RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15878
(693 letters)
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 233 bits (596), Expect = 1e-66
Identities = 163/685 (23%), Positives = 271/685 (39%), Gaps = 66/685 (9%)
Query: 4 EKYQSLAKAAEEFKFYLEEYAGVKGQYPPTKRQLNKKSIYICTIEKGSKLI---GSLIQE 60
EKY+ ++ + G Y +L + + + T EK L S I+E
Sbjct: 91 EKYEEFSR----LEELGIRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEE 146
Query: 61 NRIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIE 120
+ L+VIDE H+L + RGP+LE +V+++ L + I+I +SAT+ N ++ ++
Sbjct: 147 -----VDLVVIDEIHLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNAEEVADWLN 201
Query: 121 GITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYA-DNLDYSLTGSGPDAVLHLVQGN 179
+ RP V F DGK T DNL + VL +
Sbjct: 202 AKLVESDWRPVPLRRGV-PYVGAFLGADGKKKTWPLLIDNLAL-------ELVLESLAEG 253
Query: 180 LMVLIFCSSKIACSNLALRL-QFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECI 238
VL+F S+ A +L + + K E L E L E +
Sbjct: 254 GQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELV 313
Query: 239 LYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRD-----SYV 293
L GVA+HHA L +R+L+E+A+ G ++++ T TLAAGVNLPA+ VII+D
Sbjct: 314 LRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKG 373
Query: 294 GRDFISLNMYKQMVGRAGRTGLQESGESIMLCKTM-QDFLRFSSMMNAGPEPISSHM-DP 351
G I + QM GRAGR G + GE+I+L + + + + PEPI S + D
Sbjct: 374 GIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELEYLAELYIQSEPEPIESKLGDE 433
Query: 352 PTLVDLILEVVAANLCSSLEDVKTLIKHTLFYQ--LKSPEDQQTFLETTLSEIVASLLAS 409
L +L V++ D + ++ T FY+ +P+ + EI+ASL
Sbjct: 434 LNLRTFLLGVISV------GDAVSWLELTDFYERTFYNPQTYGEGMLR--EEILASLRYL 485
Query: 410 KGTMLTMNEA-GHLSLTSIAKAAVQAGLSHDVCLIIYSDLLHNKLNFCLLNSLHMLFLVI 468
+ L ++ L T + K + + + I L L + L+++ L
Sbjct: 486 EENGLILDADWEALHATELGKLVSRLYIDPESAKIFRDLLAELALEPTEIGLLYLISL-- 543
Query: 469 PLEYRIPSDGILLSRSKVYDRYTKFHPQTLRVAEALGVTENLVALNVTGKLKDEKKALLC 528
D + + R + L E + + +L E LL
Sbjct: 544 ------TPDLMPIKL-----RERESSELVLDELEEQS---DYLLGERLDELAVEYNLLLQ 589
Query: 529 RFFHACILYD-VLNFDNHQKVAKMYGIQNSHLQNFLNVTSYFASKVYRFC---EELPELW 584
A L D + D ++ YG+ L + ++ + E L ++
Sbjct: 590 ALKTAARLLDWINEAD-EDEILNAYGVAPGDLLRIAETAEWLSADLLALGKAAERLAKIL 648
Query: 585 CYKQLLTDLPQTL-----MYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIARADAK 639
+ + L R+ L L+++ GV RAR+L NAGY SLE +
Sbjct: 649 GLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGRVRARKLYNAGYKSLEDLRLIADP 708
Query: 640 EMVAKIRHLPLRSARNLISAAKLHF 664
+ + + R ++ +
Sbjct: 709 AELLPLTGIGERLVEAILESLGRDV 733
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 200 bits (512), Expect = 3e-55
Identities = 125/423 (29%), Positives = 201/423 (47%), Gaps = 58/423 (13%)
Query: 4 EKYQSLAKAAEEFKFYLEEYAGVK-----GQYPPTKRQLNKKSIYICTIEKGSKLIGSLI 58
EK+ EEF+ + EE GV+ G Y L I + T EK + SL+
Sbjct: 82 EKF-------EEFERF-EEL-GVRVGISTGDYDSRDEWLGDNDIIVATSEK----VDSLL 128
Query: 59 QENR---IDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINAL 115
+ N +D+I +V+DE H+++ RGP LE ++K+ L +Q+ A+SATIGN + L
Sbjct: 129 R-NGAPWLDDITCVVVDEVHLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNADEL 187
Query: 116 STFIEGITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHL 175
+ +++ RP + + + VF + G I+ D+ + D L+L
Sbjct: 188 ADWLDAELVDSEWRP------IDLREGVF--YGGA----IHFDDSQREVEVPSKDDTLNL 235
Query: 176 V-----QGNLMVLIFCSSKIACSNLALRLQFDRFPGTKEY-KKQEKEDLIEALKEE---- 225
V +G L+F SS+ A R K+ E+ +L E L EE
Sbjct: 236 VLDTLEEGGQC-LVFVSSRRNAEGFAKRAA----SALKKTLTAAERAELAE-LAEEIREV 289
Query: 226 NDGKLSTNLEECILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQR 285
+D + S +L +C+ G A+HHA L+ R L+E+A+ +++I T TLAAG+NLPA+R
Sbjct: 290 SDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARR 349
Query: 286 VIIRD-----SYVGRDFISLNMYKQMVGRAGRTGLQESGESIMLCKTMQDFLR-FSSMMN 339
VIIRD G I + Y QM GRAGR GL GE+++L K+ + F +
Sbjct: 350 VIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYDELDELFERYIW 409
Query: 340 AGPEPISSHM-DPPTLVDLILEVVAANLCSSLEDVKTLIKHTLF-YQLKSPEDQQTFLET 397
A PE + S + P L +L +A+ + + + ++ T + Q + ++
Sbjct: 410 ADPEDVRSKLATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQTDDTGRLERVVDD 469
Query: 398 TLS 400
L
Sbjct: 470 VLD 472
Score = 40.3 bits (95), Expect = 0.003
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 608 LMDLPGVK-IGR--ARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAKLHF 664
L+DL G++ +GR AR+L NAG S + AD K +V I L + A N++ A
Sbjct: 651 LLDLVGLRGVGRVRARRLYNAGIESRADLRAAD-KSVVLAI--LGEKIAENILEQAG-RR 706
Query: 665 ITKMDKVEA 673
M
Sbjct: 707 DPSMGASSE 715
