RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17587
(231 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 136 bits (343), Expect = 4e-37
Identities = 56/118 (47%), Positives = 81/118 (68%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
+ KEL G+P L +HG Q +R + +FK GK ++IAT VA+RGLDVK + V+N+
Sbjct: 393 LTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINF 452
Query: 98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKM 155
D PN EDYVHR GRTGRAG KG +YTF+T ++ R A ++++ L + P+P +L+K+
Sbjct: 453 DFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKL 510
>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 = 130 bits (329), Expect = 3e-35
Identities = 56/139 (40%), Positives = 79/139 (56%), Gaps = 3/139 (2%)
Query: 14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
+ D IV F K + + + L K G+ +LHG + Q +RD + FK+G++
Sbjct: 268 LKDEDEGRVIV-FVRTKRLVE--ELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGEL 324
Query: 74 RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
R+L+AT VAARGLD+ ++ V+NYD P EDYVHR GRTGRAG KG A +F+T E+E
Sbjct: 325 RVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVK 384
Query: 134 AGEIIRALEASGVPIPEDL 152
+ I +P L
Sbjct: 385 KLKRIEKRLERKLPSAVLL 403
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 122 bits (308), Expect = 2e-32
Identities = 50/122 (40%), Positives = 70/122 (57%), Gaps = 3/122 (2%)
Query: 16 QYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRL 75
+ +S +V F N K + L G+ L+LHG ++Q DRD +V F N +
Sbjct: 239 HHQPESCVV-FCNTKKE--CQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSV 295
Query: 76 LIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAG 135
L+AT VAARGLD+K L V+NY+ E +VHR GRTGRAG+KG A + + E+ + A
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRAN 355
Query: 136 EI 137
I
Sbjct: 356 AI 357
>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 = 102 bits (257), Expect = 1e-28
Identities = 38/78 (48%), Positives = 52/78 (66%)
Query: 40 KELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDC 99
K L K G LHGG+ Q +R+ + DF+NGK ++L+AT VA RG+D+ +NLV+NYD
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 100 PNHYEDYVHRCGRTGRAG 117
P + Y+ R GR GRAG
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>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 = 101 bits (254), Expect = 2e-27
Identities = 35/88 (39%), Positives = 54/88 (61%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
+ + L K G +LHG Q +R+ + DF+ G++ +L+AT V ARG+D+ ++++V+NY
Sbjct: 44 LAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINY 103
Query: 98 DCPNHYEDYVHRCGRTGRAGNKGFAYTF 125
D P Y+ R GR GRAG KG A
Sbjct: 104 DLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 95.7 bits (239), Expect = 7e-26
Identities = 34/80 (42%), Positives = 50/80 (62%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
+ + L + G LHGG+ Q +R+ + F NGK+++L+AT VA RGLD+ ++LV+ Y
Sbjct: 3 LAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIY 62
Query: 98 DCPNHYEDYVHRCGRTGRAG 117
D P Y+ R GR GRAG
Sbjct: 63 DLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 97.6 bits (243), Expect = 2e-23
Identities = 50/113 (44%), Positives = 71/113 (62%), Gaps = 3/113 (2%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
+ + L + GY +L+G ++Q R+ T+ K+G++ +LIAT VAARGLDV+ ++LVVNY
Sbjct: 261 VAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNY 320
Query: 98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPE 150
D P E YVHR GRTGRAG G A F+ + R I R ++ + IPE
Sbjct: 321 DIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLT---IPE 370
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 95.3 bits (237), Expect = 6e-23
Identities = 44/108 (40%), Positives = 67/108 (62%)
Query: 32 RLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHL 91
R V + K++ + + +HG +DQ DRD + +F++G R+LI T + ARG+DV+ +
Sbjct: 277 RRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQV 336
Query: 92 NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIR 139
+LV+NYD P E+Y+HR GR+GR G KG A F+T + EI R
