 bits (411), Expect = 4e-46
Identities = 75/189 (39%), Positives = 103/189 (54%), Gaps = 15/189 (7%)
Query: 213 LKKSNYTKPTPIQKYAIPAGLEG-RDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGY 271
++K + P QK AI A L G RD++ A TGSGKT A L+P + L G
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG------ 54
Query: 272 CAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGC-NILVA 330
V++ PTREL Q E K S LK+ YGG S R+LE G +ILV
Sbjct: 55 ---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVT 111
Query: 331 TMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFS 390
T GRL D+L+ ++SL++V V+LDEA R+LD GF ++ +++ +P N Q L+ S
Sbjct: 112 TPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKL--LPK--NVQLLLLS 167
Query: 391 ATFPETIQK 399
AT PE I+
Sbjct: 168 ATPPEEIEN 176
Score = 76.0 bits (187), Expect = 1e-15
Identities = 36/95 (37%), Positives = 57/95 (60%), Gaps = 11/95 (11%)
Query: 397 IQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
++ +ILV T GRL D+L+ ++SL++V V+LDEA R+LD GF ++ +++ +P
Sbjct: 101 LESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKL--LP 158
Query: 457 DVANRQTLMFSATFPETIQK-------NYIFIAVG 484
N Q L+ SAT PE I+ + +FI VG
Sbjct: 159 K--NVQLLLLSATPPEEIENLLELFLNDPVFIDVG 191
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 166 bits (421), Expect = 3e-44
Identities = 88/258 (34%), Positives = 142/258 (55%), Gaps = 16/258 (6%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
++G ++V T GRL D+L + I L +V +VLDE D ML+ GF + + Q + P
Sbjct: 244 QQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQP-- 301
Query: 459 ANRQTLMFSATFPETIQ-------KNYIFIAVGIIGGASTDVVQTILEVPKQQKKKKLLE 511
Q L+FSAT ++ K+ I I++G + V Q + V +QKK+KL +
Sbjct: 302 ---QVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFD 358
Query: 512 LLREKD--EDGVIVFVSTIRNADFIA-CYLCETEIATTSIHGSRLQSQREQAIHDFKTKK 568
+L+ K + +VFVS+ AD +A T + SIHG + +R + + F +
Sbjct: 359 ILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418
Query: 569 MKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDG 628
+ V+VAT V RG+D+ +R VI +D+P I EY+H+IGR R+G KG A F + ++D
Sbjct: 419 VPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVN-EEDR 477
Query: 629 AIAKDLVRILEQAGQPVP 646
+ +LV +L+ +G +P
Sbjct: 478 NLFPELVALLKSSGAAIP 495
Score = 151 bits (384), Expect = 2e-39
Identities = 83/226 (36%), Positives = 116/226 (51%), Gaps = 22/226 (9%)
Query: 182 ENVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGC 241
+E+ V G+ P PI SF S GL L+ NL+ + Y PTPIQ AIPA L GR L+
Sbjct: 105 RKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVS 164
Query: 242 AQTGSGKTAAFLIPIM--------HHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEV 293
A TGSGKTA+FL+PI+ H E P ++ PTREL +Q+ +
Sbjct: 165 ADTGSGKTASFLVPIISRCCTIRSGHPSEQRN---------PLAMVLTPTRELCVQVEDQ 215
Query: 294 ACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVV 353
A K L GG + ++++G ++V T GRL D+L + I L +V +V
Sbjct: 216 AKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLV 275
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
LDE D ML+ GF + + Q + P Q L+FSAT ++K
Sbjct: 276 LDEVDCMLERGFRDQVMQIFQALSQP-----QVLLFSATVSPEVEK 316
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 151 bits (382), Expect = 9e-39
Identities = 81/196 (41%), Positives = 117/196 (59%), Gaps = 4/196 (2%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+F S L L+ L+ + +T+ TPIQ +P L G D+ G AQTG+GKT AFL+ +M+
Sbjct: 10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFN 318
LL P L P +I APTREL +QIH+ A K+ L+ L YGG
Sbjct: 70 RLLSRPA-LADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQR 128
Query: 319 RQLEKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 377
L++G ++++AT GRL D + + + +SL + VLDEADRM D+GF+ DI+ +++
Sbjct: 129 ELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRR-- 186
Query: 378 MPDVANRQTLMFSATF 393
MP+ RQTL+FSAT
Sbjct: 187 MPERGTRQTLLFSATL 202
Score = 136 bits (343), Expect = 1e-33
Identities = 83/235 (35%), Positives = 134/235 (57%), Gaps = 14/235 (5%)
Query: 397 IQKKGCNILVATMGRLKDILDRGRI-SLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTM 455
+ ++G ++++AT GRL D + + ++ SL + VLDEADRM D+GF+ DI+ +++ M
Sbjct: 130 LLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRR--M 187
Query: 456 PDVANRQTLMFSATFPETI---------QKNYIFIAVGIIGGASTDVVQTILEVPKQQKK 506
P+ RQTL+FSAT + + + + I + V Q I ++K+
Sbjct: 188 PERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETI--TAARVRQRIYFPADEEKQ 245
Query: 507 KKLLELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKT 566
LL LL + +VFV+T + +A L + G Q +RE ++ F+
Sbjct: 246 TLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQK 305
Query: 567 KKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSF 621
++++LVAT VA+RGL I G+++V NYDLP + ++YVHRIGRT R+G +G A SF
Sbjct: 306 GQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 131 bits (333), Expect = 4e-36
Identities = 48/130 (36%), Positives = 75/130 (57%), Gaps = 2/130 (1%)
Query: 494 VQTILEVPKQQKKKKLLELLREKDEDG--VIVFVSTIRNADFIACYLCETEIATTSIHGS 551
++ + + +K + LLELL+E + G V++F + + D +A L + I ++HG
Sbjct: 2 IKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGD 61
Query: 552 RLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGR 611
Q +RE+ + DF+ ++ VLVAT V +RG+D+ + VINYDLP Y+ RIGR GR
Sbjct: 62 GSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGR 121
Query: 612 VGNKGRATSF 621
G KG A
Sbjct: 122 AGQKGTAILL 131
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 122 bits (308), Expect = 1e-32
Identities = 55/158 (34%), Positives = 81/158 (51%), Gaps = 14/158 (8%)
Query: 236 RDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVAC 295
RD++ A TGSGKT A L+PI+ L G +V++ APTREL Q+ E
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKG---------GQVLVLAPTRELANQVAER-L 50
Query: 296 KYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLD 355
K + +K+ GG S + L +I+V T GRL D L+R ++SL + ++LD
Sbjct: 51 KELFGEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILD 110
Query: 356 EADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATF 393
EA R+L+ GF ++ +RQ L+ SAT
Sbjct: 111 EAHRLLNQGFGLLGLKILLKL----PKDRQVLLLSATP 144
Score = 66.6 bits (163), Expect = 4e-13
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 390 SATFPETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHV 449
S E + +I+V T GRL D L+R ++SL + ++LDEA R+L+ GF +
Sbjct: 68 SIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKI 127
Query: 450 MQHSTMPDVANRQTLMFSATF 470
+ +RQ L+ SAT
Sbjct: 128 LLKL----PKDRQVLLLSATP 144
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 127 bits (320), Expect = 1e-31
Identities = 76/235 (32%), Positives = 123/235 (52%), Gaps = 12/235 (5%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