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 171 bits (434), Expect = 4e-45
Identities = 116/387 (29%), Positives = 177/387 (45%), Gaps = 51/387 (13%)
Query: 28 GQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLNEPQRGPILE 87
G Y + + + I T EK LI I+++GLIV DE H++ + RGP LE
Sbjct: 100 GDYDDPPDFIKRYDVVILTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPTLE 157
Query: 88 CVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGITYVENSRPTKHSEYVTVDKRVFQSF 147
V+S Y+ +I A+SAT+ N N L+ ++ N RP + KR+
Sbjct: 158 TVLSSARYVNPDARILALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLI--L 215
Query: 148 DGKSLTEIYADNLDYSLTGSGPDAVLHLVQGNLMVLIFCSSKIACSNLALRLQFDRFPGT 207
DG +++ ++L + V VL+F SS+
Sbjct: 216 DGYERSQVDINSL-----------IKETVNDGGQVLVFVSSR------------------ 246
Query: 208 KEYKKQEK--EDLIEALKEENDGKLSTN--------LEECILYGVAYHHADLTAGERRLI 257
K E E LI+ E ND K+S+ L E + +GVA+HHA L+ +RR I
Sbjct: 247 ---KNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFI 303
Query: 258 EEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRD-SYVGRDFISL--NM-YKQMVGRAGRT 313
EE + +++I T TLAAGVNLPA+ VI+RD + G I NM KQM+GRAGR
Sbjct: 304 EEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRP 363
Query: 314 GLQESGESIMLCKTMQDFLRFSSMMNAGPEPISSHMDPPTLVDL-ILEVVAANLCSSLED 372
G + G + + + ++ PEP+ S+M V L ++ L SS+ED
Sbjct: 364 GYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISYMGSQRKVRFNTLAAISMGLASSMED 423
Query: 373 VKTLIKHTLFYQLKSPEDQQTFLETTL 399
+ TL ++ ++E++L
Sbjct: 424 LILFYNETLMAIQNGVDEIDYYIESSL 450
Score = 35.2 bits (81), Expect = 0.11
Identities = 26/106 (24%), Positives = 50/106 (47%), Gaps = 4/106 (3%)
Query: 533 ACILYDVLNFDNHQKVAKMYGIQNSHLQNFLNVTSYFASKVYRFCEEL-PELWCYKQLLT 591
A +L ++ + QK+ YGI +Q + + + + R PE+ ++ L
Sbjct: 541 AMVLRGWISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSSIYKPEM---RRKLE 597
Query: 592 DLPQTLMYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIARAD 637
L + +L L+ +P V RAR+L +AG+ +++ IAR+
Sbjct: 598 ILNIRIKEGIREDLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSS 643
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 143 bits (363), Expect = 9e-36
Identities = 125/433 (28%), Positives = 205/433 (47%), Gaps = 51/433 (11%)
Query: 1 MVHEKYQSLAKAAEEFKFYLEEYAGVK-----GQYPPTKRQLNKKSIYICTIEKGSKLI- 54
+ EKY+ EFK + E G++ G Y T L K I I T EK L+
Sbjct: 80 LAEEKYR-------EFKDW--EKLGLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLR 130
Query: 55 -GSLIQENRIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNIN 113
GS + I ++ L+V DE H++ RG LE +++ +L QI +SAT+GN
Sbjct: 131 HGS----SWIKDVKLVVADEIHLIGSYDRGATLEMILTHML---GRAQILGLSATVGNAE 183
Query: 114 ALSTFIEGITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVL 173
L+ ++ V + RP K + V +F DGK E + ++ + V
Sbjct: 184 ELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWE-DGK--IERFPNSWE--------SLVY 232
Query: 174 HLVQGNLMVLIFCSSKIACSNLALRL--QFDRFPGTKEYKKQEKEDLIEALKEENDGKLS 231
V+ L+F +++ + AL L + RF E + ++L ++L EEN +
Sbjct: 233 DAVKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPE--LRALKELADSL-EEN--PTN 287
Query: 232 TNLEECILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDS 291
L++ + GVA+HHA L ER LIE+A+ G +++I T TL+AG+NLPA RVIIRD+
Sbjct: 288 EKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDT 347
Query: 292 YVGRDF----ISLNMYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMMNAGPEPISS 347
+F I + +QM+GRAGR E GE+I++ T + + PE + S
Sbjct: 348 KRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMERYIFGKPEKLFS 407
Query: 348 HM-DPPTLVDLILEVVAANLCSSLEDVKTLIKHTL-FYQLKSPEDQQTFLETTLSEIVAS 405
+ + +L ++ S+ +++ ++ T +Q K LE EIV
Sbjct: 408 MLSNESAFRSQVLALITNFGVSNFKELVNFLERTFYAHQRKDLYS----LEEKAKEIVYF 463
Query: 406 LLASKGTMLTMNE 418
LL ++ + + +
Sbjct: 464 LLENEFIDIDLED 476
Score = 40.6 bits (95), Expect = 0.003
Identities = 32/114 (28%), Positives = 49/114 (42%), Gaps = 6/114 (5%)
Query: 533 ACILYDVLNFDNHQKVAKMYGIQNSHLQNFLNVTS---YFASKVYRFCEELPELWCYKQL 589
A +L D +N ++ + Y I L L + Y ++Y+ E E+ Y
Sbjct: 572 AKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLDY--- 628
Query: 590 LTDLPQTLMYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVA 643
L L + + L LM LP + RAR L NAG+ S+E I A E++
Sbjct: 629 LETLHLRVKHGVREELLELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLK 682
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 102 bits (257), Expect = 1e-22
Identities = 79/330 (23%), Positives = 136/330 (41%), Gaps = 64/330 (19%)
Query: 60 ENRIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFI 119
+ +IG +VIDE H L + +RGP L+ ++ ++ YL Q +SAT+GN L+ +
Sbjct: 333 GKDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNPEELAKKL 392