Sbjct: 337 SLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 94.2 bits (235), Expect = 2e-22
Identities = 44/113 (38%), Positives = 64/113 (56%)
Query: 30 KVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK 89
+ R V + L KAG C L G + Q R+ I +G+V +L+AT VAARG+D+
Sbjct: 253 RTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDID 312
Query: 90 HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
++ V+N+D P + Y+HR GRTGRAG KG A + + G+I R +E
Sbjct: 313 DVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIE 365
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 94.1 bits (234), Expect = 3e-22
Identities = 44/105 (41%), Positives = 67/105 (63%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
+ ++L K G ++HG Q R + DFK+G +R+L+AT +AARGLD++ L VVNY
Sbjct: 261 LAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNY 320
Query: 98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
+ PN EDYVHR GRTGRA G A + + +++ + +I + L+
Sbjct: 321 ELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLK 365
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 85.0 bits (211), Expect = 3e-19
Identities = 36/77 (46%), Positives = 45/77 (58%), Gaps = 6/77 (7%)
Query: 52 LHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL---DVKHLNLVVNYDCPNHYEDYVH 108
L G + Q R + +F G + +L+AT VAARGL V H V NYD P+ EDYVH
Sbjct: 285 LTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTH---VFNYDLPDDCEDYVH 341
Query: 109 RCGRTGRAGNKGFAYTF 125
R GRTGRAG G + +
Sbjct: 342 RIGRTGRAGASGHSISL 358
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 83.0 bits (205), Expect = 2e-18
Identities = 37/88 (42%), Positives = 55/88 (62%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
I + L+K G L G + Q+ R T+ F+ GK+R+L+AT VA RG+ + ++ V+N+
Sbjct: 351 IEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINF 410
Query: 98 DCPNHYEDYVHRCGRTGRAGNKGFAYTF 125
P +DYVHR GRTGRAG G + +F
Sbjct: 411 TLPEDPDDYVHRIGRTGRAGASGVSISF 438
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 81.9 bits (202), Expect = 5e-18
Identities = 45/109 (41%), Positives = 61/109 (55%), Gaps = 5/109 (4%)
Query: 26 FKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG 85
F N K V + + L + GY L G + Q R+S + F+ G++ +L+AT VAARG
Sbjct: 263 FVNTKA--FVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARG 320
Query: 86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHA 134
L + + V NYD P EDYVHR GRT R G +G A +F ER+A
Sbjct: 321 LHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC---ERYA 366
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 80.6 bits (199), Expect = 1e-17
Identities = 37/107 (34%), Positives = 59/107 (55%)
Query: 46 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
G LS+HG +R + F G+V +++AT V RG+D+ + V+ +D PN ++
Sbjct: 392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKE 451
Query: 106 YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDL 152
Y+H+ GR R G KG A F+ E E++ L++SG IP +L
Sbjct: 452 YIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPREL 498
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 52.7 bits (127), Expect = 4e-08
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 55 GIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTG 114
G+ Q ++ I F+ G+ +L+ATSV GLD+ ++LV+ Y+ + R GRTG
Sbjct: 408 GMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTG 467
Query: 115 RAGNKGFAYTFIT 127
R KG +T
Sbjct: 468 R-KRKGRVVVLVT 479
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 46.0 bits (110), Expect = 8e-06
Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 26/98 (26%)
Query: 37 AIVKELMKAGYPCLSLHGGIDQYDRDS-----------TIVDFKNGKVRLLIATSVAARG 85
IV L K G + G Q +D + F+ G+ +L++TSVA G
Sbjct: 380 KIVDLLEKEGIKAVRFVG---QASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEG 436
Query: 86 LDVKHLNLVVNYDCPNHYED------YVHRCGRTGRAG 117
LD+ ++LV+ YE + R GRTGR
Sbjct: 437 LDIPSVDLVI------FYEPVPSEIRSIQRKGRTGRQE 468
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 45.4 bits (108), Expect = 1e-05
