RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7952
(444 letters)
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 276 bits (707), Expect = 8e-87
Identities = 139/414 (33%), Positives = 213/414 (51%), Gaps = 60/414 (14%)
Query: 34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRV-RI 92
+E LK +FG+ SF+ Q++ I +L D V MPTG +S +I
Sbjct: 3 EEAQQVLKQVFGYASFR-PGQQEIIDALLSG-KDTLVVMPTG---------GGKSLCYQI 51
Query: 93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
P +L G +SP++S L +D + + + + S ++ E +
Sbjct: 52 P---ALLLEGLTLV----VSPLIS---LM-KDQ---VDQLEAAGIRAAYLNSTLSREERQ 97
Query: 153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
+L +L ++KLLY++PER ++ F LL+ L ++ + +DEAHC+S+WGHDFR
Sbjct: 98 QVLN--QLKSGQLKLLYISPERLMSPRFLELLKRL----PISLVAIDEAHCISQWGHDFR 151
Query: 213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
P YRRLG LR N P++ALTATA P V+ DI L +F+ S R NL V
Sbjct: 152 PDYRRLGRLRAGLPN-PPVLALTATATPRVRDDIREQLGLQDA-NIFRGSFDRPNLALKV 209
Query: 273 IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------- 323
+ D A + + + GIIYC TR+ +LA+ LR+
Sbjct: 210 VEKGEPSDQLAFLATVLPQLSK-------SGIIYCLTRKKVEELAEWLRKNGISAGAYHA 262
Query: 324 -VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG 382
++ ER RVQ++F+ EI V+ AT +FGMGID+ +VRFV+H+ +P SI +YYQE+GRAG
Sbjct: 263 GLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAG 322
Query: 383 RDGLQSYCRIYHSEHSKKSLEYVIKT----DTSTKREQLELKFKNYLSMLEYCE 432
RDGL + + +S + Y+I+ + + E +L+ M+ YCE
Sbjct: 323 RDGLPAEAILLYSPEDIRWQRYLIEQSKPDEEQKQIELAKLR-----QMIAYCE 371
>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 = 263 bits (674), Expect = 2e-83
Identities = 145/413 (35%), Positives = 215/413 (52%), Gaps = 70/413 (16%)
Query: 40 LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTG-AVSLVGSVVSARSRVRIPPGADF 98
LK +FG SF+ +Q + I + +L D FV MPTG SL ++P
Sbjct: 3 LKTVFGLSSFR-PVQLEVI-NAVLLGRDCFVVMPTGGGKSLC---------YQLPA---L 48
Query: 99 ILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLE-------LIVSGQTKTEN 151
+G ISP++S +D+ + QL+ + S Q+K +
Sbjct: 49 CSDGITLV----ISPLIS-----LMEDQ---------VLQLKASGIPATFLNSSQSKEQQ 90
Query: 152 KAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDF 211
K +L +L+ +IKLLYVTPE+ + LLQ L + I VDEAHC+S+WGHDF
Sbjct: 91 KNVLTDLKD--GKIKLLYVTPEKCSASN--RLLQTLEERKGITLIAVDEAHCISQWGHDF 146
Query: 212 RPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD 271
RP Y+ LG L+Q N +PI+ALTATA PSV++DI+ L P +F TS R NL+Y+
Sbjct: 147 RPDYKALGSLKQKFPN-VPIMALTATASPSVREDILRQLNLKNPQ-IFCTSFDRPNLYYE 204
Query: 272 VI--FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------ 323
V +L+D + FI K + GIIYC +R+ + + +L+
Sbjct: 205 VRRKTPKILED----LLRFIRKEFKGKS-----GIIYCPSRKKSEQVTASLQNLGIAAGA 255
Query: 324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
+ R V F R EI V+ AT++FGMGI++ +VRFV+H+ +P S+ +YYQESG
Sbjct: 256 YHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESG 315
Query: 380 RAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
RAGRDGL S C ++++ L ++ + ++ +LK M+EYC
Sbjct: 316 RAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQQRTYKLKL---YEMMEYCL 365
>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 = 254 bits (650), Expect = 2e-78
Identities = 139/410 (33%), Positives = 206/410 (50%), Gaps = 66/410 (16%)
Query: 40 LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA-VSLVGSVVSARSRVRIPPGADF 98
LK FG+D F+ Q++ I H+L D+ V MPTG SL V P
Sbjct: 5 LKRTFGYDDFR-PGQEEIISHVL-DGRDVLVVMPTGGGKSLCYQV----------PA--L 50
Query: 99 ILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEEL 158
+L G ISP++S K + R+ + S + E + I E
Sbjct: 51 LLKGLTVV----ISPLISLM-------KDQVDQLRAAGVAAAYLNSTLSAKEQQDI--EK 97
Query: 159 RLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRL 218
LV +KLLYV PER + F +LQ + +A + VDEAHCVS+WGHDFRP Y+RL
Sbjct: 98 ALVNGELKLLYVAPERLEQDYFLNMLQRI----PIALVAVDEAHCVSQWGHDFRPEYQRL 153
Query: 219 GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI----- 273
G L + +P IALTATA+ +QDI +L+ + F TS R NL + V+
Sbjct: 154 GSLAE-RFPQVPRIALTATADAETRQDIRELLRLADANE-FITSFDRPNLRFSVVKKNNK 211
Query: 274 FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------- 323
LL ++++K G+ GIIY +R+ +LA+ L +
Sbjct: 212 QKFLL--------DYLKKHRGQS------GIIYASSRKKVEELAERLESQGISALAYHAG 257
Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
++ R+ QE F+ ++ V+ AT +FGMGID+ NVRFV+H+ MP ++ +YYQE+GRAGR
Sbjct: 258 LSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGR 317
Query: 384 DGLQSYCRIYHSEHSKKSLEYVIKTDTST-KREQLELKFKNYLSMLEYCE 432
DGL + + +S L+ I+ + +Q+E + +M+ YCE
