RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10680
(537 letters)
>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 = 245 bits (626), Expect = 1e-74
Identities = 135/521 (25%), Positives = 210/521 (40%), Gaps = 155/521 (29%)
Query: 39 KNSGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKE 98
K+ G+ +PT IQ + P+ L+GRD++G AQTG+GKT +
Sbjct: 45 KDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAA---------------------- 82
Query: 99 ESSWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTM 158
++LP L ILK E AL+LAPTRELA QI +
Sbjct: 83 -------------FLLPLLQKILK---SVERKYVSALILAPTRELAVQIAEEL------- 119
Query: 159 RIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRML 218
R L + + R+ +
Sbjct: 120 -----------------RKLGKNLGGL-------------------RVAVVYGG------ 137
Query: 219 DMGFEPQIRKIIQMTRTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRML 278
+ QI L RG +IVVATPGRL+D ++ G +++ + LVLDEADRML
Sbjct: 138 -VSIRKQIEA---------LKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRML 187
Query: 279 DMGFEPQIRKIIQMTRHAHPVVPVSLF-------ISERRDTILH-------FLESGTTNV 324
DMGF I KI++ + LF I E L+ +E +
Sbjct: 188 DMGFIDDIEKILKALPPDRQTL---LFSATMPDDIRELARRYLNDPVEIEVSVEKLERTL 244
Query: 325 NRIT--YLVLDEADRMLDMGFEPQIRKIIQMTRFNTCVFLGYVLYFWFILVAGIERWVFM 382
+I YL ++ + L++ + K+++ + VF
Sbjct: 245 KKIKQFYLEVESEEEKLEL-----LLKLLKDEDEGRVI-------------------VF- 279
Query: 383 EINHNGTETKH--YGVSSSL----YRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVA 436
TK ++ SL ++ +HGD Q RD+ L F+ G + VL+A+DVA
Sbjct: 280 ------VRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVA 333
Query: 437 SRGLDVEDIKYVVNYDFPDNTENYVHRIGRTARSTKTGISYTLFTPLNGNKAQDLIDILN 496
+RGLD+ D+ +V+NYD P + E+YVHRIGRT R+ + G++ + T + + L I
Sbjct: 334 ARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEE--EEVKKLKRIEK 391
Query: 497 EAHQFVPDRLLLLAAKNKPITTRQWKREYWRRKSSEILAEW 537
+ +P +LL + + + R +S
Sbjct: 392 RLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEESDISDEIK 432
Score = 33.2 bits (76), Expect = 0.33
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 19 FRSGYINVLIASDVASRGL 37
F+ G + VL+A+DVA+RGL
Sbjct: 319 FKDGELRVLVATDVAARGL 337
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 236 bits (603), Expect = 6e-71
Identities = 106/221 (47%), Positives = 127/221 (57%), Gaps = 54/221 (24%)
Query: 39 KNSGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKE 98
KN+G+ +PT IQ Q WPI LSGRD+IGIA+TGSGKTL+
Sbjct: 146 KNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLA---------------------- 183
Query: 99 ESSWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTM 158
++LPA+ HI P L GDGPI LVLAPTRELA+QI+ + F +
Sbjct: 184 -------------FLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASS 230
Query: 159 RIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRML 218
+IR+ YGG K Q L RG EI++A PGRLIDFLES TN+ R+TYLVLDEADRML
Sbjct: 231 KIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRML 290
Query: 219 DMGFEPQIRKIIQMTR-------------------TRDLCR 240
DMGFEPQIRKI+ R RDLC+
Sbjct: 291 DMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCK 331
Score = 137 bits (347), Expect = 7e-35
Identities = 60/120 (50%), Positives = 80/120 (66%), Gaps = 1/120 (0%)
Query: 403 AMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVH 462
A+ IHGDK Q R L +F++G ++IA+DVASRGLDV+D+KYV+N+DFP+ E+YVH
Sbjct: 404 ALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVH 463
Query: 463 RIGRTARSTKTGISYTLFTPLNGNKAQDLIDILNEAHQFVPDRLLLLAAKNKPITT-RQW 521
RIGRT R+ G SYT TP A+DL+ +L EA Q VP L L+ + T R+W
Sbjct: 464 RIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERSNGTERRRW 523
Score = 81.4 bits (201), Expect = 3e-16
Identities = 31/40 (77%), Positives = 34/40 (85%)
Query: 316 FLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTR 355
FLES TN+ R+TYLVLDEADRMLDMGFEPQIRKI+ R
Sbjct: 267 FLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIR 306
Score = 30.5 bits (69), Expect = 2.4
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 19 FRSGYINVLIASDVASRGL 37
F++G ++IA+DVASRGL
Sbjct: 423 FKTGKSPIMIATDVASRGL 441
>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 = 219 bits (561), Expect = 8e-69
Identities = 88/201 (43%), Positives = 113/201 (56%), Gaps = 39/201 (19%)
Query: 35 RGLGKNSGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSN 94
RG+ G+ KPT IQA++ P LSGRD+IG AQTGSGKT +
Sbjct: 12 RGI-YALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAA------------------ 52
Query: 95 TSKEESSWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIF 154
+++P L + PK DGP AL+LAPTRELA QI V
Sbjct: 53 -----------------FLIPILEKLDPSPKK---DGPQALILAPTRELALQIAEVARKL 92
Query: 155 SRTMRIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEA 214
+ ++ +YGGTS Q R L RG IVVATPGRL+D LE G +++++ YLVLDEA
Sbjct: 93 GKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEA 152
Query: 215 DRMLDMGFEPQIRKIIQMTRT 235
DRMLDMGFE QIR+I+++
Sbjct: 153 DRMLDMGFEDQIREILKLLPK 173
Score = 71.7 bits (177), Expect = 2e-14
Identities = 24/43 (55%), Positives = 34/43 (79%)
Query: 313 ILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTR 355
+L LE G +++++ YLVLDEADRMLDMGFE QIR+I+++
Sbjct: 130 LLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLP 172
>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 = 148 bits (377), Expect = 2e-42
Identities = 72/192 (37%), Positives = 96/192 (50%), Gaps = 42/192 (21%)
Query: 47 TSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESSWWNNN 106
T IQAQ+ P LSG+D++ A TGSGKTL+
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLA------------------------------ 30
Query: 107 VVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLY 166
++LP L +L + GP ALVLAPTRELA+QI + + + +R A L
Sbjct: 31 -----FLLPILQALLP-----KKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLT 80
Query: 167 GGTSKMYQTRDLCRG-AEIVVATPGRLIDFLESGTTNV-NRITYLVLDEADRMLDMGFEP 224
GGTS Q R L +G A+I+V TPGRL+D L G + + LVLDEA R+LDMGF
