RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17637
(150 letters)
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 141 bits (358), Expect = 8e-41
Identities = 49/94 (52%), Positives = 71/94 (75%)
Query: 49 ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN 108
E+A++L + + L LHGD++Q +R+ V+ +F + C +LVATDVAARGLDI + V+N
Sbjct: 257 EVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVIN 316
Query: 109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
Y+LARD + H HRIGRTGRAG+KG+A +LV ++
Sbjct: 317 YELARDPEVHVHRIGRTGRAGSKGLALSLVAPEE 350
Score = 29.0 bits (66), Expect = 0.82
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 1 RAGNKGVAYTLVTDKDKEFAGHLVRNLE 28
RAG+KG+A +LV ++ +E
Sbjct: 335 RAGSKGLALSLVAPEE----MQRANAIE 358
>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 = 132 bits (335), Expect = 2e-37
Identities = 56/103 (54%), Positives = 73/103 (70%)
Query: 46 NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
EELA SL + + V LHGD+ Q ER+ + KFK E R+LVATDVAARGLDIP +
Sbjct: 285 LVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSH 344
Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELR 148
V+NYDL D + + HRIGRTGRAG KGVA + VT++++ +L+
Sbjct: 345 VINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLK 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 = 115 bits (291), Expect = 4e-34
Identities = 43/91 (47%), Positives = 54/91 (59%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
+ELA L V LHGD Q ER V+ F+ E +LVATDV ARG+D+P++ V
Sbjct: 41 LDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVV 100
Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
+NYDL ++ RIGR GRAG KG A L
Sbjct: 101 INYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 104 bits (263), Expect = 1e-30
Identities = 33/76 (43%), Positives = 47/76 (61%)
Query: 54 LTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR 113
L V LHG + Q ER ++ F+ + ++LVATDVA RG+D+P + V+NYDL
Sbjct: 3 LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPW 62
Query: 114 DIDTHTHRIGRTGRAG 129
+ ++ RIGR GRAG
Sbjct: 63 NPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 103 bits (259), Expect = 6e-30
Identities = 38/82 (46%), Positives = 49/82 (59%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
EELA L V LHG + Q ER ++ KF + ++LVATDVA RGLD+P + V+
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
YDL ++ RIGR GRAG
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 110 bits (277), Expect = 2e-29
Identities = 44/91 (48%), Positives = 57/91 (62%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
ELA L + L G+M Q++RN I + +LVATDVAARG+DI + V+
Sbjct: 259 HELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVI 318
Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLV 138
N+D+ R DT+ HRIGRTGRAG KG A +LV
Sbjct: 319 NFDMPRSADTYLHRIGRTGRAGRKGTAISLV 349
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 106 bits (266), Expect = 1e-27
Identities = 44/99 (44%), Positives = 64/99 (64%), Gaps = 1/99 (1%)
Query: 46 NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
A+ L L + + L +HGD Q ER V+ +FK + I++ATDVA+RGLD+ ++
Sbjct: 389 GADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKY 448
Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVT-DKDK 143
V+N+D I+ + HRIGRTGRAG KG +YT +T DK +
Sbjct: 449 VINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYR 487
Score = 47.5 bits (113), Expect = 5e-07
Identities = 19/44 (43%), Positives = 24/44 (54%)
Query: 1 RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQ 44
RAG KG +YT +T A LV+ L A Q VPP L L+ +
Sbjct: 470 RAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNE 513
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 96.0 bits (239), Expect = 3e-24
Identities = 38/95 (40%), Positives = 60/95 (63%)
Query: 50 LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
L + +++ V +HGDMDQ +R+ ++ +F+ R+L+ TD+ ARG+D+ + V+NY
Sbjct: 283 LTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINY 342
