RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4150
(395 letters)
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 184 bits (469), Expect = 5e-53
Identities = 91/229 (39%), Positives = 129/229 (56%), Gaps = 23/229 (10%)
Query: 34 SLASALENLVTYGLRSFYNNLVEVSKE-----DGSCPILGKDNDLQNLLQQLKPKLDINI 88
LA ALE L T G+R FY L ++ +E + L D K L + I
Sbjct: 286 KLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAAKSLLADPYF-------KRALRLLI 338
Query: 89 MSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVK 148
+ E H K +LREIL+ EK ++VI+F YR EI + LK + +
Sbjct: 339 RADESGVEHPKLEKLREILKEQL----EKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKAR 394
Query: 149 ASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ 203
F+GQ+S G++Q+EQKEI+ +FR GE+N L+ATSVGEEGLDI E+DLVI ++
Sbjct: 395 -VRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPV 453
Query: 204 KSPIKMVQRLGRTGRKRNGRCVILLTQG-REAHNFQTSMQTCKSYVEKI 251
S I+ +QR GRTGRKR GR V+L+T+G R+ + +S + + +E I
Sbjct: 454 PSEIRSIQRKGRTGRKRKGRVVVLVTEGTRDEAYYYSSRRKEQKMIESI 502
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 150 bits (381), Expect = 9e-40
Identities = 63/140 (45%), Positives = 91/140 (65%), Gaps = 11/140 (7%)
Query: 97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQS 156
H K +LREI++ +L ++I+F YR +I D+L+ + +KA FVGQ+
Sbjct: 346 HPKLEKLREIVKE--QLGKNPDS--RIIVFTQYRDTAEKIVDLLE--KEGIKAVRFVGQA 399
Query: 157 S-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ 211
S G++Q+EQ EI+ KFRAGEFN L++TSV EEGLDI +DLVI ++ S I+ +Q
Sbjct: 400 SKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQ 459
Query: 212 RLGRTGRKRNGRCVILLTQG 231
R GRTGR+ GR V+L+ +G
Sbjct: 460 RKGRTGRQEEGRVVVLIAKG 479
>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 = 95.0 bits (237), Expect = 1e-23
Identities = 43/130 (33%), Positives = 74/130 (56%), Gaps = 12/130 (9%)
Query: 99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
K L E+L + H +KG KV+IF + ++ E+ ++L+ +P +K + G
Sbjct: 13 KLEALLELL----KEHLKKGG--KVLIFCPSKKMLDELAELLR--KPGIKVAALHGD--- 61
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
+Q+E++E++K FR GE L+AT V G+D+ + +VI +D SP +QR+GR GR
Sbjct: 62 GSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGR 121
Query: 219 -KRNGRCVIL 227
+ G ++L
Sbjct: 122 AGQKGTAILL 131
>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 = 86.4 bits (215), Expect = 3e-21
Identities = 25/62 (40%), Positives = 43/62 (69%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
G++Q+E++EI++ FR G+ L+AT V G+D+ +++LVI +D +P +QR+GR
Sbjct: 15 GGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRA 74
Query: 217 GR 218
GR
Sbjct: 75 GR 76
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 82.3 bits (204), Expect = 1e-19
Identities = 29/63 (46%), Positives = 42/63 (66%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
G++Q+E++EI+ KF G+ L+AT V E GLD+ +DLVI +D SP +QR+GR
Sbjct: 19 GGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78
Query: 217 GRK 219
GR
Sbjct: 79 GRA 81
>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 = 87.5 bits (217), Expect = 9e-19
Identities = 47/241 (19%), Positives = 87/241 (36%), Gaps = 15/241 (6%)
Query: 97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQS 156
K L ++L+ + +VI+F + +V E+ + L+ K +
Sbjct: 258 EEKLELLLKLLKDE--------DEGRVIVFVRTKRLVEELAESLRKRG--FKVAAL---H 304
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
+ Q+E+ ++KF+ GE L+AT V GLDI ++ VI +D P V R+GRT
Sbjct: 305 GDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRT 364
Query: 217 GR-KRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTP 275
GR R G + +T+ E + + + + + AK P
Sbjct: 365 GRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEE 424
Query: 276 RIKCLHI-VVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKK 334
I +K K K++ G++ + + + +