Sbjct: 81 GGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGD 140
Query: 225 QIRKIIQMTRTR 236
+ +I+
Sbjct: 141 DLEEILSRLPPD 152
Score = 51.9 bits (125), Expect = 8e-08
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 311 DTILHFLESGTTNV-NRITYLVLDEADRMLDMGFEPQIRKIIQMTRFNTCVFL 362
+L L G + + LVLDEA R+LDMGF + +I+ + + L
Sbjct: 105 GRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILL 157
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 155 bits (394), Expect = 1e-41
Identities = 122/447 (27%), Positives = 187/447 (41%), Gaps = 129/447 (28%)
Query: 42 GYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESS 101
G+ T IQAQ L+G D IG AQTG+GKT +
Sbjct: 106 GFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAA------------------------- 140
Query: 102 WWNNNVVDVKYILPALYHILKMPKLEE---GDGPIALVLAPTRELAQQIQAVISIFSRTM 158
+++ + +L+ P +E G+ P AL++APTREL QI
Sbjct: 141 ----------FLISIINQLLQTPPPKERYMGE-PRALIIAPTRELVVQIAK--------- 180
Query: 159 RIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRML 218
L + T +N +T++
Sbjct: 181 ---------------DAAALTK-------------------YTGLNVMTFVG-------- 198
Query: 219 DMGFEPQIRKIIQMTRTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRML 278
M F+ Q++++ R +I+VATPGRL+DF + G +++ + +VLDEADRML
Sbjct: 199 GMDFDKQLKQLEA--------RFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRML 250
Query: 279 DMGFEPQIRKIIQMTRHAHPVVPVSLFISERRDTILHFLESGTTNVNRITYLVLDEADRM 338
DMGF PQ+R+II+ T E R T+L S T T V++ A +
Sbjct: 251 DMGFIPQVRQIIRQTPR-----------KEERQTLLF---SAT-----FTDDVMNLAKQW 291
Query: 339 LDMGFEPQIRKIIQMTRFNTCVFL---------GYVLYFWFILVAGIERWVFMEINHNGT 389
+P I +I + V Y L + + ER + +
Sbjct: 292 T---TDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEV 348
Query: 390 ETKHYGVSSSLYRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVV 449
+ A + GD Q R +TL FR G I VL+A+DVA RG+ ++ I +V+
Sbjct: 349 RRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVI 408
Query: 450 NYDFPDNTENYVHRIGRTARSTKTGIS 476
N+ P++ ++YVHRIGRT R+ +G+S
Sbjct: 409 NFTLPEDPDDYVHRIGRTGRAGASGVS 435
Score = 33.7 bits (77), Expect = 0.24
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 4/30 (13%)
Query: 8 RLVSLEARLPYFRSGYINVLIASDVASRGL 37
R+ +LE FR G I VL+A+DVA RG+
Sbjct: 374 RIKTLEG----FREGKIRVLVATDVAGRGI 399
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 128 bits (324), Expect = 1e-34
Identities = 68/221 (30%), Positives = 106/221 (47%), Gaps = 48/221 (21%)
Query: 39 KNSGYGKPTSIQAQSWPICLSG-RDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSK 97
+ G+ Q ++ LSG RD+I A TGSGKTL+
Sbjct: 2 EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLA--------------------- 40
Query: 98 EESSWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRT 157
+LPAL + + G G LVL PTRELA+Q + +
Sbjct: 41 --------------ALLPALEALKR------GKGGRVLVLVPTRELAEQWAEELKKLGPS 80
Query: 158 MRIRHACLYGGTSKMYQTRDLCRG-AEIVVATPGRLIDFLESGTTNVNRITYLVLDEADR 216
+ ++ LYGG SK Q R L G +I+V TPGRL+D LE+ +++ + ++LDEA R
Sbjct: 81 LGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHR 140
Query: 217 MLDMGFEPQIRKIIQMTRTRDLCRGAEIVV-ATPGRLIDFL 256
+LD GF Q+ K++++ +++ +++ ATP I+ L
Sbjct: 141 LLDGGFGDQLEKLLKLLP-KNVQL---LLLSATPPEEIENL 177
Score = 51.3 bits (123), Expect = 2e-07
Identities = 16/52 (30%), Positives = 31/52 (59%)
Query: 311 DTILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTRFNTCVFL 362
+L LE+ +++ + ++LDEA R+LD GF Q+ K++++ N + L
Sbjct: 114 GRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 131 bits (332), Expect = 4e-33
Identities = 75/201 (37%), Positives = 93/201 (46%), Gaps = 50/201 (24%)
Query: 42 GYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKT----LSLTIENTQVARGSQCGRSNTSK 97
GY + T IQAQS P L+G+D+I A+TGSGKT L L
Sbjct: 23 GYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL------------------- 63
Query: 98 EESSWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRT 157
+DVK ALVL PTRELA Q+ I +R
Sbjct: 64 --------QKLDVKRF-----------------RVQALVLCPTRELADQVAKEIRRLARF 98
Query: 158 MR-IRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADR 216
+ I+ L GG Q L GA I+V TPGR++D L GT +++ + LVLDEADR
Sbjct: 99 IPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADR 158
Query: 217 MLDMGFEPQIRKII-QMTRTR 236
MLDMGF+ I II Q R
Sbjct: 159 MLDMGFQDAIDAIIRQAPARR 179
Score = 107 bits (270), Expect = 5e-25
Identities = 42/124 (33%), Positives = 68/124 (54%), Gaps = 7/124 (5%)
Query: 392 KHYGVSSSLYRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNY 451
G S A+ +HGD Q +RDQ L F + +VL+A+DVA+RGLD++ ++ V+NY
Sbjct: 263 NAQGFS-----ALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINY 317
Query: 452 DFPDNTENYVHRIGRTARSTKTGISYTLFTPLNGNKAQDLIDILNEAHQFVPDRLLLLAA 511
+ + E +VHRIGRT R+ G++ +L P +A + D L + + L L+
Sbjct: 318 ELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLG--RKLNWEPLPSLSP 375
Query: 512 KNKP 515
+
Sbjct: 376 LSGV 379
Score = 82.9 bits (206), Expect = 6e-17
Identities = 29/50 (58%), Positives = 37/50 (74%)
Query: 241 GAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKII 290
GA I+V TPGR++D L GT +++ + LVLDEADRMLDMGF+ I II
Sbjct: 123 GAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAII 172
Score = 57.5 bits (140), Expect = 8e-09
Identities = 22/39 (56%), Positives = 27/39 (69%)
Query: 313 ILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKII 351
IL L GT +++ + LVLDEADRMLDMGF+ I II
Sbjct: 134 ILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAII 172
Score = 31.7 bits (73), Expect = 1.2
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 19 FRSGYINVLIASDVASRGL 37
F + +VL+A+DVA+RGL
Sbjct: 288 FANRSCSVLVATDVAARGL 306
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 130 bits (329), Expect = 7e-33
Identities = 71/190 (37%), Positives = 97/190 (51%), Gaps = 36/190 (18%)
Query: 42 GYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESS 101
GY +PT IQ Q+ P L GRDL+ AQTG+GKT T
Sbjct: 20 GYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFT----------------------- 56