K G +++V T GR+ D++D+ + + ++ +LDEAD ML GF G I V + PDV
Sbjct: 144 KAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFK-KLPPDV 202
Query: 459 ANRQTLMFSATFPETI-------QKNYIFIAVGIIGGASTDVVQTILEVPKQQKK-KKLL 510
Q +FSAT P I ++ I V + Q + V K++ K L
Sbjct: 203 ---QVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLC 259
Query: 511 ELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMK 570
+L I++ +T R D++ + E + + +HG Q R+ + +F++ +
Sbjct: 260 DLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTR 319
Query: 571 VLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPD 625
VL+ T + +RG+D++ + VINYDLP + Y+HRIGR+GR G KG A +F PD
Sbjct: 320 VLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPD 374
Score = 115 bits (289), Expect = 1e-27
Identities = 70/203 (34%), Positives = 108/203 (53%), Gaps = 16/203 (7%)
Query: 197 IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPI 256
++SF++ L E L++ + + KP+ IQ+ I L+G D +G AQ+G+GKTA F+I
Sbjct: 27 VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAA 86
Query: 257 MHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASS 314
+ +L+ + +I APTREL QI +V A LK+ H GG
Sbjct: 87 L--------QLIDYDLNACQALILAPTRELAQQIQKVV--LALGDYLKVRCHACVGGTVV 136
Query: 315 MHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQ 374
+L+ G +++V T GR+ D++D+ + + ++ +LDEAD ML GF G I V +
Sbjct: 137 RDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFK 196
Query: 375 HSTMPDVANRQTLMFSATFPETI 397
PDV Q +FSAT P I
Sbjct: 197 -KLPPDV---QVALFSATMPNEI 215
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 103 bits (260), Expect = 6e-27
Identities = 36/77 (46%), Positives = 46/77 (59%)
Query: 537 YLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLP 596
L + I +HG Q +RE+ + DF+ K KVLVAT VA RG+D+ + VINYDLP
Sbjct: 2 LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLP 61
Query: 597 QEIDEYVHRIGRTGRVG 613
Y+ RIGR GR G
Sbjct: 62 WNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 102 bits (257), Expect = 2e-26
Identities = 38/82 (46%), Positives = 48/82 (58%)
Query: 532 DFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVI 591
+ +A L E I +HG Q +RE+ + F K+KVLVAT VA RGLD+ G+ VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 592 NYDLPQEIDEYVHRIGRTGRVG 613
YDLP Y+ RIGR GR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 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 [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 79.3 bits (196), Expect = 2e-15
Identities = 44/141 (31%), Positives = 67/141 (47%), Gaps = 4/141 (2%)
Query: 500 VPKQQKKKKLLELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQ 559
V K K+K LL+ L++ I++ S+ + + +A L I+ + H R +
Sbjct: 206 VKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAE 265
Query: 560 AIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRAT 619
DF +KV+VAT G+D +R VI+YD+P ++ Y GR GR G A
Sbjct: 266 NQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAI 325
Query: 620 SFYDPDQDGAIAKDLVRILEQ 640
Y P D A+ K R +EQ
Sbjct: 326 LLYSP-ADIALLK---RRIEQ 342
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 74.6 bits (184), Expect = 7e-14
Identities = 59/230 (25%), Positives = 94/230 (40%), Gaps = 27/230 (11%)
Query: 409 MGRLKDILDRGRISLASVRFVVLDEADRMLDMG--F------LGDIQHVMQHSTMPDVAN 460
R ++L R ISL V +DEA + G F LG + + +P+
Sbjct: 120 SPRFLELLKRLPISL-----VAIDEAHCISQWGHDFRPDYRRLGRL-----RAGLPNP-- 167
Query: 461 RQTLMFSATFPETIQK---NYIFIAVGIIGGASTDVVQTILEV-PKQQKKKKLLELL--R 514
L +AT ++ + + I S D L+V K + +L L
Sbjct: 168 -PVLALTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPSDQLAFLATVL 226
Query: 515 EKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVA 574
+ I++ T + + +A +L + I+ + H +RE+ F ++KV+VA
Sbjct: 227 PQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVA 286
Query: 575 TAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
T G+D +R VI+YDLP I+ Y GR GR G A Y P
Sbjct: 287 TNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSP 336
Score = 29.2 bits (66), Expect = 9.3
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 225 QKYAIPAGLEGRDLMGCAQTGSGKTAAFLIP 255
Q+ I A L G+D + TG GK+ + IP
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIP 52
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 70.8 bits (174), Expect = 1e-12
Identities = 46/131 (35%), Positives = 65/131 (49%), Gaps = 17/131 (12%)
Query: 501 PKQQKKKKLL-ELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIH---------G 550
PK +K +++L E L + + VIVF A+ I +L +I + G
Sbjct: 348 PKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFL--KKIGIKARVRFIGQASREG 405
Query: 551 SRLQSQREQ--AIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYD-LPQEIDEYVHRIG 607
+ SQ+EQ I F+ + VLVAT+V GLDI + VI Y+ +P EI + R G
Sbjct: 406 DKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEI-RSIQRKG 464
Query: 608 RTGRVGNKGRA 618
RTGR KGR
Sbjct: 465 RTGR-KRKGRV 474
Score = 43.9 bits (104), Expect = 2e-04
Identities = 38/150 (25%), Positives = 57/150 (38%), Gaps = 17/150 (11%)
Query: 215 KSNYTKPTPIQ----KYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTG 270
KP I+ + I A ++ + TG GKT + I + L G+
Sbjct: 5 AHPLIKPNTIEPRLYQLNIAAKALFKNTLVVLPTGLGKTFIAAMVIANRLRWFGGK---- 60
Query: 271 YCAQPEVIICAPTRELVMQIHEVACKYAYS-SVLKICLHYGGASSMHFNRQLEKGCNILV 329
V+ APT+ LV+Q H C+ +I G K + V
Sbjct: 61 ------VLFLAPTKPLVLQ-HAEFCRKVTGIPEDEIAALTGEVRPEEREELWAKK-KVFV 112
Query: 330 ATMGRLKDILDRGRISLASVRFVVLDEADR 359
AT +++ L GRI L V ++ DEA R
Sbjct: 113 ATPQVVENDLKAGRIDLDDVSLLIFDEAHR 142
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 65.5 bits (160), Expect = 3e-11
Identities = 81/440 (18%), Positives = 142/440 (32%), Gaps = 87/440 (19%)
Query: 201 ESAGLR--EILVKNLKKSNYTKPTPIQKYAIPA----GLEGRDLMGCAQTGSGKT--AAF 252
E A E L L + + P Q+ A+ A R + TG+GKT AA
Sbjct: 15 ELADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAE 74
Query: 253 LIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGA 312
+ L S ++ PT+EL+ Q E + + YGG
Sbjct: 75 ---AIAELKRS-------------TLVLVPTKELLDQWAE--ALKKFLLLNDEIGIYGG- 115
Query: 313 SSMHFNRQLEKGCNILVAT------MGRLKDILDRGRISLASVRFVVLDEADRMLDMGFL 366
+ + + VAT L + L L ++ DE + +
Sbjct: 116 -----GEKELEPAKVTVATVQTLARRQLLDEFLGN-EFGL-----IIFDEVHHLPAPSY- 163
Query: 367 GDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNILVATMGRLKDILDRGRISLASV 426
+ +++ + L +AT GR+ D+ D + +
Sbjct: 164 ---RRILELLSAA----YPRLGLTATPERE-----------DGGRIGDLFDL----IGPI 201
Query: 427 RFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKNYIFIAVGII 486
+ V ++D G+L ++V T+ E ++
Sbjct: 202 VYEV--SLKELIDEGYLAPYKYVEIKVTL------------TEDEEREYAKESARFRELL 247
Query: 487 GGASTDVVQTILEVPKQQKKKKLLE----LLREKDEDGVIVFVSTIRNADFIACYLCETE 542
T + ++K+ LL+ D ++F S + +A IA