Sbjct: 425 SDISDEIKKLKSSKKALLRGLGVRFTLSKLLANLGKEIPGAGDAVTIDPELERRSPNSAD 484
Query: 335 Q 335
Sbjct: 485 D 485
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 73.4 bits (181), Expect = 3e-14
Identities = 58/217 (26%), Positives = 94/217 (43%), Gaps = 34/217 (15%)
Query: 119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT 178
E T+ I+F R V E+ L + + G+ + Q ++ E +K+ G N
Sbjct: 244 EVTRSIVFVRTRERVHELAGWL--RKAGINCCYLEGE---MVQAKRNEAIKRLTDGRVNV 298
Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREAHNF 237
L+AT V G+DI ++ VI FD +S + R+GRTGR R G + L+ EAH+
Sbjct: 299 LVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV----EAHD- 353
Query: 238 QTSMQTCKSYVEKIINNKSIYANLAKNGPRMI----PAHVTPRIKCLHIVVKDRVTPAKP 293
+ + Y+E+ + R+I P P K K AK
Sbjct: 354 HLLLGKIERYIEEPLK------------ARVIDELRPKTKAPSEKKTGKPSKK--VLAKR 399
Query: 294 SKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAK 330
++KK KE EK K + + +++ GK+ K +
Sbjct: 400 AEKKEKEKEKPKVKKRHR-----DTKNIGKRRKPSGT 431
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 63.2 bits (154), Expect = 7e-11
Identities = 32/123 (26%), Positives = 54/123 (43%), Gaps = 11/123 (8%)
Query: 102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVT- 160
R + HA K +IFA+ + + + A V +G T
Sbjct: 268 RKIAAVRGLLLKHAR---GDKTLIFASDV-------EHAYEIAKLFLAPGIVEAITGETP 317
Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR 220
++E++ I+++FR G L+ V +EG+DI + D++I S +QRLGR R
Sbjct: 318 KEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPA 377
Query: 221 NGR 223
G+
Sbjct: 378 EGK 380
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 59.2 bits (144), Expect = 2e-09
Identities = 38/147 (25%), Positives = 69/147 (46%), Gaps = 20/147 (13%)
Query: 83 KLDINIMSSEYAWSHLKFI------RLREILESHFRLHAEKGETTKVIIFANYRVVVAEI 136
KL+I ++S + + + R+ E+++ H +IF N R +
Sbjct: 220 KLEIKVISPVEDLIYDEELWAALYERIAELVKKH----------RTTLIFTNTRSGAERL 269
Query: 137 FDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDL 196
LK L P + ++++ + E+ ++ + GE ++ATS E G+DIG+IDL
Sbjct: 270 AFRLKKLGPDIIEV----HHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDL 325
Query: 197 VICFDAQKSPIKMVQRLGRTGRKRNGR 223
VI + KS + +QR+GR G +
Sbjct: 326 VIQLGSPKSVNRFLQRIGRAGHRLGEV 352
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 56.8 bits (137), Expect = 9e-09
Identities = 35/98 (35%), Positives = 51/98 (52%), Gaps = 7/98 (7%)
Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTLI 180
+V++FAN + V I + L VK + Q SG V Q ++ + ++ FR G+ L+
Sbjct: 337 RVMVFANRKDEVRRIEERL------VKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLV 390
Query: 181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
AT V G+ I I VI F + P V R+GRTGR
Sbjct: 391 ATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGR 428
>gnl|CDD|213060 cd12091, FANCM_ID, insert domain of FANCM helicase and similar
proteins. FANCM and related proteins, like Mph1 and
Fml1, are DNA junction-specific helicases/translocases
that bind to and process perturbed replication forks and
intermediates of homologous recombination. FANCM
contains an N-terminal superfamily 2 helicase (SF2)
domain, although FANCM, in contrast to other members of
this family, does not exhibit DNA helicase activity. The
SF2 helicase domain is comprised of 3 structural
domains, the 2 generally conserved helicase domains and
a helical domain inserted between the two domains. FANCM
is a component of the Fanconi anaemia (FA) core complex.
FA is a rare genetic disease in humans that is
associated with progressive bone marrow failure, a
variety of developmental abnormalities, and a high
incidence of cancer. A key role of this complex is to
monoubiquitination of FANCD2 and FANCI during S-phase
and in response to DNA damage. The role of FANCM during
this process seems to be the recruitment of the complex
to chromatin.