Query: 102 WWNNNVVDVKYILPALYHILKMPKLEEGDGPI-ALVLAPTRELAQQIQAVISIFSRTMRI 160
LP L H++ +G P+ AL+L PTRELA QI + +S+ + I
Sbjct: 57 ------------LPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNI 104
Query: 161 RHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDM 220
R ++GG S Q L G +++VATPGRL+D ++++ LVLDEADRMLDM
Sbjct: 105 RSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDM 164
Query: 221 GFEPQIRKII 230
GF IR+++
Sbjct: 165 GFIHDIRRVL 174
Score = 101 bits (254), Expect = 4e-23
Identities = 42/78 (53%), Positives = 60/78 (76%)
Query: 402 RAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYV 461
R+ IHG+KSQ R + L DF+SG I VL+A+D+A+RGLD+E++ +VVNY+ P+ E+YV
Sbjct: 271 RSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYV 330
Query: 462 HRIGRTARSTKTGISYTL 479
HRIGRT R+ TG + +L
Sbjct: 331 HRIGRTGRAAATGEALSL 348
Score = 66.4 bits (162), Expect = 1e-11
Identities = 28/60 (46%), Positives = 40/60 (66%), Gaps = 3/60 (5%)
Query: 231 QMTRTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKII 290
QM + R G +++VATPGRL+D ++++ LVLDEADRMLDMGF IR+++
Sbjct: 118 QMMKLRG---GVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVL 174
Score = 43.6 bits (103), Expect = 2e-04
Identities = 16/29 (55%), Positives = 23/29 (79%)
Query: 323 NVNRITYLVLDEADRMLDMGFEPQIRKII 351
++++ LVLDEADRMLDMGF IR+++
Sbjct: 146 KLDQVEILVLDEADRMLDMGFIHDIRRVL 174
Score = 31.7 bits (72), Expect = 1.1
Identities = 12/19 (63%), Positives = 17/19 (89%)
Query: 19 FRSGYINVLIASDVASRGL 37
F+SG I VL+A+D+A+RGL
Sbjct: 291 FKSGDIRVLVATDIAARGL 309
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 129 bits (326), Expect = 1e-32
Identities = 68/198 (34%), Positives = 98/198 (49%), Gaps = 36/198 (18%)
Query: 39 KNSGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKE 98
++ GY +PT+IQA++ P L GRD++G A TG+GKT +
Sbjct: 17 QDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAA---------------------- 54
Query: 99 ESSWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTM 158
++LPAL H+L P+ + G P L+L PTRELA Q+ ++
Sbjct: 55 -------------FLLPALQHLLDFPRRKSGP-PRILILTPTRELAMQVADQARELAKHT 100
Query: 159 RIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRML 218
+ A + GG + M +IVVATPGRL+ +++ + + L+LDEADRML
Sbjct: 101 HLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRML 160
Query: 219 DMGFEPQIRKIIQMTRTR 236
DMGF I I TR R
Sbjct: 161 DMGFAQDIETIAAETRWR 178
Score = 93.9 bits (234), Expect = 1e-20
Identities = 32/83 (38%), Positives = 56/83 (67%), Gaps = 5/83 (6%)
Query: 402 RAMGIH-----GDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDN 456
R GI+ G+ Q R++ ++ G +NVL+A+DVA+RG+D++D+ +V+N+D P +
Sbjct: 266 RKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRS 325
Query: 457 TENYVHRIGRTARSTKTGISYTL 479
+ Y+HRIGRT R+ + G + +L
Sbjct: 326 ADTYLHRIGRTGRAGRKGTAISL 348
Score = 68.8 bits (169), Expect = 2e-12
Identities = 26/52 (50%), Positives = 33/52 (63%)
Query: 244 IVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTRH 295
IVVATPGRL+ +++ + + L+LDEADRMLDMGF I I TR
Sbjct: 126 IVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRW 177
Score = 46.1 bits (110), Expect = 4e-05
Identities = 18/42 (42%), Positives = 24/42 (57%)
Query: 314 LHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTR 355
L +++ + + L+LDEADRMLDMGF I I TR
Sbjct: 135 LQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETR 176
Score = 35.3 bits (82), Expect = 0.072
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 19 FRSGYINVLIASDVASRGL 37
G +NVL+A+DVA+RG+
Sbjct: 291 LTDGRVNVLVATDVAARGI 309
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 127 bits (320), Expect = 4e-31
Identities = 75/193 (38%), Positives = 105/193 (54%), Gaps = 47/193 (24%)
Query: 42 GYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESS 101
GY KP+ IQA+ P L+GRD++G+AQTGSGKT + +
Sbjct: 25 GYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFS----------------------- 61
Query: 102 WWNNNVVDVKYILPALYHI---LKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTM 158
LP L+++ LK P++ LVLAPTRELA Q+ ++ FS+ M
Sbjct: 62 ------------LPLLHNLDPELKAPQI--------LVLAPTRELAVQVAEAMTDFSKHM 101
Query: 159 R-IRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRM 217
R + LYGG Q R L +G +IVV TPGRL+D L+ GT ++++++ LVLDEAD M
Sbjct: 102 RGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEM 161
Query: 218 LDMGFEPQIRKII 230
L MGF + I+
Sbjct: 162 LRMGFIEDVETIM 174
Score = 91.4 bits (227), Expect = 2e-19
Identities = 39/74 (52%), Positives = 55/74 (74%)
Query: 401 YRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENY 460
Y + ++GD +Q R+QTL + G +++LIA+DVA+RGLDVE I VVNYD P ++E+Y
Sbjct: 270 YNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESY 329
Query: 461 VHRIGRTARSTKTG 474
VHRIGRT R+ + G
Sbjct: 330 VHRIGRTGRAGRAG 343
Score = 62.2 bits (151), Expect = 3e-10
Identities = 28/55 (50%), Positives = 40/55 (72%)
Query: 236 RDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKII 290
R L +G +IVV TPGRL+D L+ GT ++++++ LVLDEAD ML MGF + I+
Sbjct: 120 RALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIM 174
Score = 38.3 bits (89), Expect = 0.009
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 18/77 (23%)
Query: 293 TRHAHPVVPVSLFISERRDT------------------ILHFLESGTTNVNRITYLVLDE 334
++H V V+L+ +R D +L L+ GT ++++++ LVLDE
Sbjct: 98 SKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDE 157
Query: 335 ADRMLDMGFEPQIRKII 351
AD ML MGF + I+
Sbjct: 158 ADEMLRMGFIEDVETIM 174
Score = 29.0 bits (65), Expect = 7.8
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 13 EARLPYFRSGYINVLIASDVASRGL 37
E L + G +++LIA+DVA+RGL
Sbjct: 285 EQTLERLKDGRLDILIATDVAARGL 309
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 121 bits (305), Expect = 7e-30
Identities = 64/191 (33%), Positives = 92/191 (48%), Gaps = 39/191 (20%)
Query: 40 NSGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEE 99
G+ T IQA + P+ L+GRD+ G AQTG+GKT++
