RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3145
(396 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 = 143 bits (361), Expect = 5e-38
Identities = 69/225 (30%), Positives = 102/225 (45%), Gaps = 17/225 (7%)
Query: 140 DRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK 199
++ LL L+ + ++FV TKR E+ L G K LHG+L Q R +L K
Sbjct: 259 EKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEK 318
Query: 200 FKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMA- 258
FKD E VL+ATDVAARGLDI V VINY +P E Y+HR+GRT RAG+ GV++S
Sbjct: 319 FKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVT 378
Query: 259 GEVDRKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPPPPLAEIVDKYRAKVEAIEGEVQ 318
E + K +K++ K + + + PL E D K ++
Sbjct: 379 EEEEVKKLKRIEKRLERKLPSAV--------------LLPLDEPEDAKLLKT--TRPGLE 422
Query: 319 KILTEEKHDRLLNKADEQVSKAEKMLKEKKPLHENPPREWFQTKK 363
+ + L + + + + + L N +E
Sbjct: 423 EESDISDEIKKLKSSKKALLRGLGVRFTLSKLLANLGKEIPGAGD 467
>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 = 115 bits (291), Expect = 2e-31
Identities = 49/118 (41%), Positives = 69/118 (58%), Gaps = 1/118 (0%)
Query: 141 RKALLAALVCRTFKDH-TMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK 199
+ALL L K +IF P+K+ E+ LL GIK LHG+ +Q R E L+
Sbjct: 14 LEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKD 73
Query: 200 FKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSM 257
F++ E VL+ATDV ARG+D+ V VINY +P S Y+ R+GR RAG+ G ++ +
Sbjct: 74 FREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 122 bits (309), Expect = 3e-31
Identities = 70/207 (33%), Positives = 107/207 (51%), Gaps = 16/207 (7%)
Query: 147 ALVCRTFKDH----TMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKD 202
AL+C K +++FV T+ HE+ L GI L G + Q R E++++ D
Sbjct: 234 ALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTD 293
Query: 203 EETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAGEVD 262
+VL+ATDVAARG+DI V VIN+ MP S + Y+HR+GRT RAG+ G ++S+ D
Sbjct: 294 GRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHD 353
Query: 263 RKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPPPPLAEIVDKYRAKVEAIEGEVQKILT 322
L+ ++ + + P+K R+I P+ K PS K KV A E +K
Sbjct: 354 HLLLGKIERYIEEPLKARVIDELRPKTKAPSEKKTG------KPSKKVLAKRAE-KKEKE 406
Query: 323 EEKHDRLLNKADEQVSKAEKMLKEKKP 349
+EK K ++ + + K +KP
Sbjct: 407 KEK-----PKVKKRHRDTKNIGKRRKP 428
>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 = 107 bits (269), Expect = 7e-29
Identities = 38/77 (49%), Positives = 49/77 (63%)
Query: 173 LLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMP 232
LL GIK LHG L+Q R E L F++ ++ VL+ATDVA RG+D+ V VINY +P
Sbjct: 2 LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLP 61
Query: 233 HSLEHYIHRVGRTARAG 249
+ YI R+GR RAG
Sbjct: 62 WNPASYIQRIGRAGRAG 78
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 109 bits (274), Expect = 3e-26
Identities = 51/157 (32%), Positives = 79/157 (50%)
Query: 140 DRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK 199
+R L L+ + ++F TK+E E+ L G A LHG+L Q R + L +
Sbjct: 228 ERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVR 287
Query: 200 FKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAG 259
F + VL+ATDVAARGLDI+ ++ VINY + E ++HR+GRT RAG G+++S+
Sbjct: 288 FANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVA 347
Query: 260 EVDRKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPP 296
+ + + + +P P P P
Sbjct: 348 PEEMQRANAIEDYLGRKLNWEPLPSLSPLSGVPLLPE 384
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 99 bits (250), Expect = 4e-26
Identities = 43/81 (53%), Positives = 51/81 (62%)
Query: 169 EMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVIN 228
E+ LL LGIK LHG L+Q R E L KF + + VL+ATDVA RGLD+ GV VI
Sbjct: 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVII 61
Query: 229 YRMPHSLEHYIHRVGRTARAG 249
Y +P S YI R+GR RAG
Sbjct: 62 YDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 109 bits (273), Expect = 7e-26
Identities = 61/165 (36%), Positives = 93/165 (56%), Gaps = 16/165 (9%)
Query: 130 CFRIRKDTHL----DRKALLAALVCRTFKDHT--MIFVPTKREAHEMHILLGLLGIKAGE 183
C I+++ + +++ L L+ R +D +IFV TK+ A + L L G A
Sbjct: 347 CHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALC 406
Query: 184 LHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVG 243
