RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780952|ref|YP_003065365.1| DNA helicase II [Candidatus
Liberibacter asiaticus str. psy62]
(685 letters)
>gnl|CDD|30559 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA
replication, recombination, and repair].
Length = 655
Score = 499 bits (1286), Expect = e-142
Identities = 246/650 (37%), Positives = 363/650 (55%), Gaps = 32/650 (4%)
Query: 28 KGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQA 87
LN +Q AV PD PLL+LAGAG+GKT VL R+ +LI + P +ILA+TFTN+A
Sbjct: 1 SKLNPEQREAVLHPDG-PLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKA 59
Query: 88 IQEMKNRLACYLG---EKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQ 144
EM+ RL LG + + TFHSF ILR+HGE +GL +F ILDS + +IK+
Sbjct: 60 AAEMRERLLKLLGLPAAEGLTVGTFHSFALRILRRHGERLGLNANFTILDSDDQLALIKE 119
Query: 145 LLKDLQ-IDDKDYDPHEVIEKIDYWQNRGWNPKDIP----QSSLTEDAEIPKAIYIQYVA 199
LL+ +DDK+ P E + I +N +P + + +E + +Y +Y
Sbjct: 120 LLRRELNLDDKELLPREALRYISEAKNALLSPLEASALLLAAIKSEAEKKLAELYEEYQE 179
Query: 200 YLQKTKSCDFGGLIIKTIEVL-HHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQK 258
L+ + DF L++ + +L +P VL+ + YI+VDE+QD N QY LL+LL
Sbjct: 180 LLRLNNALDFDDLLLLALRLLEENPEVLEALQARFRYILVDEFQDTNPLQYELLKLLAGN 239
Query: 259 EDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTAN 318
A + VGD++Q IY +RGA +IL+F+KDF A +IKLEQNYRST +IL AN
Sbjct: 240 -----AANLFVVGDDDQSIYGFRGADPENILDFEKDFPAAKVIKLEQNYRSTPNILAAAN 294
Query: 319 KLISHNKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIIN-IQNTGMSLNNIA 377
K+I++NK+R K L T+ + KV + ++ + E I EI I+ ++ ++IA
Sbjct: 295 KVIANNKKRQAKTLRTEVE-GSGEKVVLLLANDEEDEARWIASEIDALIEIGKVNYSDIA 353
Query: 378 ILVRTSWQTRKFEDAFLEQEIPHKVIGG--SFYDRQEIRDALAYFRLVCQEHRDEDFKRI 435
IL RT+ Q+R E+A IP++++ G SF++R+EI+D LAY RLV D F RI
Sbjct: 354 ILYRTNAQSRLIEEALRAAGIPYRIVIGGTSFFERKEIKDLLAYLRLVLNPDDDAAFLRI 413
Query: 436 INCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNN 495
+N PKRGIG +L K+ A + ++SLL+A + L+ + + L +F + I
Sbjct: 414 LNLPKRGIGDATLKKLLELARERNLSLLEALKALLSFIRLSERGLALLLDFAELIEELRE 473
Query: 496 CSKKMDPAPIANMILEQSGYMAMWKNNKSSEKSQERLDNLRELLSII----EKHETLEGF 551
+ +LE GY+ S +++RL+NL ELL ++ E E+L F
Sbjct: 474 AILLSTALELIRELLEALGYLEALLEAGSLVAAEDRLENLEELLDVLKRYAEPRESLRAF 533
Query: 552 VLQAPLRENLGSF--IPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGN-- 607
+ + L N + + +MT+HAAKGLEF VF+ G E+GL P S++EG+
Sbjct: 534 LSELSLLANDEEEEEPDEDGQVNLMTIHAAKGLEFPYVFLVGLEEGLFPADRSLDEGDEP 593
Query: 608 VEGERRLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLEL 657
+E ERRL YV ITRAKKK +L Y +R+ E S+F+ EL
Sbjct: 594 LEEERRLLYVAITRAKKKLYLTYAASRKLWGKEVEEEP-----SRFVSEL 638
>gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family
helicases are composed of four structural domains. The
Rep family function as dimers. REP helicases catalyse
ATP dependent unwinding of double stranded DNA to single
stranded DNA. Bacillus subtilis addA and Escherichia
coli exodeoxyribonuclease V beta have large insertions
near to the carboxy-terminus relative to other members
of the family.