Sbjct: 25 KKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAF---------------------- 62
Query: 100 SSWWNNNVVDVKYILPALY-HILKMPKLEEG--DGPIALVLAPTRELAQQIQAVISIFSR 156
L A + ++L P E+ + P AL++APTRELA QI A ++
Sbjct: 63 --------------LTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQ 108
Query: 157 TMRIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADR 216
++ YGG Q + L G +I++ T GRLID+ + N+ I +VLDEADR
Sbjct: 109 ATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADR 168
Query: 217 MLDMGFEPQIR 227
M D+GF IR
Sbjct: 169 MFDLGFIKDIR 179
Score = 88.9 bits (221), Expect = 6e-19
Identities = 34/72 (47%), Positives = 51/72 (70%)
Query: 408 GDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVHRIGRT 467
GD +Q R + L +F G +++L+A+DVA+RGL + + +V NYD PD+ E+YVHRIGRT
Sbjct: 287 GDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRT 346
Query: 468 ARSTKTGISYTL 479
R+ +G S +L
Sbjct: 347 GRAGASGHSISL 358
Score = 62.3 bits (152), Expect = 2e-10
Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 9/67 (13%)
Query: 221 GFEPQIRKIIQMTRTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDM 280
G++ Q K+++ G +I++ T GRLID+ + N+ I +VLDEADRM D+
Sbjct: 122 GYDKQ-LKVLE--------SGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDL 172
Query: 281 GFEPQIR 287
GF IR
Sbjct: 173 GFIKDIR 179
Score = 43.0 bits (102), Expect = 3e-04
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 313 ILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIR 348
++ + + N+ I +VLDEADRM D+GF IR
Sbjct: 144 LIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIR 179
Score = 30.3 bits (69), Expect = 2.4
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 19 FRSGYINVLIASDVASRGL 37
F G +++L+A+DVA+RGL
Sbjct: 301 FTRGDLDILVATDVAARGL 319
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 120 bits (302), Expect = 1e-29
Identities = 83/260 (31%), Positives = 124/260 (47%), Gaps = 30/260 (11%)
Query: 233 TRTRD----LCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRK 288
T RD L G +VV TPGR+ D ++ V+ + +LDEAD ML GF+ QI
Sbjct: 134 TVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYD 193
Query: 289 IIQMTRHAHPVVPVSLFISERRDTILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIR 348
+ + P V V+LF + + IL TT R +L + D + G IR
Sbjct: 194 VF---KKLPPDVQVALFSATMPNEILEL----TTKFMRDPKRILVKKDELTLEG----IR 242
Query: 349 KIIQMT-----RFNT-CVFLGYVLYFWFILVAGIERWVFMEINHNGTETKHYGVSSSLYR 402
+ +F+T C + I+ R V + + + VS
Sbjct: 243 QFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKV--DYLTKKMHERDFTVSC---- 296
Query: 403 AMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVH 462
+HGD Q +RD +R+FRSG VLI +D+ +RG+DV+ + V+NYD P + ENY+H
Sbjct: 297 ---MHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIH 353
Query: 463 RIGRTARSTKTGISYTLFTP 482
RIGR+ R + G++ TP
Sbjct: 354 RIGRSGRFGRKGVAINFVTP 373
Score = 102 bits (256), Expect = 1e-23
Identities = 64/191 (33%), Positives = 89/191 (46%), Gaps = 42/191 (21%)
Query: 42 GYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESS 101
G+ KP++IQ + L G D IG AQ+G+GKT + I Q+
Sbjct: 47 GFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL----------------- 89
Query: 102 WWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIR 161
+ Y L A AL+LAPTRELAQQIQ V+ +++R
Sbjct: 90 --------IDYDLNACQ---------------ALILAPTRELAQQIQKVVLALGDYLKVR 126
Query: 162 -HACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDM 220
HAC+ GGT L G +VV TPGR+ D ++ V+ + +LDEAD ML
Sbjct: 127 CHACV-GGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSR 185
Query: 221 GFEPQIRKIIQ 231
GF+ QI + +
Sbjct: 186 GFKGQIYDVFK 196
>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 = 107 bits (268), Expect = 2e-27
Identities = 55/175 (31%), Positives = 77/175 (44%), Gaps = 44/175 (25%)
Query: 61 RDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESSWWNNNVVDVKYILPALYHI 120
RD++ A TGSGKTL+ +LP L +
Sbjct: 1 RDVLLAAPTGSGKTLA-----------------------------------ALLPILELL 25
Query: 121 LKMPKLEEGDGPIALVLAPTRELAQQIQAVIS-IFSRTMRIRHACLYGGTSKMYQTRDLC 179
G LVLAPTRELA Q+ + +F +++ L GGTS Q + L
Sbjct: 26 DS------LKGGQVLVLAPTRELANQVAERLKELFGEGIKV--GYLIGGTSIKQQEKLLS 77
Query: 180 RGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTR 234
+IVV TPGRL+D LE ++ ++ L+LDEA R+L+ GF KI+
Sbjct: 78 GKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLP 132
Score = 46.2 bits (110), Expect = 4e-06
Identities = 16/52 (30%), Positives = 26/52 (50%)
Query: 311 DTILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTRFNTCVFL 362
+L LE ++ ++ L+LDEA R+L+ GF KI+ + V L
Sbjct: 88 GRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLL 139
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 113 bits (284), Expect = 1e-26
Identities = 80/257 (31%), Positives = 125/257 (48%), Gaps = 44/257 (17%)
Query: 238 LCRGAEIVVATPGRLIDFL-ESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQM---- 292
L +G ++++ATPGRLID++ + +++ VLDEADRM D+GF IR +++
Sbjct: 131 LQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPER 190
Query: 293 -TRH--------AHPVVPVSL-FISERRDTILHFLESGTTNVNRITYLVLDEADRMLDMG 342
TR +H V+ ++ ++E ++ V + Y DE + L +G
Sbjct: 191 GTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLG 250
Query: 343 FEPQIRKIIQMTRFNTCVFLGYVLYFWFILVAGIERWVFMEINHNGTETKHYGVSSSLYR 402
+ M NT F +ER V + +G YR
Sbjct: 251 LLSRSEGARTMVFVNTKAF--------------VER-VARTLERHG------------YR 283
Query: 403 AMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVH 462
+ GD Q R+ L F+ G + +L+A+DVA+RGL ++ +KYV NYD P + E+YVH
Sbjct: 284 VGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVH 343
Query: 463 RIGRTARSTKTG--ISY 477
RIGRTAR + G IS+
Sbjct: 344 RIGRTARLGEEGDAISF 360
Score = 106 bits (265), Expect = 3e-24
Identities = 64/194 (32%), Positives = 98/194 (50%), Gaps = 38/194 (19%)
Query: 41 SGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEES 100
+G+ + T IQA + P+ L G D+ G AQTG+GKTL+
Sbjct: 27 AGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLA------------------------ 62