+HG+ Q R L +FK ++ ++IATDVA+RGLD++ VK VIN+ P+ +E Y+HR+G
Sbjct: 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIG 466
Query: 244 RTARAGKGGVSVSM----AGEVDRKLVKQVIKNAKNPVKHRIIPP 284
RT RAG G S + + R LVK V++ AK P +PP
Sbjct: 467 RTGRAGAKGASYTFLTPDKYRLARDLVK-VLREAKQP-----VPP 505
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 102 bits (256), Expect = 6e-24
Identities = 51/121 (42%), Positives = 69/121 (57%)
Query: 140 DRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK 199
++ LL L+ + D +IF TK E+ L G + G L G++ Q RL L +
Sbjct: 241 EKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEE 300
Query: 200 FKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAG 259
F + D+L+ATDVAARGL I V V NY +P E Y+HR+GRT RAG G S+S+A
Sbjct: 301 FTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLAC 360
Query: 260 E 260
E
Sbjct: 361 E 361
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 102 bits (255), Expect = 9e-24
Identities = 51/123 (41%), Positives = 74/123 (60%)
Query: 140 DRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK 199
D+ LL LV + + M+F K E + L GI A +L G++ Q R+++L
Sbjct: 321 DKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEG 380
Query: 200 FKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAG 259
F++ + VL+ATDVA RG+ I G+ VIN+ +P + Y+HR+GRT RAG GVS+S AG
Sbjct: 381 FREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAG 440
Query: 260 EVD 262
E D
Sbjct: 441 EDD 443
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 101 bits (252), Expect = 2e-23
Identities = 53/158 (33%), Positives = 88/158 (55%), Gaps = 9/158 (5%)
Query: 141 RKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKF 200
++ LL+ ++ + ++F TK A+ + L GI++ +HGN +Q +R +L F
Sbjct: 232 KRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADF 291
Query: 201 KDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAGE 260
K + VL+ATD+AARGLDI + V+NY +P+ E Y+HR+GRT RA G ++S+
Sbjct: 292 KSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCV 351
Query: 261 VDRKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPPPP 298
+ KL++ + K K + PR+ P + P P
Sbjct: 352 DEHKLLRDIEKLLKKEI---------PRIAIPGYEPDP 380
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 98.4 bits (245), Expect = 3e-22
Identities = 70/230 (30%), Positives = 111/230 (48%), Gaps = 36/230 (15%)
Query: 155 DHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVA 214
D +IFV TK E+ L G + L+G++ Q R ++L + KD D+LIATDVA
Sbjct: 246 DAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVA 305
Query: 215 ARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAGEVDRKLVKQVIKNAK 274
ARGLD+ + V+NY +P E Y+HR+GRT RAG+ G ++ +R+L++ +
Sbjct: 306 ARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNI----- 360
Query: 275 NPVKHRIIPPGYPRLKTPSFPPPPLAEIVDKYRAKVEAIEGEVQKILTEEKHDR---LLN 331
R + P ++ P+ AE++ K R +E +VQ+ L D+ LL
Sbjct: 361 ----ERTMKLTIPEVELPN------AELLGKRR--LEKFAAKVQQQLESSDLDQYRALLA 408
Query: 332 KADEQVSKAE-----------KMLKEKKPLHENP-----PREWFQTKKER 365
K E KM + ++PL P P+ F+ + +R
Sbjct: 409 KIQPTAEGEELDLETLAAALLKMAQGERPLILPPDAPMRPKREFRDRDDR 458
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 94.2 bits (234), Expect = 7e-21
Identities = 51/121 (42%), Positives = 73/121 (60%)
Query: 140 DRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK 199
+++ LL L+ R+ TM+FV TK + L G + G L G++ Q R L +
Sbjct: 243 EKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNR 302
Query: 200 FKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAG 259
F+ + ++L+ATDVAARGL I GVK V NY +P E Y+HR+GRTAR G+ G ++S A
Sbjct: 303 FQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC 362
Query: 260 E 260
E
Sbjct: 363 E 363
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 83.7 bits (207), Expect = 9e-18
Identities = 36/86 (41%), Positives = 58/86 (67%)
Query: 184 LHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVG 243
+HG++ Q R +R+F+ T VLI TD+ ARG+D++ V VINY +P S E+YIHR+G
Sbjct: 297 MHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIG 356
Query: 244 RTARAGKGGVSVSMAGEVDRKLVKQV 269
R+ R G+ GV+++ D + +K++
Sbjct: 357 RSGRFGRKGVAINFVTPDDIEQLKEI 382
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 81.0 bits (200), Expect = 1e-16
Identities = 36/122 (29%), Positives = 64/122 (52%), Gaps = 6/122 (4%)
