RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy576
(159 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 = 137 bits (346), Expect = 8e-39
Identities = 46/121 (38%), Positives = 70/121 (57%), Gaps = 3/121 (2%)
Query: 42 LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
LL E V+VFV++K +EL L G V +H D Q++RD + F+ G + +
Sbjct: 267 LLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRV 326
Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ-DAPLL 158
L+ T++ RG+D V V+NYD P Y+HRIGR GR GR+G A++F T++ + L
Sbjct: 327 LVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKL 386
Query: 159 R 159
+
Sbjct: 387 K 387
>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 = 121 bits (307), Expect = 2e-36
Identities = 45/102 (44%), Positives = 65/102 (63%)
Query: 48 PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
VL+F SK+ EL L GI V +H D +Q++R+ V++ FR G I +L+ T+++
Sbjct: 30 KVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIA 89
Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF 149
RGID V +V+NYD P S SY+ RIGRAGR G++G A+
Sbjct: 90 RGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 106 bits (266), Expect = 6e-28
Identities = 47/110 (42%), Positives = 69/110 (62%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
+++ ++ + L ++ V +H D QK RD ++R FR+G +LITT+LL RG
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330
Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
ID + V LV+NYD P+S +YIHRIGR+GR GR+G A+ F T D L+
Sbjct: 331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLK 380
>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 = 96.8 bits (242), Expect = 3e-27
Identities = 35/77 (45%), Positives = 49/77 (63%)
Query: 65 ELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP 124
L GI V +H +Q++R+ ++ FR G+ +L+ T++ GRGID V LV+NYD P
Sbjct: 2 LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLP 61
Query: 125 SSAISYIHRIGRAGRGG 141
+ SYI RIGRAGR G
Sbjct: 62 WNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 96.9 bits (242), Expect = 4e-27
Identities = 35/82 (42%), Positives = 50/82 (60%)
Query: 60 QELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV 119
+EL L GI V +H +Q++R+ ++ F G+I +L+ T++ RG+D V LV+
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 120 NYDFPSSAISYIHRIGRAGRGG 141
YD P S SYI RIGRAGR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 103 bits (259), Expect = 2e-26
Identities = 44/105 (41%), Positives = 67/105 (63%)
Query: 47 PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL 106
+L+FV++K+ A L EL DG IH D+ Q++R V+ F+TG+ I+I T++
Sbjct: 378 DKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVA 437
Query: 107 GRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT 151
RG+D + V+ V+N+DFP+ Y+HRIGR GR G +G + TF T
Sbjct: 438 SRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLT 482
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 96.9 bits (242), Expect = 2e-24
Identities = 43/108 (39%), Positives = 64/108 (59%)
Query: 51 VFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI 110
VFV+++ER EL L GIN + + Q +R+ ++ GR+ +L+ T++ RGI
Sbjct: 250 VFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGI 309
Query: 111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL 158
D V V+N+D P SA +Y+HRIGR GR GR+G A++ D LL
Sbjct: 310 DIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLL 357
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 91.4 bits (227), Expect = 4e-22
Identities = 43/112 (38%), Positives = 69/112 (61%), Gaps = 1/112 (0%)
Query: 47 PPVLVFVQSKERAQELYNEL-IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
PP +VFV S+ A L N + + G+ IH +++ K+R V++SF G + +++ T +
Sbjct: 368 PPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGV 427
Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL 157
LGRG+D VR V+ +D P++ YIH+IGRA R G +G A+ F ++D L
Sbjct: 428 LGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNL 479
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 89.9 bits (224), Expect = 9e-22
Identities = 35/116 (30%), Positives = 60/116 (51%), Gaps = 2/116 (1%)
Query: 42 LLGIEPPV--LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
LL P +VF +K+ QE+ + L G + +H D Q+ RD V+ F +
Sbjct: 236 LLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSV 295
Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
L+ T++ RG+D + + V+NY+ ++HRIGR GR G +G A++ ++
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEM 351
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 86.9 bits (215), Expect = 1e-20
Identities = 38/107 (35%), Positives = 59/107 (55%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
V+VF K+ + + L+ DGIN + D Q +R + FR G+I +L+ T++ GR
Sbjct: 338 VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGR 397
Query: 109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
GI + V+N+ P Y+HRIGR GR G G +++F + DA