Sbjct: 318 DGLPAEAILLYSPADIALLKRRIEQSEADDDYKQIEREKLR--AMIAYCE 365
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 222 bits (568), Expect = 2e-66
Identities = 129/374 (34%), Positives = 196/374 (52%), Gaps = 65/374 (17%)
Query: 31 VSEQELTAK--LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA-VSLVGSVVSAR 87
V E AK L+ FG+ F+ Q I +L D V MPTG SL
Sbjct: 6 VLNLESLAKQVLQETFGYQQFRPGQQ--EIIDAVLSGRDCLVVMPTGGGKSLC------- 56
Query: 88 SRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQT 147
+IP +L+G +SP++S K + ++ + S QT
Sbjct: 57 --YQIPA---LVLDGLTLV----VSPLISLM-------KDQVDQLLANGVAAACLNSTQT 100
Query: 148 KTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW 207
+ + ++ R +IKLLY+ PER + ++F L+HL +N A + VDEAHC+S+W
Sbjct: 101 REQQLEVMAGCR--TGQIKLLYIAPERLMMDNF---LEHLAHWN-PALLAVDEAHCISQW 154
Query: 208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN 267
GHDFRP Y LG+LRQ +P +ALTATA+ + +QDI+ +L N P + +S R N
Sbjct: 155 GHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDPL-IQISSFDRPN 212
Query: 268 LFYDVI-----FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR 322
+ Y ++ D L++ ++++ GK GIIYC +R D A L+
Sbjct: 213 IRYTLVEKFKPLDQLMR--------YVQEQRGK------SGIIYCNSRAKVEDTAARLQS 258
Query: 323 K----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIP 372
+ ++ R+ VQE+F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I
Sbjct: 259 RGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIE 318
Query: 373 AYYQESGRAGRDGL 386
+YYQE+GRAGRDGL
Sbjct: 319 SYYQETGRAGRDGL 332
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 214 bits (547), Expect = 4e-61
Identities = 152/429 (35%), Positives = 226/429 (52%), Gaps = 69/429 (16%)
Query: 34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIP 93
++L K +FG SF+ Q++ I + + +D+FV MPTG G ++ + I
Sbjct: 446 KKLEVNNKKVFGNHSFRPN-QREII-NATMSGYDVFVLMPTGG----GKSLTYQLPALIC 499
Query: 94 PGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKA 153
PG + ISP++S +D +++ L +G E
Sbjct: 500 PGITLV-----------ISPLVS----LIQDQIMNLLQANIPAASLS---AGMEWAEQLE 541
Query: 154 ILEELRLVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNK---LAYIVVDEAHCVSEWGH 209
IL+EL + KLLYVTPE+ A ++S LL+HL N LA V+DEAHCVS+WGH
Sbjct: 542 ILQELSSEYSKYKLLYVTPEKVAKSDS---LLRHLENLNSRGLLARFVIDEAHCVSQWGH 598
Query: 210 DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLF 269
DFRP Y+ LG L+Q N IP++ALTATA SVK+D++ L VF+ S R NL+
Sbjct: 599 DFRPDYQGLGILKQKFPN-IPVLALTATATASVKEDVVQALGLVNCV-VFRQSFNRPNLW 656
Query: 270 YDVI--FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR----- 322
Y V+ L+D + +FI K+N + CGIIYC +R +A+ L+
Sbjct: 657 YSVVPKTKKCLED----IDKFI-----KENHFDECGIIYCLSRMDCEKVAERLQEFGHKA 707
Query: 323 -----KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQE 377
++ +R+ VQ+ + + EIN+I AT++FGMGI++ +VRFV+H +P SI Y+QE
Sbjct: 708 AFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQE 767
Query: 378 SGRAGRDGLQSYCRIYHSEHSKKSLEYVI--------------KTDTSTKREQLELKFKN 423
GRAGRDG +S C +Y+S ++++I S+ R LE +N
Sbjct: 768 CGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMAMGYNRMASSGR-ILETNTEN 826
Query: 424 YLSMLEYCE 432
L M+ YCE
Sbjct: 827 LLRMVSYCE 835
>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 = 85.8 bits (213), Expect = 4e-20
Identities = 38/137 (27%), Positives = 64/137 (46%), Gaps = 16/137 (11%)
Query: 267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR---- 322
+ V+ + K + E +++ L K K +I+C +++ +LA+ LR+
Sbjct: 1 PIKQYVLPVEDEKLEA--LLELLKEHLKKGGKV----LIFCPSKKMLDELAELLRKPGIK 54
Query: 323 ------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
++ ER V + F GEI V+ AT GID NV V+++ +P S +Y Q
Sbjct: 55 VAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQ 114
Query: 377 ESGRAGRDGLQSYCRIY 393
GRAGR G + +
Sbjct: 115 RIGRAGRAGQKGTAILL 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 = 68.3 bits (168), Expect = 1e-14
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD 384
++ ER + E F G+ V+ AT G GID +V V+++ +P + +Y Q GRAGR
Sbjct: 18 SQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRAGRA 77
Query: 385 G 385
G
Sbjct: 78 G 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 67.6 bits (166), Expect = 2e-14
Identities = 22/61 (36%), Positives = 33/61 (54%)
Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD 384
++ ER + + F G+I V+ AT G+D V V+ + +P S +Y Q GRAGR
Sbjct: 22 SQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81
Query: 385 G 385
G
Sbjct: 82 G 82
>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 = 66.1 bits (162), Expect = 7e-13