Length = 122
Score = 51.5 bits (124), Expect = 3e-08
Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 1 MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
+ A+DK+ + + I+ DF + SLA A+E L+ +G+R FY+ L E++ E
Sbjct: 38 LQARDKFRANPPGNNEGQK---GSIEGDFALLISLAHAMELLLEHGIRPFYDYLKEIATE 94
Query: 61 DGSCPI-----LGKDNDLQNLLQQLK 81
S L + + + L+ +L+
Sbjct: 95 TKSKKSKSKKELANNPNFKELMDELE 120
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 54.1 bits (130), Expect = 6e-08
Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 7/99 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
T+ II+ N R V D L + M + V G + Q+++ IM++FR+G L
Sbjct: 268 TQAIIYCNTRRKV----DYLT--KKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVL 321
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
I T + G+D+ ++ LVI +D SP + R+GR+GR
Sbjct: 322 ITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGR 360
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 51.4 bits (124), Expect = 5e-07
Identities = 48/157 (30%), Positives = 74/157 (47%), Gaps = 16/157 (10%)
Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTG 217
E+ EI++ R GEF+ L+ ++ EGLD+ E+ LV DA K S ++Q +GR
Sbjct: 484 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAA 543
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRI 277
R NG+ VIL A SMQ E+ + N ++G + P + +I
Sbjct: 544 RNVNGK-VILY-----ADKITDSMQKAIDETER-RREIQMAYN-EEHG--ITPQTIKKKI 593
Query: 278 KCLHIVVKDRV-TPAKPSKKKPKENEKANKKSKKKLE 313
+ + + AK KK K ++K +K KKLE
Sbjct: 594 RDILDGEYEEDEYKAKIEKKASKMSKKELEKLIKKLE 630
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 50.2 bits (121), Expect = 1e-06
Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 15/100 (15%)
Query: 124 IIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGV-----TQQEQKEIMKKFRAGEFNT 178
++F N + E+ D L G S+ Q+++ +++ +F +
Sbjct: 246 VVFCNTKKECQEVADALN----------AQGFSALALHGDLEQRDRDQVLVRFANRSCSV 295
Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
L+AT V GLDI ++ VI ++ + P V R+GRTGR
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGR 335
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 49.1 bits (117), Expect = 3e-06
Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK- 219
Q +++ +++ + G + LIAT V GLD+ I LV+ +D V R+GRTGR
Sbjct: 281 QALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340
Query: 220 RNGRCVILLTQGRE 233
R GR +L + RE
Sbjct: 341 RAGR-ALLFVENRE 353
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 49.2 bits (117), Expect = 3e-06
Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 149 ASMFVGQS--SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSP 206
+ +F+ +S V+++++ + ++GE ++ATS E G+D+G +DLVI S
Sbjct: 299 SDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSV 358
Query: 207 IKMVQRLGRTGRKRNG 222
+QR+GR G + G
Sbjct: 359 ASGLQRIGRAGHQVGG 374
>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 = 47.4 bits (113), Expect = 6e-06
Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 10/117 (8%)
Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK--FRAGEFNTL 179
V I N E + LK P + + + + + +KE F+ E +
Sbjct: 220 SVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFT-EKDRAKKEAELLLEFKKSEKFVI 278
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPI-KMVQRLGRTGRK--RNGRCVILLTQGRE 233
+AT V E LDI +D++I + +PI ++QRLGR R +NG V ++T +
Sbjct: 279 VATQVIEASLDI-SVDVMI---TELAPIDSLIQRLGRLHRYGEKNGEEVYIITDAPD 331
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 47.8 bits (114), Expect = 6e-06
Identities = 22/58 (37%), Positives = 34/58 (58%)
Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
Q+E+ ++ +F+ G+ +IAT V GLD+ ++ VI FD V R+GRTGR
Sbjct: 413 QEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGR 470
>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 = 48.1 bits (115), Expect = 6e-06
Identities = 31/85 (36%), Positives = 45/85 (52%), Gaps = 11/85 (12%)
Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTG 217
E+ EI++ R GEF+ L+ ++ EGLD+ E+ LV DA K S ++Q +GR
Sbjct: 480 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAA 539
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQ 242
R NG+ VI+ A SMQ
Sbjct: 540 RNVNGK-VIMY-----ADKITDSMQ 558
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 47.3 bits (112), Expect = 1e-05
Identities = 41/152 (26%), Positives = 68/152 (44%), Gaps = 11/152 (7%)
Query: 117 KGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGE 175
+ E + ++F N + V V + LE + VG SG V Q++++ ++ +F+ G+