Sbjct: 398 GIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDA 444
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 86.1 bits (213), Expect = 2e-20
Identities = 43/110 (39%), Positives = 65/110 (59%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
++FV++K E+ L +G N ++ D Q R+ + + GR+ ILI T++ RG
Sbjct: 249 IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARG 308
Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
+D + LVVNYD P + SY+HRIGR GR GR G+A+ F ++ LLR
Sbjct: 309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLR 358
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 83.7 bits (207), Expect = 1e-19
Identities = 41/111 (36%), Positives = 63/111 (56%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
VLVF ++K A L +L DGI IH +++Q R + F++G I +L+ T++ R
Sbjct: 248 VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAAR 307
Query: 109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
G+D + VVNY+ P+ Y+HRIGR GR G+A++ + LLR
Sbjct: 308 GLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLR 358
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 75.4 bits (185), Expect = 1e-16
Identities = 43/122 (35%), Positives = 68/122 (55%), Gaps = 5/122 (4%)
Query: 33 PVQAQDETILLGI-----EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDN 87
P + +T+LLG+ +VFV +K + + L G V V+ D QK+R++
Sbjct: 239 PADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRES 298
Query: 88 VVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAV 147
++ F+ G++ IL+ T++ RG+ V+ V NYD P A Y+HRIGR R G EG A+
Sbjct: 299 LLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAI 358
Query: 148 TF 149
+F
Sbjct: 359 SF 360
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 72.3 bits (178), Expect = 1e-15
Identities = 35/100 (35%), Positives = 55/100 (55%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
++F +K R +E++ L DG V ++ D QK+R ++ F G + IL+ T++ RG
Sbjct: 259 IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARG 318
Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF 149
+ V V NYD P Y+HRIGR GR G G +++
Sbjct: 319 LHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 70.8 bits (174), Expect = 5e-15
Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 10/116 (8%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVI---HSDR------TQKQRDNVVRSFRTGRIWI 99
V+VF + ++ A+E+ N L GI V + R +QK++ ++ FR G +
Sbjct: 369 VIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNV 428
Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
L+ T + G+D V LV+ Y+ S I I R GR GR R+G+ V T+
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-KRKGRVVVLVTEGTR 483
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 70.4 bits (173), Expect = 6e-15
Identities = 33/112 (29%), Positives = 60/112 (53%)
Query: 48 PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
+++ ++++ +EL L +GI+ H+ + ++R+ V ++F I +++ T G
Sbjct: 232 SGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFG 291
Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
GID VR V++YD P S SY GRAGR G +A+ ++ +D R
Sbjct: 292 MGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343
>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 = 62.8 bits (153), Expect = 3e-12
Identities = 33/110 (30%), Positives = 55/110 (50%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
+++ S+++ +EL L GI+ H+ + K R F + +++ T G G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287
Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
ID VR V++YD P + SY GRAGR G +A+ ++ D LL+
Sbjct: 288 IDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLK 337
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 61.4 bits (150), Expect = 1e-11
Identities = 36/120 (30%), Positives = 61/120 (50%), Gaps = 11/120 (9%)
Query: 43 LGIEPP--VLVFVQSKERAQELYNELIYDGINVD--VIHSDR------TQKQRDNVVRSF 92
LG P ++VF Q ++ A+++ + L +GI V + + +QK++ ++ F
Sbjct: 360 LGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKF 419
Query: 93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK 152
R G +L++T + G+D +V LV+ Y+ S I I R GR GR EG+ V K
Sbjct: 420 RAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGR-QEEGRVVVLIAK 478
>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 = 59.0 bits (143), Expect = 6e-11
Identities = 32/110 (29%), Positives = 53/110 (48%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
+++ S+++++++ L GI H+ RD+V F+ I +++ T G G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
I+ VR V++Y P S SY GRAGR G + F+ D LR
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLR 339
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 55.5 bits (134), Expect = 9e-10
Identities = 32/110 (29%), Positives = 54/110 (49%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
+++ S+ + ++ L GI+ H+ R +V +F+ + I++ T G G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299
Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