Query: 178 GIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEH 237
G+KA +HG + R E ++ F E V++AT V RG+D+ V+ VI + MP++++
Sbjct: 392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKE 451
Query: 238 YIHRVGRTARAGKGGVSVSMAGEVDRKLVK---QVIKNAKNPVKHRII---PPGYPRLKT 291
YIH++GR +R G+ G ++ E DR L ++K++ + + G R +
Sbjct: 452 YIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELANSRYLGSGRKRK 511
Query: 292 PS 293
Sbjct: 512 KK 513
>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 = 66.6 bits (163), Expect = 6e-12
Identities = 33/118 (27%), Positives = 58/118 (49%)
Query: 159 IFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGL 218
I+ ++++ E+ L GI A H L+ R E+ F ++ V++AT+ G+
Sbjct: 229 IYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGI 288
Query: 219 DIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMAGEVDRKLVKQVIKNAKNP 276
D V+ VI+Y MP +LE Y GR R G ++ + D L+K+ I+ ++
Sbjct: 289 DKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQSEAD 346
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 63.9 bits (156), Expect = 5e-11
Identities = 38/146 (26%), Positives = 70/146 (47%), Gaps = 1/146 (0%)
Query: 135 KDTHLDRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRL 194
K D+ A LA ++ + +I+ T+++ E+ L GI AG H L+ R
Sbjct: 212 KGEPSDQLAFLATVLPQ-LSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERE 270
Query: 195 ESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVS 254
+ F ++E V++AT+ G+D V+ VI+Y +P S+E Y GR R G +
Sbjct: 271 RVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEA 330
Query: 255 VSMAGEVDRKLVKQVIKNAKNPVKHR 280
+ + D + + +I+ +K + +
Sbjct: 331 ILLYSPEDIRWQRYLIEQSKPDEEQK 356
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 56.0 bits (136), Expect = 2e-08
Identities = 30/78 (38%), Positives = 40/78 (51%), Gaps = 14/78 (17%)
Query: 188 LTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINY-------RMPHSLEHYIH 240
++Q ++E L KF+ E +VL++T VA GLDI V VI Y R I
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS-------IQ 459
Query: 241 RVGRTARAGKGGVSVSMA 258
R GRT R +G V V +A
Sbjct: 460 RKGRTGRQEEGRVVVLIA 477
>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 = 55.2 bits (133), Expect = 3e-08
Identities = 30/92 (32%), Positives = 51/92 (55%)
Query: 158 MIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARG 217
+I+ P+++++ ++ L LGI AG H L +R + KF+ +E V++AT G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 218 LDIRGVKTVINYRMPHSLEHYIHRVGRTARAG 249
++ V+ VI+Y +P S+E Y GR R G
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDG 321
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 52.8 bits (127), Expect = 1e-07
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 1/96 (1%)
Query: 157 TMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAAR 216
T+IF A+E+ L GI + G + R L +F+ VL+ V
Sbjct: 286 TLIFASDVEHAYEIAKLFLAPGIVEA-ITGETPKEEREAILERFRTGGIKVLVTVKVLDE 344
Query: 217 GLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGG 252
G+DI +I R S +I R+GR R +G
Sbjct: 345 GVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGK 380
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 50.4 bits (121), Expect = 9e-07
Identities = 28/71 (39%), Positives = 37/71 (52%)
Query: 188 LTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTAR 247
++Q + E + +F+ E +VL+AT V GLDI V VI Y S I R GRT R
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR 468
Query: 248 AGKGGVSVSMA 258
KG V V +
Sbjct: 469 KRKGRVVVLVT 479
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 46.9 bits (112), Expect = 1e-05
Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 6/104 (5%)
Query: 157 TMIFVPTKREAHEM--HILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVA 214
T+IF T+ A E L L HG+L++ RLE + K+ E ++AT
Sbjct: 256 TLIFTNTRSGA-ERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314
Query: 215 ARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGGVSVSMA 258
G+DI + VI P S+ ++ R+G RAG VS
Sbjct: 315 ELGIDIGDIDLVIQLGSPKSVNRFLQRIG---RAGHRLGEVSKG 355
>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 = 43.9 bits (104), Expect = 1e-04
Identities = 25/110 (22%), Positives = 40/110 (36%), Gaps = 17/110 (15%)
Query: 185 HGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMP-HSLEHYIHRVG 243
L + R +FK+ E +IAT+ G+DI + VI Y P S+ + R G