Identities = 24/88 (27%), Positives = 41/88 (46%)
Query: 38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
+ + L K G + H G+ +R+ F N ++++++AT+ G+D + V++Y
Sbjct: 246 LAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHY 305
Query: 98 DCPNHYEDYVHRCGRTGRAGNKGFAYTF 125
D P E Y GR GR G A
Sbjct: 306 DLPGSIESYYQETGRAGRDGLPAEAILL 333
>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 = 41.2 bits (97), Expect = 2e-04
Identities = 24/80 (30%), Positives = 37/80 (46%)
Query: 46 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
G L+ H G+ R DF V++++AT+ G+D ++ V++YD P + E
Sbjct: 248 GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLES 307
Query: 106 YVHRCGRTGRAGNKGFAYTF 125
Y GR GR G A
Sbjct: 308 YYQEAGRAGRDGLPAEAILL 327
>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 = 40.9 bits (96), Expect = 3e-04
Identities = 20/77 (25%), Positives = 35/77 (45%)
Query: 41 ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
L G + H G++ RD F+ ++++++AT G++ + V++Y P
Sbjct: 245 SLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLP 304
Query: 101 NHYEDYVHRCGRTGRAG 117
E Y GR GR G
Sbjct: 305 KSMESYYQESGRAGRDG 321
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 36.7 bits (86), Expect = 0.009
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 25/84 (29%)
Query: 60 DRDST---------IVDFKNGKVRLLIATSVAARGLDVKHLNLV--VNYDCPNHYEDYVH 108
DRD+T + F G+ +LI T + A+G D ++ LV ++ D D+
Sbjct: 459 DRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDF-- 516
Query: 109 RC------------GRTGRAGNKG 120
R GR GRA G
Sbjct: 517 RASERTFQLLTQVAGRAGRAEKPG 540
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 35.8 bits (83), Expect = 0.017
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 47 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDY 106
Y LHG + ++++ + +F+ G+V +L+AT+V G+DV + ++V D
Sbjct: 483 YNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQ 542
Query: 107 VHRC-GRTGRAGNKGFA 122
+H+ GR GR ++ +
Sbjct: 543 LHQLRGRVGRGDHQSYC 559
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 35.3 bits (82), Expect = 0.026
Identities = 14/47 (29%), Positives = 30/47 (63%)
Query: 52 LHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD 98
+HG + ++D+ + FK G++ +L+AT+V G+DV + ++V +
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIEN 559
Score = 27.2 bits (61), Expect = 8.3
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKE 41
+HG + ++D+ + FK G++ +LV V E
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIE 544
>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 = 35.0 bits (81), Expect = 0.028
Identities = 23/94 (24%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 52 LHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLN--LVVNYDCPNHYEDYVHR 109
HG + + + + +++F G+ ++L+ T++ G+D+ + N ++ D + Y R
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLR 751
Query: 110 CGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA 143
GR GR+ K +AY + Q+ + + LEA
Sbjct: 752 -GRVGRSKKKAYAY-LLYPHQKALTEDAQKRLEA 783
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 34.9 bits (81), Expect = 0.029
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 53 HGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGR 112
HG + + R K G+++ ++ATS G+D+ ++LV+ P ++ R GR
Sbjct: 285 HGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGR 344
Query: 113 TGR 115
G
Sbjct: 345 AGH 347
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 34.9 bits (80), Expect = 0.034
Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 51 SLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRC 110
S HG + + R T K+G++R ++ATS G+D+ ++LV+ P + R
Sbjct: 306 SHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRI 365
Query: 111 GRTG 114
GR G
Sbjct: 366 GRAG 369
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 34.3 bits (79), Expect = 0.044
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 53 HGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGR 112
H G+D R F+ +++++AT G++ ++ VV++D P + E Y GR