I+ VR VV++D P + SY GRAGR G +A+ F+ D LR
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 54.2 bits (131), Expect = 3e-09
Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 1/97 (1%)
Query: 48 PVLVFVQSKERAQELYNELIY-DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL 106
L+F ++ A+ L L ++V H +++ R V + G + ++ T L
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314
Query: 107 GRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE 143
GID + LV+ P S ++ RIGRAG E
Sbjct: 315 ELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGE 351
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 54.0 bits (130), Expect = 4e-09
Identities = 28/106 (26%), Positives = 52/106 (49%), Gaps = 3/106 (2%)
Query: 48 PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
L+F E A E+ + GI V+ I + +++R+ ++ FRTG I +L+T ++L
Sbjct: 285 KTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLD 343
Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGR--GGREGKAVTFFT 151
G+D +++ S +I R+GR R G+E ++
Sbjct: 344 EGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALDYS 389
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 36/104 (34%), Positives = 50/104 (48%), Gaps = 6/104 (5%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
VLV +K+ A++L + L GI V +HS+ +R ++R R G +L+ LL
Sbjct: 445 VLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE 504
Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGREGKAV 147
G+D V LV D F S S I IGRA R GK +
Sbjct: 505 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN-GKVI 547
>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 = 47.8 bits (114), Expect = 4e-07
Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 13/101 (12%)
Query: 48 PVLVFVQSKERAQELYNELI--YDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
PVL+F E +++ L + +HS + R V +FR G+I +LITT +
Sbjct: 307 PVLIFFPEIETMEQVAAALKKKLPKETIASVHS--EDQHRKEKVEAFRDGKITLLITTTI 364
Query: 106 LGRGIDFRTVRLVV----NYDFPSSAISYIHRIGRAGRGGR 142
L RG+ F V + V + F SA+ I AGR GR
Sbjct: 365 LERGVTFPNVDVFVLGAEHRVFTESALVQI-----AGRVGR 400
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 46.8 bits (112), Expect = 9e-07
Identities = 37/104 (35%), Positives = 49/104 (47%), Gaps = 6/104 (5%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
VLV +K+ A++L L GI V +HSD +R ++R R G +L+ LL
Sbjct: 449 VLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508
Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGREGKAV 147
G+D V LV D F S S I IGRA R GK +
Sbjct: 509 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN-GKVI 551
>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 = 45.5 bits (108), Expect = 3e-06
Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 9/105 (8%)
Query: 49 VLVFVQSKERAQELYNELI-----YDGINVDVIHSDR---TQKQRDNVVRSFRTGRIWIL 100
LVF +S+++ + LY G +D + + R +++R + F+ G + +
Sbjct: 309 TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGV 368
Query: 101 ITTELLGRGIDFRTVRLVVNYDFPS-SAISYIHRIGRAGRGGREG 144
I T L GID ++ V+ Y +P S +S+ R GRAGR G+E
Sbjct: 369 IATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQES 413
>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 = 44.3 bits (105), Expect = 8e-06
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 14/86 (16%)
Query: 73 VDVIHSD--RTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV---------NY 121
+ I SD + + ++ F G+ ILI T+++ +G F V LV +
Sbjct: 287 IARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSP 346
Query: 122 DFPSS--AISYIHRI-GRAGRGGREG 144
DF ++ + ++ GRAGR G
Sbjct: 347 DFRAAERGFQLLTQVAGRAGRAEDPG 372
>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 = 42.4 bits (100), Expect = 3e-05
Identities = 22/101 (21%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 48 PVLVFVQSKERAQELYNELIYDGIN--VDVIHSDRTQKQRDN----VVRSFRTGRIWILI 101
+ + V + +RAQE Y +L + + ++HS T+K R ++ + ++++
Sbjct: 224 KIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIV 283
Query: 102 TTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGR 142
T+++ +D ++ + S I R+GR R GR
Sbjct: 284 ATQVIEASLDISADVMITE---LAPIDSLIQRLGRLHRYGR 321
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 42.3 bits (100), Expect = 4e-05
Identities = 25/92 (27%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 59 AQELYNEL--IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVR 116
A+ LY L + NV ++H +++ V+ FR G + IL+ T ++ G+D
Sbjct: 469 AEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNAT 528
Query: 117 LVVNYDFPSSAISYIHRI-GRAGRGGREGKAV 147
++V D +S +H++ GR GRG + +
Sbjct: 529 VMVIEDAERFGLSQLHQLRGRVGRGDHQSYCL 560
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 42.1 bits (99), Expect = 5e-05
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 12/100 (12%)
Query: 50 LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
+VF S+ R EL + L G+ H+ K+R +V R+F + ++TT L G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503