Sbjct: 345 RAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAG 404
Query: 244 RTARAGKGGVSVSMAG----------------EVDRKLVKQVIKNAKNPV 277
R R G+ + + + E V+ V + N
Sbjct: 405 RAGRRGQESLVLVVLRSDPLDSYYLRHPEELLETGFGPVESVRVDDNNEY 454
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 42.2 bits (100), Expect = 4e-04
Identities = 52/206 (25%), Positives = 90/206 (43%), Gaps = 32/206 (15%)
Query: 157 TMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAAR 216
++ TK+ A ++ L LGIK LH ++ R+E +R + E DVL+ ++
Sbjct: 449 VLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508
Query: 217 GLDIRGVKTVINY--------RMPHSLEHYIHRVGRTARAGKGGV-------SVSMA--- 258
GLD+ V V R SL I +GR AR G V + SM
Sbjct: 509 GLDLPEVSLVAILDADKEGFLRSERSL---IQTIGRAARNVNGKVILYADKITDSMQKAI 565
Query: 259 GEVDRKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPPPPLAEIVDKYRAKVEAIEGEVQ 318
E +R+ Q+ N +H I P +K D+Y+AK+E +
Sbjct: 566 DETERRREIQMAYNE----EHGITPQT---IKKKIRDILDGEYEEDEYKAKIEKKASK-- 616
Query: 319 KILTEEKHDRLLNKADEQVSKAEKML 344
+++++ ++L+ K ++++ +A K L
Sbjct: 617 --MSKKELEKLIKKLEKEMKEAAKNL 640
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 39.4 bits (92), Expect = 0.003
Identities = 27/119 (22%), Positives = 48/119 (40%), Gaps = 9/119 (7%)
Query: 153 FKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATD 212
++ T++F ++R HE+ L G+KA H L R R F +E ++ T
Sbjct: 439 YRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTA 498
Query: 213 VAARGLDIRGVKTV-------INYRMPHSLEHYIHRVGRTARAGKGGVSVSMAGEVDRK 264
A G+D + + I + + + R GR +G V + + E +K
Sbjct: 499 ALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYL-LV-EPGKK 555
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 38.0 bits (88), Expect = 0.008
Identities = 30/114 (26%), Positives = 54/114 (47%), Gaps = 2/114 (1%)
Query: 178 GIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEH 237
G KA HG++ R +++ +E +++ AT G++ V+ VI++ +P S+E
Sbjct: 704 GHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEG 763
Query: 238 YIHRVGRTARAGKGGVSVSMAGEVDRKLVKQVIKNAKNPVKHRIIPPGYPRLKT 291
Y GR R G+ V D VK +I ++ V+ + GY R+ +
Sbjct: 764 YHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMI--SQGGVEQSPMAMGYNRMAS 815
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 37.6 bits (88), Expect = 0.011
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 13/88 (14%)
Query: 140 DRKALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLL---GIKAGELHGNLTQPSRLES 196
D L LV + D +IFVP+ + L L GI A
Sbjct: 315 DSVEKLVELV-KRLGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGFE-----RK 368
Query: 197 LRKFKDEETDVLI--AT--DVAARGLDI 220
KF++ E DVL+ A+ V RG+D+
Sbjct: 369 FEKFEEGEVDVLVGVASYYGVLVRGIDL 396
>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 = 36.9 bits (86), Expect = 0.017
Identities = 50/206 (24%), Positives = 84/206 (40%), Gaps = 35/206 (16%)
Query: 154 KDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDV 213
+ ++ TK+ A ++ L LGIK LH + R+E +R + E DVL+ ++
Sbjct: 442 NERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINL 501
Query: 214 AARGLDIRGVKTVINY--------RMPHSLEHYIHRVGRTARAGKGGV-------SVSMA 258
GLD+ V V R SL I +GR AR G V + SM
Sbjct: 502 LREGLDLPEVSLVAILDADKEGFLRSERSL---IQTIGRAARNVNGKVIMYADKITDSMQ 558
Query: 259 ---GEVDRKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPPPPLAEIVD-KYRAKVEAIE 314
E +R+ Q+ N +H I P + P+ +I+D + + K +A +
Sbjct: 559 KAIEETERRRKIQMAYNE----EHGITPQTIRK---------PIRDILDIELKEKEDAAK 605
Query: 315 GEVQKILTEEKHDRLLNKADEQVSKA 340
+ + + + L K +Q+ K
Sbjct: 606 KKKKGEDLSDLSKKELKKLIKQLEKE 631
>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 = 35.9 bits (83), Expect = 0.033
Identities = 30/114 (26%), Positives = 46/114 (40%), Gaps = 16/114 (14%)
Query: 142 KALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLES----L 197
K A++ T + K + E I+L +H T+ R + L
Sbjct: 217 KGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIML---------IHSRFTEKDRAKKEAELL 267
Query: 198 RKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKG 251
+FK E V++AT V LDI V +I P ++ I R+GR R G+
Sbjct: 268 LEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP--IDSLIQRLGRLHRYGEK 318
>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 = 35.5 bits (82), Expect = 0.039