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
DL + + HRIGR+GR G KGVA VT D +
Sbjct: 343 DLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIE 377
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 92.3 bits (230), Expect = 8e-23
Identities = 44/90 (48%), Positives = 57/90 (63%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
EE+ L + V LL GD+ Q +R ++ +F R + ILVATDVAARGL IP + V
Sbjct: 269 EEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVF 328
Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
NYDL D + + HRIGRTGRAG G + +L
Sbjct: 329 NYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 88.8 bits (220), Expect = 2e-21
Identities = 43/95 (45%), Positives = 61/95 (64%)
Query: 49 ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN 108
E+A +L Y+ L+GDM+Q+ R + + K IL+ATDVAARGLD+ I VVN
Sbjct: 260 EVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVN 319
Query: 109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
YD+ D +++ HRIGRTGRAG G A V ++++
Sbjct: 320 YDIPMDSESYVHRIGRTGRAGRAGRALLFVENRER 354
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 81.2 bits (200), Expect = 9e-19
Identities = 41/94 (43%), Positives = 60/94 (63%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
E +A +L Y V +L GD+ Q +R S++ +F++ + ILVATDVAARGL I ++ V
Sbjct: 271 ERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVY 330
Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDK 141
NYDL D + + HRIGRT R G +G A + ++
Sbjct: 331 NYDLPFDAEDYVHRIGRTARLGEEGDAISFACER 364
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 78.4 bits (193), Expect = 9e-18
Identities = 37/89 (41%), Positives = 51/89 (57%)
Query: 54 LTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR 113
L + L GD+ Q +R + F+ + R+LVATDVA RG+ I I V+N+ L
Sbjct: 355 LVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPE 414
Query: 114 DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
D D + HRIGRTGRAG GV+ + + D
Sbjct: 415 DPDDYVHRIGRTGRAGASGVSISFAGEDD 443
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 77.5 bits (191), Expect = 2e-17
Identities = 46/114 (40%), Positives = 61/114 (53%), Gaps = 17/114 (14%)
Query: 25 RNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE 84
R GAN LA QLN + + ++ +HG+ Q R + FK +
Sbjct: 253 RTKHGANH--------LAEQLNKDGIRSAA---------IHGNKSQGARTRALADFKSGD 295
Query: 85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLV 138
R+LVATD+AARGLDI + VVNY+L + + HRIGRTGRA G A +LV
Sbjct: 296 IRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLV 349
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 73.7 bits (181), Expect = 3e-16
Identities = 40/110 (36%), Positives = 64/110 (58%), Gaps = 1/110 (0%)
Query: 35 PPALMNLAMQLNAEELANSLTV-KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV 93
PPA++ ++ +L A+ LAN++TV L +HG+ ER V+ F E ++VAT V
Sbjct: 368 PPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGV 427
Query: 94 AARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
RG+D+ +R V+ +D+ I + H+IGR R G KG A V ++D+
Sbjct: 428 LGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDR 477
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 65.0 bits (159), Expect = 4e-13
Identities = 31/98 (31%), Positives = 45/98 (45%)
Query: 46 NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
EELA L H + ER V F E +++VAT+ G+D P +R
Sbjct: 242 KVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRF 301
Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
V++YDL I+++ GR GR G A L + +D
Sbjct: 302 VIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDI 339
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 62.7 bits (153), Expect = 2e-12
Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 68 MDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYD-LARDIDTHTHRIGRTG 126
M Q E+ +I +F++ E +LVAT V GLDIP + V+ Y+ + +I + R GRTG
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRS-IQRKGRTG 467
Query: 127 RAGNKGVAYTLVTDKDKD 144
R KG LVT+ +D