Query: 110 IDFRTVRLVVNYDFPSSAI--------SYIHRIGRAGRGG 141
+DF +++ F S A+ + +GRAGR
Sbjct: 504 VDFPASQVI----FESLAMGIEWLSVREFQQMLGRAGRPD 539
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 41.7 bits (98), Expect = 6e-05
Identities = 30/107 (28%), Positives = 50/107 (46%), Gaps = 15/107 (14%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT----GRIWILITTE 104
VLV V + +RA ELY +L G V ++HS T K R+ R + +I++ T+
Sbjct: 443 VLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ 502
Query: 105 LLGRGIDFRTVRLVVNYDF----PSSAISYIHRIGRAGRGGREGKAV 147
++ G+D +++D + S I R GR R G++
Sbjct: 503 VIEAGVD-------IDFDVLITELAPIDSLIQRAGRVNRHGKKENGK 542
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 41.0 bits (96), Expect = 1e-04
Identities = 33/127 (25%), Positives = 53/127 (41%), Gaps = 35/127 (27%)
Query: 49 VLVFVQSKERAQELYNELI------------------YDGINVDVI-------HSDRTQK 83
VLVFV S++ A++ LI YD +++ H+ + +
Sbjct: 239 VLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNE 298
Query: 84 QRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD---FPSSAISYI------HRI 134
QR + FR I +++ T L G++ RLV+ D + + I Y+ I
Sbjct: 299 QRRFIEEMFRNRYIKVIVATPTLAAGVNL-PARLVIVRDITRYGNGGIRYLSNMEIKQMI 357
Query: 135 GRAGRGG 141
GRAGR G
Sbjct: 358 GRAGRPG 364
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 48 PVLVFVQSKERAQELYNELIYDG--INVDVIHSDRTQKQRDN----VVRSFRTGRIWILI 101
V + V + +RAQE Y +L G + +IHS T+K R ++ F+ ++++
Sbjct: 220 SVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIV 279
Query: 102 TTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGR 142
T+++ +D ++ + S I R+GR R G
Sbjct: 280 ATQVIEASLDISVDVMITE---LAPIDSLIQRLGRLHRYGE 317
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 40.3 bits (94), Expect = 2e-04
Identities = 24/78 (30%), Positives = 35/78 (44%)
Query: 77 HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGR 136
H QR V + + I I+ T G GI+ VR V+++ P S Y GR
Sbjct: 711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGR 770
Query: 137 AGRGGREGKAVTFFTKQD 154
AGR G+ V +++ D
Sbjct: 771 AGRDGQRSSCVLYYSYSD 788
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 39.4 bits (93), Expect = 4e-04
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 14/87 (16%)
Query: 75 VIHSD--RTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV---------NYDF 123
I D R + + ++ F G ILI T++L +G DF V LV + DF
Sbjct: 457 RIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDF 516
Query: 124 PSS--AISYIHRI-GRAGRGGREGKAV 147
+S + ++ GRAGR + G+ +
Sbjct: 517 RASERTFQLLTQVAGRAGRAEKPGEVL 543
Score = 27.4 bits (62), Expect = 4.3
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 70 GINVDVIHSDRTQKQRDNVVRSFRTGRIWILI 101
G V V+HS + +R + R + G ++I
Sbjct: 215 GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVI 246
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 39.1 bits (92), Expect = 4e-04
Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 9/92 (9%)
Query: 59 AQELYNEL--IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF--RT 114
A+ELY EL + V ++H ++D V+ +F+ G I IL+ T ++ G+D T
Sbjct: 494 AEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNAT 553
Query: 115 VRLVVNYD-FPSSAISYIHRI-GRAGRGGREG 144
V ++ N + F ++ +H++ GR GRG +
Sbjct: 554 VMVIENAERF---GLAQLHQLRGRVGRGDLQS 582
>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 = 38.6 bits (90), Expect = 7e-04
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 90 RSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF 149
R+ R G + + TT L G+D + VV FP + S + GRAGR G+ V
Sbjct: 323 RALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVV-- 380
Query: 150 FTKQDAPL 157
+D PL
Sbjct: 381 LVARDDPL 388
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 38.8 bits (90), Expect = 7e-04
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 77 HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGR 136
H +++QR ++ ++G + ++ T L GID V LV+ P S S + RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
Query: 137 AG 138
AG
Sbjct: 368 AG 369
>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 = 38.3 bits (90), Expect = 9e-04
Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 9/105 (8%)
Query: 50 LVFVQSKERAQELYNELIYDGINVD---VI---HSDRTQKQRDNVVRSFRTGRIWILITT 103
LVF ++ +A+ + L N + I H ++QR V + GR+ ++ T
Sbjct: 251 LVFTNTRSQAELWFQALWE--ANPEFALPIALHHGSLDREQRRWVEAAMAAGRLRAVVCT 308
Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAG-RGGREGKAV 147
L G+DF V LV+ P + R GR+ R G +A+
Sbjct: 309 SSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRAL 353
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 36.4 bits (85), Expect = 0.003
Identities = 27/88 (30%), Positives = 38/88 (43%), Gaps = 13/88 (14%)
Query: 50 LVFVQS---KERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-- 104
L+FV S KE A+EL L GIN ++ S +K F G + +L+
Sbjct: 332 LIFVPSDKGKEYAEELAEYLEDLGINAELAISGFERKFEK-----FEEGEVDVLVGVASY 386
