RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18034
(251 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 = 127 bits (320), Expect = 7e-34
Identities = 48/106 (45%), Positives = 64/106 (60%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+VF TK VE + + L G ++ DL R KF+ G++RVLV TDVAAR
Sbjct: 276 VIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAAR 335
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
G+DIP + VINY+ P + +VHR+GR RAGR GVA S V+ +E
Sbjct: 336 GLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEE 381
>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 = 103 bits (259), Expect = 5e-28
Identities = 36/101 (35%), Positives = 57/101 (56%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
++F +K ++ + ++L GI ++ D R+ F+ G+I VLV TDV AR
Sbjct: 31 VLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIAR 90
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSL 102
GID+P++ VINY+ P ++ R+GR RAG+ G A L
Sbjct: 91 GIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 107 bits (269), Expect = 7e-27
Identities = 45/106 (42%), Positives = 60/106 (56%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
VVF TK + V L G S+ ++ DL+ R +F VLV TDVAAR
Sbjct: 245 CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAAR 304
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
G+DI +L+AVINY ++ VHR+GR RAG G+A SLV+ +E
Sbjct: 305 GLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEE 350
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 102 bits (257), Expect = 3e-25
Identities = 42/102 (41%), Positives = 59/102 (57%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
++VF T+ V + L AGI+ Y+ ++ R + G++ VLV TDVAAR
Sbjct: 248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAAR 307
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
GIDI + VIN++ P A ++HR+GR RAGR G A SLV
Sbjct: 308 GIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV 349
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 97.2 bits (242), Expect = 3e-23
Identities = 47/105 (44%), Positives = 63/105 (60%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+VFT TK+ ++ + L GI S I+ + AR A F++G IRVLV TD+AARG
Sbjct: 249 LVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARG 308
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+DI L V+NY P + +VHR+GR RA +G A SLV DE
Sbjct: 309 LDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDE 353
>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 = 89.1 bits (222), Expect = 4e-23
Identities = 32/78 (41%), Positives = 45/78 (57%)
Query: 17 KILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNF 76
K+L GI ++ L R+ F+ GK +VLV TDVA RGID+P ++ VINY+
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 77 PCKAKLFVHRVGRCARAG 94
P ++ R+GR RAG
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 86.1 bits (214), Expect = 5e-22
Identities = 33/82 (40%), Positives = 47/82 (57%)
Query: 13 EYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVI 72
E + ++L GI ++ L R+ KF GKI+VLV TDVA RG+D+P +D VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 73 NYNFPCKAKLFVHRVGRCARAG 94
Y+ P ++ R+GR RAG
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 82.5 bits (204), Expect = 5e-18
Identities = 37/105 (35%), Positives = 64/105 (60%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
++F TK +++ K L L G + I+ D R +F+TGK +++ TDVA+RG
Sbjct: 381 LIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRG 440
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
+D+ + VIN++FP + + +VHR+GR RAG G +Y+ ++ D+
Sbjct: 441 LDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDK 485
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 79.5 bits (196), Expect = 4e-17
Identities = 36/106 (33%), Positives = 65/106 (61%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ T+ V+Y+ K + + + ++ D+D R + +F++G RVL+ TD+ ARG
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDEL 108
ID+ + VINY+ P + ++HR+GR R GR GVA + V+ D++
Sbjct: 331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDI 376
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 79.6 bits (196), Expect = 5e-17
Identities = 46/119 (38%), Positives = 62/119 (52%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+VF K V + + L GI++ + D+ R F+ GKIRVLV TDVA RG
Sbjct: 339 MVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRG 398