Identities = 31/114 (27%), Positives = 44/114 (38%), Gaps = 16/114 (14%)
Query: 142 KALLAALVCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSR----LESL 197
K A++ T + K A E I+L LH T+ R E L
Sbjct: 221 KGGKIAIIVNTVDRAQEFYQQLKENAPEEEIML---------LHSRFTEKDRAKKEAELL 271
Query: 198 RKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKG 251
+ K E V++AT V LDI +I P ++ I R+GR R G+
Sbjct: 272 EEMKKNEKFVIVATQVIEASLDI-SADVMITELAP--IDSLIQRLGRLHRYGRK 322
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 34.7 bits (80), Expect = 0.084
Identities = 33/99 (33%), Positives = 43/99 (43%), Gaps = 9/99 (9%)
Query: 157 TMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRK----FKDEETDVLIATD 212
++ V T A E++ L G K LH T R E R+ FK E +++AT
Sbjct: 443 VLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ 502
Query: 213 VAARGLDIRGVKTVINYRMP-HSLEHYIHRVGRTARAGK 250
V G+DI +I P SL I R GR R GK
Sbjct: 503 VIEAGVDI-DFDVLITELAPIDSL---IQRAGRVNRHGK 537
>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 = 0.11
Identities = 13/74 (17%), Positives = 27/74 (36%)
Query: 149 VCRTFKDHTMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVL 208
+ ++ P+ ++ LL ++ G + SR + L +FK + +L
Sbjct: 4 LLEAIPGGVLVLFPSYSLLEQVAELLASELLEKGIELLVQGEGSREKLLERFKKGKGAIL 63
Query: 209 IATDVAARGLDIRG 222
G+D G
Sbjct: 64 FGVGSFWEGIDFPG 77
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 33.9 bits (78), Expect = 0.14
Identities = 19/72 (26%), Positives = 35/72 (48%)
Query: 178 GIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEH 237
GI A H L R + F+ ++ +++AT G++ V+ V+++ +P ++E
Sbjct: 260 GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES 319
Query: 238 YIHRVGRTARAG 249
Y GR R G
Sbjct: 320 YYQETGRAGRDG 331
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 32.6 bits (75), Expect = 0.16
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 143 ALLAALVCRTFKDHTMIFVPTKREAHEMHI----LLGLLGIKAGELHGNLTQPSRLESLR 198
+L AL+ + ++ PT+ A +++ L +LG++ L G + + L+
Sbjct: 34 PILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLK 93
Query: 199 KFKDEETDVLIAT 211
K + D+L+ T
Sbjct: 94 K---GKADILVGT 103
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 33.7 bits (77), Expect = 0.20
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 185 HGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGR 244
HG++++ R + + K E ++AT G+D+ V VI P S+ + R+G
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIG- 366
Query: 245 TARAGK--GGVS 254
RAG GGVS
Sbjct: 367 --RAGHQVGGVS 376
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 33.3 bits (77), Expect = 0.23
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 176 LLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDI 220
L +K G +HG + + + FK+ E D+L+AT V G+D+
Sbjct: 505 LPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|233644 TIGR01932, hflC, HflC protein. HflK and HflC are paralogs encoded
by tandem genes in Proteobacteria, spirochetes, and some
other bacterial lineages. The HflKC complex is anchored
in the membrane and exposed to the periplasm. The
complex is not active as a protease, but rather binds to
and appears to modulate the ATP-dependent protease FtsH.
The overall function of HflKC is not fully described
[Protein fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 317
Score = 32.8 bits (75), Expect = 0.27
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 298 PLAEIVDKYRAKVEAIEGEVQKILTEEKHDRLLN 331
P E V + AK++ ++G +I T+EK D +++
Sbjct: 57 PFIEHVKIFDAKIQTMDGRPDRIPTKEKKDIIID 90
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 32.7 bits (75), Expect = 0.36
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 182 GELHGNLTQPSRLESLRKFKDEETDVLIATDVAARGLDI 220
G LHG + + + +F++ E D+L+AT V G+D+
Sbjct: 486 GLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDV 524
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 32.7 bits (76), Expect = 0.39
Identities = 16/59 (27%), Positives = 37/59 (62%), Gaps = 6/59 (10%)
Query: 296 PPPLAEIVDKYRAKVEAIEGEVQK-ILT-EEKHDRLL---NKADEQVSKA-EKMLKEKK 348
PP EI+++ +V IE + ++ ++T E++++++ +KA ++V+KA K L + +
Sbjct: 625 PPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDQ 683
>gnl|CDD|204605 pfam11178, DUF2963, Protein of unknown function (DUF2963). This
family of proteins with unknown function appears to be
restricted to Mollicutes.