Query: 105 --LLGRGIDF-RTVRLVVNYDFPSSAIS 129
+L RGID +R + Y P S
Sbjct: 387 YGVLVRGIDLPERIRYAIFYGVPKFKFS 414
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 35.9 bits (82), Expect = 0.006
Identities = 24/107 (22%), Positives = 39/107 (36%), Gaps = 8/107 (7%)
Query: 38 DETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR- 96
D+ + G VL+F Q L + L GI + K+R ++ F
Sbjct: 703 DKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEE 762
Query: 97 -IWILITTELLGRGIDFRTVRLVV------NYDFPSSAISYIHRIGR 136
L++ + G G++ V+ N AI HRIG+
Sbjct: 763 EKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQ 809
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 35.8 bits (83), Expect = 0.007
Identities = 27/87 (31%), Positives = 41/87 (47%), Gaps = 14/87 (16%)
Query: 75 VIHSDRTQKQRDN--VVRSFRTGRIWILITTELLGRGIDFRTVRLVV---------NYDF 123
I SD T+++ ++ F G ILI T+++ +G DF V LV + DF
Sbjct: 511 RIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDF 570
Query: 124 PSS---AISYIHRIGRAGRGGREGKAV 147
+S + GRAGR G+ G+ V
Sbjct: 571 RASERTFQLLMQVAGRAGRAGKPGEVV 597
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 33.3 bits (77), Expect = 0.023
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
VLV S +++ L + + + + + R+ ++ F+ G+ IL
Sbjct: 12 VLVLFPSYSLLEQVAELLASELLEKGIELLVQGEGSREKLLERFKKGKGAILFGVGSFWE 71
Query: 109 GIDF--RTVRLVV 119
GIDF +RLV+
Sbjct: 72 GIDFPGDALRLVI 84
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 32.7 bits (75), Expect = 0.066
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 13/89 (14%)
Query: 49 VLVFVQS---KERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE- 104
L+FV +E+A+EL L GIN ++IH+++ + + F G + +L+
Sbjct: 338 GLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKEEA-----LEDFEEGEVDVLVGVAS 392
Query: 105 ---LLGRGIDF-RTVRLVVNYDFPSSAIS 129
+L RG+D +R V Y P
Sbjct: 393 YYGVLVRGLDLPHRIRYAVFYGVPKFRFR 421
>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 = 32.5 bits (74), Expect = 0.087
Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 12/85 (14%)
Query: 49 VLVFVQS---KERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE- 104
+V+V KE+A+E+ L G+ H+ + ++ F G I +LI
Sbjct: 329 GIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPKE----DYEKFAEGEIDVLIGVAS 384
Query: 105 ---LLGRGIDF-RTVRLVVNYDFPS 125
L RG+D VR V P
Sbjct: 385 YYGTLVRGLDLPERVRYAVFLGVPK 409
>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 = 32.3 bits (74), Expect = 0.11
Identities = 19/95 (20%), Positives = 44/95 (46%), Gaps = 2/95 (2%)
Query: 53 VQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF 112
++S E+ EL+ + + + H T+ + + V+ F G +L+ T ++ GID
Sbjct: 670 IESIEKLATQLRELVPE-ARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDI 728
Query: 113 RTVRLVVNYDFPSSAISYIHRI-GRAGRGGREGKA 146
++ ++ ++++ GR GR ++ A
Sbjct: 729 PNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYA 763
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 31.8 bits (72), Expect = 0.14
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 13/88 (14%)
Query: 50 LVFV---QSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-- 104
L+FV + E+A+E+ L+ DG ++++ + + F G I LI
Sbjct: 334 LIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAKNKKGFDL-----FEEGEIDYLIGVATY 388
Query: 105 --LLGRGIDF-RTVRLVVNYDFPSSAIS 129
L RG+D +R V Y P
Sbjct: 389 YGTLVRGLDLPERIRFAVFYGVPKFRFR 416
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 31.7 bits (73), Expect = 0.15
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 59 AQELYNEL--IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
A+E Y EL + + V ++H ++D V+ +F+ G I IL+ T
Sbjct: 492 AEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVAT 538
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 30.9 bits (70), Expect = 0.23
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 17/122 (13%)
Query: 48 PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
PVLV Q ++EL L+ G+ +V+++ ++ + + G + ++T++ G
Sbjct: 427 PVLVGTQDVAESEELAEALLEAGVPCNVLNAKNDAEEAAIIAEAGDIGA--VTVSTQMAG 484
Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRI---------------GRAGRGGREGKAVTFFTK 152
RG D R + + +H I GRAGR G G +V F +
Sbjct: 485 RGTDIRLGGSDEADHDRVAELGGLHVIGTGRHRTARLDNQLRGRAGRQGDPGSSVFFVSL 544
Query: 153 QD 154
+D
Sbjct: 545 ED 546
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 30.9 bits (70), Expect = 0.28
Identities = 26/100 (26%), Positives = 36/100 (36%), Gaps = 8/100 (8%)
Query: 57 ERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVR 116
E Y E +++ Q DN + + RI IT +LL G+D V
Sbjct: 444 EALVNEYPEYNGRYAMKITGDAEQAQALIDNFIDKEKYPRI--AITVDLLTTGVDVPEVV 501
Query: 117 LVVNYDFPSSAISYIHRIGRAGR-----GGREGKAVTFFT 151
+V S + +GR R GG E FFT
Sbjct: 502 NLVFDRKVRSKTKFKQMVGRGTRLCPDLGGPEQDK-EFFT 540
>gnl|CDD|223961 COG1030, NfeD, Membrane-bound serine protease (ClpP class)
[Posttranslational modification, protein turnover,
chaperones].