Length = 494
Score = 392 bits (1008), Expect = e-109
Identities = 195/505 (38%), Positives = 285/505 (56%), Gaps = 30/505 (5%)
Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89
LN +Q AVT PLL+LAGAGTGKT VL R+ +LI I P +ILA+TFTN+A +
Sbjct: 1 LNPEQRKAVT-HLGGPLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAR 59
Query: 90 EMKNRLACYLGEKIPR---IQTFHSFCASILRKHGEVVG-LPTDFAILDSAESRTIIKQL 145
EMK R+ LG+ I TFHSFC ILRK+ +G L +F+ILD + ++K++
Sbjct: 60 EMKERILKLLGKAEASELNISTFHSFCLRILRKYANRIGDLLPNFSILDELDQLALLKEI 119
Query: 146 LKDLQIDDKDYDPH------EVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKA--IYIQY 197
LK D D D E+ E I +N +P+++ Q+S A Y +Y
Sbjct: 120 LKK---DRLDLDSKLLRPLLELKELISKAKNELLSPEELQQASYAATPRDKLAAEFYQEY 176
Query: 198 VAYLQKTKSCDFGGLIIKTIEVLH-HPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLC 256
L++ + DF L++ T+E+L P +L+ Y E+ YI+VDE+QD N QY LL+LL
Sbjct: 177 QERLKENNALDFDDLLLLTLELLRSDPELLEAYRERFKYILVDEFQDTNPIQYELLKLLA 236
Query: 257 QKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNT 316
+ VGD +Q IY +RGA +IL F+KDF A +I LEQNYRST ILN
Sbjct: 237 -----GGHPNLFLVGDPDQSIYGFRGADIENILKFEKDFPAAKVITLEQNYRSTPEILNA 291
Query: 317 ANKLISHNKQRFDK-KLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQNTG--MSL 373
ANKLIS+N R +K L++Q+ KV+++ ++++ E I EI + +G +
Sbjct: 292 ANKLISNNTARKEKRLLWSQKG--SGEKVTVYEAETEQEEAEFIADEIKALHKSGAAIPF 349
Query: 374 NNIAILVRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDF 432
+IA+LVR++ Q+R E+A L+ IP+K++GG SF+DR+EI+D LA RL+ D
Sbjct: 350 GDIAVLVRSNSQSRAIEEALLKAGIPYKILGGLSFFDRKEIKDLLALLRLIDNPKDDLAL 409
Query: 433 KRIINCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIR--QSLQNFVKDI 490
RI+N PKRGIG +L K++ A ISL +A +L++ R + L F+ I
Sbjct: 410 LRILNTPKRGIGPTTLDKLRNLAKDRQISLFKALNQLLEKLNELLSARAYKKLLLFLALI 469
Query: 491 RRWNNCSKKMDPAPIANMILEQSGY 515
++ + + +LE GY
Sbjct: 470 EELEKLLLEILLEALLDEVLELLGY 494
>gnl|CDD|31272 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 144 bits (365), Expect = 6e-35
Identities = 104/528 (19%), Positives = 174/528 (32%), Gaps = 100/528 (18%)
Query: 191 KAIYIQYVAYLQKTKSCDFGGLIIKTIEVLHHPH--VLKKYHEKIPYIMVDEYQDINTPQ 248
+ + +Y A ++ + DF LI + ++L + + E+ P+I++DE+QD + Q
Sbjct: 335 EELIERYDAEKRQRNALDFDDLIHRLAKLLTSEGEELAESLREQYPHILIDEFQDTDPQQ 394
Query: 249 YLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYR 308
+ +L L + VGD Q IY +RGA L K I LE NYR
Sbjct: 395 WRILSRLFAGFKAGNRTLFL-VGDPKQSIYRFRGADIFTFLEAASSEKAFARITLETNYR 453
Query: 309 STTHILNTANKLISHNKQRFDK---------------------------KLFTQRDCHDD 341
ST +LN N L + F + +
Sbjct: 454 STPELLNAVNALFKQAMFAYPGEIDYDPVAELGARNGSPGSVNGEPLPALKFWEEEDDWT 513
Query: 342 AKVSIHVSQSDN-SELSTIIQEIINIQNTG--------MSLNNIAILVRTSWQTRKFEDA 392
A + + E I + + + +IA+LVR+ + E A
Sbjct: 514 APENEEDEREIADLEARQIAAWLRELIEGEAVLDGERPIRAGDIAVLVRSRNEAAAIERA 573
Query: 393 FLEQEIPHKVIGG---SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKRGIGKESLH 449
+ I V S ++ E +D LA R + D ++ P G+ ++ L
Sbjct: 574 LKKAGII-PVYLSNRSSLFETLEAQDLLALLRAILNPEDDLPLAALLRSPLFGLTEDDLA 632