Length = 52
Score = 29.2 bits (66), Expect = 0.43
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 63 EYQPKKFKTKKITDFDNDFSFVSSIEEYNKDTE 95
EY P+ K K T + +D + I EY+K T
Sbjct: 13 EYDPQTGKLIKKTYYQDDGKTIDYINEYDKQTG 45
>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 = 32.7 bits (75), Expect = 0.44
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 184 LHGNLTQPSRLES-LRKFKDEETDVLIATDVAARGLDIRGVKTVI 227
HG +T + LE + +F E VL+ T + G+DI T+I
Sbjct: 692 AHGQMT-ENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII 735
>gnl|CDD|235356 PRK05170, PRK05170, hypothetical protein; Provisional.
Length = 147
Score = 30.7 bits (70), Expect = 0.62
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 197 LRKFKDEETDVLIATDVAARGLDI 220
L K +DE+T + T+VA R LDI
Sbjct: 32 LHKLEDEDTGEIYYTNVACRLLDI 55
>gnl|CDD|201257 pfam00485, PRK, Phosphoribulokinase / Uridine kinase family. In
Arabidopsis the region carries two binding domains, a
phosphoribosylpyrophosphate-binding domain and, at the
very C-terminus, a uracil-binding domain.
Length = 197
Score = 30.8 bits (70), Expect = 0.78
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 209 IATDVAARGLDIRGVKTVINYRMPHSLEHYI 239
I D+A RG + V I R P +YI
Sbjct: 148 IQRDMAERGHSLEAVTDSILRRKP-DYVNYI 177
>gnl|CDD|177698 PLN00068, PLN00068, photosystem II CP47 chlorophyll A apoprotein;
Provisional.
Length = 508
Score = 31.4 bits (71), Expect = 0.82
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 160 FVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAA 215
FVP +H HI G LGI AG H ++ P RL + + ET ++++ +AA
Sbjct: 193 FVPGGIASH--HIAAGTLGILAGLFHLSVRPPQRLYKGLRMGNIET--VLSSSIAA 244
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 31.6 bits (71), Expect = 0.96
Identities = 16/64 (25%), Positives = 26/64 (40%)
Query: 157 TMIFVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDVAAR 216
+IF + L LGIK L G+ R E + +F +E + + + A
Sbjct: 714 VLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAG 773
Query: 217 GLDI 220
GL +
Sbjct: 774 GLGL 777
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 31.2 bits (71), Expect = 1.1
Identities = 28/106 (26%), Positives = 40/106 (37%), Gaps = 28/106 (26%)
Query: 207 VLIATDVAARGLDIR---GVK------TVINYRMPHSLEHYIHRV-----GRTARAGKGG 252
V +AT +A RG DI+ GV + RM +S RV GR+ R G G
Sbjct: 475 VTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENS------RVDLQLRGRSGRQGDPG 528
Query: 253 VS---VSMAGEV-----DRKLVKQVIKNAKNPVKHRIIPPGYPRLK 290
S VS+ ++ L K K + K + R +
Sbjct: 529 SSQFFVSLEDDLIKRWSPSWLKKYYKKYSVKDSKLKPSALFKRRFR 574
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 31.0 bits (71), Expect = 1.4
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 300 AEIVDKYRAKVEAIEGEVQKILT--EEKHDRLLNKADEQVSKAEKMLKEKKPLHENPPRE 357
AE + + E ++ E+++ +E+ D+LL +A+++ +A K K++ R+
Sbjct: 536 AEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQ 595
Query: 358 WFQTKKERAAIKTSQAGEGLAAL 380
K A++K + E L
Sbjct: 596 --LQKGGYASVKAHELIEARKRL 616
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 30.7 bits (69), Expect = 1.5
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 163 TKREAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETD 206
RE E + LL +K G + R+E LR D+ +
Sbjct: 161 EDREGDERDVYRLLLKVKNG------GKRMRMEGLRILTDKAVN 198
>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 = 30.5 bits (69), Expect = 1.9
Identities = 47/186 (25%), Positives = 68/186 (36%), Gaps = 27/186 (14%)
Query: 193 RLESLRKFKDEETDVLIATDVAARGLDIRGVKTVINYRMPHSLEHYIHRVGRTARAGKGG 252
LE R +D E + T+ G+DI G+ V+ P + + GR R G+G
Sbjct: 320 ELE--RALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGA 377
Query: 253 VSVSMAGE--VDRKLVKQVIKNAKNPVKHRIIPPGYPRLKTPSFPPPPLAEIVDKYRAKV 310
+ V +A + +D LV PV+ + P P + P A
Sbjct: 378 LVVLVARDDPLDTYLVHHPEALFDRPVEATVFDPDNPYVLGPHL-----------CCAAA 426
Query: 311 EAIEGEVQKILTEEKHDRLLNKADEQVSKAEKMLKEKKPLHENPPREWFQTKKERAAIKT 370
E LTE + L A +V L E+ L P WF T++ERA
Sbjct: 427 EL-------PLTEADLE-LFGPAAAEVLDQ---LVEQGLLRRRPAG-WFWTRRERAHDAV 474
Query: 371 SQAGEG 376
G G
Sbjct: 475 DIRGGG 480
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 30.3 bits (69), Expect = 2.2
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 185 HGNLTQPSRLES-LRKFKDEETDVLIATDVAARGLDIRGVKTVI 227
HG + LE + F + E DVL+ T + G+DI T+I
Sbjct: 836 HGQMR-ERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII 878
>gnl|CDD|184696 PRK14474, PRK14474, F0F1 ATP synthase subunit B; Provisional.