Sbjct: 267 HAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGR 326
Query: 113 TGRAG 117
GR G
Sbjct: 327 AGRDG 331
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 33.1 bits (76), Expect = 0.11
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 19/78 (24%)
Query: 56 IDQYDRDST---------IVDFKNGKVRLLIATSVAARGLDVKHLNL--VVNYDCPNHYE 104
I + D D+T + F NGK +LI T + A+G ++ L V++ D H
Sbjct: 287 IARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSP 346
Query: 105 DYVHRCGRTGRAGNKGFA 122
D+ RA +GF
Sbjct: 347 DF--------RAAERGFQ 356
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 32.8 bits (74), Expect = 0.14
Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 8/82 (9%)
Query: 40 KELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK--VRLLIATSVAARGLDVKHLNLVVNY 97
L G + L G R I F + L++ GL++ + V+ +
Sbjct: 729 DYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILF 788
Query: 98 D-CPNH-----YEDYVHRCGRT 113
D N D HR G+
Sbjct: 789 DPWWNPAVELQAIDRAHRIGQK 810
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 32.9 bits (75), Expect = 0.15
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 36 CAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLV 94
C V E ++ G+ HG +D R + ++ ++ AT G++ + V
Sbjct: 693 CEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFV 752
Query: 95 VNYDCPNHYEDYVHRCGRTGRAGNK 119
+++ P E Y CGR GR G +
Sbjct: 753 IHHSLPKSIEGYHQECGRAGRDGQR 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 = 32.7 bits (75), Expect = 0.17
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 77 IATSVAARGLDVK---------HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT 127
+ATS+A RG D+K L ++ N D R GR+GR G+ G + F++
Sbjct: 477 VATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVDLQLR-GRSGRQGDPGSSQFFVS 535
Query: 128 LE 129
LE
Sbjct: 536 LE 537
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 32.6 bits (75), Expect = 0.17
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 23/83 (27%)
Query: 53 HGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRC-- 110
HG + + + + ++DF NG+ +L+ T++ G+D+ + N ++ + R
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII-----------IERADK 884
Query: 111 ----------GRTGRAGNKGFAY 123
GR GR+ + +AY
Sbjct: 885 FGLAQLYQLRGRVGRSNKQAYAY 907
>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 = 32.1 bits (73), Expect = 0.23
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 39 VKELMKAGYPCL---SLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNL-V 94
V +K P S+H DQ R + F++GK+ LLI T++ RG+ ++++ V
Sbjct: 321 VAAALKKKLPKETIASVHS-EDQ-HRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFV 378
Query: 95 VNYDCPNHYED-YVHRCGRTGR 115
+ + E V GR GR
Sbjct: 379 LGAEHRVFTESALVQIAGRVGR 400
>gnl|CDD|225652 COG3110, COG3110, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 216
Score = 31.7 bits (72), Expect = 0.24
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 146 VPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRA-----LEASGVP 200
+ + D + LIV F A N + L ER A + I+ L+ G P
Sbjct: 67 IRLGSDRRLYISPPLIVT---FNAQNIDLVFFLPRLRNEREANKFIKTPRWQLLDGDGTP 123
Query: 201 IPEDLDKILAEGLVWLRDYKQ 221
I D + EGL R+Y+
Sbjct: 124 IAVKQDVLAQEGLQKGRNYEV 144
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 31.5 bits (72), Expect = 0.34
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 60 DRDST---------IVDFKNGKVRLLIATSVAARGLDVKHLNLVV 95
D D+T + F NG+ +LI T + A+G D ++ LV
Sbjct: 513 DSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVG 557
>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 = 31.2 bits (71), Expect = 0.42
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 37 AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN 96
+V+E K + G+ + +R +FK G++ +IAT+ G+D+ L+ V+
Sbjct: 329 RLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIA 388
Query: 97 YDCPNH-YEDYVHRCGRTGRAGNKGFAY 123
Y P + R GR GR G +
Sbjct: 389 YGYPGVSVLSFRQRAGRAGRRGQESLVL 416
>gnl|CDD|237255 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 31.3 bits (71), Expect = 0.45