Sbjct: 468 R-KRKGRVVVLVTEGTRD 484
>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 = 57.4 bits (139), Expect = 2e-10
Identities = 27/95 (28%), Positives = 46/95 (48%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
EELA L + L H + R F + +++VAT+ G+D P++R V+
Sbjct: 238 EELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVI 297
Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
+YD+ +++++ GR GR G A L + D
Sbjct: 298 HYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPAD 332
>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 = 57.1 bits (138), Expect = 3e-10
Identities = 25/82 (30%), Positives = 44/82 (53%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
E++ SL H ++ S R+ V KF+R E +++VAT G++ P +R V+
Sbjct: 240 EQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVI 299
Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
+Y L + ++++ GR GR G
Sbjct: 300 HYSLPKSMESYYQESGRAGRDG 321
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 54.7 bits (132), Expect = 1e-09
Identities = 26/82 (31%), Positives = 44/82 (53%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
E+ A L + H +D R V F+R + +I+VAT G++ P++R VV
Sbjct: 250 EDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
++D+ R+I+++ GR GR G
Sbjct: 310 HFDIPRNIESYYQETGRAGRDG 331
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 53.5 bits (129), Expect = 4e-09
Identities = 34/107 (31%), Positives = 54/107 (50%), Gaps = 4/107 (3%)
Query: 46 NAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
AE L L +Y+V LLHG M E+ +V+ +F+ E ILVAT V G+D+P+
Sbjct: 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNA 527
Query: 104 RTVVNYDLARDIDTHTHRI-GRTGRAGNKGVAYTLVTD-KDKDGELR 148
+V D R + H++ GR GR ++ + + K + + R
Sbjct: 528 TVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKR 574
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 53.3 bits (129), Expect = 4e-09
Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 68 MDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA----RDIDTHTHRIG 123
M Q E+ ++ KF+ E +LV+T VA GLDIP + V+ Y+ R I R G
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSI----QRKG 462
Query: 124 RTGRAGNKGVAYTLVTDKDKD 144
RTGR +G L+ +D
Sbjct: 463 RTGR-QEEGRVVVLIAKGTRD 482
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 52.2 bits (126), Expect = 1e-08
Identities = 25/58 (43%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 46 NAEELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP 101
AEEL L + E V L+HG M +E+++V+ FK E ILVAT V G+D+P
Sbjct: 493 AAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVP 550
>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 = 50.0 bits (120), Expect = 8e-08
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 9/93 (9%)
Query: 56 VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV-----NYD 110
V E + + HG M ++E V+ +F + E ++LV T + G+DIP+ T++ +
Sbjct: 684 VPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFG 743
Query: 111 LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
LA + R GR GR+ K AY L +
Sbjct: 744 LA---QLYQLR-GRVGRSKKKAYAYLLYPHQKA 772
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 48.2 bits (115), Expect = 3e-07
Identities = 33/100 (33%), Positives = 44/100 (44%), Gaps = 8/100 (8%)
Query: 46 NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
ELA++LT K H + ER SV F QE +V T A G+D P
Sbjct: 452 RCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFP-ASQ 510
Query: 106 VVNYDLARDIDTHTHR-----IGRTGRAG--NKGVAYTLV 138
V+ LA I+ + R +GR GR ++G Y LV
Sbjct: 511 VIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLV 550
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 47.8 bits (114), Expect = 4e-07
Identities = 32/137 (23%), Positives = 56/137 (40%), Gaps = 21/137 (15%)
Query: 15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERN 74
K G L+++ G + + + +A E+A V + G+ + ER
Sbjct: 269 KIAAVRGLLLKHARGDKTLIFASDVE-----HAYEIAKLFLAPGI-VEAITGETPKEERE 322