Query: 450 KIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMI 509
L E + + + F + W +K +
Sbjct: 633 ------------ALAQDEAEWEFLWENLRQLADIWRFRGVLAMWRALAKITPLHDLIAER 680
Query: 510 LEQSGYMAMWKNNKSSEKSQERLDNLRELLSIIEKHET-----LEGFVLQAPLRENLGSF 564
L + N + L+ELL+ +E LE F+ +
Sbjct: 681 LLSTNLGERDLTNGL-----HAQELLQELLTRALSYEHGLLRWLERFI-ALIENNDEEQA 734
Query: 565 I---PDSNCIQIMTLHAAKGLEFDTVFISG-------------------------WEQGL 596
D + ++IMT+H +KGLEF VF+ +
Sbjct: 735 RRLESDRDLVRIMTIHKSKGLEFPIVFLPFILSKRFNDSDVPLLVYYDGLRFELFDDLKS 794
Query: 597 LPHQLS------INEGNVEGERRLAYVGITRAKKKCHLFYTINRRTHD 638
P S E + E RL YV +TRAK++ L ++R
Sbjct: 795 YPTPESQANKELAEEEALAEELRLLYVALTRAKEQLILIGAPSKREKS 842
Score = 75.9 bits (186), Expect = 3e-14
Identities = 41/163 (25%), Positives = 62/163 (38%), Gaps = 43/163 (26%)
Query: 46 LLILAGAGTGKTTVLIARMLHLICHKE-IPPSKILAMTFTNQAIQEMKNRLACYLGEKIP 104
+L+ A AGTGKT VL R+L L+ + +IL +TFT A EMK R+ L E +
Sbjct: 19 VLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLKEALQ 78
Query: 105 ----------------------------------------RIQTFHSFCASILRKHGEVV 124
I T H FC ILR+
Sbjct: 79 ENDEKLASDDELLEALAALIQALIQAIRLFALALETNDEAAIFTIHGFCQRILRQFALEA 138
Query: 125 GLPTDFAILDSAESRTIIKQLLKDLQIDDKDYDPHEVIEKIDY 167
G+ DF +L+ + + +L++D P E+ + +
Sbjct: 139 GISFDFELLE--DESDLFLELVEDFWRRRFYPLPAELAQLVAQ 179
>gnl|CDD|37319 KOG2108, KOG2108, KOG2108, 3'-5' DNA helicase [Replication,
recombination and repair].
Length = 853
Score = 143 bits (363), Expect = 1e-34
Identities = 147/643 (22%), Positives = 229/643 (35%), Gaps = 70/643 (10%)
Query: 26 YLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTN 85
LN Q + P ++AG G+GKT VL R+ +LI I P +IL T TN
Sbjct: 10 LYSLLNKSQRFSALSPLRR-KRVIAGPGSGKTLVLTERVAYLINFNNIKPDEILINTGTN 68
Query: 86 QAIQEMKNRLACYLG-----EKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRT 140
+A +K L L ++I I TFHS + G ++ L + I D ++
Sbjct: 69 KAADSIKLNLIAILRTSKCSKEI--IGTFHSIAVKYSLRDGPLLPLSENCRIQDLPDTYA 126
Query: 141 IIKQLLKDL--QIDD---------KDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEI 189
I+ + L +I + P + N I L E
Sbjct: 127 ILGDNIWALLAKIKLPSSSSNRKQRLLFPLRRPDSTVTKPNVTETLYSIAVLLLAMFEEG 186
Query: 190 PK-----AIYIQYVAYLQKTKSCDFGGLIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDI 244
I Y YLQ + D L + +++VL P V KI +++VDE+QDI
Sbjct: 187 INVSNRDDYEIYYYLYLQTLE--DSCTLAMNSLKVLQRPRVCSN---KITHVLVDEFQDI 241
Query: 245 NTPQYLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDAN---II 301
Q L++L + GD +Q IY++ G + I F
Sbjct: 242 LKIQLEPLQVL-------KIKAFAGTGDTDQSIYKFAGKW-AEIRILYVTFNKFIATQAE 293
Query: 302 KLEQNYRSTTHILNTANKLISHNKQRFDKK-LFTQRDCHDDAKVSIHVSQSDNSELSTII 360
+L N RS I + A I Q K L + + + +
Sbjct: 294 RLFPNNRSCKTIHSLAYGAIGRQYQEKKKLLLRKLTPS--ELNSVLAEFKGGFPKAKLKC 351
Query: 361 QEIINIQNTGMSL---NNIAILVRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDA 416
+ N N+ AIL +S Q FE +EQ +K+I SF D E R
Sbjct: 352 RTEENFLVAADIEFTINDHAILWCSSSQLSSFESVLVEQREKYKLIAVASFLDSNERRLG 411
Query: 417 LAYFRLVCQEHRDEDFKRIINCPKRGIGKESLHKIQYHASQ------HHISLLQASEKLI 470