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 58 QYDRDSTIVDFKNGKVRLLIATSVAARGLDVK------HLNLVVNYDCPNHYEDYVHRC- 110
Q+DR++ IV K + IAT++A RG D+K L + H + R
Sbjct: 632 QHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQL 691
Query: 111 -GRTGRAGNKGFAYTFITLEQE 131
GR GR G+ G + +++LE E
Sbjct: 692 RGRAGRQGDPGESVFYVSLEDE 713
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 31.3 bits (72), Expect = 0.49
Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 41 ELMKAGYPCLS---LHGGIDQYDRDSTIVDFKNGKVRLLIATSV 81
E ++ +P L LHG + ++D+ + FK G++ +L+AT+V
Sbjct: 497 EELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTV 540
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 30.9 bits (70), Expect = 0.54
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 19 RDSTIVDFKNGKVRLLVC-AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLI 77
R TIV F + R C + L G H G+ +R S F ++ ++
Sbjct: 440 RGQTIV-FTYSRRR---CHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVV 495
Query: 78 ATSVAARGLD 87
T+ A G+D
Sbjct: 496 TTAALAAGVD 505
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 30.9 bits (70), Expect = 0.55
Identities = 10/57 (17%), Positives = 30/57 (52%)
Query: 39 VKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV 95
+ +L A ++ G + +R++ + F+ G +++L+ V G+D+ ++++
Sbjct: 299 IAKLFLAPGIVEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLI 355
>gnl|CDD|215298 PLN02542, PLN02542, fructose-1,6-bisphosphatase.
Length = 412
Score = 29.8 bits (67), Expect = 1.1
Identities = 16/29 (55%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 10 LHGGIDQYDRDSTIVDFKNGKVRLLV-CA 37
L+GGI Y RD KNGK+RLL CA
Sbjct: 337 LYGGIYGYPRDKKS---KNGKLRLLYECA 362
Score = 29.5 bits (66), Expect = 1.8
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 52 LHGGIDQYDRDSTIVDFKNGKVRLL 76
L+GGI Y RD KNGK+RLL
Sbjct: 337 LYGGIYGYPRDKKS---KNGKLRLL 358
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 29.6 bits (67), Expect = 1.4
Identities = 30/121 (24%), Positives = 48/121 (39%), Gaps = 23/121 (19%)
Query: 40 KELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK---------- 89
L +AG P L+ D ++ IV + R+ +AT++A RG D+K
Sbjct: 491 ALLREAGLPHQVLNAKQDA--EEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGG 548
Query: 90 -HLNLVVNYDCPNHYEDYVHR--CGRTGRAGNKGFAYTFITLEQE---RHAGEIIRALEA 143
H+ L +D + R GR GR G+ G ++LE + G A+
Sbjct: 549 LHVILTERHDSAR-----IDRQLAGRCGRQGDPGSYEAILSLEDDLLQSFLGSRGLAIRR 603
Query: 144 S 144
Sbjct: 604 M 604
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 29.9 bits (67), Expect = 1.4
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 10/83 (12%)
Query: 53 HGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYV----- 107
H G+ R F+N +++++AT A G+++ LV+ D + +
Sbjct: 292 HAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLP-ARLVIVRDITRYGNGGIRYLSN 350
Query: 108 ----HRCGRTGRAGNKGFAYTFI 126
GR GR G + +I
Sbjct: 351 MEIKQMIGRAGRPGYDQYGIGYI 373
>gnl|CDD|107250 cd01537, PBP1_Repressors_Sugar_Binding_like, Ligand-binding
domain of the LacI-GalR family of transcription
regulators and the sugar-binding domain of ABC-type
transport systems. Ligand-binding domain of the
LacI-GalR family of transcription regulators and the
sugar-binding domain of ABC-type transport systems, all
of which contain the type I periplasmic binding
protein-like fold. Their specific ligands include
lactose, ribose, fructose, xylose, arabinose,
galactose/glucose, and other sugars. The LacI family of
proteins consists of transcriptional regulators related
to the lac repressor; in general the sugar binding
domain in this family binds a sugar, which in turn
changes the DNA binding activity of the repressor
domain. The core structure of the periplasmic binding
proteins is classified into two types and they differ
in number and order of beta strands in each domain:
type I, which has six beta strands, and type II, which
has five beta strands. These two distinct structural
arrangements may have originated from a common
ancestor.