Sbjct: 254 RSEGARTMVFVNTKAFVER---VARTLE---RHGYRVGVLSGDVPQKKRESLLNRFQKGQ 307
Query: 176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAH 235
L+AT V GL I + V +D V R+GRT R I R A
Sbjct: 308 LEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYA- 366
Query: 236 NFQTSMQTCKSYVEKIINNKSIYANLAKNGPR 267
S+ ++Y+E+ I + + A L PR
Sbjct: 367 ---MSLPDIEAYIEQKIPVEPVTAELLTPLPR 395
>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 = 47.4 bits (113), Expect = 1e-05
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 3/88 (3%)
Query: 133 VAEIFDVLKPLEPMV-KASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDI 191
+ I + L +V +A + + +T+ E +E+M +F GEF L+ T++ E G+DI
Sbjct: 670 IESIEKLATQLRELVPEARIAIAHGQ-MTENELEEVMLEFYKGEFQVLVCTTIIETGIDI 728
Query: 192 GEIDLVICFDAQKSPIKMVQRL-GRTGR 218
+ +I A K + + +L GR GR
Sbjct: 729 PNANTIIIERADKFGLAQLYQLRGRVGR 756
>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 = 47.0 bits (112), Expect = 1e-05
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPI----KMVQR 212
+G+ ++E++ I +F+ GE +IAT+ E G+DIG +D VI A P QR
Sbjct: 346 AGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVI---AYGYPGVSVLSFRQR 402
Query: 213 LGRTGRKRNGRCVILLTQGREA 234
GR GR R ++L+ +
Sbjct: 403 AGRAGR-RGQESLVLVVLRSDP 423
>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 = 45.1 bits (107), Expect = 3e-05
Identities = 31/123 (25%), Positives = 50/123 (40%), Gaps = 12/123 (9%)
Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK--FRAGEFNTL 179
K+ I N E + LK P + + + + + +KE + E +
Sbjct: 224 KIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFT-EKDRAKKEAELLEEMKKNEKFVI 282
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPI-KMVQRLGRTGRK----RNGRCVILLTQGREA 234
+AT V E LDI D++I + +PI ++QRLGR R V ++T E
Sbjct: 283 VATQVIEASLDI-SADVMI---TELAPIDSLIQRLGRLHRYGRKNGENFEVYIITIAPEG 338
Query: 235 HNF 237
F
Sbjct: 339 KLF 341
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 43.0 bits (102), Expect = 2e-04
Identities = 32/98 (32%), Positives = 48/98 (48%), Gaps = 7/98 (7%)
Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTLI 180
+ IIFAN + EI+ L VG +G V Q+++ I+++F G+ + L+
Sbjct: 257 RAIIFANTKHRCEEIWGHLA------ADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILV 310
Query: 181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
AT V GL I + V +D V R+GRTGR
Sbjct: 311 ATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGR 348
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 42.5 bits (100), Expect = 3e-04
Identities = 23/87 (26%), Positives = 42/87 (48%)
Query: 160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK 219
+ +E++E+MK F GE ++AT V G+D+ + VI FD + + + ++GR R
Sbjct: 403 SMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRM 462
Query: 220 RNGRCVILLTQGREAHNFQTSMQTCKS 246
I+ + + F + KS
Sbjct: 463 GEKGTAIVFVNEEDRNLFPELVALLKS 489
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 42.0 bits (100), Expect = 5e-04
Identities = 30/71 (42%), Positives = 38/71 (53%), Gaps = 14/71 (19%)
Query: 166 EIMKKFRAGEFNTLIATSVG----EEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRT 216
EI++ R GEF+ L VG EGLDI E+ LV DA K S ++Q +GR
Sbjct: 487 EIIRDLRLGEFDVL----VGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA 542
Query: 217 GRKRNGRCVIL 227
R NG+ VIL
Sbjct: 543 ARNVNGK-VIL 552
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 41.7 bits (98), Expect = 5e-04
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
F++G+ L+AT + GLDI E+ V+ ++ P V R+GRTGR
Sbjct: 291 FKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGR 338
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 40.4 bits (95), Expect = 0.001
Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 4/87 (4%)
Query: 133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIG 192
+++ LK P + G+ + E++ +M++FR GE + L+AT+V E G+D+
Sbjct: 469 AEALYERLKKAFPKYNVGLLHGR---MKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP 525
Query: 193 EIDLVICFDAQKSPIKMVQRL-GRTGR 218
+++ DA++ + + +L GR GR
Sbjct: 526 NATVMVIEDAERFGLSQLHQLRGRVGR 552
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 39.5 bits (93), Expect = 0.003
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDI 191
E+++ LK P +K + G+ E+ +M+ F+ GE + L+AT+V E G+D+
Sbjct: 494 AEELYEELKSFLPELKVGLVHGRMKP---AEKDAVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 39.5 bits (93), Expect = 0.003
Identities = 20/52 (38%), Positives = 35/52 (67%)