Query: 120 EGITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQGN 179
+ + RP V L+ HLV
Sbjct: 393 GAKLVLYDERP--------VP-------------------LER-----------HLV--- 411
Query: 180 LMVLIFCSSKIACSNLALRL---QFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEE 236
F ++ ++ RL +F +K Y+ Q ++ +L+ L
Sbjct: 412 -----FARNESEKWDIIARLVKREFST-ESSKGYRGQT---IVFTYSRRRCHELADALTG 462
Query: 237 CILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRD 296
L Y HA L ER+ +E A+ A L + T+ LAAGV+ PA +VI +G +
Sbjct: 463 KGLKAAPY-HAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIE 521
Query: 297 FISLNMYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSS---------MMNAGPEPISS 347
++S+ ++QM+GRAGR + G+ +L + + + ++ + PEP+
Sbjct: 522 WLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKYHASMEETEDEVAFKLLESEPEPVIV 581
Query: 348 HMDPPTLVDLILEVVAA-NLCSSLEDVKTL 376
D + +L N S +E V +L
Sbjct: 582 EYDEEDEEENVLASAGVTNSLSVIERVNSL 611
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 97.5 bits (243), Expect = 8e-21
Identities = 89/375 (23%), Positives = 153/375 (40%), Gaps = 70/375 (18%)
Query: 65 EIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGI-- 122
+I +V DE H + + +RG + E V+ + L ++ +SAT+ N + +I+ +
Sbjct: 229 DIEWVVFDEVHYIGDRERGVVWEEVI---ILLPDHVRFVFLSATVPNAEEFAEWIQRVHS 285
Query: 123 --TYV--ENSRPTKHSEYVTVDKRVFQSFDGKS--LTEIYA------------------- 157
+V RP +V V K +F D K E +
Sbjct: 286 QPIHVVSTEHRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCFSEKVRETDDG 345
Query: 158 DNLDYSLTGSG-----------PDAVLHLVQGNLM-VLIFCSSKIACSNLALRLQFDRFP 205
D Y+ P+ V L + NL+ ++F S+ C A L
Sbjct: 346 DVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLV 405
Query: 206 GTKEYKKQEKEDLIEA----LKEENDG------KLSTNLEECILYGVAYHHADLTAGERR 255
T+E K++ ++I+ L EE+ ++S L L G+A HHA L +
Sbjct: 406 LTEE-KERAIREIIDHAIGDLAEEDRELPLQILEISALL----LRGIAVHHAGLLPAIKE 460
Query: 256 LIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRD-----FISLNMYKQMVGRA 310
L+EE + G ++++ T T A G+N+PA+ V+ S D ++S Y QM GRA
Sbjct: 461 LVEELFQEGLVKVVFATETFAIGINMPARTVVFT-SLSKFDGNGHRWLSPGEYTQMSGRA 519
Query: 311 GRTGLQESGESIMLCKTMQDFLR-FSSMMNAGPEPISSHMDPPTLVDLILEVVAANLCSS 369
GR GL G I++ + + + + +P+ S + L L V
Sbjct: 520 GRRGLDVLGTVIVIEPPFESEPSEAAGLASGKLDPLRSQFRLSYNMILNLLRV-----EG 574
Query: 370 LEDVKTLIKHTLFYQ 384
L+ + L++ + F Q
Sbjct: 575 LQTAEDLLERS-FAQ 588
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 69.9 bits (172), Expect = 6e-15
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 240 YGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLP-AQRVIIRDSYVGRDFI 298
VA H L+ ER I + + G ++++ T G++LP VII D
Sbjct: 12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-----PW 66
Query: 299 SLNMYKQMVGRAGRTG 314
S Y Q +GRAGR G
Sbjct: 67 SPASYIQRIGRAGRAG 82
>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 = 62.5 bits (153), Expect = 2e-12
Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 240 YGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLP-AQRVIIRDSYVGRDFI 298
VA H L+ ER I E + G +++ T G++LP VI D
Sbjct: 8 IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL-----PW 62
Query: 299 SLNMYKQMVGRAGRTG 314
+ Y Q +GRAGR G
Sbjct: 63 NPASYIQRIGRAGRAG 78
>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 = 61.9 bits (151), Expect = 2e-11
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 240 YGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFIS 299
VA H D + ER + + + G + ++ T +A G++LP V+I + S
Sbjct: 53 IKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVI---NYDLPW-S 108
Query: 300 LNMYKQMVGRAGRTGLQESGESIML 324
+ Y Q +GRAGR G + G +I+L
Sbjct: 109 PSSYLQRIGRAGRAG--QKGTAILL 131
>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 = 56.0 bits (136), Expect = 6e-08
Identities = 52/227 (22%), Positives = 82/227 (36%), Gaps = 54/227 (23%)
Query: 69 IVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGITYVENS 128
+V+DE+H L +RG LE ++++ L ++ + +SATIGN+ + G
Sbjct: 144 VVVDEWHELAGSKRGDQLELALARLRRLAPGLRRWGLSATIGNLEEARRVLLG------- 196
Query: 129 RPTKHSEYVTVDKRVFQSFDGK-----SLTEIYADNLDYS--LTGSGPDAVLHLVQGNLM 181
+ + K SL + ++ L V +
Sbjct: 197 -------VGGAPAVLVRGKLPKAIPVISLLPESEERFPWAGHLGLRALPEVYAEIDQART 249
Query: 182 VLIFCSSKIACSNLALRLQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYG 241
L+F ++ R Q E Q L EA E +
Sbjct: 250 TLVFTNT---------RSQ-------AELWFQA---LWEAN-PEFALPI----------- 278
Query: 242 VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVN-LPAQRVI 287
A HH L +RR +E A AG L+ + CTS+L GV+ P VI
Sbjct: 279 -ALHHGSLDREQRRWVEAAMAAGRLRAVVCTSSLDLGVDFGPVDLVI 324