Length = 250
Score = 29.4 bits (66), Expect = 2.9
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 304 DKYRAKVEAIEGEVQKILT------EEKHDRLLNKADEQVSKAEKMLKEKKPLHENPPRE 357
++YR K +++E + + +E+ LLN+A E V+ A E+ E +E
Sbjct: 60 ERYRQKQQSLEQQRASFMAQAQEAADEQRQHLLNEAREDVATARDEWLEQL---EREKQE 116
Query: 358 WFQTKKERA 366
+F+ +++
Sbjct: 117 FFKALQQQT 125
>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 = 29.2 bits (66), Expect = 3.0
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 12/65 (18%)
Query: 209 IATDVAARGLDIRGVKTVINYRMPH----SLEHYIHRVGRTARAGKGGVSVSMAGEVDRK 264
IA +A RG D+ VINYR + I +G A + VS +V+
Sbjct: 14 IALRLAERGADV-----VINYRKSKDAAAEVAAEIEELGGKAVVVRA--DVSQPQDVEE- 65
Query: 265 LVKQV 269
+ V
Sbjct: 66 MFAAV 70
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 29.7 bits (68), Expect = 3.1
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 166 EAHEMHILLGLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIATDV 213
E +E + ++ G LHG + + + FK E D+L+AT V
Sbjct: 494 ETYE-ELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTV 540
>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 = 29.4 bits (66), Expect = 3.5
Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 12/81 (14%)
Query: 189 TQPSRLESLRKFKDEETDVLIATDVAARGLDIRGVKT-VINYRMP----HSLEHYIHRVG 243
R E + F+D + +LI T + RG+ V V+ +L RVG
Sbjct: 340 EDQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVG 399
Query: 244 RTARAGKG-------GVSVSM 257
R+ G G S +M
Sbjct: 400 RSLERPTGDVLFFHYGKSKAM 420
>gnl|CDD|214350 CHL00062, psbB, photosystem II 47 kDa protein.
Length = 504
Score = 29.7 bits (67), Expect = 3.5
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 160 FVPTKREAHEMHILLGLLGIKAGELHGNLTQPSRL 194
FVP +H HI G LGI AG H ++ P RL
Sbjct: 193 FVPGGIASH--HIAAGTLGILAGLFHLSVRPPQRL 225
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 28.6 bits (64), Expect = 4.4
Identities = 30/97 (30%), Positives = 44/97 (45%), Gaps = 15/97 (15%)
Query: 143 ALLAALVC--RTFKDHTMIFVPTK----REAHEMHILLGLLGIKAGELHGNLTQPSRLES 196
ALL AL R ++ VPT+ + A E+ L LG+K L+G S+ E
Sbjct: 41 ALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGD---SKREQ 97
Query: 197 LRKFKDEETDVLIAT------DVAARGLDIRGVKTVI 227
LRK + +TD+L+ T + L + V VI
Sbjct: 98 LRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVI 134
>gnl|CDD|227162 COG4825, COG4825, Uncharacterized membrane-anchored protein
conserved in bacteria [Function unknown].
Length = 395
Score = 29.1 bits (65), Expect = 4.7
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 191 PSRLESLRKFKDEETDVLIATDVAARGLDIRGVK 224
L+SL+ F E VLI D AA L G K
Sbjct: 193 EDDLKSLKPFIKEYQPVLIGVDGAADVLRKAGYK 226
>gnl|CDD|225798 COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alpha subunit
[Energy production and conversion].
Length = 441
Score = 28.9 bits (65), Expect = 5.0
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 310 VEAIEGEVQKILTEEKHDRLLNKADEQVSKAEKMLKEKKPLHEN 353
V A+ G V K L+EE ++LL++A E + A++ ++ K L E
Sbjct: 160 VNAVPGGVAKNLSEEAREKLLDRAKEALELADRTVELFKELLER 203
>gnl|CDD|233579 TIGR01798, cit_synth_I, citrate synthase I (hexameric type). This
model describes one of several distinct but closely
homologous classes of citrate synthase, the protein that
brings carbon (from acetyl-CoA) into the TCA cycle. This
form, class I, is known to be hexameric and
allosterically inhibited by NADH in Escherichia coli,
Acinetobacter anitratum, Azotobacter vinelandii,
Pseudomonas aeruginosa, etc. In most species with a
class I citrate synthase, a dimeric class II isozyme is
found. The class II enzyme may act primarily on
propionyl-CoA to make 2-methylcitrate or be
bifunctional, may be found among propionate utilization
enzymes, and may be constitutive or induced by
propionate. Some members of this model group as class I
enzymes, and may be hexameric, but have shown regulatory
properties more like class II enzymes [Energy
metabolism, TCA cycle].