Query: 101 SWWNNNVVDVKYILPALYHILKMPKL--EEGDGPIALVLAPTRELAQQIQAVISIFSRTM 158
+++ + +L P L + + P AL+LAPTRELA QI F +
Sbjct: 63 -----------FLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL 111
Query: 159 RIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFL-ESGTTNVNRITYLVLDEADRM 217
+R A +YGG Q L +G ++++ATPGRLID++ + +++ VLDEADRM
Sbjct: 112 GLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRM 171
Query: 218 LDMGFEPQIRKIIQ 231
D+GF IR +++
Sbjct: 172 FDLGFIKDIRFLLR 185
Score = 29.1 bits (65), Expect = 6.4
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 13 EARLPYFRSGYINVLIASDVASRGL 37
E+ L F+ G + +L+A+DVA+RGL
Sbjct: 297 ESLLNRFQKGQLEILVATDVAARGL 321
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 109 bits (275), Expect = 1e-25
Identities = 61/191 (31%), Positives = 91/191 (47%), Gaps = 33/191 (17%)
Query: 41 SGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEES 100
+GY PT IQ Q+ P LSGR L+ A TGSGKT S + ++R + S++
Sbjct: 139 AGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLV--PIISRCCTIRSGHPSEQR- 195
Query: 101 SWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRI 160
P+A+VL PTREL Q++ + + +
Sbjct: 196 ------------------------------NPLAMVLTPTRELCVQVEDQAKVLGKGLPF 225
Query: 161 RHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDM 220
+ A + GG + Q + +G E++V TPGRLID L ++ ++ LVLDE D ML+
Sbjct: 226 KTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLER 285
Query: 221 GFEPQIRKIIQ 231
GF Q+ +I Q
Sbjct: 286 GFRDQVMQIFQ 296
Score = 76.8 bits (189), Expect = 7e-15
Identities = 36/130 (27%), Positives = 66/130 (50%), Gaps = 5/130 (3%)
Query: 402 RAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYV 461
+A+ IHG+KS R + ++ F G + V++A+ V RG+D+ ++ V+ +D P+ + Y+
Sbjct: 394 KALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYI 453
Query: 462 HRIGRTARSTKTGISYTLFTPLNGNKAQDLIDILNEAHQFVPDRLLLLAAKNKPITTRQW 521
H+IGR +R + G + + N +L+ +L + +P L N
Sbjct: 454 HQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELA-----NSRYLGSGR 508
Query: 522 KREYWRRKSS 531
KR+ RR S
Sbjct: 509 KRKKKRRYGS 518
Score = 32.1 bits (73), Expect = 0.88
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 313 ILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQ 352
++ L ++ ++ LVLDE D ML+ GF Q+ +I Q
Sbjct: 257 LIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQ 296
>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 = 96.2 bits (240), Expect = 1e-23
Identities = 33/79 (41%), Positives = 52/79 (65%)
Query: 401 YRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENY 460
+ +HGD SQ R++ L+DFR G I VL+A+DV +RG+D+ ++ V+NYD P + +Y
Sbjct: 53 IKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSY 112
Query: 461 VHRIGRTARSTKTGISYTL 479
+ RIGR R+ + G + L
Sbjct: 113 LQRIGRAGRAGQKGTAILL 131
Score = 28.4 bits (64), Expect = 4.4
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 19 FRSGYINVLIASDVASRGL 37
FR G I VL+A+DV +RG+
Sbjct: 74 FREGEIVVLVATDVIARGI 92
>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 = 92.2 bits (230), Expect = 5e-23
Identities = 32/69 (46%), Positives = 45/69 (65%)
Query: 401 YRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENY 460
+ +HG SQ R++ L DFR+G VL+A+DVA RG+D+ D+ V+NYD P N +Y
Sbjct: 8 IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASY 67
Query: 461 VHRIGRTAR 469
+ RIGR R
Sbjct: 68 IQRIGRAGR 76
Score = 29.8 bits (68), Expect = 0.55
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 19 FRSGYINVLIASDVASRGL 37
FR+G VL+A+DVA RG+
Sbjct: 29 FRNGKSKVLVATDVAGRGI 47
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 84.2 bits (209), Expect = 5e-20
Identities = 29/69 (42%), Positives = 42/69 (60%)
Query: 401 YRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENY 460
+ +HG SQ R++ L F +G I VL+A+DVA RGLD+ + V+ YD P + +Y
Sbjct: 12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASY 71
Query: 461 VHRIGRTAR 469
+ RIGR R
Sbjct: 72 IQRIGRAGR 80
Score = 28.7 bits (65), Expect = 1.5
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 19 FRSGYINVLIASDVASRGL 37
F +G I VL+A+DVA RGL
Sbjct: 33 FNNGKIKVLVATDVAERGL 51
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 53.1 bits (128), Expect = 2e-07
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 411 SQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTE-NYVHRIGRTAR 469
SQ + + + FR G NVL+A+ V GLD+ ++ V+ Y+ P +E + R GRT R
Sbjct: 410 SQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYE-PVPSEIRSIQRKGRTGR 468
Query: 470 STKTGISYTLFT 481
K G L T
Sbjct: 469 KRK-GRVVVLVT 479
Score = 31.5 bits (72), Expect = 1.1
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 19/92 (20%)
Query: 134 ALVLAPTREL-AQQIQAVISIFSRTMRIRH---ACLYGGTS-----KMYQTRDLCRGAEI 184
L LAPT+ L Q + + I A L G +++ + +
Sbjct: 61 VLFLAPTKPLVLQHAEF----CRKVTGIPEDEIAALTGEVRPEEREELWAKKK------V 110
Query: 185 VVATPGRLIDFLESGTTNVNRITYLVLDEADR 216
VATP + + L++G +++ ++ L+ DEA R
Sbjct: 111 FVATPQVVENDLKAGRIDLDDVSLLIFDEAHR 142
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 44.2 bits (105), Expect = 1e-04
Identities = 48/247 (19%), Positives = 95/247 (38%), Gaps = 43/247 (17%)
Query: 250 GRLIDFLESGTTNVNRITYLVLDEADRMLDMG--FEPQIRKIIQMTRHAHPVVPVSLFIS 307
R ++ L+ I+ + +DEA + G F P R++ ++ P PV +
Sbjct: 121 PRFLELLKRL-----PISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGL-PNPPVLALTA 174
Query: 308 ----ERRDTILHFLESGTTNV-----NR--ITYLVLDEADRMLDMGFEPQIRKIIQMTRF 356
RD I L N+ +R + V+++ + + F + ++ +
Sbjct: 175 TATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPSDQLAF---LATVLP--QL 229
Query: 357 NTCVFLGYVLYFWFILVAGIERWVFMEINHNGTETKHYGVSSSLYRAMGIHGDKSQWNRD 416
+ + Y L +E + NG Y H S R+
Sbjct: 230 SKSG-IIYCLTRK-----KVEELAE-WLRKNGISAGAY------------HAGLSNEERE 270
Query: 417 QTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVHRIGRTARSTKTGIS 476
+ + F + I V++A++ G+D D+++V++YD P + E+Y GR R +
Sbjct: 271 RVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEA 330