Query: 166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
E+ +K + GE +++++ E G+DIG IDLV+ + KS +++QR+GR G
Sbjct: 331 EVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 39.6 bits (93), Expect = 0.003
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 133 VAEIFDVLKPLEPMV-KASMFV--GQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGL 189
V I + L +V +A + V GQ + ++E +E+M F GE++ L+ T++ E G+
Sbjct: 813 VESIEKKAERLRELVPEARIAVAHGQ---MRERELEEVMLDFYNGEYDVLVCTTIIETGI 869
Query: 190 DIGEIDLVICFDAQK 204
DI + +I A K
Sbjct: 870 DIPNANTIIIERADK 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 = 39.0 bits (91), Expect = 0.004
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 9/100 (9%)
Query: 123 VIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIAT 182
V+IF + ++ LK P + + Q +KE ++ FR G+ LI T
Sbjct: 308 VLIFFPEIETMEQVAAALKKKLPKETIASVHSED-----QHRKEKVEAFRDGKITLLITT 362
Query: 183 SVGEEGLDIGEIDLVICFDAQKSPIK---MVQRLGRTGRK 219
++ E G+ +D+ + A+ +VQ GR GR
Sbjct: 363 TILERGVTFPNVDVFV-LGAEHRVFTESALVQIAGRVGRS 401
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 39.0 bits (91), Expect = 0.004
Identities = 43/200 (21%), Positives = 79/200 (39%), Gaps = 30/200 (15%)
Query: 24 MIQRDFHVTHSLASA-LENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKP 82
+ V L SA L + L+ EV + CP + LK
Sbjct: 364 EALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDE--------PGLKR 415
Query: 83 KLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP 142
K +++ + E ++ K KV++ N E+++ LK
Sbjct: 416 KERVDVEDGPQEE---LIELISEEVKE------GK----KVLVIVNTVDRAIELYEKLKE 462
Query: 143 LEPMVKASMFVGQ-SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD 201
P K + + + +++++E+ K F+ E ++AT V E G+DI + D++I
Sbjct: 463 KGP--KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-DFDVLI--- 516
Query: 202 AQKSPIK-MVQRLGRTGRKR 220
+ +PI ++QR GR R
Sbjct: 517 TELAPIDSLIQRAGRVNRHG 536
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 36.7 bits (86), Expect = 0.024
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDI 191
E+ +M F+AGE + L+AT+V E G+D+
Sbjct: 518 AEKDAVMAAFKAGEIDILVATTVIEVGVDV 547
>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 = 36.0 bits (84), Expect = 0.034
Identities = 18/57 (31%), Positives = 29/57 (50%)
Query: 172 RAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILL 228
AG ++ TS + G+D G +DLVI + K +++QR GR+ + LL
Sbjct: 298 AAGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRALL 354
>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 = 35.5 bits (82), Expect = 0.057
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
+G ++++E+ + R GE + T+ E G+DI +D V+ + + Q+ GR
Sbjct: 311 AGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRA 370
Query: 217 GRKRNGRCVILL 228
GR+ G V+L+
Sbjct: 371 GRRGQGALVVLV 382
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 34.7 bits (80), Expect = 0.068
Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 12/119 (10%)
Query: 243 TCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKP-----SKKK 297
T KS ++ I S L+K ++ + + V K KK
Sbjct: 16 TQKSKLQPISYIYSNVLVLSKEI-------LSTFSEEENKVATTSTKKDKKEDKNNESKK 68
Query: 298 PKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKKQPMMTQSNDIRTCFENITKKKK 356
E +K KK KK+ +++G ++ K K + K KK P + D+ F I + +
Sbjct: 69 KSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAE 127
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 34.5 bits (80), Expect = 0.094
Identities = 36/123 (29%), Positives = 52/123 (42%), Gaps = 31/123 (25%)
Query: 133 VAEIFDVLKPLEPMVKASMFV----GQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEG 188
V EI V + L V + + + G S + +Q QK I+ AG ++AT++ E
Sbjct: 222 VGEIQRVQEQLASRVASDVLLCPLYGALS-LAEQ-QKAILPA-PAGRRKVVLATNIAETS 278
Query: 189 LDIGEIDLVI--------CFD-------------AQKSPIKMVQRLGRTGRKRNGRCVIL 227
L I I LV+ FD +Q S M QR GR GR G C+ L
Sbjct: 279 LTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQAS---MTQRAGRAGRLEPGICLHL 335
Query: 228 LTQ 230
++
Sbjct: 336 YSK 338
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 34.0 bits (78), Expect = 0.14
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 187 EGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGR 223
EG+D+ +D VI FD + S + +VQ +GR RK G+
Sbjct: 540 EGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGK 576
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 33.2 bits (76), Expect = 0.28
Identities = 33/146 (22%), Positives = 65/146 (44%), Gaps = 16/146 (10%)