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 53.8 bits (130), Expect = 2e-07
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 242 VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLN 301
+HA L+ ER +++A+L ++++ T+ G++ P R +I G S+
Sbjct: 257 AGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPG----SIE 312
Query: 302 MYKQMVGRAGRTGLQESGESIML 324
Y Q GRAGR GL E+I+L
Sbjct: 313 SYYQETGRAGRDGL--PAEAILL 333
>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 = 51.3 bits (123), Expect = 1e-06
Identities = 55/311 (17%), Positives = 99/311 (31%), Gaps = 81/311 (26%)
Query: 57 LIQENRID--EIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATI-GNIN 113
LI+ ++D + +V+DE + + +E ++ L Q SAT+ +I
Sbjct: 164 LIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKA---LPPDRQTLLFSATMPDDIR 220
Query: 114 ALS-------TFIE-GITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLT 165
L+ IE + +E + Y+ V+ + K
Sbjct: 221 ELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESE-----EEK--------------- 260
Query: 166 GSGPDAVLHLVQGNL--MVLIFCSSKIACSNLALRLQFDRFPGTKEYKKQEKEDLIEALK 223
+ +L L++ V++F +K LA L+ F
Sbjct: 261 ---LELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFK------------------ 299
Query: 224 EENDGKLSTNLEECILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPA 283
VA H DL ER E + G L+++ T A G+++P
Sbjct: 300 ------------------VAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPD 341
Query: 284 QRVIIRDSYVGRDFISLNMYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMMNAGPE 343
+I Y Y +GR GR G G +I ++ + +
Sbjct: 342 VSHVIN--YDLPL--DPEDYVHRIGRTGRAGR--KGVAISFVTEEEEVKKLKRIEKRLER 395
Query: 344 PISSHMDPPTL 354
+ S + P
Sbjct: 396 KLPSAVLLPLD 406
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 51.8 bits (124), Expect = 1e-06
Identities = 31/113 (27%), Positives = 54/113 (47%), Gaps = 8/113 (7%)
Query: 229 KLSTNLEECILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVII 288
K++ L+E + A++H + +R +++ + + IIC T G+N P R +I
Sbjct: 695 KVAERLQEF-GHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVI 753
Query: 289 RDSYVGRDFISLNMYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMMNAG 341
S S+ Y Q GRAGR G + S +L + D++R M++ G
Sbjct: 754 HHSLPK----SIEGYHQECGRAGRDGQR---SSCVLYYSYSDYIRVKHMISQG 799
>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 = 48.2 bits (115), Expect = 1e-05
Identities = 52/255 (20%), Positives = 83/255 (32%), Gaps = 54/255 (21%)
Query: 68 LIVIDEFHMLNEPQRGPI---LECVVSKVL----YLKKSIQIFAMSATIGNI-NALSTF- 118
+V+DE H RG + ++ ++L +QI SAT+ N
Sbjct: 198 YLVVDELHTY----RGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAEELF 253
Query: 119 -IEGITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQ 177
+ V+ + Y + + +S+ L LV+
Sbjct: 254 GRDFEVPVDEDGSPRGLRYFVRREPPIR-ELAESIRRSALAELATLAA--------LLVR 304
Query: 178 GNLMVLIFCSSKIACSNLALRLQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEEC 237
+ L+F S + L R L E GKL
Sbjct: 305 NGIQTLVFFRS---RKQVELLYLSPR----------------RRLVRE-GGKLLDA---- 340
Query: 238 ILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDF 297
V+ + A L ERR IE + G L + T+ L G+++ + +I Y G
Sbjct: 341 ----VSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSV 396
Query: 298 ISLNMYKQMVGRAGR 312
+S Q GRAGR
Sbjct: 397 LSFR---QRAGRAGR 408
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 45.9 bits (109), Expect = 2e-05
Identities = 27/136 (19%), Positives = 52/136 (38%), Gaps = 10/136 (7%)
Query: 2 VHEKYQSLAKAAEEFKF-YLEEYAGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQE 60
+ + L K + Y G + K + K I + T + L+ L +
Sbjct: 67 AEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGR---LLDLLEND 123
Query: 61 N-RIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGN--INALST 117
+ + L+++DE H L + G LE ++ L K++Q+ +SAT N L
Sbjct: 124 KLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKL---LPKNVQLLLLSATPPEEIENLLEL 180
Query: 118 FIEGITYVENSRPTKH 133
F+ +++
Sbjct: 181 FLNDPVFIDVGFTPLE 196
>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 = 44.2 bits (105), Expect = 5e-05
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 42 IYICTIEKGSKLIGSLIQENRID---EIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKK 98
I + T + + L++ ++ + L+V+DE H L + G LE ++S+ L
Sbjct: 99 ILVGTPGR----LLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSR---LPP 151
Query: 99 SIQIFAMSATI 109
QI +SAT+
Sbjct: 152 DRQILLLSATL 162
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 43.9 bits (104), Expect = 3e-04
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 242 VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLN 301