Sbjct: 248 RARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPG 307
Query: 543 IATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEY 602
I +I G + +RE + F+T +KVLV V G+DI +I +
Sbjct: 308 I-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLF 366
Query: 603 VHRIGRTGR-VGNKGRATSF 621
+ R+GR R K +
Sbjct: 367 IQRLGRGLRPAEGKEDTLAL 386
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 63.8 bits (156), Expect = 2e-10
Identities = 46/153 (30%), Positives = 75/153 (49%), Gaps = 11/153 (7%)
Query: 209 LVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKT-AAFLIPIMHHLLE-SPGE 266
V+ K +T TP Q+YAIP G +++ A TGSGKT AAFL P+++ LL G+
Sbjct: 11 RVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFL-PVINELLSLGKGK 69
Query: 267 LVTG-YCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGC 325
L G Y + +P + L I + +++ + +G + L+
Sbjct: 70 LEDGIYA-----LYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPP 124
Query: 326 NILVATMGRLKDILD--RGRISLASVRFVVLDE 356
+IL+ T L +L+ + R L VR+V++DE
Sbjct: 125 HILITTPESLAILLNSPKFRELLRDVRYVIVDE 157
Score = 48.8 bits (117), Expect = 9e-06
Identities = 31/110 (28%), Positives = 51/110 (46%), Gaps = 7/110 (6%)
Query: 507 KKLLELLRE--KDEDGVIVFVSTIRNADFIACYLCETEIATTSI---HGSRLQSQREQAI 561
L E + E K ++F +T A+ +A L ++ I HGS + R +
Sbjct: 240 AALYERIAELVKKHRTTLIFTNTRSGAERLAFRL--KKLGPDIIEVHHGSLSRELRLEVE 297
Query: 562 HDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGR 611
K ++K +VAT+ G+DI I VI P+ ++ ++ RIGR G
Sbjct: 298 ERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 62.6 bits (153), Expect = 5e-10
Identities = 44/127 (34%), Positives = 66/127 (51%), Gaps = 17/127 (13%)
Query: 505 KKKKLLELLRE----KDEDGVIVFVSTIRN-ADFIACYLCETEIAT------TSIHGSRL 553
K +KL E+++E + +IVF + R+ A+ I L + I S G +
Sbjct: 348 KLEKLREIVKEQLGKNPDSRIIVF-TQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKG 406
Query: 554 QSQREQ--AIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYD-LPQEIDEYVHRIGRTG 610
SQ+EQ + F+ + VLV+T+VA GLDI + VI Y+ +P EI + R GRTG
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEI-RSIQRKGRTG 465
Query: 611 RVGNKGR 617
R +GR
Sbjct: 466 R-QEEGR 471
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 61.7 bits (150), Expect = 7e-10
Identities = 34/126 (26%), Positives = 59/126 (46%), Gaps = 5/126 (3%)
Query: 504 QKKKKLLE-----LLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQRE 558
+K K+LE + +E I++ + + ++ + L IA + H S R+
Sbjct: 207 RKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARD 266
Query: 559 QAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRA 618
H F+ +++V+VAT G++ +R VI+Y LP+ ++ Y GR GR G
Sbjct: 267 DVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSEC 326
Query: 619 TSFYDP 624
FY P
Sbjct: 327 HLFYAP 332
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 51.6 bits (124), Expect = 1e-06
Identities = 35/138 (25%), Positives = 59/138 (42%), Gaps = 19/138 (13%)
Query: 223 PIQKYAIPAGL-EGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICA 281
Q+ A+ GL +++ A TGSGKT L+ I+ LLE G +V+
Sbjct: 34 NPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGG----------KVVYIV 83
Query: 282 PTRELVMQIHEVACKYA-YSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILD 340
P + L + +E + +++ + G + + +++V T +L D L
Sbjct: 84 PLKALAEEKYEEFSRLEELG--IRVGISTG---DYDLDDERLARYDVIVTTPEKL-DSLT 137
Query: 341 RGRISLAS-VRFVVLDEA 357
R R S V VV+DE
Sbjct: 138 RKRPSWIEEVDLVVIDEI 155
Score = 34.7 bits (80), Expect = 0.17
Identities = 59/290 (20%), Positives = 86/290 (29%), Gaps = 92/290 (31%)
Query: 400 KGCNILVATMGRLKDILDRGRISLAS-VRFVVLDEA----------------DRMLDMGF 442
+++V T +L D L R R S V VV+DE RM +
Sbjct: 121 ARYDVIVTTPEKL-DSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRLN- 178
Query: 443 LGDIQHVMQHSTMP---DVA-----NRQTLMFS-ATFPETIQKNYIFIAVGIIGGASTDV 493
I+ V +T+P +VA + + F+ G G T
Sbjct: 179 -ELIRIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFL--GADGKKKTW- 234
Query: 494 VQTILEVPKQQKKKKLLELLREKDEDG--VIVFVS----TIRNADFIACYLCETEIATTS 547
LEL+ E +G V+VFV + A + + T
Sbjct: 235 --------PLLIDNLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEK 286
Query: 548 IHGSRLQS-------------------QREQAIHD--------------FKTKKMKVLVA 574
I S R A H F+ K+KVLV+
Sbjct: 287 IVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVS 346
Query: 575 TAVASRG------LDIKGIRHVINYDL---PQEID--EYVHRIGRTGRVG 613
T + G I I+ YD +I + + GR GR G
Sbjct: 347 TPTLAAGVNLPARTVI--IKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPG 394
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 51.6 bits (124), Expect = 1e-06
Identities = 35/125 (28%), Positives = 59/125 (47%), Gaps = 5/125 (4%)
Query: 504 QKKKKLLELLR----EKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQ 559
+K K L +L+R ++ + G+I S + D A L I+ + H R
Sbjct: 219 EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVED-TAARLQSRGISAAAYHAGLDNDVRAD 277
Query: 560 AIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRAT 619
F+ ++++VAT G++ +R V+++D+P+ I+ Y GR GR G A
Sbjct: 278 VQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAM 337
Query: 620 SFYDP 624
FYDP
Sbjct: 338 LFYDP 342
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 51.6 bits (124), Expect = 1e-06
Identities = 24/72 (33%), Positives = 33/72 (45%)
Query: 193 PPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAF 252
S E L L K+ + Q A+ EGR+++ TGSGKT +F
Sbjct: 43 ARPGKTSEFPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESF 102
Query: 253 LIPIMHHLLESP 264
L+PI+ HLL P
Sbjct: 103 LLPILDHLLRDP 114
Score = 35.8 bits (83), Expect = 0.094
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 546 TSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLP-QEIDEYVH 604
++ + +R + +FK ++ ++AT G+DI + VI Y P + +
Sbjct: 342 STYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQ 401
Query: 605 RIGRTGRVGN 614
R GR GR G
Sbjct: 402 RAGRAGRRGQ 411
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 50.7 bits (122), Expect = 3e-06
Identities = 51/160 (31%), Positives = 79/160 (49%), Gaps = 24/160 (15%)
Query: 215 KSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKT-AAFLIPIMHHL--LESPGELVTG- 270
K + TP Q+YAIP EG++++ + TGSGKT AAFL I+ L L GEL
Sbjct: 27 KEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA-IIDELFRLGREGELEDKV 85
Query: 271 YCAQPEVIICAPTRELVMQIH-----------EVACKYAYSSV-LKICLHYGGASSMHFN 318
YC + +P R L IH E+A + +++ + G SS
Sbjct: 86 YC-----LYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQ 140
Query: 319 RQLEKGCNILVATMGRLKDILD--RGRISLASVRFVVLDE 356
+ L+K +IL+ T L +L+ + R L +V++V++DE
Sbjct: 141 KMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDE 180
>gnl|CDD|201366 pfam00641, zf-RanBP, Zn-finger in Ran binding protein and others.