Query: 99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
K+ + +++ F + KG + I+F R E+ D L +KA+ + +G
Sbjct: 419 KWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALT--GKGLKAAPY---HAG 473
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK------SPIKMVQR 212
+ +E+K + + F A E ++ T+ G+D ++ F++ S + Q
Sbjct: 474 LPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVI--FESLAMGIEWLSVREFQQM 531
Query: 213 LGRTGRK---RNGRCVILLTQGREAH 235
LGR GR G+ +L+ G++ H
Sbjct: 532 LGRAGRPDYHDRGKVYLLVEPGKKYH 557
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 33.2 bits (76), Expect = 0.28
Identities = 65/265 (24%), Positives = 86/265 (32%), Gaps = 85/265 (32%)
Query: 21 LDRMIQRD-------------FHVTH-----SLASALENLVTYGLRSFYNNLVEVSKEDG 62
L RMIQ D FH LA AL+ V LR ED
Sbjct: 101 LTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALD--VQSSLR-----------ED- 146
Query: 63 SCPILGKDNDLQNL-LQQLKPKLDINIMSSEYAWSHLKFIRLR-----EILESHFR---L 113
IL L L L P D ++ SE S IR + LE
Sbjct: 147 -LKILAMSATLDGERLSSLLP--DAPVVESE-GRSFPVEIRYLPLRGDQRLEDAVSRAVE 202
Query: 114 HAEKGETTKVIIF----ANYRVVVAEIFDVLKP---LEPMVKASMFVGQSSGVTQQEQKE 166
HA ET +++F A R V ++ + L + P+ Q
Sbjct: 203 HALASETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSL---------AAQDR 253
Query: 167 IMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI--------CFD-------------AQKS 205
+K G ++AT++ E L I I +VI FD +Q S
Sbjct: 254 AIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQAS 313
Query: 206 PIKMVQRLGRTGRKRNGRCVILLTQ 230
QR GR GR G C L ++
Sbjct: 314 ---ATQRAGRAGRLEPGVCYRLWSE 335
>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 = 32.7 bits (75), Expect = 0.35
Identities = 24/112 (21%), Positives = 50/112 (44%), Gaps = 10/112 (8%)
Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG 222
E++E++++F +G L+A +EG+DI + +P + +QR GR R G
Sbjct: 327 EREELLRQFESGLLQGLVAIRCLDEGVDIPATRTAYILASSSNPRQFIQRRGRVLRPHPG 386
Query: 223 R--------CVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGP 266
+ V+ T+ + + +S +++ + +A LA+N
Sbjct: 387 KNRATIYDFIVVPPTEADDL--DDNTFNVERSLLKRELKRFVEFAQLAENAG 436
>gnl|CDD|233953 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3, subtype
Dpsyc. This model describes a CRISPR-associated
putative DEAH-box helicase, or Cas3, of a subtype found
in Actinomyces naeslundii MG1, Geobacter sulfurreducens
PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea
psychrophila. This protein includes both DEAH and HD
motifs [Mobile and extrachromosomal element functions,
Other].
Length = 862
Score = 32.6 bits (74), Expect = 0.46
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIK-MVQRLGRTGR 218
++ATS GE G D+ + D ++ P + +VQR GR R
Sbjct: 352 VVATSTGEVGADL-DFDHLVT---DLCPFESLVQRFGRVNR 388
>gnl|CDD|153159 cd04887, ACT_MalLac-Enz, ACT_MalLac-Enz CD includes the N-terminal
ACT domain of putative NAD-dependent malic enzyme 1,
Bacillus subtilis YqkI and related domains. The
ACT_MalLac-Enz CD includes the N-terminal ACT domain of
putative NAD-dependent malic enzyme 1, Bacillus subtilis
YqkI, a malolactic enzyme (MalLac-Enz) which converts
malate to lactate, and other related ACT domains. The
yqkJ product is predicted to convert malate directly to
lactate, as opposed to related malic enzymes that
convert malate to pyruvate. Members of this CD belong to
the superfamily of ACT regulatory domains.
Length = 74
Score = 29.2 bits (66), Expect = 0.64
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 180 IATSVGEEGLDIGEIDLV 197
+ T++GE G DIG IDLV
Sbjct: 16 VTTAIGEAGGDIGAIDLV 33
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 31.9 bits (73), Expect = 0.70
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 156 SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGR 215
+G++ +E++ + + F E ++AT+ G+D ++ VI +D S Q GR
Sbjct: 261 HAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGR 320
Query: 216 TGR 218
GR
Sbjct: 321 AGR 323
>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 = 31.6 bits (72), Expect = 0.78
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 13/80 (16%)
Query: 160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDL--VICFD----------AQKSPI 207
+ + ++ +F G+ + LI T + +G + L V+ D A++
Sbjct: 297 RKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQ 356
Query: 208 KMVQRLGRTGR-KRNGRCVI 226
+ Q GR GR + G+ +I
Sbjct: 357 LLTQVAGRAGRAEDPGQVII 376
>gnl|CDD|107110 PHA02088, PHA02088, hypothetical protein.