Query: 75 SVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHR--IGRTGR----A 128
+++ +F+ ++LV V G+DIP ++ + R T + R I R GR A
Sbjct: 323 AILERFRTGGIKVLVTVKVLDEGVDIPDADVLI---ILR--PTGSRRLFIQRLGRGLRPA 377
Query: 129 GNKGVA----YTLVTDK 141
K Y+LV D
Sbjct: 378 EGKEDTLALDYSLVPDD 394
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 47.8 bits (115), Expect = 4e-07
Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 45 LNAEELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP 101
+AEE L E V LLHG M +E+++V+ FK E ILVAT V G+D+P
Sbjct: 490 QSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 46.5 bits (111), Expect = 1e-06
Identities = 30/102 (29%), Positives = 45/102 (44%), Gaps = 11/102 (10%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
AE L V E + + HG M + E V+ F E +LV T + G+DIP+ T+
Sbjct: 820 AERLREL--VPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTI 877
Query: 107 V-----NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
+ + LA + R GR GR+ + AY L +
Sbjct: 878 IIERADKFGLA---QLYQLR-GRVGRSNKQAYAYFLYPPQKA 915
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 46.4 bits (110), Expect = 1e-06
Identities = 27/99 (27%), Positives = 50/99 (50%), Gaps = 2/99 (2%)
Query: 44 QLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
+++ E++A L + HG MD ++R V ++ + E I+ AT G++ P +
Sbjct: 690 RMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDV 749
Query: 104 RTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTD 140
R V+++ L + I+ + GR GR G + V Y +D
Sbjct: 750 RFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSD 788
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 42.3 bits (100), Expect = 3e-05
Identities = 31/113 (27%), Positives = 52/113 (46%), Gaps = 17/113 (15%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
AE L + + ++L L+G + E+ V + ++++AT++A L IP IR V
Sbjct: 276 AEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYV 335
Query: 107 VNYDLAR----DIDTHTHR-----------IGRTGRAGN--KGVAYTLVTDKD 142
++ LA+ D T R R GRAG G+ Y L +++D
Sbjct: 336 IDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICYRLYSEED 388
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 41.7 bits (98), Expect = 6e-05
Identities = 30/99 (30%), Positives = 48/99 (48%), Gaps = 11/99 (11%)
Query: 46 NAEELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
N ++ A L V E + + HG M + E V+ F Q +LV T + G+DIP
Sbjct: 821 NIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA 880
Query: 104 RTVV-----NYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
T++ ++ LA+ H R GR GR+ ++ A+ L
Sbjct: 881 NTIIIERADHFGLAQ---LHQLR-GRVGRSHHQAYAWLL 915
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 38.7 bits (91), Expect = 5e-04
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 5/86 (5%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
AE+L L V LH D+D ER +I + E +LV ++ GLD+P + V
Sbjct: 459 AEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV 518
Query: 107 VNYD-----LARDIDTHTHRIGRTGR 127
D R + IGR R
Sbjct: 519 AILDADKEGFLRSERSLIQTIGRAAR 544
>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 = 38.6 bits (90), Expect = 6e-04
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 56 VKEYDVLLLHGDMDQSER----NSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL 111
E +++L+H + +R ++ +FK+ E ++VAT V LDI V+ +L
Sbjct: 242 GPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIVATQVIEASLDISV--DVMITEL 299
Query: 112 ARDIDTHTHRIGRTGRAGNK 131
A ID+ R+GR R G K
Sbjct: 300 A-PIDSLIQRLGRLHRYGEK 318
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 38.4 bits (90), Expect = 7e-04
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 47 AEELANSL-TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
AE LA L + + + HG + + R V + K E + +VAT G+DI I
Sbjct: 266 AERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDL 325
Query: 106 VVNYDLARDIDTHTHRIGRTGR 127
V+ + ++ RIGR G
Sbjct: 326 VIQLGSPKSVNRFLQRIGRAGH 347
>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 = 38.2 bits (89), Expect = 7e-04