A +HA L R ++EA+ LQI+ T G+N P R ++ + R+ S
Sbjct: 263 AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFD-IPRNIES-- 319
Query: 302 MYKQMVGRAGRTGLQESGESIML 324
Y Q GRAGR GL E+++
Sbjct: 320 -YYQETGRAGRDGL--PAEAMLF 339
>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 = 42.4 bits (100), Expect = 6e-04
Identities = 27/98 (27%), Positives = 38/98 (38%), Gaps = 12/98 (12%)
Query: 243 AYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLNM 302
AYH A L R + + +Q++ T G+N P R +I S + +M
Sbjct: 255 AYH-AGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYS------LPKSM 307
Query: 303 --YKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMM 338
Y Q GRAGR GL L D R ++
Sbjct: 308 ESYYQESGRAGRDGLP---SECHLFYAPADINRLRRLL 342
>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 = 40.0 bits (94), Expect = 7e-04
Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 13/104 (12%)
Query: 13 AEEFKFYLE-----EYAGVKGQYPPTKRQLNKKS-IYICTIEKGSKLIGSLIQEN-RIDE 65
AE K Y ++ L+ K+ I + T + L+ L + + +
Sbjct: 47 AERLKELFGEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGR---LLDELERLKLSLKK 103
Query: 66 IGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATI 109
+ L+++DE H L G + ++ K L K Q+ +SAT
Sbjct: 104 LDLLILDEAHRLLNQGFGLLGLKILLK---LPKDRQVLLLSATP 144
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 42.2 bits (100), Expect = 8e-04
Identities = 43/217 (19%), Positives = 76/217 (35%), Gaps = 57/217 (26%)
Query: 69 IVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEG------I 122
+++DE H L E +RG L + ++ L Q +SAT+G ++ F+ G I
Sbjct: 153 VIVDEIHALAESKRGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEI 212
Query: 123 TYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQGNLMV 182
V ++ + V+ ++ +L E A+ LV+ +
Sbjct: 213 VDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAE----------------LVKKHRTT 256
Query: 183 LIFCSSKIACSNLALRLQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYGV 242
LIF +++ E L LK+ +
Sbjct: 257 LIFTNTR-----------------------SGAERLAFRLKKLGPDI------------I 281
Query: 243 AYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGV 279
HH L+ R +EE G L+ + TS+L G+
Sbjct: 282 EVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGI 318
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 40.6 bits (96), Expect = 0.002
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 608 LMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L DLPGV A +L AGY ++E IA A KE+ ++ + +A +I AA+
Sbjct: 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKEL-SEAAGIGESTAAKIIEAAR 60
>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 = 0.005
Identities = 34/118 (28%), Positives = 57/118 (48%), Gaps = 9/118 (7%)
Query: 209 EYKKQEKED--LIEALKEENDGKLSTNLEECILYGVAYHHADLTAGERRLIEEAYLAGTL 266
+Y K+ + +I A + +L+ LE + +AYH A L+ R +E +L +
Sbjct: 217 DYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYH-AGLSNKVRAENQEDFLYDDV 275
Query: 267 QIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLNMYKQMVGRAGRTGLQESGESIML 324
+++ T+ G++ P R +I G +L Y Q GRAGR GL E+I+L
Sbjct: 276 KVMVATNAFGMGIDKPNVRFVIHYDMPG----NLESYYQEAGRAGRDGLP--AEAILL 327
>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA.
This family consists exclusively of archaeal RadA
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239), and archaeal RadB
(TIGR02237). This protein is involved in DNA repair and
recombination. The member from Pyrococcus horikoshii
contains an intein [DNA metabolism, DNA replication,
recombination, and repair].
Length = 310
Score = 38.6 bits (90), Expect = 0.008
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 608 LMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L DLPGV A +L AGY + E IA A KE +++I + +A +I AA+
Sbjct: 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKE-LSEIAGISEGTAAKIIQAAR 53
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 36.7 bits (85), Expect = 0.042
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 8/78 (10%)
Query: 246 HADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNL-PAQRVIIRDSYVGRDFISLNMYK 304
H + + ERR + +++L G + +I T L GV+L ++VII D ++ Y
Sbjct: 399 HGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPN-----TIKEYI 453
Query: 305 QMVGRAGRTGLQESGESI 322
+GRA R G E G +I
Sbjct: 454 HQIGRASRMG--EKGTAI 469
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 36.8 bits (85), Expect = 0.051
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 245 HHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLNMYK 304
HH ++ +R + E+A +G L+ + TS+L G+++ A ++I+ + +S+
Sbjct: 307 HHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATP----LSVASGL 362