Length = 125
Score = 30.1 bits (67), Expect = 0.80
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 39 LENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLL--QQLKPKLDI 86
R Y L ++ K+D + P + +L ++L Q K + I
Sbjct: 73 FSECKGINFRKAYKMLEQIRKDDIANPDFDQTGNLMSILYLSQAKIEKTI 122
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 31.7 bits (72), Expect = 0.88
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 14/60 (23%)
Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMV-QRLGRTGR-KRNGR--------CVILL 228
L+AT V E+ LD+ + D +I Q P+ ++ QRLGR R R R +LL
Sbjct: 625 LVATQVVEQSLDL-DFDWLI---TQLCPVDLLFQRLGRLHRHHRKYRPAGFEIPVATVLL 680
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 31.6 bits (72), Expect = 0.95
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRL-GRTGRK 219
++E + +M F FN L+ T++ E G+DI + +I A + + +L GR GR
Sbjct: 847 ERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRS 906
Query: 220 RNGRCVILLT 229
+ LLT
Sbjct: 907 HHQAYAWLLT 916
>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
Length = 470
Score = 31.2 bits (71), Expect = 1.00
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 10/82 (12%)
Query: 285 KDRVTPAKPSKKKPKENEKANKKSKKKLETD---------GNSEPAGKQNKTNAKKTKKQ 335
++ V K K+ K +K NKKSKK ++ D N E KQN KK KK+
Sbjct: 7 ENEVKQQKQQNKQ-KGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKK 65
Query: 336 PMMTQSNDIRTCFENITKKKKT 357
+ ++ +
Sbjct: 66 KKKKNLGEAYDLAYDLPVVWSS 87
>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 = 31.3 bits (71), Expect = 1.1
Identities = 16/62 (25%), Positives = 29/62 (46%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
+G+ + ++ KF+ E ++AT G++ ++ VI + KS Q GR
Sbjct: 258 AGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRA 317
Query: 217 GR 218
GR
Sbjct: 318 GR 319
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 31.2 bits (70), Expect = 1.1
Identities = 47/182 (25%), Positives = 76/182 (41%), Gaps = 24/182 (13%)
Query: 47 LRSFYNN--LVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLR 104
LR N+ LV+ E I+ + ++ KP + ++ K L
Sbjct: 648 LRQICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKG---------KLQALD 698
Query: 105 EILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQ 164
E+L +L E G KV+IF+ + V+ + D LK L K G + +
Sbjct: 699 ELLLD--KLLEE-GHYHKVLIFSQFTPVLDLLEDYLKALGI--KYVRLDGS---TPAKRR 750
Query: 165 KEIMKKFRAGEFNT--LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ---RLGRTGRK 219
+E++ +F A E L++ G GL++ D VI FD +P +Q R R G+K
Sbjct: 751 QELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQK 810
Query: 220 RN 221
R
Sbjct: 811 RP 812
>gnl|CDD|187827 cd09696, Cas3_I, CRISPR/Cas system-associated protein Cas3;
Distinct Cas3 family with HD domain fused to C-termus of
Helicase domain. 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; DNA helicase Cas3; This protein includes
both DEAH and HD motifs; signature gene for Type I.
Length = 843
Score = 31.1 bits (70), Expect = 1.2
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIK-MVQRLGRTGR 218
L+ TS GE G++I D ++C +P + M QR GR R
Sbjct: 339 LVCTSAGEVGVNI-SADHLVC---DLAPFESMQQRFGRVNR 375
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 30.1 bits (69), Expect = 2.1
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 291 AKPSKKKPKENEKANKKSKKKLETDGNSEPAGK 323
A K P + A K S+K + SE GK
Sbjct: 825 ADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 29.9 bits (67), Expect = 2.3
Identities = 15/45 (33%), Positives = 18/45 (40%), Gaps = 8/45 (17%)
Query: 290 PAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKK 334
AK +KK K+ K K+ KK A K K AK K
Sbjct: 248 AAKKAKKTAKKALKKAAKAVKK--------AAKKAAKAAAKAAKG 284
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 30.2 bits (68), Expect = 2.4
Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 14/91 (15%)
Query: 123 VIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIAT 182
+++F +Y ++ ++D+L L P + + Q G+ K I K+F GE L+ T
Sbjct: 678 LVLFTSYEMLHM-VYDMLNEL-PEFEGYEVLAQ--GINGSRAK-IKKRFNNGEKAILLGT 732
Query: 183 SVGEEGLDIGEIDLVICFDAQKSPIKMVQRL 213
S EG+D F ++ RL
Sbjct: 733 SSFWEGVD---------FPGNGLVCLVIPRL 754
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 30.2 bits (68), Expect = 2.5
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 3/62 (4%)
Query: 289 TPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKKQPMMTQSNDIRTCF 348
TP P +KK K +K+ K +T K K + P+ T S +
Sbjct: 742 TPKTPYEKKTKAKKKSASTKGKAAKTVKKK---SKAKSKKTTKKRAGPLYTPSPALAAMI 798
Query: 349 EN 350
Sbjct: 799 GA 800
>gnl|CDD|204792 pfam11947, DUF3464, Protein of unknown function (DUF3464). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 137 to 196
amino acids in length.
Length = 149
Score = 28.8 bits (65), Expect = 2.6
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 291 AKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKKQ 335
A K+ P E +++ KK K L ++ KQ K +K+ +
Sbjct: 2 ASSRKRLPFEPKRSRKKGVKALRKAAVAKSKDKQKKPKSKRAASE 46
>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62.
Length = 217
Score = 29.4 bits (66), Expect = 2.7
Identities = 11/47 (23%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 291 AKPSKKKPKENEKANKKSKKKLE-TDGNSEPAGKQNKTNAKKTKKQP 336
+ K N + K KL +E K + K+ KK+P
Sbjct: 27 KGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKP 73
>gnl|CDD|200066 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
type. This model finds organelle (chloroplast and
mitochondrial) ribosomal protein S4 as well as bacterial
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 200
Score = 29.2 bits (66), Expect = 2.8
Identities = 12/37 (32%), Positives = 15/37 (40%)
Query: 249 EKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVK 285
EK + NL NG R IP+ + K L V
Sbjct: 141 EKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVL 177
>gnl|CDD|224223 COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48
and related proteins) [Coenzyme transport and
metabolism].