Identities = 40/203 (19%), Positives = 70/203 (34%), Gaps = 50/203 (24%)
Query: 54 QKKAIRHILLRTHDIFVSMPTGAVSLVG-SVVSARSRVRIPPGADFILNGNVRSRNGWIS 112
Q +AI IL D+ V PTG+ G ++ P +L + ++
Sbjct: 4 QAQAIPAIL-SGKDVLVQAPTGS----GKTLAFLL------PILQALLPKKGGPQALVLA 52
Query: 113 P-------ILSSF--YLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKP 163
P I + + +++TG G + E + +L K
Sbjct: 53 PTRELAEQIYEELKKLFKILGLRVALLTG------------GTSLKE-----QARKLKKG 95
Query: 164 RIKLLYVTPERAVTESFHYLLQH--LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGEL 221
+ +L TP R LL+ L L +V+DEAH + + G F +
Sbjct: 96 KADILVGTPGR-----LLDLLRRGKLKLLKNLKLLVLDEAHRLLDMG--FGDDLEEILSR 148
Query: 222 RQFTGNSIPIIALTATAEPSVKQ 244
I+ L+AT +++
Sbjct: 149 LP---PDRQILLLSATLPRNLED 168
>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 = 61.0 bits (148), Expect = 5e-10
Identities = 35/148 (23%), Positives = 60/148 (40%), Gaps = 22/148 (14%)
Query: 283 AHVKEFIEKCLGKDNKA-----------NNCGIIYCRTREHTTDLADALRR--------- 322
+K+F + ++ K I++ RT+ +LA++LR+
Sbjct: 245 KKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALH 304
Query: 323 -KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRA 381
+ + ER R E F GE+ V+ AT G+D +V V+++ +P Y GR
Sbjct: 305 GDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRT 364
Query: 382 GRDGLQSYC-RIYHSEHSKKSLEYVIKT 408
GR G + E K L+ + K
Sbjct: 365 GRAGRKGVAISFVTEEEEVKKLKRIEKR 392
>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 = 60.5 bits (147), Expect = 9e-10
Identities = 66/311 (21%), Positives = 108/311 (34%), Gaps = 98/311 (31%)
Query: 145 GQTK-TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL-----QHLVRYNKLAYIVV 198
G T E +AI+ P I L P+ HYLL L L Y+VV
Sbjct: 153 GDTPPEERRAIIRN----PPDI--LLTNPDM-----LHYLLLRNHDAWLWLLRNLKYLVV 201
Query: 199 DEAHCVSEWGHDFRPTY------------RRLGELRQFTGNSIPIIALTATA-------- 238
DE H TY RRL + G+ + II +AT
Sbjct: 202 DELH-----------TYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAE 250
Query: 239 ------------EPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVK 286
E + + ++ P + S RS A +
Sbjct: 251 ELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSA--------------LAELA 296
Query: 287 EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKH------------------E 328
+ + +++ R+R+ L + RR++ + E
Sbjct: 297 TLAALLVRNGIQ----TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREE 352
Query: 329 RSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQ 387
R R++ F GE+ + AT + +GID ++ V+ +G P S+ ++ Q +GRAGR G +
Sbjct: 353 RRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQE 412
Query: 388 SY-CRIYHSEH 397
S + S+
Sbjct: 413 SLVLVVLRSDP 423
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 55.8 bits (135), Expect = 2e-09
Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 15/98 (15%)
Query: 140 ELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVD 199
++ G + + + +L+ + ++ TP R L + + KL +++D
Sbjct: 61 GYLIGGTSIKQ------QEKLLSGKTDIVVGTPGRL----LDELERLKLSLKKLDLLILD 110
Query: 200 EAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT 237
EAH + G ++ ++ L+AT
Sbjct: 111 EAHRLLNQGFGLLGL-----KILLKLPKDRQVLLLSAT 143
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 56.3 bits (136), Expect = 3e-09
Identities = 37/200 (18%), Positives = 70/200 (35%), Gaps = 41/200 (20%)
Query: 54 QKKAIRHILLRTHDIFVSMPTGA-VSLVGSVVSARSRVRIPPGADFI------LNGNVRS 106
QK+AI +L D+ ++ PTG+ +L + + + R G + L
Sbjct: 13 QKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAE 72
Query: 107 RNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIK 166
L + G S QL + SG+T
Sbjct: 73 E-------LKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTD------------------ 107
Query: 167 LLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG 226
+L TP R L + + + +++DEAH + + G F +L +L
Sbjct: 108 ILVTTPGRL----LDLLENDKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLLKL---LP 158
Query: 227 NSIPIIALTATAEPSVKQDI 246
++ ++ L+AT ++ +
Sbjct: 159 KNVQLLLLSATPPEEIENLL 178
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 53.3 bits (128), Expect = 1e-07
Identities = 68/249 (27%), Positives = 109/249 (43%), Gaps = 60/249 (24%)
Query: 165 IKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF 224
++L+ TP R + L +H + + ++ +V+DE C+ E G FR ++ F
Sbjct: 247 VELIVGTPGRLID----LLSKHDIELDNVSVLVLDEVDCMLERG--FRDQVMQI-----F 295
Query: 225 TGNSIPIIAL-TATAEPSVKQ---------DIISVLKFNKPYKVFK-------TSTFRSN 267
S P + L +AT P V++ +IS+ N+P K K T +
Sbjct: 296 QALSQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQK 355
Query: 268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR-----R 322