Query: 305 QMVGRAG 311
Q +GRAG
Sbjct: 363 QRIGRAG 369
>gnl|CDD|216709 pfam01798, Nop, Putative snoRNA binding domain. This family
consists of various Pre RNA processing
ribonucleoproteins. The function of the aligned region
is unknown however it may be a common RNA or snoRNA or
Nop1p binding domain. Nop5p (Nop58p) from yeast is the
protein component of a ribonucleoprotein protein
required for pre-18s rRNA processing and is suggested to
function with Nop1p in a snoRNA complex. Nop56p and
Nop5p interact with Nop1p and are required for ribosome
biogenesis. Prp31p is required for pre-mRNA splicing in
S. cerevisiae.
Length = 149
Score = 34.6 bits (80), Expect = 0.056
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 572 KVYRFCEELPELWCYKQLLTDLPQTLMYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLE 631
+ FCE + L Y++ L + ++ M APNL AL+ G +G AR + +AG SL
Sbjct: 1 NILEFCERILSLAEYRKQLEEYIESKMSKIAPNLTALV---GELVG-ARLISHAG--SLT 54
Query: 632 LIARADA 638
+A+ A
Sbjct: 55 NLAKLPA 61
>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 = 35.9 bits (83), Expect = 0.076
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 242 VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLN 301
VA + A +RR +E A G L + T+ L GV++ ++ + G
Sbjct: 306 VAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGT----RA 361
Query: 302 MYKQMVGRAGRTGLQES 318
Q GRAGR G Q +
Sbjct: 362 SLWQQAGRAGRRG-QGA 377
>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 = 33.9 bits (78), Expect = 0.34
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 225 ENDGKLSTNLEECILYG-VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLP- 282
E+ KL+T L E + +A H +T E + + G Q++ CT+ + G+++P
Sbjct: 671 ESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPN 730
Query: 283 AQRVIIRDSYVGRDFISLNMYKQMVGRAGRTGLQ 316
A +II + D L Q+ GR GR+ +
Sbjct: 731 ANTIIIERA----DKFGLAQLYQLRGRVGRSKKK 760
>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 = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 240 YGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLP-AQRVIIRDSYVGRDFI 298
Y V H + + E+ + E + G + I+ T+ + GV++P A ++I D+ +
Sbjct: 483 YNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDA----ERF 538
Query: 299 SLNMYKQMVGRAGRTGLQ 316
L+ Q+ GR GR Q
Sbjct: 539 GLSQLHQLRGRVGRGDHQ 556
>gnl|CDD|220319 pfam09622, DUF2391, Putative integral membrane protein (DUF2391).
This entry is found in Nostoc sp. PCC 7120,
Agrobacterium tumefaciens, Rhizobium meliloti, and
Gloeobacter violaceus in a conserved two-gene
neighborhood. Proteins containing this entry appear to
span the membrane seven times.
Length = 267
Score = 32.7 bits (75), Expect = 0.59
Identities = 27/101 (26%), Positives = 35/101 (34%), Gaps = 22/101 (21%)
Query: 345 ISSHMDPPTLVDLILEVVAANLCSSLEDVKTLIKHTLFYQL-----KSPEDQQTFLETTL 399
I+ M P L+ LIL +SL LI H Y K +Q + L
Sbjct: 167 IAYKMSPWHLLALIL--------ASL-----LIMHGFVYAAEFRGQKKRRQEQGLFQAFL 213
Query: 400 SEIVA----SLLASKGTMLTMNEAGHLSLTSIAKAAVQAGL 436
E V SLL S + T L+ A + GL
Sbjct: 214 RETVVGYLISLLVSLYMLWTFGRLDGDGLSQWLSATIVLGL 254
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 32.9 bits (76), Expect = 0.64
Identities = 52/255 (20%), Positives = 104/255 (40%), Gaps = 60/255 (23%)
Query: 69 IVIDEFHMLNEPQRGPILECVVSKVLYL-KKSIQIFAMSATIGNINALSTFIEGITYVEN 127
+++DE H L E +RG L + ++ L +SATI + ++ F+ G
Sbjct: 176 VIVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPLEEVAKFLVGYEDDGE 235
Query: 128 SRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYS----LTGSGPDAVLHLVQGNLMVL 183
R VD R + FD K ++ + D+L ++ ++ + + + L++ + L
Sbjct: 236 PRD-----CEIVDARFVKPFDIKVISPV--DDLIHTPAEEISEALYETLHELIKEHRTTL 288
Query: 184 IFCSSKIACSNLALRLQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYGVA 243
IF +++ + L+ K + ++ ED I A
Sbjct: 289 IFTNTRSGAERVLYNLR-------KRFPEEYDEDNIGA---------------------- 319
Query: 244 YHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFI----- 298
HH+ L+ R +EE G L+++ +++L G+++ Y+ D +
Sbjct: 320 -HHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIG---------YI--DLVVLLGS 367
Query: 299 --SLNMYKQMVGRAG 311
S++ Q +GRAG
Sbjct: 368 PKSVSRLLQRIGRAG 382
>gnl|CDD|221191 pfam11731, Cdd1, Pathogenicity locus. Cdd1 is expressed as part of
the pathogenicity locus operon in several different
orders of bacteria. Many members of the family are
annotated as being putative mitomycin resistance
proteins but this could not be confirmed.
Length = 92
Score = 30.3 bits (69), Expect = 0.65
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 599 YCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAK 644
L+ L DLP + A+ L G +S +A D E+ +
Sbjct: 5 KVDRSALKELTDLPNIGKATAKDLRLLGINSPAQLAGRDPLELYER 50
>gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X
DNA Polymerases. X family polymerases fill in short
gaps during DNA repair. They are relatively inaccurate
enzymes and play roles in base excision repair, in
non-homologous end joining (NHEJ) which acts mainly to
repair damage due to ionizing radiation, and in V(D)J
recombination. This family includes eukaryotic Pol beta,
Pol lambda, Pol mu, and terminal deoxyribonucleotidyl
transferase (TdT). Pol beta and Pol lambda are primarily
DNA template-dependent polymerases. TdT is a DNA
template-independent polymerase. Pol mu has both
template dependent and template independent activities.
This subgroup belongs to the Pol beta-like NT
superfamily. In the majority of enzymes in this
superfamily, two carboxylates, Dx[D/E], together with a
third more distal carboxylate, coordinate two divalent
metal cations involved in a two-metal ion mechanism of
nucleotide addition. These three carboxylate residues
are fairly well conserved in this family.
Length = 307
Score = 32.2 bits (74), Expect = 0.94
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 586 YKQLLTDLPQTLMYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKI 645
++L D+P L L+ +PGV AR+L G +LE + +A ++ I
Sbjct: 73 LEELREDVPPGL--------LLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGAKLEQNI 124
Query: 646 R 646
Sbjct: 125 L 125
>gnl|CDD|224986 COG2075, RPL24A, Ribosomal protein L24E [Translation, ribosomal
structure and biogenesis].