L Y +L D K ++ P+R G I +Q ++ L+Q +
Sbjct: 412 LNYEKLHANMTPDGYLK-LLQLPERPNGLAKFDYIILDEAQDCTPCIQNLILIQKHNIKV 470
Query: 471 DSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMILEQSGYMAMWKNNKSSEKSQE 530
G F I R N+ + P + + + K E E
Sbjct: 471 FVGDFHQSI--------YSFRGANSALFNLATLPDTLVECLTKSFRFGNEVAKVKETILE 522
Query: 531 RLDNLRELLSIIEKHETLEGFVLQAPLRENLGSFIPDSNC-----IQIMTLHAAKGLEFD 585
+ +R+L + H ++ L S + +QI TLH+AKGLE+
Sbjct: 523 KKKRVRKLTLVSNNHFYFLSIPGDVSGQKFLLSRTLSNLTQEEEELQISTLHSAKGLEWP 582
Query: 586 TVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHL 628
V I + ++P + + + V TRA++ HL
Sbjct: 583 VVSIGLCRENIIPILFQ---DEEDEDGQNLVVKDTRARRLLHL 622
Score = 31.1 bits (70), Expect = 1.0
Identities = 24/75 (32%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 559 ENLGSFIPDS-NCIQIMTLHAAKGLEFDTVFIS-------GWEQGLLPHQLSINEGNVEG 610
EN D + + T+H AKGLEFD V + G E E
Sbjct: 662 ENFHIRDLDKAENVILGTIHQAKGLEFDNVHLQNDFVKVFGSVSNFERLPSFRVETYNED 721
Query: 611 ERRLAYVGITRAKKK 625
E YV +TRAKK+
Sbjct: 722 EWNFLYVAVTRAKKR 736
>gnl|CDD|37014 KOG1803, KOG1803, KOG1803, DNA helicase [Replication, recombination
and repair].
Length = 649
Score = 42.3 bits (99), Expect = 5e-04
Identities = 29/133 (21%), Positives = 55/133 (41%), Gaps = 7/133 (5%)
Query: 25 NYLKGLNAQQTHAVT--IPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMT 82
+ K LN+ Q AV+ I + L+I GTGKT L+ + L+ K+ ++L
Sbjct: 181 FFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKK----RVLVCA 236
Query: 83 FTNQAIQEMKNRLACYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTII 142
+N A+ + RL +L + R+ S+ +++ D + S+ I
Sbjct: 237 PSNVAVDNIVERLT-HLKLNLVRVGHPARLLESVADHSLDLLSNTKDNSQNAKDISKDID 295
Query: 143 KQLLKDLQIDDKD 155
K+ + +
Sbjct: 296 ILFQKNTKTKNDK 308
>gnl|CDD|110446 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles at
different stages of viral RNA replication, as dissected
by mutational analysis.
Length = 226
Score = 37.4 bits (87), Expect = 0.014
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 9/59 (15%)
Query: 571 IQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629
++ T+H +GL FD+V + + + L YV +TR +K H+
Sbjct: 176 VRATTVHEVQGLTFDSVTL---------VLDKDTDLLSISDPELLYVALTRHRKSLHIL 225
>gnl|CDD|30853 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 36.6 bits (84), Expect = 0.022
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 12/56 (21%)
Query: 574 MTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629
MT+H ++G EFD V + LLP + R L Y ITRA+ + L+
Sbjct: 625 MTIHKSQGSEFDRVIV------LLP------SHSPMLSRELLYTAITRARDRLILY 668
>gnl|CDD|33753 COG3972, COG3972, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 660
Score = 35.4 bits (81), Expect = 0.048
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89
+ QT A I AG+GKT +L + L H + P S+I FT
Sbjct: 163 FDTDQTKAAFQSGFGKQRIRGLAGSGKTELLAHKAAEL--HSKNPDSRIAFTFFTKILAS 220
Query: 90 EMKNRL 95
M+ +
Sbjct: 221 TMRTLV 226
>gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA
processing and modification].