LF D+LK S H K +++ +R LA+A+ +
Sbjct: 356 LF------DILK-SKQHFKP--------------PAVVFVSSRLGADLLANAITVVTGLK 394
Query: 323 KVNKH------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
++ H ER V +SF+ GE+ VI AT G G+D VR V+ + MP++I Y
Sbjct: 395 ALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIH 454
Query: 377 ESGRAGRDG 385
+ GRA R G
Sbjct: 455 QIGRASRMG 463
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 53.4 bits (129), Expect = 2e-07
Identities = 59/270 (21%), Positives = 104/270 (38%), Gaps = 85/270 (31%)
Query: 159 RLVK--PRIKLLYVTPERAVTESFHYLL------QHL--VRYNKLAYIVVDEAHCV--SE 206
+++K P I L TPE S LL + L VRY ++VDE H + S+
Sbjct: 118 KMLKNPPHI--LITTPE-----SLAILLNSPKFRELLRDVRY-----VIVDEIHALAESK 165
Query: 207 WGH----------DFRPTYRRLG---------ELRQF-TGNSIP--IIALTATAEPSVKQ 244
G + ++R+G E+ +F G P I+ ++A + +K
Sbjct: 166 RGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIK- 224
Query: 245 DIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGI 304
+ + Y + ++ L + + E ++K + +
Sbjct: 225 --VISPVEDLIY-------------DEELWAALYER----IAELVKK--------HRTTL 257
Query: 305 IYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRGEINVITATISFGMG 353
I+ TR LA L++ +++ R V+E GE+ + AT S +G
Sbjct: 258 IFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELG 317
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
ID ++ V+ G P S+ + Q GRAG
Sbjct: 318 IDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 48.3 bits (115), Expect = 5e-06
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
IIYC TR L + + +++ +R + F G V+ T G
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
ID Q V V+++ +P+S Y GR+GR G
Sbjct: 331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 47.0 bits (112), Expect = 1e-05
Identities = 47/240 (19%), Positives = 73/240 (30%), Gaps = 59/240 (24%)
Query: 191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL 250
N+ I+ DE H H P+YRR+ EL + P + LTAT E I +
Sbjct: 145 NEFGLIIFDEVH------HLPAPSYRRILELLS---AAYPRLGLTATPEREDGGRIGDLF 195
Query: 251 ------------------KFNKPYK---VFKTST-------------FRSNLFYD----V 272
+ PYK + T T FR L
Sbjct: 196 DLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRA 255
Query: 273 IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKV-------- 324
+ + K + L + + +I+ EH ++A
Sbjct: 256 ENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVEAITGE 315
Query: 325 -NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
K ER + E F G I V+ G+D + ++ P+ + R GR
Sbjct: 316 TPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLII-LRPTGSRRLFI--QRLGR 372
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 46.9 bits (112), Expect = 1e-05
Identities = 30/98 (30%), Positives = 43/98 (43%), Gaps = 16/98 (16%)
Query: 308 RTREHTTDLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMG------- 353
E + DLAD + + H R V+++F I VI++T + G
Sbjct: 290 SDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARR 349
Query: 354 -IDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSY 389
I R R+ GM P + Y+Q +GRAGR GL Y
Sbjct: 350 VIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPY 387
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 44.1 bits (104), Expect = 1e-04
Identities = 21/64 (32%), Positives = 31/64 (48%)
Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
V +H+R + E F G+I V+ AT G GI + V+++ +P Y GR GR
Sbjct: 369 VPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGR 428
Query: 384 DGLQ 387
G
Sbjct: 429 AGAS 432
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 44.2 bits (105), Expect = 1e-04
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 10/93 (10%)
Query: 303 GIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGM 352
I++ RTRE +LA LR+ ++ + +R+ + G +NV+ AT
Sbjct: 248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAAR 307
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
GID +V V+++ MP S Y GR GR G
Sbjct: 308 GIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG 340
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 43.9 bits (104), Expect = 1e-04
Identities = 74/321 (23%), Positives = 118/321 (36%), Gaps = 81/321 (25%)
Query: 139 LELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVV 198
+ L+ K +LE + +I L+ T H L+Q V + +LA +++
Sbjct: 315 VALLTGSLKGKRRKELLETIA--SGQIHLVVGT---------HALIQEKVEFKRLALVII 363
Query: 199 DEAHCVSEWGHDFRPTYRRLGE------LRQFTGNSIP-IIALTATAEPSVKQDIISVLK 251
DE H +G + R R G+ + + IP +ALT + + II L
Sbjct: 364 DEQH---RFGVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGD--LDTSIIDELP 418