Query: 477 YTLFTPL 483
L++P
Sbjct: 331 ILLYSPE 337
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 44.1 bits (105), Expect = 2e-04
Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 408 GDK--SQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTE-NYVHRI 464
GDK SQ + + L FR+G NVL+++ VA GLD+ + V+ Y+ P +E + R
Sbjct: 403 GDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEIRSIQRK 461
Query: 465 GRTARSTK 472
GRT R +
Sbjct: 462 GRTGRQEE 469
Score = 29.8 bits (68), Expect = 4.7
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 21/93 (22%)
Query: 134 ALVLAPTRELAQQIQAVISIFSRTMRIRH---ACLYGGTS-----KMYQTRDLCRGAEIV 185
L+LAPT+ L +Q F + + I G S ++++ A+++
Sbjct: 61 VLILAPTKPLVEQHAE---FFRKFLNIPEEKIVVFTGEVSPEKRAELWEK------AKVI 111
Query: 186 VATPGRLI--DFLESGTTNVNRITYLVLDEADR 216
VATP ++I D + +G ++ ++ L+ DEA R
Sbjct: 112 VATP-QVIENDLI-AGRISLEDVSLLIFDEAHR 142
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 43.0 bits (102), Expect = 3e-04
Identities = 24/108 (22%), Positives = 38/108 (35%), Gaps = 35/108 (32%)
Query: 41 SGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEES 100
+ T Q + P SG +++ IA TGSGKT +
Sbjct: 18 RKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAA----------------------- 54
Query: 101 SWWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQ 148
LP + +L + K + DG AL ++P + L I+
Sbjct: 55 ------------FLPVINELLSLGKGKLEDGIYALYISPLKALNNDIR 90
>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 = 39.7 bits (93), Expect = 0.004
Identities = 24/95 (25%), Positives = 43/95 (45%)
Query: 388 GTETKHYGVSSSLYRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKY 447
E + S A+ H S R + DF + V++A++ G+D ++++
Sbjct: 236 KVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRF 295
Query: 448 VVNYDFPDNTENYVHRIGRTARSTKTGISYTLFTP 482
V++YD P N E+Y GR R + L++P
Sbjct: 296 VIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSP 330
>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 = 39.4 bits (92), Expect = 0.004
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 415 RDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVHRIGRTAR 469
RD F+ I V++A+ G++ D+++V++Y P + E+Y GR R
Sbjct: 265 RDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGR 319
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 36.6 bits (85), Expect = 0.034
Identities = 28/125 (22%), Positives = 47/125 (37%), Gaps = 15/125 (12%)
Query: 125 KLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQTRDLCRGAEI 184
L EG G + + P + LA++ S + IR T + ++
Sbjct: 71 TLLEGGGK-VVYIVPLKALAEEKYEEFSRLEE-LGIRVGIS---TGDYDLDDERLARYDV 125
Query: 185 VVATPGRLIDFLESGTTN----VNRITYLVLDEADRMLDMGFEPQIRKIIQMTRTRDLCR 240
+V TP + L+S T + + +V+DE + D P + I+ R R L
Sbjct: 126 IVTTPEK----LDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIV--ARMRRLNE 179
Query: 241 GAEIV 245
IV
Sbjct: 180 LIRIV 184
>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 = 36.6 bits (85), Expect = 0.035
Identities = 46/218 (21%), Positives = 73/218 (33%), Gaps = 59/218 (27%)
Query: 7 VRLVSLEARLPYFRSGYINVLIASDVASRGLGKNSGYGKPTSIQAQSWPICLSGRDLIGI 66
+R +EAR L + S + +G + S Q + + GR+++
Sbjct: 36 LRDPEIEARPGKTSE--FPELRDESLKSALV--KAGIERLYSHQVDALRLIREGRNVVVT 91
Query: 67 AQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESSWWNNNVVDVKYILPALYHILKMPKL 126
TGSGKT S ++LP L H+L+ P
Sbjct: 92 TGTGSGKTES-----------------------------------FLLPILDHLLRDPSA 116
Query: 127 EEGDGPIALVLAPTRELAQ-QIQAVISIFSRTMRIRHACLYGGTSKMYQTRDLCRG-AEI 184
AL+L PT LA Q + + + S Y G + + R + R +I
Sbjct: 117 R------ALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDI 170
Query: 185 VVATPGRLIDFLES----GTTNVNRIT----YLVLDEA 214
++ P D L + YLV+DE
Sbjct: 171 LLTNP----DMLHYLLLRNHDAWLWLLRNLKYLVVDEL 204
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 35.9 bits (83), Expect = 0.053
Identities = 61/371 (16%), Positives = 109/371 (29%), Gaps = 103/371 (27%)
Query: 134 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSK----------MYQTRDLCRGAE 183
LVL PT+EL Q ++ + +YGG K QT
Sbjct: 83 TLVLVPTKELLDQWAE--ALKKFLLLNDEIGIYGGGEKELEPAKVTVATVQT-------- 132
Query: 184 IVVATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQMTRTRDLCRGAE 243
+A L +FL N ++ DE + + R+I+++ A
Sbjct: 133 --LARRQLLDEFLG------NEFGLIIFDEVHHLPAPSY----RRILEL------LSAAY 174
Query: 244 IVV---ATPGRLIDFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKI-----IQMTRH 295
+ ATP R L P + ++ I
Sbjct: 175 PRLGLTATPEREDGGRI------------------GDLFDLIGPIVYEVSLKELIDEGYL 216
Query: 296 AHPV---VPVSLFISERRDTILHFLESGTTNVNRITYLVLDEADRMLDMGFEPQIRKIIQ 352
A + V+L E R+ + R + E + + ++
Sbjct: 217 APYKYVEIKVTLTEDEEREYAKESARFR--ELLRARGTLRAENEARRIAIASERKIAAVR 274
Query: 353 MTRFNTCVFLGYVLYFW-----FILVAGIERW-VFMEINHNGTETKHYGVSSSLYRAMGI 406
G +L I + +E ++ + I
Sbjct: 275 ----------GLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVEA------------I 312
Query: 407 HGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTEN---YVHR 463
G+ + R+ L FR+G I VL+ V G+D+ D ++ T + ++ R
Sbjct: 313 TGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLI---ILRPTGSRRLFIQR 369
Query: 464 IGRTARSTKTG 474
+GR R +
Sbjct: 370 LGRGLRPAEGK 380
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 35.1 bits (81), Expect = 0.10
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 395 GVSSSLYRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFP 454
G+S++ Y A G+ D ++ RD + +++A+ G++ ++++VV++D P
Sbjct: 260 GISAAAYHA-GLDNDVRADVQEAFQRD----DLQIVVATVAFGMGINKPNVRFVVHFDIP 314
Query: 455 DNTENYVHRIGRTAR 469
N E+Y GR R
Sbjct: 315 RNIESYYQETGRAGR 329
>gnl|CDD|184558 PRK14188, PRK14188, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 296
Score = 33.8 bits (78), Expect = 0.19
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 11/48 (22%)
Query: 230 IQMTRTRDL---CRGAEIVVATPGR--LI--DFLESGTT----NVNRI 266
I +RTRDL CR A+I+VA GR ++ D+++ G T +NRI
Sbjct: 187 IAHSRTRDLPAVCRRADILVAAVGRPEMVKGDWIKPGATVIDVGINRI 234