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 58 EYDVLLLHGDMDQSER----NSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR 113
E +++LLH + +R ++ + K+ E ++VAT V LDI V+ +LA
Sbjct: 248 EEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDISA--DVMITELA- 304
Query: 114 DIDTHTHRIGRTGRAGNK 131
ID+ R+GR R G K
Sbjct: 305 PIDSLIQRLGRLHRYGRK 322
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 37.8 bits (88), Expect = 0.001
Identities = 34/114 (29%), Positives = 46/114 (40%), Gaps = 17/114 (14%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSER----NSVITKFKRQECRILVATDVAARGLDIPH 102
A EL L K VLLLH +R + FK+ E I+VAT V G+DI
Sbjct: 453 AIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-- 510
Query: 103 IRTVVNYDLA-RD---IDTHTHRIGRTGRAGNK--GVAYTLVTDKDKDGELRSQ 150
++D+ + ID+ R GR R G K G Y ++ S
Sbjct: 511 -----DFDVLITELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEERGPYLKYSY 559
>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 = 35.4 bits (82), Expect = 0.006
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 77 ITKFKRQECRILVATDVAARGLDIPHIRT--VVNYDLA----------RDIDTHTHRIGR 124
+ +F + IL+ T + A+G P++ V++ D R T GR
Sbjct: 305 LNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGR 364
Query: 125 TGRAGNKG 132
GRA + G
Sbjct: 365 AGRAEDPG 372
>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 = 35.3 bits (82), Expect = 0.008
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
AE+L + L V LH ++D ER +I + E +LV ++ GLD+P + V
Sbjct: 455 AEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV 514
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 34.3 bits (79), Expect = 0.018
Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT----DVAARGLDIPH 102
AEELA L + L+H +E+ + F+ E +LV V RGLD+PH
Sbjct: 351 AEELAEYLRSHGINAELIH-----AEKEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPH 405
Query: 103 -IRTVVNYD 110
IR V Y
Sbjct: 406 RIRYAVFYG 414
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 34.0 bits (78), Expect = 0.021
Identities = 32/108 (29%), Positives = 50/108 (46%), Gaps = 18/108 (16%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
E+LA L + + L+G++ + ++ I + ++++AT++A L I IR V
Sbjct: 226 QEQLAERLD-SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVV 284
Query: 107 VNYDLAR----DIDT-----HTHRIG------RTGRAGN--KGVAYTL 137
++ LAR D T T RI R GRAG GV Y L
Sbjct: 285 IDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRL 332
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 34.0 bits (78), Expect = 0.023
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 46 NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
+A E+ ++ ++L L+ + E+ V + RI++AT+VA L +P I
Sbjct: 294 DAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPHSGR--RIVLATNVAETSLTVPGIHY 351
Query: 106 VVNYDLARDIDTHTHRIGR 124
V IDT T RI R
Sbjct: 352 V--------IDTGTARISR 362
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 33.8 bits (78), Expect = 0.028
Identities = 22/89 (24%), Positives = 34/89 (38%), Gaps = 16/89 (17%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILV--AT--DVAARGLDIPH 102
AEELA L + L ++ KF+ E +LV A+ V RG+D+P
Sbjct: 344 AEELAEYLEDLGINAELAISGFERK-----FEKFEEGEVDVLVGVASYYGVLVRGIDLPE 398
Query: 103 -IRTVVNYDL------ARDIDTHTHRIGR 124
IR + Y + + + R
Sbjct: 399 RIRYAIFYGVPKFKFSLEEELAPPFLLLR 427
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 32.0 bits (73), Expect = 0.10
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 11/78 (14%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
A+ L N L ++ ++L L+ + SE+N V + RI++AT+VA L +P I+ V
Sbjct: 303 ADAL-NKLNLRHTEILPLYARLSNSEQNRVFQSHSGR--RIVLATNVAETSLTVPGIKYV 359
Query: 107 VNYDLARDIDTHTHRIGR 124
ID T RI R
Sbjct: 360 --------IDPGTARISR 369
>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 = 31.1 bits (71), Expect = 0.15
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 41 LAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT 91