Query: 252 FNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE 311
K T +I D Y EFIE+ + K +A ++Y E
Sbjct: 419 --PGRKPITTV---------LIKHDEKDIVY----EFIEEEIAKGRQAY---VVYPLIEE 460
Query: 312 -HTTDLADA------------------LRRKVNKHERSRVQESFMRGEINVITATISFGM 352
DL A L ++ E+ V E F GE++++ AT +
Sbjct: 461 SEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEV 520
Query: 353 GIDRQNV---------RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH----SEHSK 399
G+D N RF + +Q GR GR QSYC + + SE +K
Sbjct: 521 GVDVPNATVMVIEDAERF--------GLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAK 572
Query: 400 KSLEYVIKTDTSTKREQLELK 420
K L + T + +L+
Sbjct: 573 KRLRVMADTLDGFVIAEEDLE 593
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 42.9 bits (101), Expect = 3e-04
Identities = 26/92 (28%), Positives = 45/92 (48%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
II+ RT+ T ++A+AL R +N+ R + E G ++++ AT G
Sbjct: 249 IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARG 308
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+D + + VV++ +P +Y GR GR G
Sbjct: 309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 42.6 bits (100), Expect = 4e-04
Identities = 22/75 (29%), Positives = 37/75 (49%)
Query: 308 RTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM 367
R + +A + V+K +R+ +++ GE+ + AT S +GID V V+
Sbjct: 295 RVQSSDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVAT 354
Query: 368 PSSIPAYYQESGRAG 382
P S+ + Q GRAG
Sbjct: 355 PLSVASGLQRIGRAG 369
>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 = 40.9 bits (96), Expect = 0.001
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 328 ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
+R ++ + GE+ + T + +G+D + VV G P + + +Q++GRAGR G
Sbjct: 317 DRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG 374
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 40.5 bits (95), Expect = 0.002
Identities = 27/115 (23%), Positives = 52/115 (45%), Gaps = 18/115 (15%)
Query: 283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR------------RKVNKHERS 330
+K +++ + +K +I+ T++ L LR +K + ER+
Sbjct: 364 GKLKMLLQRIMRDGDKI----LIFVETKKGADFLTKELRLDGWPALCIHGDKK--QEERT 417
Query: 331 RVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
V F G+ ++ AT G+D ++V++V+++ P+ I Y GR GR G
Sbjct: 418 WVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAG 472
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 37.5 bits (87), Expect = 0.014
Identities = 28/84 (33%), Positives = 38/84 (45%), Gaps = 17/84 (20%)
Query: 316 LADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVV----- 363
L ALR V H ER ++++F G I VITAT + GI+ R ++
Sbjct: 290 LKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKR 349
Query: 364 --HWGMPSSIPAY--YQESGRAGR 383
++G IP Q GRAGR
Sbjct: 350 YSNFGW-EDIPVLEIQQMMGRAGR 372
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 37.1 bits (86), Expect = 0.018
Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 20/107 (18%)
Query: 304 IIYCRTREHTTDLADALRRKVNK----------HERSRVQESFMRGEINVITATISFGMG 353
I++ +R +LADAL K K ER V+ +F E+ + T + G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503
Query: 354 ID--RQNVRFV-----VHWGMPSSIPAYYQESGRAGRDGLQSYCRIY 393
+D V F + W + Q GRAGR ++Y
Sbjct: 504 VDFPASQVIFESLAMGIEWLSVRE---FQQMLGRAGRPDYHDRGKVY 547
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 36.6 bits (85), Expect = 0.025
Identities = 31/122 (25%), Positives = 53/122 (43%), Gaps = 16/122 (13%)
Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMG--------IDRQNV 359
+LA+ + R V H +R V+++F +G+I V+ +T + G I +
Sbjct: 308 ELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTR 367
Query: 360 RFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLE 418
R+ G+ + Q +GRAGR G Y S LEY+ + ++ E +E
Sbjct: 368 RYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELEYLAELYIQSEPEPIE 427
Query: 419 LK 420
K
Sbjct: 428 SK 429
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 36.4 bits (85), Expect = 0.028
Identities = 21/54 (38%), Positives = 29/54 (53%)
Query: 329 RSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG 382
R V+E RGE+ V+ ++ S +GID + VV G P S+ Q GRAG
Sbjct: 329 RLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 33.6 bits (78), Expect = 0.23
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 11/65 (16%)
Query: 138 QLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV 197
++ L+ E + ILE + ++ T H L+Q V ++ L ++
Sbjct: 340 RVALLTGSLKGKERREILEAIA--SGEADIVIGT---------HALIQDDVEFHNLGLVI 388
Query: 198 VDEAH 202
+DE H
Sbjct: 389 IDEQH 393