Length = 66
Score = 28.9 bits (65), Expect = 1.4
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 176 VQGNLMVLIFCSSKIAC-SNLALRLQFDRFPGTKEYKKQEKEDLIE 220
V+ + VL FCSSK C L + TK+Y+K K+++ E
Sbjct: 22 VRNDGKVLRFCSSK--CEKLFKLGRNPRKLKWTKKYRKMHKKEIKE 65
>gnl|CDD|234230 TIGR03491, TIGR03491, RecB family nuclease, putative, TM0106
family. Members of this uncharacterized protein family
are found broadly but sporadically among bacteria. The
N-terminal region is homologous to the Cas4 protein of
CRISPR systems, although this protein family shows no
signs of association with CRISPR repeats.
Length = 457
Score = 31.5 bits (72), Expect = 1.4
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 608 LMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L +PG+ R R L G +LE +A AD + L A L+ A+
Sbjct: 209 LSLVPGIGPSRYRLLQELGIHTLEDLAAAD-PNDLEDFGEQGLGVAEQLVQQAR 261
>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 = 31.2 bits (71), Expect = 1.6
Identities = 29/111 (26%), Positives = 44/111 (39%), Gaps = 9/111 (8%)
Query: 21 EEYAGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGL----IVIDEFHM 76
EE+ + Y + L I +CTI++ K + + ++ DE H
Sbjct: 75 EEFEHLFPLYIHSNDTLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHF 134
Query: 77 LNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGITYVEN 127
+E IL V +VL + I MSAT+ L + E I YVE
Sbjct: 135 YDEYTLALIL--AVLEVL-KDNDVPILLMSATLPKF--LKEYAEKIGYVEE 180
>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 = 31.3 bits (71), Expect = 1.7
Identities = 34/139 (24%), Positives = 55/139 (39%), Gaps = 9/139 (6%)
Query: 21 EEYAGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGL----IVIDEFHM 76
EE+ + Y + +L I +CTI++ K + + ++ DE H
Sbjct: 76 EEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHF 135
Query: 77 LNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGITYVENSRPTKHSEY 136
+E IL V +VL + I MSAT+ L + E I YVE + P E
Sbjct: 136 YDEYTLALIL--AVLEVL-KDNDVPILLMSATLPKF--LKEYAEKIGYVEFNEPLDLKEE 190
Query: 137 VTVDKRVFQSFDGKSLTEI 155
++ F + + EI
Sbjct: 191 RRFERHRFIKIESDKVGEI 209
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 31.3 bits (71), Expect = 1.8
Identities = 51/262 (19%), Positives = 81/262 (30%), Gaps = 44/262 (16%)
Query: 64 DEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSI---QIFAMSATI-----GNINAL 115
+E GLI+ DE H P S L+ ++AT G I L
Sbjct: 145 NEFGLIIFDEVH------HLPA----PSYRRILELLSAAYPRLGLTATPEREDGGRIGDL 194
Query: 116 STFIEGITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHL 175
I I Y + + Y+ + + + E + + A L
Sbjct: 195 FDLIGPIVYEVSLKELIDEGYL-APYKYVEIKVTLTEDEEREYAKESARFRELLRARGTL 253
Query: 176 VQGNLM--VLIFCSSKIACSNLALRLQFDRFPGTK---EYKKQEKEDLIEALKEENDGKL 230
N + I KIA + L L+ R T + E I
Sbjct: 254 RAENEARRIAIASERKIA-AVRGLLLKHARGDKTLIFASDVEHAYE--IAK-------LF 303
Query: 231 STNLEECILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRD 290
+ G ER I E + G ++++ L GV++P V+I
Sbjct: 304 LAPGIVEAITGETPKE------EREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLI-- 355
Query: 291 SYVGRDFISLNMYKQMVGRAGR 312
+ R S ++ Q +GR R
Sbjct: 356 --ILRPTGSRRLFIQRLGRGLR 375
>gnl|CDD|234519 TIGR04244, nitrous_NosZ_RR, nitrous-oxide reductase, TAT-dependent.
Members of this family are the nitrous-oxide reductase
structural protein, NosZ, with an N-terminal
twin-arginine translocation (TAT) signal sequence (see
TIGR01409). The TAT system replaces the Sec system for
export of proteins with bound cofactor.
Length = 627
Score = 30.9 bits (70), Expect = 2.5
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 475 PSDGILLSRSK-----VYDRYTKFHPQTLRVAEALGVTE 508
P D I++ RSK VYDR P + A+A GV
Sbjct: 484 PHDSIIVHRSKVKPRSVYDRDDPMFPDARKQAKADGVLL 522
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
Length = 936
Score = 30.6 bits (69), Expect = 3.3
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 608 LMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L+ +PG+ +L AG +L+ AD K+ +AK+ + + RNL + AK
Sbjct: 879 LLSVPGLGETTLEKLYLAGVYDGDLLVSADPKK-LAKVTGIDEKKLRNLQAYAK 931
>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p
homolog [Translation, ribosomal structure and
biogenesis].
Length = 395
Score = 30.1 bits (68), Expect = 4.7
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 576 FCEELPELWCYKQLLTDLPQTLMYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIAR 635
E + EL+ ++ L + ++ M APNL AL+ G +G AR + +AG L +A+
Sbjct: 215 LAEIILELYELREQLEEYIESKMSEIAPNLTALV---GPVLG-ARLISHAG--GLTRLAK 268
Query: 636 ADA 638
A
Sbjct: 269 MPA 271
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 27.0 bits (61), Expect = 4.7
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 208 KEYKKQEKEDLIEALKEENDGKLSTNLEECIL 239
+ YKK+ +DL + +K E S + E+ +L
Sbjct: 24 QAYKKRYGKDLEDDIKSE----TSGDFEKLLL 51
>gnl|CDD|216753 pfam01872, RibD_C, RibD C-terminal domain. The function of this
domain is not known, but it is thought to be involved in
riboflavin biosynthesis. This domain is found in the C
terminus of RibD/RibG, in combination with pfam00383, as
well as in isolation in some archaebacterial proteins.