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDELCYYLDLLLFLGRK 121
I I + VIN+ P +VHR+GR RAG SGV+ S D+ ++ LGRK
Sbjct: 399 IHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRK 457
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 79.6 bits (196), Expect = 5e-17
Identities = 41/101 (40%), Positives = 56/101 (55%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+VF TK VE V + L G + D+ R+ +FQ G++ +LV TDVAAR
Sbjct: 260 TMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAAR 319
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSL 102
G+ I + V NY+ P A+ +VHR+GR AR G G A S
Sbjct: 320 GLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 78.0 bits (192), Expect = 2e-16
Identities = 36/106 (33%), Positives = 61/106 (57%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
++F TK V + L G +S + D++ R+ + + G++ +L+ TDVAAR
Sbjct: 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAAR 307
Query: 62 GIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVSSDE 107
G+D+ + V+NY+ P ++ +VHR+GR RAGR+G A V + E
Sbjct: 308 GLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRE 353
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 74.2 bits (183), Expect = 2e-15
Identities = 29/59 (49%), Positives = 40/59 (67%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSL 102
+F G + +LV TDVAARG+ IP++ V NY+ P + +VHR+GR RAG SG + SL
Sbjct: 300 EFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 58.1 bits (141), Expect = 8e-10
Identities = 29/102 (28%), Positives = 48/102 (47%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ T+ VE + + L GIS+ ++ L R+ F +I+V+V T+ G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLVS 104
ID P + VI+Y+ P + + GR R G A L S
Sbjct: 294 IDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYS 335
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 53.6 bits (129), Expect = 3e-08
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T++F + H + K+ GI I + R+ +F+TG I+VLV V
Sbjct: 286 TLIFASDVEHAYEIAKLFLAPGIVE-AITGETPKEEREAILERFRTGGIKVLVTVKVLDE 344
Query: 62 GIDIPSLDAVI 72
G+DIP D +I
Sbjct: 345 GVDIPDADVLI 355
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 50.2 bits (120), Expect = 4e-07
Identities = 22/69 (31%), Positives = 38/69 (55%)
Query: 38 RKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSG 97
R+ F G++ V+V T V RG+D+ + VI ++ P K ++H++GR +R G G
Sbjct: 407 RREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKG 466
Query: 98 VAYSLVSSD 106
A V+ +
Sbjct: 467 TAIVFVNEE 475
>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 = 50.1 bits (120), Expect = 4e-07
Identities = 31/87 (35%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 26 STYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFP-CKAKLFV 84
STY + L R+ A+F+ G++ ++ T+ GIDI SLDAVI Y +P F
Sbjct: 342 STY-RAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFR 400
Query: 85 HRVGRCARAGRSGVAYSLVSSDELCYY 111
R GR R G+ + ++ SD L Y
Sbjct: 401 QRAGRAGRRGQESLVLVVLRSDPLDSY 427
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 49.3 bits (118), Expect = 7e-07
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
+F+ G+ VLV T V G+DIP +D VI Y + R GR R R G LV
Sbjct: 420 QFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-KRKGRVVVLV 478
Query: 104 SSDE 107
+
Sbjct: 479 TEGT 482
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 46.0 bits (110), Expect = 8e-06
Identities = 41/162 (25%), Positives = 63/162 (38%), Gaps = 17/162 (10%)
Query: 43 AKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSL 102
KF+ G+ VLV T VA G+DIPS+D VI Y + R GR R G L
Sbjct: 417 DKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGR-QEEGRVVVL 475
Query: 103 VS---SDELCYYLDLLLFLGRKPVLADDSMKGKIRHQDGMFGKIPQGLMEDQISEIMNWV 159
++ DE Y+ RK + MK ++++ G+ K Q L E+Q E
Sbjct: 476 IAKGTRDEAYYWSSR-----RK----EKKMKEELKNLKGILNKKLQELDEEQKGEEEE-- 524
Query: 160 ELDADMEGIQKTCNNAYKKYVKSRPGASVESVKKVKELELAT 201
+ + + K+ + + + E E
Sbjct: 525 --KDEQLSLDDFVKSKGKEEEEEEEKEEKDKETEEDEPEGPK 564
>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 = 42.0 bits (99), Expect = 2e-04
Identities = 21/78 (26%), Positives = 33/78 (42%)
Query: 35 PTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAG 94
P R+ + G++ + T+ G+DI LDAV+ FP + GR R G
Sbjct: 315 PEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG 374
Query: 95 RSGVAYSLVSSDELCYYL 112
+ + + D L YL
Sbjct: 375 QGALVVLVARDDPLDTYL 392