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 32.9 bits (75), Expect = 0.31
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 10/90 (11%)
Query: 304 IIYCRTREHTTDLADALRRKV--------NKHE--RSRVQESFMRGEINVITATISFGMG 353
+++ RT+ LA+ L + NK + R+R F G+I V+ AT G
Sbjct: 249 LVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARG 308
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
+D + + VV++ +P+ Y GR GR
Sbjct: 309 LDIEELPHVVNYELPNVPEDYVHRIGRTGR 338
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 32.6 bits (75), Expect = 0.42
Identities = 67/299 (22%), Positives = 101/299 (33%), Gaps = 101/299 (33%)
Query: 138 QLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV 197
++ L+ K ILE +L I ++ T H L+Q V ++ L ++
Sbjct: 341 RVALLTGSLKGKARKEILE--QLASGEIDIVVGT---------HALIQDKVEFHNLGLVI 389
Query: 198 VDEAHCVSEWGHDFRPTYRRLG-----ELR----------QFTGNSIP-IIALTATAEPS 241
+DE H R G LR T IP +ALTA +
Sbjct: 390 IDEQH--------------RFGVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLD 435
Query: 242 VKQDIISVLKFNKPY--KVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKA 299
V S++ P K T VI + V E I + + K +A
Sbjct: 436 V-----SIID-ELPPGRKPITTV---------VIPH----ERRPEVYERIREEIAKGRQA 476
Query: 300 NNCGIIYCRTRE-HTTDLADALRR---------KVNK---H------ERSRVQESFMRGE 340
++ E +L A ++ H E+ V E+F GE
Sbjct: 477 Y---VVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGE 533
Query: 341 INVITATISFGMGIDRQNV---------RFVVHWGMPSSIPAYYQESGRAGRDGLQSYC 390
I+++ AT +G+D N RF + +Q GR GR LQSYC
Sbjct: 534 IDILVATTVIEVGVDVPNATVMVIENAERF--------GLAQLHQLRGRVGRGDLQSYC 584
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 32.3 bits (74), Expect = 0.49
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 325 NKHERSRVQESFMRGEINVITATISFG-MGIDRQNVRFVVHW-GMPSSIPAYYQESGRAG 382
++ E+ + + F +GE NV+ AT S G G+D V V+ + +PS I Q GR G
Sbjct: 410 SQKEQKEIIDQFRKGEYNVLVAT-SVGEEGLDIPEVDLVIFYEPVPSEI-RSIQRKGRTG 467
Query: 383 RD 384
R
Sbjct: 468 RK 469
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 32.2 bits (73), Expect = 0.56
Identities = 56/267 (20%), Positives = 98/267 (36%), Gaps = 50/267 (18%)
Query: 164 RIKLLYVTPERAVTESFH--YLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR-PTYRRLGE 220
R ++ +T E+A + H Y++ N + IV DE H + G + R PT +
Sbjct: 111 RYDVVILTSEKADSLIHHDPYII------NDVGLIVADEIHII---GDEDRGPTLETVLS 161
Query: 221 LRQFTGNSIPIIALTATAE-----------PSVKQDIISV-LKFNKPYK--VFKTSTFRS 266
++ I+AL+AT +K + V LK Y+ + RS
Sbjct: 162 SARYVNPDARILALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERS 221
Query: 267 NLFYDVIFDDLLKD---------SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLA 317
+ + + + + D S + +++ E + + N+ + + L
Sbjct: 222 QVDINSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLN 281
Query: 318 DALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGIDRQN----VRFVVHWG 366
+ L V H +R ++E F I VI AT + G++ VR + +G
Sbjct: 282 EMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYG 341
Query: 367 MPSSIP----AYYQESGRAGRDGLQSY 389
Q GRAGR G Y
Sbjct: 342 NGGIRYLSNMEIKQMIGRAGRPGYDQY 368
>gnl|CDD|116050 pfam07429, Glyco_transf_56, 4-alpha-L-fucosyltransferase glycosyl
transferase group 56. This family contains the
bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc
transferase) (EC 2.4.1.-) (approximately 360 residues
long). This catalyzes the synthesis of
Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the
biosynthetic pathway of enterobacterial common antigen
(ECA), a polysaccharide comprised of the trisaccharide
repeat unit Fuc4NAc-ManNAcA-GlcNAc.
Length = 361
Score = 32.0 bits (73), Expect = 0.70
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 21/81 (25%)
Query: 357 QNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ 416
NVR +V G P++ AY ++ +AG ++ ++L+ + E+
Sbjct: 213 DNVRIIVPMGYPANNQAYIEQVRQAGL-------ALF----PAENLQIL--------TEK 253
Query: 417 LELKFKNYLSMLEYCEQGYFL 437
L F +YL++L C+ GYF+
Sbjct: 254 LA--FDDYLALLRQCDLGYFI 272
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 32.0 bits (73), Expect = 0.72
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 328 ERSRVQESFMRGEINVITATISFGMGID--RQNVRF--VVHWG----MPSSIPAYYQESG 379
+ V+E F G + V+ AT +F +GI+ + V F + + S Y Q SG
Sbjct: 458 IKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSG 517
Query: 380 RAGRDGL 386
RAGR GL
Sbjct: 518 RAGRRGL 524
>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 = 31.9 bits (73), Expect = 0.85
Identities = 72/297 (24%), Positives = 113/297 (38%), Gaps = 79/297 (26%)
Query: 140 ELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVD 199