Length = 264
Score = 29.3 bits (66), Expect = 1.5
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 8/72 (11%)
Query: 2 KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCA--------IVKELMKAGYPCLSLH 53
AGY L + D + S + + V ++ A IVK KAG P + +
Sbjct: 27 AAGYQVLLANSQNDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKAGIPVVLVD 86
Query: 54 GGIDQYDRDSTI 65
I DR ++
Sbjct: 87 RDIPDGDRVPSV 98
>gnl|CDD|220636 pfam10222, DUF2152, Uncharacterized conserved protein (DUF2152).
This is a family of proteins conserved from worms to
humans. Its function is unknown.
Length = 603
Score = 29.5 bits (66), Expect = 1.8
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVC 36
P +S+ + ++T+V+FK G V C
Sbjct: 118 SPIVSVAIDGAGPEAEATVVEFKEGLVHRFRC 149
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 28.8 bits (65), Expect = 1.9
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 23 IVDFKN-GKVRLLVCAIVKELMKAGY-PCL--SLHGGIDQYDRDS 63
++ FK+ GK L + I+K L + GY H D+ D D+
Sbjct: 6 VIGFKDSGKTTL-IEKILKNLKERGYRVATAKHTHHEFDKPDTDT 49
>gnl|CDD|227174 COG4837, COG4837, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 106
Score = 27.5 bits (61), Expect = 2.8
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 10/94 (10%)
Query: 143 ASGVPIPEDLDKM-WAEDLIVRTFCFRAGNKGFAYTFITLEQ---ERHAGEIIRALEASG 198
AS V P D W E + R + N+ F YT+I + E H + +E
Sbjct: 17 ASCVNAPTSKDTYEWLEAALKRKY----PNQPFKYTYIDITNPPLEDHDLQFAEKIEQDE 72
Query: 199 VPIPEDL--DKILAEGLVWLRDYKQRVDQRIARE 230
P + D+I+AEG L+D + +D + E
Sbjct: 73 YFYPLIVVEDEIVAEGNPRLKDIYRVMDDKGYNE 106
>gnl|CDD|216422 pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has
been shown to bind preferentially to dsRNA. The domain
is found in SUA5 as well as HypF and YrdC. It has also
been shown to be required for telomere recombniation in
yeast.
Length = 178
Score = 28.2 bits (64), Expect = 3.0
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 10 LHGGIDQYDRDSTIVDFKNGKVRLL 34
L GG DST+VD +GK R+L
Sbjct: 151 LDGGRIPVGVDSTVVDLTDGKPRIL 175
Score = 28.2 bits (64), Expect = 3.0
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 52 LHGGIDQYDRDSTIVDFKNGKVRLL 76
L GG DST+VD +GK R+L
Sbjct: 151 LDGGRIPVGVDSTVVDLTDGKPRIL 175
>gnl|CDD|131482 TIGR02429, pcaI_scoA_fam, 3-oxoacid CoA-transferase, A subunit.
Various members of this family are characterized as the
A subunits of succinyl-CoA:3-ketoacid-CoA transferase
(EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase
(EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase
(EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase
(EC 2.8.3.9). This represents a very distinct clade
with strong sequence conservation within the larger
family defined by pfam01144. The B subunit represents a
different clade in pfam01144, described by TIGR02428.
The two are found in general as tandem genes and
occasionally as a fusion.