Length = 29
Score = 40.4 bits (95), Expect = 4e-05
Identities = 14/28 (50%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 105 PGDWMCS-CGASNFAKRDACFKCSEPKP 131
GDW CS C NFA C C PKP
Sbjct: 1 EGDWDCSKCLVQNFATSTKCVACQAPKP 28
>gnl|CDD|219205 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 = 436
Score = 46.1 bits (110), Expect = 5e-05
Identities = 39/173 (22%), Positives = 70/173 (40%), Gaps = 44/173 (25%)
Query: 461 RQTLMFSATFPETIQKNYIF----------------IAVGIIGGASTDVVQT-------- 496
RQT++FS+ T + N +F G+IG V Q
Sbjct: 211 RQTILFSSY--ITPEINSLFNSKCVNYRGKVKLKPIYKSGVIGQVGLKVRQVFQRFDASS 268
Query: 497 ILEVPKQQKK---KKLLE-LLREKDEDGVIVFVST------IRNADFIACYLCETEIATT 546
I++ P + K K +L L + G ++F+ + +RN YL + ++
Sbjct: 269 IVDDPDARFKFFTKNVLPQLRKSSYISGTLIFIPSYFDFVRLRN------YLKKENVSFA 322
Query: 547 SIHGSRLQSQREQAIHDFKTKKMKVLVAT--AVASRGLDIKGIRHVINYDLPQ 597
+I + +A F + ++ VL+ T R +IKG+++VI Y P+
Sbjct: 323 AISEYTSPKKISRARTLFFSGRINVLLYTERLHFFRRYEIKGVKNVIFYGPPE 375
>gnl|CDD|197784 smart00547, ZnF_RBZ, Zinc finger domain. Zinc finger domain in
Ran-binding proteins (RanBPs), and other proteins. In
RanBPs, this domain binds RanGDP.
Length = 25
Score = 40.0 bits (94), Expect = 6e-05
Identities = 13/25 (52%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 106 GDWMCS-CGASNFAKRDACFKCSEP 129
GDW C C NFA R CF C P
Sbjct: 1 GDWECPACTFLNFASRSKCFACGAP 25
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 45.9 bits (108), Expect = 7e-05
Identities = 29/118 (24%), Positives = 45/118 (38%), Gaps = 10/118 (8%)
Query: 502 KQQKKKKLL--ELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQ 559
K Q +LL +LL E V++F D + YL I + GS +R++
Sbjct: 693 KLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQE 752
Query: 560 AIHDFKTKK--MKVLVATAVASRGLDIKGIRHVINYDLPQEIDEY------VHRIGRT 609
I F + L++ GL++ G VI +D HRIG+
Sbjct: 753 LIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQK 810
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 44.0 bits (104), Expect = 2e-04
Identities = 81/417 (19%), Positives = 126/417 (30%), Gaps = 134/417 (32%)
Query: 241 CAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKY-AY 299
A TG GKT A LI LL+ +L + VI P R ++ ++ A +
Sbjct: 220 EAPTGYGKTEASLIL-ALALLDEKIKL------KSRVIYVLPFRTIIEDMYRRAKEIFGL 272
Query: 300 SSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADR 359
SV+ LH + + L ++ LA +
Sbjct: 273 FSVIGKSLHSSSKEPLLLEPDQDILLT--------LTTNDSYKKLLLALI---------- 314
Query: 360 MLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNILVATMGRLKDILDRG 419
+ IQ ++ S
Sbjct: 315 -----VVTPIQILI-FSVKGFKFEFL---------------------------------A 335
Query: 420 RISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP-----------DVANRQTLMFSA 468
+ + V +LDE H+ TM + LM SA
Sbjct: 336 LLLTSLV---ILDEV-------------HLYADETMLAALLALLEALAEAGVPVLLM-SA 378
Query: 469 TFPETIQKNYIFIAVGIIGGASTDVVQTILEVPK----QQKKKK-----------LLELL 513
T P K + A+G +VV+ PK K+K+ L+EL+
Sbjct: 379 TLP-PFLKEKLKKALG----KGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELI 433
Query: 514 REKDEDGVIVFVSTIRN--ADFIACY-LCETEIATTS-IHGSRLQSQREQAI----HDFK 565
E+ ++G V V I N I Y + + +H RE+ FK
Sbjct: 434 SEEVKEGKKVLV--IVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFK 491
Query: 566 TKKMKVLVATAVASRGLDIKGIRHVINYDL----PQEIDEYVHRIGRTGRVGNKGRA 618
+ ++VAT V G+D I++D+ ID + R GR R G K
Sbjct: 492 QNEGFIVVATQVIEAGVD-------IDFDVLITELAPIDSLIQRAGRVNRHGKKENG 541
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 40.1 bits (94), Expect = 0.003
Identities = 37/184 (20%), Positives = 64/184 (34%), Gaps = 48/184 (26%)
Query: 464 LMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPKQQKKKKL-LELLREKDEDG-- 520
L+ SAT P+ +++ I V K++++ + + E D+ G
Sbjct: 159 LLMSATLPKFLKEYAEKIGY---------VEFNEPLDLKEERRFERHRFIKIESDKVGEI 209
Query: 521 ---------------VIVFVSTIRNADFIACYLCETEIATTS----IHGSRLQSQRE--- 558
+ + V+T+ A Y E A +H + R
Sbjct: 210 SSLERLLEFIKKGGKIAIIVNTVDRA--QEFYQQLKENAPEEEIMLLHSRFTEKDRAKKE 267
Query: 559 -QAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDL----PQEIDEYVHRIGRTGRVG 613
+ + + K + V+VAT V LD I+ D+ ID + R+GR R G
Sbjct: 268 AELLEEMKKNEKFVIVATQVIEASLD-------ISADVMITELAPIDSLIQRLGRLHRYG 320
Query: 614 NKGR 617
K
Sbjct: 321 RKNG 324
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 39.9 bits (93), Expect = 0.006
Identities = 35/124 (28%), Positives = 58/124 (46%), Gaps = 7/124 (5%)
Query: 505 KKKKLLE----LLREK--DEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQRE 558
K KK LE ++E DE G+I +S + + + +A L E HGS +QR
Sbjct: 662 KTKKCLEDIDKFIKENHFDECGIIYCLSRM-DCEKVAERLQEFGHKAAFYHGSMDPAQRA 720
Query: 559 QAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRA 618
+ ++ ++ AT G++ +R VI++ LP+ I+ Y GR GR G +
Sbjct: 721 FVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSC 780
Query: 619 TSFY 622
+Y
Sbjct: 781 VLYY 784
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 38.2 bits (89), Expect = 0.015
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 14/75 (18%)
Query: 220 KPTPIQKYAI----PAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQP 275
+P P Q+ A G L+ A TG+GKT A+L+P + + E
Sbjct: 15 EPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE----------GK 64
Query: 276 EVIICAPTRELVMQI 290
+VII T+ L Q+
Sbjct: 65 KVIISTRTKALQEQL 79
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 36.4 bits (85), Expect = 0.020
Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 11/89 (12%)
Query: 509 LLELLREKDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQ----REQAIHDF 564
+LELL GV+V + + +A L + G L Q RE+ + F
Sbjct: 1 ILELLEAI-PGGVLVLFPSYSLLEQVAELLASELLEK----GIELLVQGEGSREKLLERF 55
Query: 565 KTKKMKVLVATAVASRGLDIKG--IRHVI 591
K K +L G+D G +R VI
Sbjct: 56 KKGKGAILFGVGSFWEGIDFPGDALRLVI 84
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 37.5 bits (87), Expect = 0.026
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 213 LKKSNYTKPTPIQKYAIPAGL-EGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELV 268
LK+ + P+Q A+ AGL EG +L+ + T SGKT + + LL +++
Sbjct: 209 LKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKML 265
Score = 34.0 bits (78), Expect = 0.29
Identities = 23/95 (24%), Positives = 37/95 (38%), Gaps = 6/95 (6%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
IVF + R +A L + H +R+ F +++ +V TA + G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503
Query: 582 LDIKGIRHVINYDLPQEID-----EYVHRIGRTGR 611
+D VI L I+ E+ +GR GR
Sbjct: 504 VDFPA-SQVIFESLAMGIEWLSVREFQQMLGRAGR 537
>gnl|CDD|233032 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 transcribed 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 [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 36.9 bits (86), Expect = 0.042
Identities = 35/138 (25%), Positives = 61/138 (44%), Gaps = 18/138 (13%)
Query: 512 LLREKDEDGVIVFV-STIRNADFIACYLCETEIATTSI---HGSRLQSQREQAIHDFKTK 567
+ RE G + +V + I + + +A L + I HG +++ E+ + +F
Sbjct: 653 IRRELLRGGQVFYVHNRIESIEKLATQL-RELVPEARIAIAHGQMTENELEEVMLEFYKG 711
Query: 568 KMKVLVATAVASRGLDIKG-----IRHVINYDLPQEIDEYVHRI-GRTGRVGNKGRATSF 621
+ +VLV T + G+DI I + L Q ++++ GR GR K A