Score = 30.7 bits (70), Expect = 1.6
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 11/43 (25%)
Query: 175 TRDL---CRGAEIVVATPGR--LI--DFLESGTT----NVNRI 206
TRDL CR A+I+VA GR ++ D+++ G T +NRI
Sbjct: 192 TRDLPAVCRRADILVAAVGRPEMVKGDWIKPGATVIDVGINRI 234
>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 = 33.6 bits (77), Expect = 0.29
Identities = 55/234 (23%), Positives = 82/234 (35%), Gaps = 73/234 (31%)
Query: 42 GYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARGSQCGRSNTSKEESS 101
G +P QA++ + +GR ++ T SGK+L+
Sbjct: 33 GIHRPWQHQARAAELAHAGRHVVVATGTASGKSLA------------------------- 67
Query: 102 WWNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQ-QIQAVISIFSRTMRI 160
Y LP L L + AL LAPT+ LA Q++AV + T+R
Sbjct: 68 ----------YQLPVL------SALADDPRATALYLAPTKALAADQLRAVREL---TLRG 108
Query: 161 RHACLYGGTSKMYQTRDLCRGAEIVVATPGRLIDFLESG--------TTNVNRITYLVLD 212
Y G + + R A V+ P D L G + R+ Y+V+D
Sbjct: 109 VRPATYDGDTPTEERRWAREHARYVLTNP----DMLHRGILPSHARWARFLRRLRYVVID 164
Query: 213 EADRMLDMGFEPQIRKIIQMTRTRDLCR--GAEIVV-----------ATPGRLI 253
E + F + +++ R R LC GA V A RLI
Sbjct: 165 ECHSYRGV-FGSHVALVLR--RLRRLCARYGASPVFVLASATTADPAAAASRLI 215
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 33.3 bits (76), Expect = 0.43
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 410 KSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVHRIGRTAR 469
+ QW++D+ IN++ A+ G++ D+++V+++ P + E Y GR R
Sbjct: 723 QKQWSKDE---------INIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGR 773
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 32.9 bits (76), Expect = 0.47
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 415 RDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYD-----FPDNTENYVHRIGRTAR 469
R + +RD R G +VL+ ++ GLD+ ++ V D F + + + IGR AR
Sbjct: 485 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 544
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 33.0 bits (76), Expect = 0.47
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 402 RAMGIHGDKSQWNRDQTLRDFRSGYINVLI--AS--DVASRGLDV-EDIKYVVNYDFP 454
+GI+ + + ++ F G ++VL+ AS V RG+D+ E I+Y + Y P
Sbjct: 352 EDLGINAELAISGFERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVP 409
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 32.3 bits (74), Expect = 0.67
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 402 RAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYD-----FPDN 456
+ +H + R + +RD R G +VL+ ++ GLD+ ++ V D F +
Sbjct: 468 KVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRS 527
Query: 457 TENYVHRIGRTAR 469
+ + IGR AR
Sbjct: 528 ERSLIQTIGRAAR 540
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 32.2 bits (73), Expect = 0.77
Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 6/105 (5%)
Query: 389 TETKHYGVSSSLYRAMGIHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYV 448
T + + R+ HG S+ R T + +SG + ++A+ G+D+ + V
Sbjct: 292 TSNRVQSSDVFIARSH--HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLV 349
Query: 449 VNYDFPDNTENYVHRIGRTARSTKTGISYTLFTPLNGNKAQDLID 493
+ P + + + RIGR G+S LF P +DL+D
Sbjct: 350 IQVATPLSVASGLQRIGRAGHQVG-GVSKGLFFP---RTRRDLVD 390
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 31.3 bits (72), Expect = 0.87
Identities = 31/113 (27%), Positives = 44/113 (38%), Gaps = 29/113 (25%)
Query: 237 DLCRGAEIVVATPGRLIDFLESGTTN---------------VNRITYLVLDEADRMLDMG 281
+ E V + PG L +E G N + + LVLDEA +D
Sbjct: 114 ERVGLKEFVESLPGGLDTVVEEGGENLSVGQRQLLCLARALLRKSKILVLDEATASVDPE 173
Query: 282 FEPQIRKIIQMTRHAHPVVPVSLFISERRDTILHFLESGTTNVNRITYLVLDE 334
+ I+K I+ V L I+ R DTI+ +RI LVLD+
Sbjct: 174 TDALIQKTIREAFKDCTV----LTIAHRLDTIIDS--------DRI--LVLDK 212
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 30.9 bits (70), Expect = 2.1
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 28 IASDVASRGLGKNSGYGKPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSLTIENTQVARG 87
I + A R LG P +Q L+G D+I +A TG GKTL+ + T A
Sbjct: 64 ILREAAERTLGMR-----PFDVQLLGALRLLAG-DVIEMA-TGEGKTLAGAMAATGFALL 116
>gnl|CDD|233040 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) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 30.0 bits (68), Expect = 3.0
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 12/72 (16%)
Query: 416 DQTLRDFRSGYINVLIASDVASRGLDVEDIKY--VVNYD----FPD-----NTENYVHRI 464
+ L F +G ++LI + + ++G ++ V++ D PD + ++
Sbjct: 302 EALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQV 361
Query: 465 -GRTARSTKTGI 475
GR R+ G
Sbjct: 362 AGRAGRAEDPGQ 373
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 30.1 bits (68), Expect = 3.1
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 9/60 (15%)
Query: 223 EPQIRKIIQMTRTRDLCRGAEIVVATPGRLID----FLESGTTNVNRITYLVLDEADRML 278
+ R+ ++ T+ R+L + A+ VV + D FLE + Y+V D+ R
Sbjct: 437 DEAERERLRTTQMRELIQPAQTVVPPTASVADMTRVFLEYPVKYL----YVV-DDDGRFR 491
Score = 29.7 bits (67), Expect = 4.8
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 152 SIFSRTMRIRHACLYGGTSKMYQTRDLCRGAEIVVATPGRLID----FLESGTTNVNRIT 207
S++ T+R + Q R+L + A+ VV + D FLE +
Sbjct: 426 SMYEITLRRHQDEAERERLRTTQMRELIQPAQTVVPPTASVADMTRVFLEYPVKYL---- 481
Query: 208 YLVLDEADRML 218
Y+V D+ R
Sbjct: 482 YVV-DDDGRFR 491
>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 = 30.2 bits (69), Expect = 3.2
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 45 KPTSIQAQSWPICLSGRDLIGIAQTGSGKTLSL 77
P Q + W L GR + IA TGSGKTL+
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAG 45
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 30.0 bits (68), Expect = 3.4
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 325 NRITYLVLDEADRMLDM-GFEPQIRKIIQMTRFNTCV 360
R + +DE ++LD F IR ++ R V
Sbjct: 633 GRPFLIFIDEFWKLLDNPKFADFIRDWLKTLRKLNGV 669
>gnl|CDD|217673 pfam03687, UPF0164, Uncharacterized protein family (UPF0164). This
family of uncharacterized proteins are only found in
Treponema pallidum. They contain a putative signal
peptide so may be secreted proteins.