Length = 222
Score = 27.8 bits (62), Expect = 3.7
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 3 AGYPCLSLHGGIDQYDRDSTIVD-------------FKNGKVRLLVCAIVKELMKAGYPC 49
AG P + ID +D TIV K G+VR L+C+ ++ +
Sbjct: 30 AGQPFELIDALIDTGAKDLTIVSNNAGNGEIGLAALLKAGQVRKLICSFPRQSDSYVFDE 89
Query: 50 LSLHGGID 57
L G I+
Sbjct: 90 LYRAGKIE 97
>gnl|CDD|220262 pfam09485, CRISPR_Cse2, CRISPR-associated protein Cse2
(CRISPR_cse2). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This family of proteins,
represented by CT1973 from Chlorobaculum tepidum, is
encoded by genes found in the CRISPR/Cas subtype Ecoli
regions of many bacteria (most of which are mesophiles),
and not in Archaea. It is designated Cse2.
Length = 143
Score = 27.3 bits (61), Expect = 3.7
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 182 EQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIARE 230
E R ++R L GVP+ D LA L++ D QRV +R AR+
Sbjct: 96 ELLRRLRRLVRLLRGDGVPV--DYAD-LARDLLYWNDETQRVRRRWARD 141
>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 = 28.2 bits (63), Expect = 3.8
Identities = 21/110 (19%), Positives = 38/110 (34%), Gaps = 19/110 (17%)
Query: 52 LHGGIDQYDRDS----TIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYV 107
LH + DR + + K + +++AT V LD+ ++++ P + +
Sbjct: 254 LHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLI 310
Query: 108 HRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA-SGVPIPEDLDKMW 156
R GR R G K E+ A G P + +
Sbjct: 311 QRLGRLHRYGRK-----------NGENFEVYIITIAPEGKLFPYPYELVE 349
>gnl|CDD|192316 pfam09533, DUF2380, Predicted lipoprotein of unknown function
(DUF2380). This family consists of at least 9 paralogs
in Myxococcus xanthus, a member of the
Deltaproteobacteria. One appears truncated toward the
N-terminus; the others are predicted lipoproteins. The
function is unknown.
Length = 191
Score = 27.5 bits (61), Expect = 4.7
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGF-----AYTFITLEQ-ERHAGEI 137
RG+ + L + P +H G G A N+ + + E+ RHAGE+
Sbjct: 119 RGVKIHDYTLPI----PRDVHRRIHGGGGRGGAWNQAWRDFRRRNPGASPEEIFRHAGEL 174
Query: 138 IRALEASGVPI 148
I E +G PI
Sbjct: 175 IFRFELTGGPI 185
>gnl|CDD|238033 cd00078, HECTc, HECT domain; C-terminal catalytic domain of a
subclass of Ubiquitin-protein ligase (E3). It binds
specific ubiquitin-conjugating enzymes (E2), accepts
ubiquitin from E2, transfers ubiquitin to substrate
lysine side chains, and transfers additional ubiquitin
molecules to the end of growing ubiquitin chains.
Length = 352
Score = 27.9 bits (63), Expect = 4.7
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 203 EDLDKILAEGLVWLRDYKQRVD 224
E+LD L + L L D D
Sbjct: 131 EELDPELYKSLKELLDNDGDED 152
>gnl|CDD|224133 COG1212, KdsB, CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell
envelope biogenesis, outer membrane].
Length = 247
Score = 27.6 bits (62), Expect = 5.0
Identities = 34/165 (20%), Positives = 48/165 (29%), Gaps = 43/165 (26%)
Query: 82 AARGLDVKHLNLVVNY--DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEII- 138
L + ++VN D P + + N A TL + E
Sbjct: 83 VVEKLGLPDDEIIVNVQGDEPFIEPEVIRAVAENLENSNADMA----TLAVKITDEEEAF 138
Query: 139 -------------RALEASGVPIPEDLDKMWAEDLI--VRTFCFRAGNKGFAYTFIT--- 180
AL S PIP D + + + +R GF F+
Sbjct: 139 NPNVVKVVLDKEGYALYFSRAPIPYGRDNFGGTPFLRHIGIYAYR---AGFLERFVALKP 195
Query: 181 --------LEQER--HAGEIIRALEASGVPI-----PEDLDKILA 210
LEQ R GE I VP PEDL+++
Sbjct: 196 SPLEKIESLEQLRVLENGEKIHVEIVKEVPSIGVDTPEDLERVRK 240
>gnl|CDD|180413 PRK06128, PRK06128, oxidoreductase; Provisional.