Length = 436
Score = 30.4 bits (69), Expect = 0.38
Identities = 16/59 (27%), Positives = 20/59 (33%), Gaps = 7/59 (11%)
Query: 92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF 150
F T I ++ LGR F+ +LV S G G GK VT
Sbjct: 337 FLTLAILSILFKVFLGRLPAFKIYKLVRATKSKS-------GTGNEELIGLVGKTVTPL 388
>gnl|CDD|225028 COG2117, COG2117, Predicted subunit of
tRNA(5-methylaminomethyl-2-thiouridylate)
methyltransferase, contains the PP-loop ATPase domain
[Translation, ribosomal structure and biogenesis].
Length = 198
Score = 29.7 bits (67), Expect = 0.43
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
L R I V +++ +P +AI YIH + RE + T++D
Sbjct: 59 LDREILEDAVEMIIEDGYPRNAIQYIHEMALEALASREVDRIADGTRRD 107
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 28.8 bits (65), Expect = 1.3
Identities = 11/51 (21%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 70 GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT-ELLGRGIDFRTVRLVV 119
+ ++V+ R+ K++ +++ G++ I+I T LL + + F+ + L++
Sbjct: 671 PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLI 721
>gnl|CDD|219205 pfam06862, DUF1253, Protein of unknown function (DUF1253). This
family represents the C-terminal portion (approximately
500 residues) of several hypothetical eukaryotic
proteins of unknown function.
Length = 436
Score = 28.4 bits (64), Expect = 1.6
Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 8/102 (7%)
Query: 62 LYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG--RGIDFRTVRLVV 119
L N L + ++ I + K+ F +GRI +L+ TE L R + + V+ V+
Sbjct: 310 LRNYLKKENVSFAAISEYTSPKKISRARTLFFSGRINVLLYTERLHFFRRYEIKGVKNVI 369
Query: 120 NY------DFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
Y F S + + + G+ ++K DA
Sbjct: 370 FYGPPENPQFYSELVRMLGKSVFEGKDLAAASVRALYSKYDA 411
>gnl|CDD|184745 PRK14561, PRK14561, hypothetical protein; Provisional.
Length = 194
Score = 27.5 bits (62), Expect = 2.3
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 103 TELLGRGIDFRTVRLVVNYDFPSSAISYIHR 133
L R I + V +++ +P++AI Y+H
Sbjct: 55 VLELDREILEKAVDMIIEDGYPNNAIQYVHE 85
>gnl|CDD|234724 PRK00315, PRK00315, potassium-transporting ATPase subunit C;
Reviewed.
Length = 193
Score = 27.5 bits (62), Expect = 2.5
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 8 TNPALKRRVKSNLARMYRETEGAGSPV 34
+NPAL +K+ +A + GA SPV
Sbjct: 91 SNPALDDAIKARVAALRAANPGASSPV 117
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 28.1 bits (63), Expect = 2.6
Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 61 ELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN 120
E EL+ G+ H+ ++ R V +FR G+I +L++T L G++ R V+
Sbjct: 307 EELAELVLRGVAFH--HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNL-PARTVII 363
Query: 121 YDF----PSSAISYIHR------IGRAGRGG 141
D P I I GRAGR G
Sbjct: 364 KDTRRYDPKGGIVDIPVLDVLQMAGRAGRPG 394
>gnl|CDD|187617 cd05359, ChcA_like_SDR_c, 1-cyclohexenylcarbonyl_coenzyme
A_reductase (ChcA)_like, classical (c) SDRs. This
subgroup contains classical SDR proteins, including
members identified as 1-cyclohexenylcarbonyl coenzyme A
reductase. ChcA of Streptomyces collinus is implicated
in the final reduction step of shikimic acid to
ansatrienin. ChcA shows sequence similarity to the SDR
family of NAD-binding proteins, but it lacks the
conserved Tyr of the characteristic catalytic site. This
subgroup also contains the NADH-dependent
enoyl-[acyl-carrier-protein(ACP)] reductase FabL from
Bacillus subtilis. This enzyme participates in bacterial
fatty acid synthesis, in type II fatty-acid synthases
and catalyzes the last step in each elongation cycle.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 27.7 bits (62), Expect = 2.6
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT-----GRIWILI 101
V+ + +SK+ A E+ E+ G V+ +D +Q Q +V F GR+ +L+
Sbjct: 26 VINYRKSKDAAAEVAAEIEELGGKAVVVRADVSQPQ--DVEEMFAAVKERFGRLDVLV 81
>gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed.