Sbjct: 712 EFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQ-----LYQLRGRVGRSKKKAYAYLL 766
Query: 622 YDPDQDGAIAKDLVRILE 639
Y P Q A+ +D + LE
Sbjct: 767 Y-PHQK-ALTEDAQKRLE 782
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 36.2 bits (84), Expect = 0.073
Identities = 42/153 (27%), Positives = 59/153 (38%), Gaps = 36/153 (23%)
Query: 220 KPTPIQKYAIPAGLEGRDLMGCAQTGSGKT--AAFLIPIMHHLLESPGELVTGYCAQPEV 277
+ P Q+ AI G ++ CA T SGKT A + I L G+ V
Sbjct: 119 ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAI----ALALRDGQ---------RV 165
Query: 278 IICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKG---CN----ILVA 330
I +P + L Q KY + +G + M L G N LV
Sbjct: 166 IYTSPIKALSNQ------KYR-----DLLAKFGDVADM---VGLMTGDVSINPDAPCLVM 211
Query: 331 TMGRLKDILDRGRISLASVRFVVLDEADRMLDM 363
T L+++L RG SL + +VV DE + D
Sbjct: 212 TTEILRNMLYRGSESLRDIEWVVFDEVHYIGDR 244
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 36.1 bits (84), Expect = 0.085
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 13/81 (16%)
Query: 512 LLREKDEDGVIVF----VSTIRNADFIACYLC----ETEIATTSIHGSRLQSQREQAIHD 563
+LRE G + + V +I A L E IA HG + + E+ + D
Sbjct: 796 ILRELLRGGQVFYVHNRVESIEK---KAERLRELVPEARIAV--AHGQMRERELEEVMLD 850
Query: 564 FKTKKMKVLVATAVASRGLDI 584
F + VLV T + G+DI
Sbjct: 851 FYNGEYDVLVCTTIIETGIDI 871
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 35.5 bits (82), Expect = 0.090
Identities = 40/176 (22%), Positives = 65/176 (36%), Gaps = 35/176 (19%)
Query: 464 LMFSATFPETIQKNYIFIAVGIIGGAST------DVVQTILE----VPKQQKKKKLLELL 513
L+ SAT P+ +++ +G + + I V + ++LLE +
Sbjct: 158 LLMSATLPKFLKEYA--EKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSLERLLEFI 215
Query: 514 REKDEDGVIVFVSTIRNADFIACYLCETEIATTS----IHGSRLQSQR----EQAIHDFK 565
K V + V+T+ A Y E IH + R + + +FK
Sbjct: 216 --KKGGSVAIIVNTVDRA--QEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFK 271
Query: 566 TKKMKVLVATAVASRGLDIKGIRHVINYDL----PQEIDEYVHRIGRTGRVGNKGR 617
+ V+VAT V LD I+ D+ ID + R+GR R G K
Sbjct: 272 KSEKFVIVATQVIEASLD-------ISVDVMITELAPIDSLIQRLGRLHRYGEKNG 320
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 34.9 bits (80), Expect = 0.19
Identities = 20/64 (31%), Positives = 32/64 (50%)
Query: 547 SIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRI 606
S HGS + QR K+ +++ +VAT+ G+D+ + VI P + + RI
Sbjct: 306 SHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRI 365
Query: 607 GRTG 610
GR G
Sbjct: 366 GRAG 369
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 33.9 bits (78), Expect = 0.33
Identities = 16/71 (22%), Positives = 24/71 (33%), Gaps = 1/71 (1%)
Query: 7 VSPPVDQVVEAEVIEVEVTEVKTGHVHVVRVEEAVVAMATEVTAEVVALAMGMEVEMEVV 66
+ PV + + +V E E V V A V A+A + E VV
Sbjct: 843 IRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVA-EVVEEPVVV 901
Query: 67 EAVTEEKIGHV 77
E++ V
Sbjct: 902 AEPQPEEVVVV 912
Score = 33.1 bits (76), Expect = 0.58
Identities = 24/126 (19%), Positives = 33/126 (26%), Gaps = 32/126 (25%)
Query: 6 EVSPPVDQVVEAEVIE--VEVTEVKTGHVHVVRVEEA--VVAMATEVTAEVVALAMGMEV 61
+V D V EV E V E + + E VV EV A+ A +
Sbjct: 929 QVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVA 988
Query: 62 EMEVVEAVTEEKIGHVRVVRAIL----------------------------RPDSRFSSG 93
E ++ +V A + RP F
Sbjct: 989 AEVETVTAVEPEVAPAQVPEATVEHNHATAPMTRAPAPEYVPEAPRHSDWQRPTFAFEGK 1048
Query: 94 GGGGGD 99
G GG
Sbjct: 1049 GAAGGH 1054
Score = 32.3 bits (74), Expect = 0.96
Identities = 17/78 (21%), Positives = 23/78 (29%), Gaps = 13/78 (16%)
Query: 7 VSPPVDQVVEAEVIEVEVTEVKTGHVHVV------------RVEEAVVAMATEVTAEVVA 54
+ VV AE EV V+T H V+ + AV E VV
Sbjct: 892 AEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVE 951
Query: 55 LAMGMEVEMEVVEAVTEE 72
++E E
Sbjct: 952 PQ-DETADIEEAAETAEV 968
Score = 31.5 bits (72), Expect = 1.7
Identities = 21/71 (29%), Positives = 25/71 (35%), Gaps = 5/71 (7%)
Query: 4 TSEVSPPVDQVVEAEVIEVEVTEVKTGHVHVVRVEEAVVAMATEVTAEVVALAMGMEVEM 63
E + V+ V EV V V V V A+A V VV A E+
Sbjct: 855 VEEQREAEEVQVQPVVAEVPVAAA----VEPVVSAPVVEAVAEVVEEPVVV-AEPQPEEV 909
Query: 64 EVVEAVTEEKI 74
VVE E I
Sbjct: 910 VVVETTHPEVI 920
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 33.5 bits (77), Expect = 0.44
Identities = 43/205 (20%), Positives = 78/205 (38%), Gaps = 27/205 (13%)
Query: 395 ETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 454
ETI +++V T +++ ++ + V++DE R G Q
Sbjct: 332 ETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHR------FGVEQRKKLREK 380
Query: 455 MPDVANRQTLMFSAT-FPETIQKN-YIFIAVGIIGGASTDVVQTILEVPKQQKKKKLLEL 512
L+ SAT P T+ Y + II + K +K + E
Sbjct: 381 GQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEF 440
Query: 513 LREKDEDG--VIVFVSTIRNADFI----ACYLCET------EIATTSIHGSRLQSQ-REQ 559
+ E+ G V I ++ + A L E + +HG R++S +E
Sbjct: 441 IEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHG-RMKSDEKEA 499
Query: 560 AIHDFKTKKMKVLVATAVASRGLDI 584
+ +F+ ++ +LVAT V G+D+
Sbjct: 500 VMEEFREGEVDILVATTVIEVGVDV 524
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 33.0 bits (76), Expect = 0.64
Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 24/123 (19%)
Query: 521 VIVFVSTIRNADFIACYLCE--TEIATTSIHGSRLQSQRE--QAIHDFKTKKMKVLVATA 576
IVFV+++ + YL + IHG ++ + E + ++ +K ++++T
Sbjct: 398 GIVFVASVSQCEEYKKYLEKRLPIYDFYIIHG-KVPNIDEILEKVYS--SKNPSIIISTP 454
Query: 577 VASRGLDIKGIRHVINYD-----LPQEID---------EYVHRIGRTGRVGNKGRATSFY 622
+ I+ HV YD +P+ R GR GRV + G FY
Sbjct: 455 YLESSVTIRNATHV--YDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFY 511
Query: 623 DPD 625
D D
Sbjct: 512 DLD 514
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 32.4 bits (74), Expect = 0.88
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 25/84 (29%)
Query: 516 KDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVAT 575
+ EDG V V+T R DF+ C L S+ + + E ++++ +V T
Sbjct: 551 ETEDGDTVVVTTTRPGDFVVCNL-------ASLSLGNIDLEDE--------EELEEVVRT 595
Query: 576 AVASRGLDIKGIRHVIN---YDLP 596
V R LD +VI+ Y +P
Sbjct: 596 VV--RALD-----NVIDLNFYPVP 612
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 32.5 bits (75), Expect = 0.99
Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 220 KPTPIQKYAIPAGLEGRDLMGCAQTGSGKT-AAFLIPIMHHLL-ESPGE 266
P P Q A LEGR + A TGSGKT A FL ++ E P +
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKK 61
Score = 32.1 bits (74), Expect = 1.3
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 549 HGSRLQSQR---EQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHR 605
HGS + QR E A+ +++ +V T+ G+D + VI P+ + + R
Sbjct: 282 HGSLDREQRRWVEAAMAA---GRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQR 338
Query: 606 IGRTG-RVGNKGRAT 619
GR+ R G RA
Sbjct: 339 AGRSNHRPGEPSRAL 353
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 32.3 bits (73), Expect = 1.3
Identities = 17/59 (28%), Positives = 26/59 (44%)
Query: 5 SEVSPPVDQVVEAEVIEVEVTEVKTGHVHVVRVEEAVVAMATEVTAEVVALAMGMEVEM 63
S+V P D VE + E + ++ VVA T E++ LAM ME ++
Sbjct: 1591 SKVPPVADVTVETSTLAAESAPAIDLNDYIQSTMMTVVADKTGYPTEMLELAMDMEADL 1649
>gnl|CDD|225398 COG2842, COG2842, Uncharacterized ATPase, putative transposase
[General function prediction only].