LA Q+ EEL + V LL G E+ K K+ + ILV T
Sbjct: 57 LAEQI-YEELKKLFKILGLRVALLTGGTSLKEQ---ARKLKKGKADILVGT 103
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 30.9 bits (70), Expect = 0.22
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 47 AEELANSL---TVKEYDVLLLHGDMDQSER----NSVITKF----KRQECRILVATDVAA 95
A++L L + D+ L H ++R VI F KR + RILVAT V
Sbjct: 573 AQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVE 632
Query: 96 RGLDI 100
+ LD+
Sbjct: 633 QSLDL 637
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 30.9 bits (71), Expect = 0.25
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 14/72 (19%)
Query: 77 ITKFKRQECRILVATDVAARGLDIPHIRT---VVNYDLA----------RDIDTHTHRIG 123
+ +F R E IL+ T + A+G D P++ T V++ DL R T G
Sbjct: 473 LAQFARGEADILIGTQMLAKGHDFPNV-TLVGVLDADLGLFSPDFRASERTFQLLTQVAG 531
Query: 124 RTGRAGNKGVAY 135
R GRA G
Sbjct: 532 RAGRAEKPGEVL 543
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 30.8 bits (70), Expect = 0.25
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 13/92 (14%)
Query: 65 HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR--------DID 116
H + + +R V F++ + ++LV+T A G+++P RTV+ D R DI
Sbjct: 321 HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLP-ARTVIIKDTRRYDPKGGIVDIP 379
Query: 117 THTHR--IGRTGRAG--NKGVAYTLVTDKDKD 144
GR GR G + G A L T D+
Sbjct: 380 VLDVLQMAGRAGRPGYDDYGEAIILATSHDEL 411
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 29.8 bits (67), Expect = 0.48
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ-ECRILVATDVAARGLDIPH--I 103
+ +A L + + +L + ER ++ KFK E ILV G+D P +
Sbjct: 492 LKRVAERLKDERSTLPVL--TQGEDEREELLEKFKASGEGLILVGGGSFWEGVDFPGDAL 549
Query: 104 RTVV 107
R VV
Sbjct: 550 RLVV 553
>gnl|CDD|197335 cd09101, INPP5c_SHIP2-INPPL1, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of SH2 domain containing
inositol 5-phosphatase-2 and related proteins. This
subfamily contains the INPP5c domain of SHIP2 (SH2
domain containing inositol 5-phosphatase-2, also called
INPPL1) and related proteins. It belongs to a family of
Mg2+-dependent inositol polyphosphate 5-phosphatases,
which hydrolyze the 5-phosphate from the inositol ring
of various 5-position phosphorylated phosphoinositides
(PIs) and inositol phosphates (IPs), and to the large
EEP (exonuclease/endonuclease/phosphatase) superfamily
that contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. SHIP2 catalyzes the dephosphorylation of the PI,
phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3],
to phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2].
SHIP2 is widely expressed, most prominently in brain,
heart and in skeletal muscle. SHIP2 is an inhibitor of
the insulin signaling pathway. It is implicated in actin
structure remodeling, cell adhesion and cell spreading,
receptor endocytosis and degradation, and in the
JIP1-mediated JNK pathway. Its interacting partners
include filamin/actin, p130Cas, Shc, Vinexin,
Interesectin 1, and c-Jun NH2-terminal kinase
(JNK)-interacting protein 1 (JIP1). A large variety of
extracellular stimuli appear to lead to the tyrosine
phosphorylation of SHIP2, including epidermal growth
factor (EGF), platelet-derived growth factor (PDGF),
insulin, macrophage colony-stimulating factor (M-CSF)
and hepatocyte growth factor (HGF). SHIP2 is localized
to the cytosol in quiescent cells; following growth
factor stimulation and /or cell adhesion, it relocalizes
to membrane ruffles. In addition to this INPP5c domain,
SHIP2 has an N-terminal SH2 domain, a C-terminal
proline-rich domain (PRD), which includes a WW-domain
binding motif (PPLP), an NPXY motif and a sterile alpha
motif (SAM) domain. The gene encoding SHIP2 is a
candidate for conferring a predisposition for type 2
diabetes; it has been suggested that suppression of
SHIP2 may be of benefit in the treatment of obesity and
thereby prevent type 2 diabetes. SHIP2 and SHIP1 have
little overlap in their in vivo functions.