>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 = 39.3 bits (92), Expect = 0.002
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 3/95 (3%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ +++ VE + + L GIS+ ++ L R N F ++V+V T+ G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSG 97
ID P++ VI+Y+ P + + G RAGR G
Sbjct: 288 IDKPNVRFVIHYDMPGNLESYYQEAG---RAGRDG 319
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 37.2 bits (87), Expect = 0.007
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 1/89 (1%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIY-SDLDPTARKINAAKFQTGKIRVLVVTDVAA 60
T++FT T+ E + L G ++ L R + + G+++ +V T
Sbjct: 256 TLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLE 315
Query: 61 RGIDIPSLDAVINYNFPCKAKLFVHRVGR 89
GIDI +D VI P F+ R+GR
Sbjct: 316 LGIDIGDIDLVIQLGSPKSVNRFLQRIGR 344
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 36.7 bits (85), Expect = 0.010
Identities = 16/66 (24%), Positives = 29/66 (43%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
T+VFT ++ + L G+ + ++ L RK F ++ +V T A
Sbjct: 443 TIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAA 502
Query: 62 GIDIPS 67
G+D P+
Sbjct: 503 GVDFPA 508
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 36.1 bits (84), Expect = 0.017
Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 15/78 (19%)
Query: 4 VFTATKYHVEYVHKILGL---AGISSTYIYSDLDPTARKINAAKFQTGKIRVLV----VT 56
+F + EY ++ GI++ S + KF+ G++ VLV
Sbjct: 333 IFVPSDKGKEYAEELAEYLEDLGINAELAISGFER-----KFEKFEEGEVDVLVGVASYY 387
Query: 57 DVAARGIDIPSLDAVINY 74
V RGID+P I Y
Sbjct: 388 GVLVRGIDLP---ERIRY 402
>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 = 34.7 bits (80), Expect = 0.040
Identities = 28/95 (29%), Positives = 48/95 (50%), Gaps = 3/95 (3%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ ++ E V L GI++ ++ L+ +AR KFQ +I+V+V T G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSG 97
I+ P + VI+Y+ P + + G RAGR G
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESG---RAGRDG 321
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 32.1 bits (73), Expect = 0.27
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 41 NAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKL-FVHRVGRCAR 92
F+ + ++L + G+D+P+LD+VI ++ P + + V VGR R
Sbjct: 520 LKNTFEPNECKILSNARCLSEGVDVPALDSVIFFD-PRSSMVDIVQAVGRVMR 571
>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 = 31.6 bits (72), Expect = 0.40
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVI--NYNFPCKAKLFVHRVGRCARAGRSGVAYS 101
+F G+ +VLV T + GIDIP+ + +I + A+L+ R GR R+ + AY
Sbjct: 707 EFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLR-GRVGRSKKKAYAYL 765
Query: 102 LVSSDE 107
L +
Sbjct: 766 LYPHQK 771
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 31.0 bits (70), Expect = 0.65
Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 3/101 (2%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ ++ E V + L G + + + +DP R ++ +I ++ T G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSGVAYSLV 103
I+ P + VI+++ P K+ H+ C RAGR G S V
Sbjct: 744 INKPDVRFVIHHSLP-KSIEGYHQ--ECGRAGRDGQRSSCV 781
>gnl|CDD|148288 pfam06589, CRA, Circumsporozoite-related antigen (CRA). This
family consists of several circumsporozoite-related
antigen (CRA) or exported protein-1 (EXP1) sequences
found specifically in Plasmodium species. The function
of this family is unknown.
Length = 157
Score = 29.9 bits (67), Expect = 0.77
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 172 CNNAYKKYVKSRPGASVESVKKVKELE-LATMQVHPLFRNIGSAEQEKFNLLTKMSEYRP 230
N+A K + G+ KK K+ + VH L ++ E+E L S Y+
Sbjct: 16 VNDALGKNKNGKYGSGNVIKKKNKKGSGEPLIDVHDLISDMVRKEEELVKLTKNKSSYKL 75
Query: 231 PSTVL 235
+ VL
Sbjct: 76 ATVVL 80
>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 = 30.7 bits (70), Expect = 0.78
Identities = 27/96 (28%), Positives = 46/96 (47%), Gaps = 5/96 (5%)
Query: 2 TVVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAAR 61
+V T TK E + L GI Y++S++D R + G+ VLV ++
Sbjct: 445 VLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE 504
Query: 62 GIDIP--SLDAVINYN---FPCKAKLFVHRVGRCAR 92
G+D+P SL A+++ + F + + +GR AR
Sbjct: 505 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 540
>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 = 30.1 bits (68), Expect = 1.0