EL+ ++ E IL+EL K I +L T H LLQ V++ L +++D
Sbjct: 532 ELLSRFRSAKEQNEILKELASGK--IDILIGT---------HKLLQKDVKFKDLGLLIID 580
Query: 200 EAH--CVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP-------SVKQDIISVL 250
E V + +L ELR S+ ++ L+AT P S +D+ S++
Sbjct: 581 EEQRFGVKQ--------KEKLKELRT----SVDVLTLSATPIPRTLHMSMSGIRDL-SII 627
Query: 251 KFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTR 310
P TF +D L V+E I + L + + + Y R
Sbjct: 628 A-TPPEDRLPVRTFVME------YDPEL------VREAIRRELLRGGQ-----VFYVHNR 669
Query: 311 -EHTTDLADALRR------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQ 357
E LA LR ++ ++E V F +GE V+ T GID
Sbjct: 670 IESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIP 729
Query: 358 NVRFVV-----HWGMPSSIPAYYQESGRAGRDGLQSYCR--IYH----SEHSKKSLE 403
N ++ +G+ YQ GR GR ++Y H +E ++K LE
Sbjct: 730 NANTIIIERADKFGLAQ----LYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLE 782
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 31.6 bits (72), Expect = 1.0
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 14/103 (13%)
Query: 280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRT---REHTTDLADALRRKVNK-----HERSR 331
D Y E +EK + K + G+I+ RE +LA+ LR E+
Sbjct: 316 DIYVES-ESLEKVVELVKKLGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKEE 374
Query: 332 VQESFMRGEINVITATISF-GM---GIDR-QNVRFVVHWGMPS 369
E F GE++V+ S+ G+ G+D +R+ V +G+P
Sbjct: 375 ALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK 417
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 31.4 bits (72), Expect = 1.1
Identities = 14/58 (24%), Positives = 27/58 (46%)
Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG 382
++ +R V+ + G + + T S +G+D V V+ G P + Q +GR+
Sbjct: 286 DREQRRWVEAAMAAGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSN 343
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 29.1 bits (66), Expect = 1.5
Identities = 28/95 (29%), Positives = 42/95 (44%), Gaps = 27/95 (28%)
Query: 144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC 203
SG+T T I RL K + K+L+V P + + E + I++DEAH
Sbjct: 29 SGKTLTAAALIA---RLAKGKKKVLFVVPRKDLLE-------------QALVIIIDEAH- 71
Query: 204 VSEWGHDFRPT-YRRLGELRQFTGNSIPIIALTAT 237
H T YR++ L +F ++ LTAT
Sbjct: 72 -----HSSAKTKYRKI--LEKFKPAF--LLGLTAT 97
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 31.0 bits (70), Expect = 1.6
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 241 SVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKAN 300
S K+DI V K + +TF N +YD SY +++E + G +AN
Sbjct: 1194 SYKKDIDQVKKNMSKERNDHLTTFEYNAYYDK-----ATASYENIEELTTEAKGLKGEAN 1248
Query: 301 N 301
Sbjct: 1249 R 1249
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 30.9 bits (70), Expect = 1.8
Identities = 31/124 (25%), Positives = 50/124 (40%), Gaps = 18/124 (14%)
Query: 264 FRSNLFYDVIFD-DLLK---DSYAHVKEFIEKCLGKDNKANNCGIIYCRT---REHTTDL 316
FR L ++V D L+ D Y ++ E L K GI+Y +E ++
Sbjct: 286 FRELLGFEVGGGSDTLRNVVDVYVEDEDLKETLLEIVKKLGTGGIVYVSIDYGKEKAEEI 345
Query: 317 ADALRRK------VNKHERSRVQESFMRGEINVITATISF----GMGIDR-QNVRFVVHW 365
A+ L + + E F GEI+V+ S+ G+D + VR+ V
Sbjct: 346 AEFLENHGVKAVAYHATKPKEDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFL 405
Query: 366 GMPS 369
G+P
Sbjct: 406 GVPK 409
>gnl|CDD|203028 pfam04494, TFIID_90kDa, WD40 associated region in TFIID subunit.
This region, possibly a domain is found in subunits of
transcription factor TFIID. The function of this region
is unknown.
Length = 141
Score = 28.7 bits (65), Expect = 2.8
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 13/72 (18%)
Query: 117 SFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAV 176
SF+ +F D + G D+ +L I + EN + R K RI+L
Sbjct: 62 SFFDKFHGD-FEQLHG-EDIEKLRSISLPEHLKEN-ELARAFRDNKYRIRL--------- 109
Query: 177 TE-SFHYLLQHL 187
+ SF LL+ L
Sbjct: 110 SRDSFSLLLRFL 121
>gnl|CDD|226642 COG4174, COG4174, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 364
Score = 28.9 bits (65), Expect = 5.7
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 2 AEGESKDASSAVGKSSSLTGNQQDRKGGKVSEQELTAKLKALFGFD 47
G DAS A G +++ +Q +G + + EL A+++ +GFD
Sbjct: 52 LGGGGVDASGAGGGVGNISDSQ--YRGAQGLDPELIAEIEKQYGFD 95
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 29.0 bits (66), Expect = 6.0
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 12/49 (24%)
Query: 253 NKPYKVFK-TSTFRSNLFYDVIFD---------DLLKDSYAHVKEFIEK 291
NK YK K S+F +N V+FD ++LK+ H E ++
Sbjct: 277 NKLYKKTKLQSSFSTNNL--VLFDGGPKYLNLKEILKEFLEHRLEVYKR 323
>gnl|CDD|223004 PHA03173, PHA03173, UL37 tegument protein; Provisional.