Length = 360
Score = 29.6 bits (67), Expect = 2.9
Identities = 19/64 (29%), Positives = 22/64 (34%), Gaps = 15/64 (23%)
Query: 19 RDLDRMIQR----DFHVTHSLASALENLVTYG--LRSFY------NNLVEVSKEDGSCPI 66
DL R QR FH A E+ VT +F L EV D S
Sbjct: 2 ADLRRAAQRRLPKAFHYIDGGA---EDEVTLRRNREAFEDIALRPRVLPEVDDIDLSTTF 58
Query: 67 LGKD 70
LG+
Sbjct: 59 LGQK 62
>gnl|CDD|237612 PRK14108, PRK14108, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 986
Score = 30.0 bits (68), Expect = 3.1
Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 23/66 (34%)
Query: 168 MKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPI-----------KMVQRLGRT 216
M K AGE N +S +IDL++ FD + ++ +RL R
Sbjct: 192 MGKLGAGELNY---SS---------DIDLIVFFDETAPILGDPIEAQPFFVRLTRRLVRI 239
Query: 217 GRKRNG 222
++R G
Sbjct: 240 LQERTG 245
>gnl|CDD|224738 COG1825, RplY, Ribosomal protein L25 (general stress protein Ctc)
[Translation, ribosomal structure and biogenesis].
Length = 93
Score = 27.2 bits (61), Expect = 4.7
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIK 208
+ E K R ++T+I V G+ V+ D Q+ P+
Sbjct: 43 DHHEFAKALRKLGYSTVITLEVD------GKEIKVLVKDVQRHPLT 82
>gnl|CDD|215318 PLN02581, PLN02581, red chlorophyll catabolite reductase.
Length = 267
Score = 28.5 bits (64), Expect = 5.4
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 245 KSYVEK---IINNKSIYANLAKNGPRMIPAHVTPRI 277
++Y+EK +I +KS+ +L+ N PR+ V R+
Sbjct: 222 RAYLEKRDRMIRSKSVEVDLSSNMPRLFGQEVADRV 257
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 28.9 bits (65), Expect = 5.6
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 153 VGQSSGVTQQEQKEIMKKFRAGEFNTLIATS 183
V S + +E++E +++ +G+F+ LI TS
Sbjct: 159 VVYHSALPTKEKEEALERIESGDFDILITTS 189
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.7 bits (65), Expect = 6.2
Identities = 8/28 (28%), Positives = 20/28 (71%)
Query: 156 SSGVTQQEQKEIMKKFRAGEFNTLIATS 183
S + ++E++E +++ + G+F+ L+ TS
Sbjct: 160 HSSLKKKEKEEFLERLKEGDFDILVTTS 187
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 28.4 bits (64), Expect = 6.7
Identities = 33/113 (29%), Positives = 51/113 (45%), Gaps = 10/113 (8%)
Query: 115 AEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG 174
A+KGE T ++F Y ++++LK + V +V SG E + MKK G
Sbjct: 341 AKKGENT-FVMF-KYVEHGKPLYEMLKKVYDKV---YYV---SGEVDTEDRNEMKKIAEG 392
Query: 175 EFNTLIATSVG--EEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCV 225
+I S G G+ I + VI KS I ++Q +GR RK + +
Sbjct: 393 GKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSI 445
>gnl|CDD|130427 TIGR01360, aden_kin_iso1, adenylate kinase, isozyme 1 subfamily.
Members of this family are adenylate kinase, EC 2.7.4.3.
This clade is found only in eukaryotes and includes
human adenylate kinase isozyme 1 (myokinase). Within the
adenylate kinase superfamily, this set appears
specifically closely related to a subfamily of
eukaryotic UMP-CMP kinases (TIGR01359), rather than to
the large clade of bacterial, archaeal, and eukaryotic
adenylate kinase family members in TIGR01351.
Length = 188
Score = 27.9 bits (62), Expect = 7.8
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 185 GEE-GLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
GEE IG LV+ FD S MV+RL +
Sbjct: 97 GEEFERRIGPPTLVLYFDC--SEDTMVKRLLKRAE 129
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 28.6 bits (64), Expect = 8.0
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATS 183
S + +E+KE M++ G+F+ LI T+
Sbjct: 160 SRLPTKEKKEFMERIENGDFDILITTT 186
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
0.316 0.132 0.369
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: 19,221,041
Number of extensions: 1812415
Number of successful extensions: 2414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2291
Number of HSP's successfully gapped: 151
Length of query: 395
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 296
Effective length of database: 6,546,556
Effective search space: 1937780576
Effective search space used: 1937780576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.8 bits)