Length = 913
Score = 28.0 bits (62), Expect = 2.8
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 48 PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
PVLV + E ++ + N L +GI V+++ +K+ + + ++ R G + I T + G
Sbjct: 451 PVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGRPGA--LTIATNMAG 508
Query: 108 RGID 111
RG D
Sbjct: 509 RGTD 512
>gnl|CDD|226383 COG3865, COG3865, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 151
Score = 27.0 bits (60), Expect = 3.3
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 123 FPSSAISYIHRIGRAGRGGREGK 145
FP S I I R GG+EGK
Sbjct: 27 FPDSKIIGITRYPEGEPGGKEGK 49
>gnl|CDD|172500 PRK13999, PRK13999, potassium-transporting ATPase subunit C;
Provisional.
Length = 201
Score = 27.4 bits (61), Expect = 3.3
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 8 TNPALKRRVKSNLARMYRETEGAGSPV 34
T+ AL RVK ++ + E GA PV
Sbjct: 102 TSKALADRVKEDVDALKAENPGAPVPV 128
>gnl|CDD|240162 cd05126, Mth938, Mth938 domain. Mth938 is a hypothetical protein
encoded by the Methanobacterium thermoautotrophicum
(Mth) genome. This protein crystallizes as a dimer,
although it is monomeric in solution, with one disulfide
bond in each monomer. The function of the protein has
not been determined.
Length = 117
Score = 26.5 bits (59), Expect = 3.4
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 29 GAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINV-DVIHS 78
G ++ ET+ + V V V E A + YNEL G V VIH
Sbjct: 67 GQSGALKVPPETVEKLEKRGVEVLVLPTEEAVKRYNELAGKGRRVLAVIHV 117
>gnl|CDD|185766 cd09243, BRO1_Brox_like, Protein-interacting Bro1-like domain of
human Brox1 and related proteins. This family contains
the Bro1-like domain of a single-domain protein, human
Brox, and related domains. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1
and Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of Brox. Human Brox can bind
to human immunodeficiency virus type 1 (HIV-1)
nucleocapsid. In addition to a Bro1-like domain, Brox
also has a C-terminal thioester-linkage site for
isoprenoid lipids (CaaX motif). This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 353
Score = 27.3 bits (61), Expect = 4.0
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIY 68
L + Y +T+G G+ + + P V ++ ER N IY
Sbjct: 283 ALCKEYAKTKGPGTTAKPDQHLFFRKLGPLVKRTLEKCERE----NGFIY 328
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 27.5 bits (62), Expect = 4.1
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 5/88 (5%)
Query: 56 KERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTV 115
++R E Y+E N+ HS +++ R V + G + +++++ L GID +
Sbjct: 305 RKRFPEEYDE-----DNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYI 359
Query: 116 RLVVNYDFPSSAISYIHRIGRAGRGGRE 143
LVV P S + RIGRAG E
Sbjct: 360 DLVVLLGSPKSVSRLLQRIGRAGHRLGE 387
>gnl|CDD|218695 pfam05691, Raffinose_syn, Raffinose synthase or seed inhibition
protein Sip1. This family consists of several raffinose
synthase proteins, also known as seed inhibition (Sip1)
proteins. Raffinose (O-alpha- D-galactopyranosyl-
(1-->6)- O-alpha- D-glucopyranosyl-(1<-->2)- O-beta-
D-fructofuranoside) is a widespread oligosaccharide in
plant seeds and other tissues. Raffinose synthase
(EC:2.4.1.82) is the key enzyme that channels sucrose
into the raffinose oligosaccharide pathway. Raffinose
family oligosaccharides (RFOs) are ubiquitous in plant
seeds and are thought to play critical roles in the
acquisition of tolerance to desiccation and seed
longevity. Raffinose synthases are alkaline
alpha-galactosidases and are solely responsible for RFO
breakdown in germinating maize seeds, whereas acidic
galactosidases appear to have other functions.