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 43 AKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGR 95
+ + + V+V T V +DI A + + R+GR R GR
Sbjct: 272 EEMKKNEKFVIVATQVIEASLDI---SADVMITELAPIDSLIQRLGRLHRYGR 321
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 30.3 bits (68), Expect = 1.2
Identities = 16/52 (30%), Positives = 26/52 (50%)
Query: 38 RKINAAKFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGR 89
R I ++G++R +V T GID+ ++D VI P + R+GR
Sbjct: 316 RAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 29.3 bits (66), Expect = 2.0
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 3/95 (3%)
Query: 3 VVFTATKYHVEYVHKILGLAGISSTYIYSDLDPTARKINAAKFQTGKIRVLVVTDVAARG 62
+++ ++ VE L GIS+ ++ LD R FQ ++++V T G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299
Query: 63 IDIPSLDAVINYNFPCKAKLFVHRVGRCARAGRSG 97
I+ P++ V++++ P + + G RAGR G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETG---RAGRDG 331
>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 = 29.3 bits (66), Expect = 2.1
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 16/82 (19%)
Query: 32 DLDPTARKINA----AKFQTGKIRVLVVTDVAARGIDIP--SLDAVINYN-------FPC 78
D D T+RK +F GK +L+ T + A+G P +L V++ + F
Sbjct: 291 DSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA 350
Query: 79 KAKLF--VHRV-GRCARAGRSG 97
+ F + +V GR RA G
Sbjct: 351 AERGFQLLTQVAGRAGRAEDPG 372
>gnl|CDD|222427 pfam13871, Helicase_C_4, Helicase_C-like. Strawberry notch
proteins carry DExD/H-box groups and Helicase_C
domains. These proteins promote the expression of
diverse targets, potentially through interactions with
transcriptional activator or repressor complexes.
Length = 263
Score = 28.7 bits (65), Expect = 2.3
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 30 YSDLDPTARKINAAKFQTGKIRVLVVTDVAARGIDIPSLDA 70
+A F G+ +LV++D + GI SL A
Sbjct: 41 ADTRAASANLAEKQAFMDGEKLILVISDAGSTGI---SLHA 78
>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 = 28.9 bits (65), Expect = 2.7
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 3/45 (6%)
Query: 51 RVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGRCARAGR 95
V+V T V +DI + + R+GR R G
Sbjct: 276 FVIVATQVIEASLDI---SVDVMITELAPIDSLIQRLGRLHRYGE 317
>gnl|CDD|237273 PRK13018, PRK13018, cell division protein FtsZ; Provisional.
Length = 378
Score = 28.1 bits (63), Expect = 4.5
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 27 TYIYSDLDPTARKINAAKFQ---TGKIRVLVV 55
+ I +LDP A I A+ GK+RV+V+
Sbjct: 296 SRITEELDPEANIIWGARIDPDMEGKVRVMVI 327
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 28.1 bits (63), Expect = 5.4
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 29 IYSDLDPTARKINA----AKFQTGKIRVLVVTDVAARGIDIPSLDAV 71
I D D T RK +F G+ +L+ T + A+G D P++ V
Sbjct: 510 IRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLV 556
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 27.8 bits (62), Expect = 8.1
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 45 FQTGKIRVLVVTDVAARGIDIPSLDAVI 72
F + VLV T + GIDIP+ + +I
Sbjct: 857 FHHQRFNVLVCTTIIETGIDIPTANTII 884
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 27.4 bits (61), Expect = 9.3
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 38 RKINAAKFQTGKIRVLVVTDVAARGIDIPSLD-AVINYNFPC--KAKL--FVHRVGR 89
RK F+ GKI +L+ T + RG+ P++D V+ ++ L RVGR
Sbjct: 344 RKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGR 400
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 27.2 bits (61), Expect = 9.4
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 44 KFQTGKIRVLVVTDVAARGIDIPSLDAVINYNFPCKAKLFVHRVGR 89
K + G+++V+V + GIDI +D V+ P + R+GR
Sbjct: 335 KLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGR 380
>gnl|CDD|227291 COG4955, COG4955, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 343
Score = 27.1 bits (60), Expect = 9.7
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 173 NNAYKKYVKSRPGASVESVKKVKELELATMQVH 205
N+ YK Y G ++E + +++L+ +T++ H
Sbjct: 244 NSTYKTYTMLLQGFTLEDIAAIRQLKTSTIEDH 276
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 0.398
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: 12,822,109
Number of extensions: 1214127
Number of successful extensions: 1011
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1003
Number of HSP's successfully gapped: 52
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
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: 58 (26.0 bits)