Length = 412
Score = 29.0 bits (65), Expect = 5.4
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 151 RTFKDHTMI-------FVPTKREAHEMHILLGLLGIKAGELHGNL 188
T HTM+ F +R+AH M +++G++G + H +L
Sbjct: 95 DTVTRHTMVHEQVTRFFNGFRRDAHPMAVMVGVVGALSAFYHDSL 139
>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 = 28.9 bits (65), Expect = 5.9
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 12/69 (17%)
Query: 196 SLRKFKDEETDVLIATDVAARGLDIRGVKTVI-----------NYRMPHSLEHYIHRV-G 243
L +F + + D+LI T + A+G V V ++R + +V G
Sbjct: 304 LLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAG 363
Query: 244 RTARAGKGG 252
R RA G
Sbjct: 364 RAGRAEDPG 372
>gnl|CDD|237571 PRK13961, PRK13961, phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 296
Score = 28.6 bits (65), Expect = 6.1
Identities = 14/27 (51%), Positives = 19/27 (70%), Gaps = 4/27 (14%)
Query: 290 KTPSFPPPPL-AEIVDKYRAK-VEAIE 314
KT P PPL A++++K RAK EA+E
Sbjct: 264 KTA--PAPPLPADVIEKTRAKYREALE 288
>gnl|CDD|215067 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 28.6 bits (64), Expect = 6.3
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 335 EQVSKAEKMLKEKKPLHENPPREWFQTKKERA 366
+Q E LK KKP E+ +E Q+K++RA
Sbjct: 151 QQYKSIEPWLKTKKPP-EDGQKEHLQSKEDRA 181
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 28.4 bits (64), Expect = 8.2
Identities = 11/37 (29%), Positives = 15/37 (40%)
Query: 175 GLLGIKAGELHGNLTQPSRLESLRKFKDEETDVLIAT 211
G K LH L+ R R+ + E V+I T
Sbjct: 267 ARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGT 303
>gnl|CDD|218422 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyze the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 28.6 bits (65), Expect = 8.3
Identities = 9/41 (21%), Positives = 22/41 (53%)
Query: 295 PPPPLAEIVDKYRAKVEAIEGEVQKILTEEKHDRLLNKADE 335
P +A ++++R V A+ ++ ++L E+ + L +A
Sbjct: 1340 QPLDIAAEIERFRPGVAALRPQLPELLPGEEREALEERAQA 1380
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 28.4 bits (63), Expect = 8.4
Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 13/90 (14%)
Query: 283 PPGYPRLKTPSFPPPPLAEIVDKYRAKVEAIEGEVQKILTEEKHD-RLLNKADEQV---- 337
PPG+ P PPPP + + R ++ V IL + L +D+ V
Sbjct: 15 PPGFEPPSQPPPPPPPGVNVKKRSRKQLS----IVGDILGHSGNPIYSLRVSDKPVKLGN 70
Query: 338 -SKAEKMLKEKKPLHENPPREWFQTKKERA 366
+K +L K P+ PP + + +
Sbjct: 71 KAKTLHVLTLKAPI---PPEHLRKIQSPCS 97
>gnl|CDD|173781 cd03361, TOPRIM_TopoIA_RevGyr, TopoIA_RevGyr : The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to the ATP-dependent reverse gyrase found in
archaea and thermophilic bacteria. Type IA DNA
topoisomerases remove (relax) negative supercoils in the
DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. Reverse gyrase is also able to
insert positive supercoils in the presence of ATP and
negative supercoils in the presence of AMPPNP. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). For topoisomerases the
conserved glutamate is believed to act as a general base
in strand joining and, as a general acid in strand
cleavage. The DXD motif may co-ordinate Mg2+, a cofactor
required for full catalytic function.
Length = 170
Score = 27.3 bits (61), Expect = 9.6
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 192 SRLESLRKFKDEETDVLIATDVAARGLDI 220
LE+LR+ E +VLIATD G I
Sbjct: 107 ETLEALRELALEVDEVLIATDPDTEGEKI 135
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
0.318 0.135 0.393
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: 20,224,707
Number of extensions: 1995530
Number of successful extensions: 2439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2425
Number of HSP's successfully gapped: 90
Length of query: 396
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 297
Effective length of database: 6,546,556
Effective search space: 1944327132
Effective search space used: 1944327132
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 (21.7 bits)
S2: 60 (26.8 bits)