Length = 742
Score = 27.4 bits (61), Expect = 4.3
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 15/43 (34%)
Query: 43 LGIEPPVLVFVQSKERAQELYNEL-IY------DGINVDVIHS 78
LG+ P ++A E Y+EL Y DG+ VDVIH
Sbjct: 354 LGLVHP--------KKAHEFYDELHSYLASAGIDGVKVDVIHI 388
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 27.2 bits (61), Expect = 4.6
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 74 DVIHSDRTQKQRDNVVRSFRTGRIWIL 100
DV H+ + NV +T +WIL
Sbjct: 453 DVYHA--PEFTYGNVHLLPKTSHLWIL 477
>gnl|CDD|179062 PRK00553, PRK00553, ribose-phosphate pyrophosphokinase;
Provisional.
Length = 332
Score = 26.8 bits (59), Expect = 5.4
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 76 IHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
IHSD+TQ D V RT +++ ELLG+
Sbjct: 135 IHSDQTQGFFDIPVDILRTYHVFLSRVLELLGK 167
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 26.5 bits (59), Expect = 5.9
Identities = 9/66 (13%), Positives = 19/66 (28%), Gaps = 1/66 (1%)
Query: 84 QRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE 143
+ R + + L G+D +V N D+ + + G
Sbjct: 53 PSKSEERKLLSREEVLENAKAQLACGLDPEKSEIVNNSDWLEH-LELAWLLRDLGNHFSL 111
Query: 144 GKAVTF 149
+ + F
Sbjct: 112 NRMLQF 117
>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent groups. This group includes enzymes from
Escherichia coli, Bacillus subtilis, Aquifex aeolicus,
the spirochete Treponema pallidum, Synechocystis
PCC6803, and one of the two prolyL-tRNA synthetases of
Saccharomyces cerevisiae. The other group includes the
Pro-specific domain of a human multifunctional tRNA
ligase and the prolyl-tRNA synthetases from the Archaea,
the Mycoplasmas, and the spirochete Borrelia burgdorferi
[Protein synthesis, tRNA aminoacylation].
Length = 568
Score = 26.7 bits (59), Expect = 7.6
Identities = 12/28 (42%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 56 KERAQELYNELIYDGINVDVIHSDRTQK 83
++ A+ELY+EL+ G VDV+ DR ++
Sbjct: 489 QQLAEELYSELLAQG--VDVLLDDRNER 514
>gnl|CDD|188660 cd08705, RGS_R7-like, Regulator of G protein signaling (RGS)
domain found in the R7 subfamily of proteins. The RGS
(Regulator of G-protein Signaling) domain is an
essential part of the R7 (Neuronal RGS) protein
subfamily of the RGS protein family, a diverse group of
multifunctional proteins that regulate cellular
signaling events downstream of G-protein coupled
receptors (GPCRs). As a major G-protein regulator, RGS
domain containing proteins are involved in many crucial
cellular processes such as regulation of intracellular
trafficking, glial differentiation, embryonic axis
formation, skeletal and muscle development, and cell
migration during early embryogenesis. The R7 subfamily
includes RGS6, RGS7, RGS9, and RGS11, all of which, in
humans, are expressed predominantly in the nervous
system, form an obligatory complex with G-beta-5, and
play important roles in the regulation of crucial
neuronal processes. In addition, R7 proteins were found
to bind many other proteins outside of the G protein
signaling pathways including: m-opioid receptor,
beta-arrestin, alpha-actinin-2, NMDAR, polycystin,
spinophilin, guanylyl cyclase, among others.
Length = 121
Score = 25.3 bits (56), Expect = 9.2
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 54 QSKERAQELYNELIYDG----INVDVIHSDRTQKQRDN 87
Q E+ QE+Y E + G IN+D + T K +
Sbjct: 51 QVPEKVQEIYQEFLAPGAPSWINIDSKTMEITLKNLKD 88
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 25.9 bits (57), Expect = 9.8
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 55 SKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRS 91
+ERA+ Y +L G V+ K+RD+ +
Sbjct: 148 VEERAKRRYKQLQIKGNEVNFEELLAEIKERDDRDSN 184
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 0.139 0.399
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: 8,219,678
Number of extensions: 755899
Number of successful extensions: 855
Number of sequences better than 10.0: 1
Number of HSP's gapped: 832
Number of HSP's successfully gapped: 95
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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: 55 (24.9 bits)