Length = 332
Score = 29.9 bits (67), Expect = 3.5
Identities = 18/53 (33%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 452 DFPDNTENYVHRIGRTARSTKTGISY---TLFTPLNGNKAQDLIDILNEAHQF 501
D T +YV R G T Y T + LN KA + I N AH F
Sbjct: 101 DSHTETLSYVGRSGNTGYGASARAFYPESTFYFSLNPKKASGFVGIANVAHNF 153
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 29.9 bits (68), Expect = 4.3
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 406 IHGDKSQWNRDQTLRDFRSGYINVLIASDVASRGLDV 442
+HG +D + F+ G I++L+A+ V G+DV
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|237272 PRK13017, PRK13017, dihydroxy-acid dehydratase; Provisional.
Length = 596
Score = 29.9 bits (68), Expect = 4.4
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 59 SGRDLIGIAQTGS 71
SG+ +IGIAQTGS
Sbjct: 45 SGKPIIGIAQTGS 57
>gnl|CDD|227101 COG4759, COG4759, Uncharacterized protein conserved in bacteria
containing thioredoxin-like domain [Posttranslational
modification, protein turnover, chaperones].
Length = 316
Score = 29.3 bits (66), Expect = 5.0
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 103 WNNNVVDVKYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRH 162
W NV+D K I L +L+ +L + G I L +AP RE +Q + I+ R +
Sbjct: 36 WTENVLDSKPIPQNLQDLLE--ELYKAGGVIPLAIAPDREYSQPGYTRVLIYRRPAK--- 90
Query: 163 ACLYGGTSK 171
L+ G SK
Sbjct: 91 --LFAGYSK 97
>gnl|CDD|172682 PRK14194, PRK14194, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 301
Score = 29.4 bits (66), Expect = 5.2
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 170 SKMYQTRDLCRGAEIVVATPG--RLID--FLESGT----TNVNRI 206
S+ + LCR A+IVVA G RLID +L+ G +NRI
Sbjct: 191 SRSTDAKALCRQADIVVAAVGRPRLIDADWLKPGAVVIDVGINRI 235
>gnl|CDD|140258 PTZ00231, PTZ00231, variable surface protein Vir17; Provisional.
Length = 385
Score = 29.1 bits (65), Expect = 6.1
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 6/46 (13%)
Query: 457 TENYVHRIGRTARSTKTGIS------YTLFTPLNGNKAQDLIDILN 496
T +Y+ I T I YT T +G DL LN
Sbjct: 30 TLDYLRSINETDNEALKNIGCSLESGYTFLTARDGETLTDLCKYLN 75
>gnl|CDD|226109 COG3581, COG3581, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 420
Score = 29.0 bits (65), Expect = 7.0
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 171 KMYQTRDLCRGAEIVVATPGRLIDFLESGTTNVNRITYLV 210
Y D+C A + + G+LID +ESG ++ L+
Sbjct: 41 LKYSNNDICLPAILTI---GQLIDAIESGEYDIENDAVLM 77
Score = 28.6 bits (64), Expect = 9.4
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 237 DLCRGAEIVVATPGRLIDFLESGTTNVNRITYLV 270
D+C A + + G+LID +ESG ++ L+
Sbjct: 47 DICLPAILTI---GQLIDAIESGEYDIENDAVLM 77
>gnl|CDD|213917 TIGR04304, GeoRSP_SPASM, GeoRSP system SPASM domain protein.
Members of this protein family are encoded by one of two
consecutive genes for SPASM domain proteins. The two are
closely homologous in the SPASM domain regions, and also
in a small N-terminal region, but the other family
(TIGR04303) has an intact radical SAM domain (pfam04055)
that this "quasi-rSAM" protein lacks. A PqqD-family
protein, TIGR04302, is always adjacent.
Length = 293
Score = 28.7 bits (64), Expect = 7.1
Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 113 ILPALYH----------ILKMPKLEEGDGPIALVLAPTRELAQQIQAV 150
LP L +L M +L G+ P L REL+ + A
Sbjct: 128 ELPELVSYCLDRGITRLVLPMQRLYGGEPPFFLTRNERRELSNALDAE 175
>gnl|CDD|237249 PRK12891, PRK12891, allantoate amidohydrolase; Reviewed.
Length = 414
Score = 29.0 bits (65), Expect = 7.3
Identities = 21/84 (25%), Positives = 27/84 (32%), Gaps = 28/84 (33%)
Query: 119 HILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYG-----GTSKMY 173
HI + LE I +V A + R L G GT+ M
Sbjct: 191 HIEQGAILERAGKTIGVVTA----------------GQGQRWYEVTLTGVDAHAGTTPMA 234
Query: 174 QTRDLCRGAEIVVATPGRLIDFLE 197
RD GA R+I FL+
Sbjct: 235 FRRDALVGA-------ARMIAFLD 251
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 28.8 bits (65), Expect = 7.4
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 411 SQWNRDQTLRDFRSGYINVLIASDVASRGLDVEDIKYVVNYDFPDNTENYVHRIGRTAR 469
S+ R++ LR F SG + L+A G+D+ + N ++ R GR R
Sbjct: 324 SKEEREELLRQFESGLLQGLVAIRCLDEGVDIPATRTAYILASSSNPRQFIQRRGRVLR 382
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
0.322 0.137 0.407
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,736,167
Number of extensions: 2751996
Number of successful extensions: 2756
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2739
Number of HSP's successfully gapped: 133
Length of query: 537
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 435
Effective length of database: 6,413,494
Effective search space: 2789869890
Effective search space used: 2789869890
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 (21.9 bits)
S2: 61 (27.2 bits)