This family appears to be related to pfam00186.
Length = 201
Score = 29.3 bits (66), Expect = 5.2
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 35 RQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIV 70
R+L ++ I +E G+ L GSL++ +DE+ L +
Sbjct: 129 RELKERGIRSLLVEGGATLAGSLLRAGLVDELRLYI 164
>gnl|CDD|188887 cd09488, SAM_EPH-R, SAM domain of EPH family of tyrosine kinase
receptors. SAM (sterile alpha motif) domain of EPH
(erythropoietin-producing hepatocyte) family of receptor
tyrosine kinases is a C-terminal signal transduction
module located in the cytoplasmic region of these
receptors. SAM appears to mediate cell-cell initiated
signal transduction via binding proteins to a conserved
tyrosine that is phosphorylated. In some cases the SAM
domain mediates homodimerization/oligomerization and
plays a role in the clustering process necessary for
signaling. EPH kinases are the largest family of
receptor tyrosine kinases. They are classified into two
groups based on their abilities to bind ephrin-A and
ephrin-B ligands. The EPH receptors are involved in
regulation of cell movement, shape, and attachment
during embryonic development; they control cell-cell
interactions in the vascular, nervous, epithelial, and
immune systems, and in many tumors. They are potential
molecular markers for cancer diagnostics and potential
targets for cancer therapy.
Length = 61
Score = 27.2 bits (61), Expect = 5.3
Identities = 11/32 (34%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 611 LPGVKIGRARQ-LLNAGYSSLELIARADAKEM 641
L +K+GR ++ AGY+SL+ +A+ A+++
Sbjct: 9 LESIKMGRYKENFTAAGYTSLDAVAQMTAEDL 40
>gnl|CDD|131636 TIGR02587, TIGR02587, putative integral membrane protein TIGR02587.
Members of this family are found in Nostoc sp. PCC
7120, Agrobacterium tumefaciens, Sinorhizobium meliloti,
and Gloeobacter violaceus in a conserved two-gene
neighborhood. This family, as defined, includes some
members of COG4711 but is narrower and strictly
bacterial. Members appear to span the membrane seven
times [Cell envelope, Other].
Length = 271
Score = 29.4 bits (66), Expect = 5.7
Identities = 25/101 (24%), Positives = 33/101 (32%), Gaps = 22/101 (21%)
Query: 345 ISSHMDPPTLVDLILEVVAANLCSSLEDVKTLIKHTLFYQL-----KSPEDQ----QTFL 395
I+ + PP + LIL + I H YQL Q FL
Sbjct: 171 IAYKISPPHIFALILASLV-------------IMHAFVYQLGFRGQHKRRQGKGIFQRFL 217
Query: 396 ETTLSEIVASLLASKGTMLTMNEAGHLSLTSIAKAAVQAGL 436
T + SLLAS + T + +A V GL
Sbjct: 218 RETTIGYLVSLLASAYMLWTFQRVDFADWSMWLEATVVLGL 258
>gnl|CDD|223381 COG0304, FabB, 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid
metabolism / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 412
Score = 29.5 bits (67), Expect = 5.8
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 387 SPEDQQTFLETTLSEIVASLLASKGTMLTMNEAGHLSLTSIAKAA--VQAGLSHDVCLI 443
SP L + VA + KG T A +I A ++ G + DV +
Sbjct: 129 SPFLVPKMLPNLAAGNVAIVFGLKGPNYTPVTACATGAHAIGDAVRLIRLGKA-DVVIA 186
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 29.7 bits (67), Expect = 5.9
Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 5/89 (5%)
Query: 275 LAAGVNLPAQRVIIRDSYVGRDFISLNMYKQMVGRAGRT-GLQESGESIMLCKTMQDFLR 333
L GV++P ++ D R S +KQMVGR R E T+ DF+
Sbjct: 491 LTTGVDVPEVVNLVFD----RKVRSKTKFKQMVGRGTRLCPDLGGPEQDKEFFTIFDFVD 546
Query: 334 FSSMMNAGPEPISSHMDPPTLVDLILEVV 362
+ PE + L + +
Sbjct: 547 NTEYFEMDPEMREGRVRVSLEQRLFADRL 575
>gnl|CDD|191413 pfam05970, PIF1, PIF1-like helicase. This family includes
homologues of the PIF1 helicase, which inhibits
telomerase activity and is cell cycle regulated. This
family includes a large number of largely
uncharacterized plant proteins. This family includes a
P-loop motif that is involved in nucleotide binding.
Length = 364
Score = 29.3 bits (66), Expect = 8.1
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 37 LNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLN 78
L + C I++GSKL ++ LI+ DE M+N
Sbjct: 80 LGIDELSTCKIKRGSKL------AELLENTSLIIWDEAPMVN 115
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 29.3 bits (66), Expect = 8.4
Identities = 25/95 (26%), Positives = 32/95 (33%), Gaps = 21/95 (22%)
Query: 493 FHPQTLRVAEALGVTENLVALNV---TGKLKDEKKALLCRFFHACILYDVLNFDNHQKVA 549
P LR E LG+ + L AL V + D+ L F D A
Sbjct: 47 LSPNALRALERLGLWDRLEALGVPPLHVMVVDDGGRRLLIF-------DAAELGRG---A 96
Query: 550 KMYGIQNSHLQNFL--------NVTSYFASKVYRF 576
Y + S L N L NVT F ++V
Sbjct: 97 LGYVVPRSDLLNALLEAARALPNVTLRFGAEVEAV 131
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
0.321 0.136 0.387
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: 34,757,376
Number of extensions: 3452492
Number of successful extensions: 3493
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3462
Number of HSP's successfully gapped: 74
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 62 (27.6 bits)