Length = 304
Score = 29.2 bits (65), Expect = 0.70
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 7/50 (14%)
Query: 39 MNLAMQLNAEELANSLTVKEYDVLLLHGDMDQ----SERNSVITKFKRQE 84
+N + ++ +E+ N +T KE+D LL +DQ E+N V +F+ +E
Sbjct: 185 LNYRLDMDIQEILNYITRKEFDPLL---AVDQLNLEREKNKVFLRFREEE 231
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 29.2 bits (66), Expect = 0.80
Identities = 29/106 (27%), Positives = 47/106 (44%), Gaps = 16/106 (15%)
Query: 48 EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP------ 101
E L+ L +L+ D E +++ + ++ RI VAT++A RG DI
Sbjct: 487 ERLSALLREAGLPHQVLNAKQDAEE-AAIVARAGQRG-RITVATNMAGRGTDIKLEPGVA 544
Query: 102 -----HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
H+ +D AR ID GR GR G+ G +++ +D
Sbjct: 545 ARGGLHVILTERHDSAR-IDRQL--AGRCGRQGDPGSYEAILSLED 587
>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 = 28.3 bits (64), Expect = 1.0
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP--HIR 104
AE LA+ L K ++L+ + R ++ +FK+ + IL G+D P +R
Sbjct: 26 AELLASELLEKGIELLV----QGEGSREKLLERFKKGKGAILFGVGSFWEGIDFPGDALR 81
Query: 105 TVV 107
V+
Sbjct: 82 LVI 84
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 29.1 bits (65), Expect = 1.1
Identities = 17/62 (27%), Positives = 27/62 (43%)
Query: 65 HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
HG + + +R K E R +VAT G+D+ + V+ + + RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
Query: 125 TG 126
G
Sbjct: 368 AG 369
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 27.3 bits (61), Expect = 1.2
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 39 MNLAMQLNAEELANSLTVKEYDVLLLHGD 67
MNL + NAEE+ + V++ +++ GD
Sbjct: 38 MNLVLD-NAEEIQDGEVVRKLGKVVIRGD 65
>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 = 28.6 bits (64), Expect = 1.3
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 18/65 (27%)
Query: 73 RNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRI---------- 122
R + F+ + +L+ T + RG+ P++ V + HR+
Sbjct: 344 RKEKVEAFRDGKITLLITTTILERGVTFPNVDVFV-------LGAE-HRVFTESALVQIA 395
Query: 123 GRTGR 127
GR GR
Sbjct: 396 GRVGR 400
>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 = 28.1 bits (63), Expect = 1.8
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 61 VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL-ARDIDTHT 119
V + + ER + +FK E ++AT+ G+DI + V+ Y + +
Sbjct: 341 VSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFR 400
Query: 120 HRIGRTGRAGN 130
R GR GR G
Sbjct: 401 QRAGRAGRRGQ 411
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 28.1 bits (63), Expect = 2.0
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 77 ITKFKRQECRILVATDVAARGLDIPHIRTVV 107
+ +F E IL+ T + A+G D P++ V
Sbjct: 527 LDQFANGEADILIGTQMIAKGHDFPNVTLVG 557
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 27.9 bits (62), Expect = 2.7
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 10/83 (12%)
Query: 65 HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHT----- 119
H + +R + F+ + +++VAT A G+++P R V+ D+ R +
Sbjct: 292 HAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLP-ARLVIVRDITRYGNGGIRYLSN 350
Query: 120 ----HRIGRTGRAGNKGVAYTLV 138
IGR GR G +
Sbjct: 351 MEIKQMIGRAGRPGYDQYGIGYI 373
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 27.5 bits (62), Expect = 3.1
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 65 HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
H + + R V K KR E +++V++ G+DI +I VV + + RIGR
Sbjct: 321 HSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGR 380
Query: 125 TG-RAGNKGVAYTLVTDKD 142
G R G +V D+D
Sbjct: 381 AGHRLGEVSKGRIIVVDRD 399
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 27.1 bits (61), Expect = 4.1
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 53 SLTVKEY-DVLLLHGDMDQSERNSVITKF 80
+ KEY V+ LHGD+ + + V +F
Sbjct: 80 LESGKEYVCVMHLHGDVPEEDIRKVFKEF 108
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 26.9 bits (60), Expect = 4.4
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 69 DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
+ ER ++ +F+ + LVA G+DIP RT
Sbjct: 324 SKEEREELLRQFESGLLQGLVAIRCLDEGVDIPATRTAY 362
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 305
Score = 26.8 bits (60), Expect = 5.1
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 86 RILVATDVAARGLD-IPHIRTVVNYDLARDID 116
+IL A ++ +GL+ + V D D D
Sbjct: 2 KILTANKISKKGLERFKKDKYEVKEDALEDPD 33
>gnl|CDD|178585 PLN03008, PLN03008, Phospholipase D delta.