Length = 297
Score = 31.2 bits (71), Expect = 1.6
Identities = 26/130 (20%), Positives = 37/130 (28%), Gaps = 51/130 (39%)
Query: 238 LMGC-----AQTGSGKTAAFLIPIMHHLLESPGELVTGYCA-QPEVIICAPTRELVMQIH 291
G G GKT A Y P ++
Sbjct: 92 KTGSLVVVYGYAGLGKTQA----------------AKNYAPSNPNALLIEADP------- 128
Query: 292 EVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISL-ASVR 350
A +L IC AT G + D+ +R I L +VR
Sbjct: 129 ---SYTALVLILIICA------------------AAFGATDGTINDLTERLMIRLRDTVR 167
Query: 351 FVVLDEADRM 360
+++DEADR+
Sbjct: 168 LIIVDEADRL 177
Score = 30.9 bits (70), Expect = 2.1
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 366 LGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNILVATMGRLKDILDRGRISL-A 424
LG Q ++ A S T I AT G + D+ +R I L
Sbjct: 105 LGKTQAAKNYAPSNPNALLIEADPSYTALVLILIICAAAFGATDGTINDLTERLMIRLRD 164
Query: 425 SVRFVVLDEADRM 437
+VR +++DEADR+
Sbjct: 165 TVRLIIVDEADRL 177
>gnl|CDD|234365 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 = 31.6 bits (72), Expect = 1.6
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 193 PPRPIESFE-SAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAA 251
P R + A +V L+ + +P Q A GR ++ T SGK+ A
Sbjct: 8 PARAGRTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLA 67
Query: 252 FLIPIMHHLLESPG 265
+ +P++ L + P
Sbjct: 68 YQLPVLSALADDPR 81
>gnl|CDD|216334 pfam01153, Glypican, Glypican.
Length = 559
Score = 31.2 bits (71), Expect = 2.2
Identities = 23/108 (21%), Positives = 36/108 (33%), Gaps = 19/108 (17%)
Query: 60 EVEMEVV--EAVTEEKIGHVRVVRAILR-----------PDSRFSSGGGGGGDRGNSKPG 106
EVE+++ + V ++I ++++ + LR S SSGG G G K
Sbjct: 442 EVEVDITKPDPVIRQQIMKLKIMTSRLRAAYSGNDVDFQDASDESSGGSGSGSGCVDKRL 501
Query: 107 DWMCSCGASNFAKRDACFKCSEPKPEGAGGGAPGGADGAPFDPAKPPL 154
C G D F +P G + A L
Sbjct: 502 RITCEGG------HDLDFSDPVIRPPLTTARPSGKSGSASGSNPSSRL 543
>gnl|CDD|237255 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 31.3 bits (71), Expect = 2.4
Identities = 29/78 (37%), Positives = 37/78 (47%), Gaps = 11/78 (14%)
Query: 554 QSQREQAIHDFKTKKMKVLVATAVASRGLDIK---GIRHVIN-YDLPQEIDEYVHRI--- 606
Q RE I +K V +AT +A RG DIK G+R + + L E E RI
Sbjct: 632 QHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHE-SRRIDRQ 690
Query: 607 --GRTGRVGNKGRATSFY 622
GR GR G+ G + FY
Sbjct: 691 LRGRAGRQGDPGESV-FY 707
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 31.1 bits (71), Expect = 2.6
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 553 LQSQREQAIHDFKTKKMKVLVATAVASRGLDIK---GIR-----HVINYDL--PQEIDEY 602
Q E AI ++ ++ VAT +A RG DIK G+ HVI + ID
Sbjct: 506 KQDAEEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQ 565
Query: 603 VHRIGRTGRVGNKGRATSF 621
+ GR GR G+ G +
Sbjct: 566 L--AGRCGRQGDPGSYEAI 582
>gnl|CDD|184433 PRK13978, PRK13978, ribose-5-phosphate isomerase A; Provisional.