Length = 300
Score = 27.9 bits (62), Expect = 5.1
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 129 EQERHAGEIIRALEASG---VPIPEDL-DKMWAEDLIVR 163
E+E+ A E+++ ++A G V +P DL D+ + L+ R
Sbjct: 89 EEEQDAAEVVQLIQAEGRKAVALPGDLKDEAFCRQLVER 127
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.0 bits (63), Expect = 6.1
Identities = 8/35 (22%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 60 DRDSTIVDFKNGKVRLLIATS----VAARGLDVKH 90
+ F+ G+V +L+ + V RG+D+
Sbjct: 364 GFERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPE 398
>gnl|CDD|227123 COG4784, COG4784, Putative Zn-dependent protease [General function
prediction only].
Length = 479
Score = 27.5 bits (61), Expect = 6.1
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 18 DRDSTIVDF-KNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLL 76
D ++ D+ ++G V L VK+ G + D++ D ++ + R L
Sbjct: 332 DSRRSLTDYIRSGWVAGLDPETVKQTTINGLEAATARASADRWQFDVAVIRAGDRVYRFL 391
Query: 77 IATSVAARGLD 87
A + L+
Sbjct: 392 TAVPKGSTALE 402
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon;
Provisional.
Length = 313
Score = 27.4 bits (61), Expect = 7.6
Identities = 28/113 (24%), Positives = 42/113 (37%), Gaps = 35/113 (30%)
Query: 57 DQYDRDSTIVD-----FKNGKVRLLIATSVAARGLD-----VKHLNLVVNYDC---PNH- 102
Y R +VD F+ G+ R++ S+A GLD + + ++N P H
Sbjct: 11 SHYPRGWAVVDVETSGFRPGQARII---SLAVLGLDADGNVEQSVVTLLNPGVDPGPTHV 67
Query: 103 -------------YEDYVHRC-----GRTGRAGNKGFAYTFITLEQERHAGEI 137
+ D GRT A N F Y+F+ E ER E+
Sbjct: 68 HGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAEL 120
>gnl|CDD|218804 pfam05908, DUF867, Protein of unknown function (DUF867). This
family consists of a number of bacterial and phage
proteins with no known function and is present in
Bacillus species and the Lambda-like viruses.
Length = 190
Score = 26.8 bits (60), Expect = 9.2
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP 48
+S+HG Y D G R L AIV+ L +AG+
Sbjct: 95 VSIHG----YKGDDEHT-LVGGTDRELAEAIVRALERAGFS 130
>gnl|CDD|132849 cd07210, Pat_hypo_W_succinogenes_WS1459_like, Hypothetical patatin
similar to WS1459 of Wolinella succinogenes.
Patatin-like phospholipase. This family predominantly
consists of bacterial patatin glycoproteins. The patatin
protein accounts for up to 40% of the total soluble
protein in potato tubers. Patatin is a storage protein,
but it also has the enzymatic activity of a lipid acyl
hydrolase, catalyzing the cleavage of fatty acids from
membrane lipids. Members of this family have also been
found in vertebrates.
Length = 221
Score = 26.9 bits (60), Expect = 9.3
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 187 AGEIIRALEASGVPIPEDLDKILAEGLVWL 216
AG ++ L ASG+ E + +L+
Sbjct: 37 AGALVGGLFASGISPDEMAELLLSLERKDF 66
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
0.323 0.142 0.431
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,470,364
Number of extensions: 1224554
Number of successful extensions: 1640
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1627
Number of HSP's successfully gapped: 102
Length of query: 231
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 137
Effective length of database: 6,768,326
Effective search space: 927260662
Effective search space used: 927260662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.6 bits)