Length = 868
Score = 27.0 bits (59), Expect = 5.2
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 60 DVLLLHGDMD----QSERNSVITKFKRQECRILVATDVAARGLD 99
DV+LLHGD+D ++ R + F R+ A + AR D
Sbjct: 8 DVMLLHGDLDLKIVKARRLPNMDMFSEHLRRLFTACNACARPTD 51
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 26.3 bits (59), Expect = 6.7
Identities = 11/33 (33%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 89 VATDVAARGLDIPHIRTVVNYDLARDIDTHTHR 121
T A GLD VV DL D R
Sbjct: 352 TTTAAAREGLDAAR---VVLIDLLLDYAAAKRR 381
>gnl|CDD|236405 PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.
Length = 565
Score = 26.2 bits (59), Expect = 8.1
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 47 AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFK 81
AE+L L +VLL D D+ ER V KF
Sbjct: 487 AEKLYAELQAAGIEVLL---D-DRKERPGV--KFA 515
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 26.1 bits (58), Expect = 9.0
Identities = 11/26 (42%), Positives = 11/26 (42%)
Query: 4 NKGVAYTLVTDKDKEFAGHLVRNLEG 29
KG V DKDKE L R L
Sbjct: 936 KKGSVLLSVRDKDKEELLDLARKLAE 961
>gnl|CDD|197333 cd09099, INPP5c_Synj2, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of synaptojanin 2. This
subfamily contains the INPP5c domains of human
synaptojanin 2 (Synj2) and related proteins. It belongs
to a family of Mg2+-dependent inositol polyphosphate
5-phosphatases, which hydrolyze the 5-phosphate from the
inositol ring of various 5-position phosphorylated
phosphoinositides (PIs) and inositol phosphates (IPs),
and to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. Synj2 can hydrolyze phosphatidylinositol
diphosphate (PIP2) to phosphatidylinositol phosphate
(PIP). In addition to this INPP5c domain, these proteins
contain an N-terminal Sac1-like domain; the Sac1 domain
can dephosphorylate a variety of phosphoinositides in
vitro. Synj2 occurs as multiple alternative splice
variants in various tissues. These variants share the
INPP5c domain and the Sac1 domain. Synj2A is recruited
to the mitochondria via its interaction with OMP25, a
mitochondrial outer membrane protein. Synj2B is found at
nerve terminals in the brain and at the spermatid
manchette in testis. Synj2B undergoes further
alternative splicing to give 2B1 and 2B2. In
clathrin-mediated endocytosis, Synj2 participates in the
formation of clathrin-coated pits, and perhaps also in
vesicle decoating. Rac1 GTPase regulates the
intracellular localization of Synj2 forms, but not
Synj1. Synj2 may contribute to the role of Rac1 in cell
migration and invasion, and is a potential target for
therapeutic intervention in malignant tumors.
Length = 336
Score = 26.1 bits (57), Expect = 9.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 113 RDIDTHTHRIGRTGRAGNKG 132
RD+ T + G G+AGNKG
Sbjct: 119 RDVAIDTVKTGMGGKAGNKG 138
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.133 0.373
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: 7,425,074
Number of extensions: 664999
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 677
Number of HSP's successfully gapped: 87
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.5 bits)