Length = 228
Score = 30.1 bits (68), Expect = 2.8
Identities = 34/124 (27%), Positives = 59/124 (47%), Gaps = 19/124 (15%)
Query: 245 GSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLK 304
G+G T L+P M L++ G +TG C ++ A +EL ++I E+ + V
Sbjct: 28 GTGSTMELLLPQMAQLIKERGYNITGVCTSNKIAFLA--KELGIKICEI------NDVDH 79
Query: 305 ICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMG 364
I L GA + + + KG + R K I + +AS RFVV+ + +++
Sbjct: 80 IDLAIDGADEVDPSLNIIKGGG---GALFREKVIDE-----MAS-RFVVVVDETKIVQ-- 128
Query: 365 FLGD 368
+LG+
Sbjct: 129 YLGE 132
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 31.1 bits (71), Expect = 2.9
Identities = 41/151 (27%), Positives = 61/151 (40%), Gaps = 25/151 (16%)
Query: 220 KPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVII 279
KP +Q+ L G A TG GKT F + +M L G+ + I
Sbjct: 80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGL-VMSLYLAKKGK---------KSYI 128
Query: 280 CAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMH-----FNRQLEKG-CNILVATMG 333
PTR LV Q+ E K+ + + Y +S F +L++G +ILV T
Sbjct: 129 IFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQ 188
Query: 334 RL---KDILDRGRISLASVRFVVLDEADRML 361
L D L + + FV +D+ D +L
Sbjct: 189 FLSKNFDELPKKKFD-----FVFVDDVDAVL 214
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 29.6 bits (67), Expect = 2.9
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 618 ATSFYDPDQDGAIAK-DLVRILEQAGQPVPE 647
A +D D DG I + +L +IL G E
Sbjct: 25 AFQLFDRDSDGLIDRNELGKILRSLGFNPSE 55
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 30.7 bits (70), Expect = 3.1
Identities = 32/148 (21%), Positives = 49/148 (33%), Gaps = 27/148 (18%)
Query: 12 DQVVEA------EVIEVEVTEVKTGHVHVVRVEEAVVAMATEVTAEVVALAMGMEVEMEV 65
+++ A + + + E V VR + V+ +T A A EV +
Sbjct: 517 PEILAAVPKRSRKTWAILLPEA---TVLGVRGDTLVLGFSTGGLARRFASPGNAEV---L 570
Query: 66 VEAVTEEKIGHVRVVRAILRPDSRFSSGGGGGGDRGNSKPGDWMCSCGASNFAKRDACFK 125
V A+ EE G +V A++ P G GG A+ A
Sbjct: 571 VTALAEELGGDWQV-EAVVGPAP----GAAGGEGPPAPASSGP-----PEEAARPAA--- 617
Query: 126 CSEPKPEGAGGGAPGGADGAPFDPAKPP 153
P AP GA AP + + P
Sbjct: 618 --PAAPAAPAAPAPAGAAAAPAEASAAP 643
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 30.4 bits (69), Expect = 3.2
Identities = 16/53 (30%), Positives = 18/53 (33%), Gaps = 5/53 (9%)
Query: 211 KNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLES 263
K KK P I P E M TG+GKT + LL S
Sbjct: 18 KLRKKDGKASPITIAGLPFPKDAEEAHTMIIGTTGTGKTT-----QIRELLAS 65
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 30.6 bits (69), Expect = 3.4
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 207 EILVKNLKKSNYTKPTPIQKYAIPAG-LEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPG 265
E + + LK+ + P Q A+ +G LEG++L+ T SGKT I +++ LL G
Sbjct: 10 ERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGG 69
Query: 266 ELV 268
+ V
Sbjct: 70 KAV 72
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 30.4 bits (69), Expect = 3.6
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 548 IHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVI 591
++G+ ++ + K KV++AT +A L I GIR+VI
Sbjct: 293 LYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVI 336
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 30.3 bits (69), Expect = 3.7
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 548 IHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDI 584
+HG ++++ + FK ++ +LVAT V G+D+
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|223726 COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA
helicase) [Intracellular trafficking and secretion].
Length = 822
Score = 30.7 bits (70), Expect = 3.7
Identities = 27/82 (32%), Positives = 36/82 (43%), Gaps = 16/82 (19%)
Query: 554 QSQREQAIHDFKTKKMKVLVATAVASRGLDIK-----------GIRHVINYDL--PQEID 600
RE I + V +AT +A RG DIK G HVI + + ID
Sbjct: 463 NHAREAEIIAQAGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRID 522
Query: 601 EYVHRIGRTGRVGNKGRATSFY 622
+ R GR GR G+ G ++ FY
Sbjct: 523 NQL-R-GRAGRQGDPG-SSRFY 541
>gnl|CDD|185748 cd09235, V_Alix, Middle V-domain of mammalian Alix and related
domains are dimerization and protein interaction
modules. This family contains the middle V-shaped (V)
domain of mammalian Alix (apoptosis-linked gene-2
interacting protein X) and related domains. It belongs
to the V_Alix_like superfamily which includes the
V-domains of Bro1 and Rim20 (also known as PalA) from
Saccharomyces cerevisiae, mammalian His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), and related domains. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1), is
part of the ESCRT (Endosomal Sorting Complexes Required
for Transport) system, and participates in membrane
remodeling processes, including the budding of enveloped
viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), the abscission reactions
of mammalian cell division, and in apoptosis. The Alix
V-domain is a dimerization domain, and contains a
binding site, partially conserved in the V_Alix_like
superfamily, for the retroviral late assembly (L) domain
YPXnL motif. In addition to the V-domain, Alix also has
an N-terminal Bro1-like domain, which binds components
of the ESCRT-III complex, in particular CHMP4. The
Bro1-like domain of Alix can also bind to human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1), and
the apoptotic protein ALG-2.
Length = 339
Score = 30.3 bits (69), Expect = 3.8
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 397 IQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD 439
I+K G + + L ++L R R +LDEA RMLD
Sbjct: 66 IEKGGIQTIDQLIKELPELLQRNR--------EILDEALRMLD 100
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 29.6 bits (67), Expect = 4.1
Identities = 27/92 (29%), Positives = 33/92 (35%), Gaps = 9/92 (9%)
Query: 61 VEMEVVEAVTEEKIGHVRVVRAILRPDSRFSSGGGGGGDRGNSKPGDWMCSCGASNFAKR 120
VE+EV E + +V RA GG GGG G+ G G A
Sbjct: 99 VELEVDEIGPSLRYATAKVTRASRGGGGGGGGGGFGGGGGGSGGGG----GGGGGGGAPG 154
Query: 121 DACFKCSEPKPE-----GAGGGAPGGADGAPF 147
+ S P + A GG GG D PF
Sbjct: 155 GGGAQASAPADDPWSSAPASGGFGGGDDEPPF 186
>gnl|CDD|215026 smart01104, CTD, Spt5 C-terminal nonapeptide repeat binding Spt4.
The C-terminal domain of the transcription elongation
factor protein Spt5 is necessary for binding to Spt4 to
form the functional complex that regulates early
transcription elongation by RNA polymerase II. The
complex may be involved in pre-mRNA processing through
its association with mRNA capping enzymes. This CTD
domain carries a regular nonapeptide repeat that can be
present in up to 18 copies, as in S. pombe. The repeat
has a characteristic TPA motif.
Length = 121
Score = 28.6 bits (64), Expect = 5.1
Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 3/38 (7%)
Query: 651 FGGGGGGYGRGGDAFGARDIRHDPDAAPVWGGSGATEP 688
+G G GG P WGG+G+ P
Sbjct: 17 WGSRTPGTAAGGAPTARG---GSGSRTPAWGGAGSRTP 51
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.0 bits (63), Expect = 5.4
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 15/72 (20%)
Query: 220 KPTPIQKYAIPAGLEGRDLMGCAQTGSGKT--AAFLIPIMHHLLESPGELVTGYCAQPEV 277
+ P Q+ AI LE + + TGSGKT AA LI L + +V
Sbjct: 3 ELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALI----ARLAKGKK---------KV 49
Query: 278 IICAPTRELVMQ 289
+ P ++L+ Q
Sbjct: 50 LFVVPRKDLLEQ 61
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 29.7 bits (68), Expect = 6.0
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 21 EVEVTEVKTG----HVHVVRVEEAVVAMATEVTAEV 52
EVT+ + VH +VEE + + EVTAEV
Sbjct: 506 VFEVTDTQKPPNGLIVHRGKVEEGELKVGDEVTAEV 541
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 29.7 bits (67), Expect = 6.0
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 510 LELLREKDEDGVIVFVSTIRNADFIACYLCE---TEIATTSIHGS-RLQSQREQAIHDFK 565
L + ++VF+ + L E +++ ++G L +Q +AI
Sbjct: 202 EHALAS-ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQD-RAIKPDP 259
Query: 566 TKKMKVLVATAVASRGLDIKGIRHVIN 592
+ KV++AT +A L I+GIR VI+
Sbjct: 260 QGRRKVVLATNIAETSLTIEGIRVVID 286
>gnl|CDD|236408 PRK09200, PRK09200, preprotein translocase subunit SecA; Reviewed.
Length = 790
Score = 29.9 bits (68), Expect = 6.1
Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 32/132 (24%)
Query: 505 KKKKLLELLREKDEDG--VIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQ---REQ 559
K K ++E ++E+ E G V++ +I ++ + L E I H + L ++ +E
Sbjct: 413 KYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIP----H-NLLNAKNAAKEA 467
Query: 560 AIHDFKTKKMKVLVATAVASRGLDIK--------GIRHVINYDLPQEIDEYV--HRI--- 606
I +K V VAT +A RG DIK G VI E + R+
Sbjct: 468 QIIAEAGQKGAVTVATNMAGRGTDIKLGEGVHELGGLAVI-------GTERMESRRVDLQ 520
Query: 607 --GRTGRVGNKG 616
GR+GR G+ G
Sbjct: 521 LRGRSGRQGDPG 532
>gnl|CDD|181905 PRK09492, treR, trehalose repressor; Provisional.