Length = 1028
Score = 28.9 bits (65), Expect = 6.9
Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 14/68 (20%)
Query: 45 GFDSFKCELQKKAIRHILLRTHDIFVSMPT---------GAVSLVGSVVS--ARSRVRIP 93
GF C L ++A+ L R + G V++VG VV S
Sbjct: 385 GFTRQHCRLLERALEDYLSRGRNRRTPEGPALDDAQQVVGCVAVVGGVVFGLLES---YG 441
Query: 94 PGADFILN 101
PGAD++
Sbjct: 442 PGADYVRA 449
>gnl|CDD|217360 pfam03087, DUF241, Arabidopsis protein of unknown function. This
family represents a number of Arabidopsis proteins.
Their functions are unknown.
Length = 230
Score = 28.1 bits (63), Expect = 7.0
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 307 CRTREHTTDLADALRRKVNKHERSRV-----QESFMRGEIN 342
+EH +L ALRRK + V ++ EI
Sbjct: 56 VEIKEHVRELQSALRRKRSGDLEVEVKAYVRSRKKLKKEIA 96
>gnl|CDD|117046 pfam08469, NPHI_C, Nucleoside triphosphatase I C-terminal. This
viral domain is found to the C-terminus of Poxvirus
nucleoside triphosphatase phosphohydrolase I (NPH I)
together with the helicase conserved C-terminal domain
(pfam00271).
Length = 148
Score = 27.7 bits (62), Expect = 7.5
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 5/38 (13%)
Query: 231 IIALTATAEPSVKQDIISVLK-----FNKPYKVFKTST 263
IIA + PSV +D++ ++K FN+ +KV K S+
Sbjct: 16 IIARLSNGRPSVDEDLLDIIKDKSKEFNQLFKVLKHSS 53
>gnl|CDD|132513 TIGR03473, HpnK, hopanoid biosynthesis associated protein HpnK.
The sequences represented by this model are members of
the pfam04794 "YdjC-like" family of uncharacterized
proteins. The member of this clade from
Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0976) is
found in the same locus as squalene-hopene cyclase (SHC,
TIGR01507) and other genes associated with the
biosynthesis of hopanoid natural products. Similarly, in
Ralstonia eutropha JMP134 (Reut_B4902) this gene is
adjacent to HpnAB, IspH and HpnH (TIGR03470), although
SHC itself is elsewhere in the genome. Notably, this
gene (here named HpnK) and three others form a conserved
set (HpnIJKL) which occur in a subset of all genomes
containing the SHC enzyme. This relationship was
discerned using the method of partial phylogenetic
profiling. This group includes Zymomonas mobilis, the
organism where the initial hopanoid biosynthesis locus
was described consisting of the genes HpnA-E and SHC
(HpnF). Continuing past SHC are found a phosphorylase
enzyme (ZMO0873, i.e. HpnG, TIGR03468) and a radical SAM
enzyme (ZMO0874), HpnH. Although discontinuous in Z.
mobilis, we continue the gene symbol sequence with
HpnIJKL.
Length = 283
Score = 28.2 bits (63), Expect = 8.6
Identities = 9/35 (25%), Positives = 13/35 (37%)
Query: 368 PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 402
P IP GR G D ++ R + + L
Sbjct: 72 PDQIPDLVDGQGRFGDDMVRDGVRYFFLPAVRAQL 106
>gnl|CDD|220606 pfam10160, Tmemb_40, Predicted membrane protein. This is a region
of 280 amino acids from a group of proteins conserved
from plants to humans. It is predicted to be a membrane
protein but its function is otherwise unknown.
Length = 261
Score = 27.9 bits (62), Expect = 9.7
Identities = 11/47 (23%), Positives = 19/47 (40%)
Query: 74 TGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYL 120
TG VS + +++ + FI N ++ GW + S L
Sbjct: 121 TGLVSALDTLLQVILEFGFGGVSLFIDNFDIGGHGGWGFWVAHSLVL 167
>gnl|CDD|232963 TIGR00410, lacE, PTS system, lactose/cellobiose family IIC
component. Bacterial PTS transporters transport and
concomitantly phosphorylate their sugar substrates, and
typically consist of multiple subunits or protein
domains. This family of proteins consists of both the
cellobiose specific and the lactose specific forms of
the phosphotransferase system (PTS) IIC component. The
IIC domain catalyzes the transfer of a phosphoryl group
from the IIB domain to the substrate. When the IIC
component and IIB components are in the same polypeptide
chain they are designated IIBC [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids,
Signal transduction, PTS].
Length = 423
Score = 28.2 bits (63), Expect = 9.8
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 341 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
+ + I+ G+ V V W MP I ++ G
Sbjct: 350 VTITVTYIAMSTGLVPPPVGIAVPWTMPPGISGFFATGG 388
>gnl|CDD|232938 TIGR00359, cello_pts_IIC, phosphotransferase system, cellobiose
specific, IIC component. The family consists of the
cellobiose specific form of the phosphotransferase
system (PTS), IIC component [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids,
Signal transduction, PTS].
Length = 423
Score = 28.2 bits (63), Expect = 9.8
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 341 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
+ + I+ G+ V V W MP I ++ G
Sbjct: 350 VTITVTYIAMSTGLVPPPVGIAVPWTMPPGISGFFATGG 388
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
0.321 0.136 0.395
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: 22,291,192
Number of extensions: 2179459
Number of successful extensions: 2139
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2089
Number of HSP's successfully gapped: 70
Length of query: 444
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 344
Effective length of database: 6,502,202
Effective search space: 2236757488
Effective search space used: 2236757488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.2 bits)