Length = 315
Score = 29.5 bits (67), Expect = 6.2
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 19/72 (26%)
Query: 483 VGII-----GGASTDVVQTILEVPKQQ--------------KKKKLLELLREKDEDGVIV 523
VGII + V+T+L +Q K + L +L+ ++ DGVI+
Sbjct: 65 VGIIVSRLDSLSENQAVRTMLPAFYEQGYDPIIMESQFSPEKVNEHLGVLKRRNVDGVIL 124
Query: 524 FVSTIRNADFIA 535
F T + +A
Sbjct: 125 FGFTGITEEMLA 136
>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed.
Length = 925
Score = 29.6 bits (67), Expect = 6.5
Identities = 35/132 (26%), Positives = 62/132 (46%), Gaps = 15/132 (11%)
Query: 502 KQQKKKKLLELLREKDEDGVIVFVST--IRNADFIACYLCETEIATTSIHGSRLQSQREQ 559
K K K +++ ++ + G + + T + +++ + L E I T ++ Q+ RE
Sbjct: 408 KHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAK--QNAREA 465
Query: 560 AIHDFKTKKMKVLVATAVASRGLDIKGIRHVIN----YDLPQEIDEYVHRI-----GRTG 610
I +K + +AT +A RG DIK + V+ Y L + E RI GR+G
Sbjct: 466 EIIAKAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAE-SRRIDNQLRGRSG 524
Query: 611 RVGNKGRATSFY 622
R G+ G + F+
Sbjct: 525 RQGDVG-ESRFF 535
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 29.3 bits (67), Expect = 7.1
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 548 IHGSRLQSQREQAIHDFKTKKMKVLVATAV 577
+HG ++++ + FK ++ +LVAT V
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTV 540
>gnl|CDD|176712 cd08364, FosX, FosX, a fosfomycin resistance protein, catalyzes the
addition of a water molecule to the C1 position of the
antibiotic with inversion of configuration at C1. This
subfamily family contains FosX, a fosfomycin resistant
protein. Fosfomycin inhibits the enzyme
UDP-Nacetylglucosamine-3-enolpyruvyltransferase (MurA),
which catalyzes the first committed step in bacterial
cell wall biosynthesis. FosX catalyzes the addition of a
water molecule to the C1 position of the antibiotic with
inversion of the configuration at C1 in the presence of
Mn(II). The hydrated fosfomycin loses the inhibition
activity. FosX is evolutionarily related to glyoxalase I
and type I extradiol dioxygenases.
Length = 131
Score = 28.2 bits (63), Expect = 7.2
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 598 EIDEYVHRIGRTG--------RVGNKGRATSFYDPD 625
++DEY RI G RV +GR+ FYD D
Sbjct: 78 DVDEYTERIKALGVEMKPPRPRVQGEGRSIYFYDFD 113
>gnl|CDD|233212 TIGR00963, secA, preprotein translocase, SecA subunit. The
proteins SecA-F and SecY, not all of which are
necessary, comprise the standard prokaryotic protein
translocation apparatus. Other, specialized
translocation systems also exist but are not as broadly
distributed. This model describes SecA, an essential
member of the apparatus. This model excludes SecA2 of
the accessory secretory system [Protein fate, Protein
and peptide secretion and trafficking].
Length = 745
Score = 29.5 bits (67), Expect = 7.2
Identities = 33/110 (30%), Positives = 43/110 (39%), Gaps = 36/110 (32%)
Query: 543 IATTSIHGSRLQSQ------------------REQAIHDFKTKKMKVLVATAVASRGLDI 584
+ TTS+ S L S RE I +K V +AT +A RG DI
Sbjct: 410 VGTTSVEKSELLSNLLKERGIPHNVLNAKNHEREAEIIAQAGRKGAVTIATNMAGRGTDI 469
Query: 585 K-------GIRHVINYDLPQEIDEYVHRI-----GRTGRVGNKGRATSFY 622
K G +VI E E RI GR+GR G+ G + F+
Sbjct: 470 KLEEVKELGGLYVIG----TERHE-SRRIDNQLRGRSGRQGDPGS-SRFF 513
>gnl|CDD|143508 cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme MccE. This subfamily is composed
of uncharacterized proteins with similarity to
Escherichia coli MccE, a hypothetical protein that is
homologous to eukaryotic ornithine decarboxylase (ODC)
and diaminopimelate decarboxylase (DapDC). ODC and DapDC
are fold type III PLP-dependent enzymes that contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Most members
of this subfamily share the same domain architecture as
ODC and DapDC. A few members, including Escherichia coli
MccE, contain an additional acetyltransferase domain at
the C-terminus.
Length = 379
Score = 29.2 bits (66), Expect = 7.5
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 617 RATSFYDPDQDGAIAKDLVRILEQAGQPVPEFLKFGGG 654
++ +P+ A AK L+ +L++ E+L GGG
Sbjct: 175 VGSNILNPEAYSAAAKKLIELLDRLFGLELEYLDLGGG 212
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 29.5 bits (67), Expect = 8.3
Identities = 13/37 (35%), Positives = 24/37 (64%)
Query: 555 SQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVI 591
+++++AI + KV++AT +A L I+GIR V+
Sbjct: 252 AEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVV 288
>gnl|CDD|216862 pfam02068, Metallothio_PEC, Plant PEC family metallothionein.
Length = 76
Score = 26.8 bits (59), Expect = 8.3
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 10/51 (19%)
Query: 87 DSRFSSGGGGGGDRGNSKPGDWMCSCGASNFAKRDACFKCSEPKPEGAGGG 137
R +SG GD+ ++ C CG + C C+ PK E G
Sbjct: 17 SCRCTSGEASAGDQEHTT-----CPCG-----EHCGCNPCTCPKTETTTSG 57
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 29.2 bits (66), Expect = 8.5
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 12/60 (20%)
Query: 567 KKMKVLVATAVASRGLDIK---------GIRHVINYDLP-QEIDEYVHRIGRTGRVGNKG 616
+K V VAT++A RG DIK G+ + + +D + GR+GR G+ G
Sbjct: 471 QKGAVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVDLQLR--GRSGRQGDPG 528
>gnl|CDD|184064 PRK13461, PRK13461, F0F1 ATP synthase subunit B; Provisional.
Length = 159
Score = 28.1 bits (63), Expect = 9.9
Identities = 31/145 (21%), Positives = 60/145 (41%), Gaps = 31/145 (21%)
Query: 474 IQKNYIFIAV-GIIGGASTDVVQTILEVPKQQKKKKLL-----ELLREKDEDGVIVFVST 527
I K++ F + +I +++ I + + QKK + L L+ E+G +
Sbjct: 21 ILKHFFFDKIKAVIDSRQSEIDNKIEKADEDQKKARELKLKNERELKNAKEEGKKIVEEY 80
Query: 528 IRNADFIACYLCETEI-------ATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASR 580
A+ + EI A I ++L++QRE+ +++ K V +A ++S+
Sbjct: 81 KSKAENVY-----EEIVKEAHEEADLIIERAKLEAQREKEKAEYEIKNQAVDLAVLLSSK 135
Query: 581 GLDIKGIRHVINYDLPQEIDEYVHR 605
L+ + IDE HR
Sbjct: 136 ALE-------------ESIDESEHR 147
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.136 0.401
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,198,542
Number of extensions: 3681436
Number of successful extensions: 4467
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4357
Number of HSP's successfully gapped: 134
Length of query: 693
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 589
Effective length of database: 6,324,786
Effective search space: 3725298954
Effective search space used: 3725298954
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.9 bits)