Length = 673
Score = 32.7 bits (74), Expect = 0.39
Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 12/106 (11%)
Query: 46 LLILAGAGTGKTTVLIARMLHLICH--------KEIPPSKILAMTFTN---QAIQEMKNR 94
+ +A G+GKT + +L I I + + T Q I+E N+
Sbjct: 285 PIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNK 344
Query: 95 LACYLGEKIPRIQTFHSFCASILR-KHGEVVGLPTDFAILDSAESR 139
LG + + SF + G + + T ++DS E+R
Sbjct: 345 FGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENR 390
>gnl|CDD|31392 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 32.0 bits (72), Expect = 0.48
Identities = 35/261 (13%), Positives = 64/261 (24%), Gaps = 46/261 (17%)
Query: 37 AVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMKNRLA 96
A + LLI A GTGKT + L + K++ T T +++
Sbjct: 28 AEALKGGEGLLIEAPTGTGKTLAYLLPALA---YAREEGKKVIISTRTKALQEQLLEED- 83
Query: 97 CYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAE-----SRTIIKQLLKDLQI 151
L H + L FA+L SR L
Sbjct: 84 --------------------LPIHKLLKKLGGKFALLKGRSNYLCLSRLERLAQLGGDDD 123
Query: 152 DDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKTKSCDFGG 211
D + + + W + D + + + C +
Sbjct: 124 DYLQSLALKALADLLVWLTETKTGDLRELTPKALDDPLWTL--VTDDKDSCLGEDCPY-- 179
Query: 212 LIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQGARICCVG 271
+ Y + + LL + ++ V
Sbjct: 180 ------------YTECFYFPARKEAENADLV-VTNHALLLADVALEESRILLPENDVVVF 226
Query: 272 DENQCIYEWRGAQFSHILNFQ 292
DE + + + S L+ +
Sbjct: 227 DEAHNLPDIARSALSIRLSER 247
>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
factor (pNORF1) [RNA processing and modification].
Length = 935
Score = 31.9 bits (72), Expect = 0.66
Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 23 VPNYLKGLNAQQTHAVTIPDDTPLLILAGA-GTGKTTVLIARMLHLICHKEIPPSKILAM 81
VPN K LNA Q++AV PL ++ G GTGKT + HL P +L
Sbjct: 405 VPNLPK-LNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGP---VLVC 460
Query: 82 TFTNQAIQEMKNRLACYLGEKIPRI 106
+N A+ ++ ++ G K+ R+
Sbjct: 461 APSNIAVDQLAEKIH-KTGLKVVRL 484
>gnl|CDD|33754 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 747
Score = 31.1 bits (70), Expect = 0.91
Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 1/89 (1%)
Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLIC-HKEIPPSKILAMTFTNQAI 88
+ +Q + + L++ AG+GKTT+ + R+ +L+ ++ +K + + N+
Sbjct: 213 IQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVF 272
Query: 89 QEMKNRLACYLGEKIPRIQTFHSFCASIL 117
E +R+ LGE+ +TF + +IL
Sbjct: 273 LEYISRVLPELGEEGVVQETFEEWALAIL 301
Score = 31.1 bits (70), Expect = 0.95
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 573 IMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLFYT 631
++ ++ AKGLEFD V + SI E E + R YV +TRA ++F
Sbjct: 697 VIPVYDAKGLEFDHVIV---------VDPSIVE-ETEQDLRDLYVAVTRALHSLYIFGE 745
>gnl|CDD|153410 cd07956, Anticodon_Ia_Arg, Anticodon-binding domain of arginyl tRNA
synthetases. This domain is found in arginyl tRNA
synthetases (ArgRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. ArgRS catalyzes the
transfer of arginine to the 3'-end of its tRNA.
Length = 156
Score = 31.0 bits (71), Expect = 1.2
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 100 GEKIPRIQTFHSFCASILRKHGEVVGLPTDFAI--LDSAESRTIIKQLLK 147
G+ P +Q H+ SILRK GE + D + L + R +I L K
Sbjct: 33 GDTGPYLQYAHARLCSILRKAGETIEAEADADLSLLPEPDERDLILLLAK 82
>gnl|CDD|30368 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 30.6 bits (69), Expect = 1.4
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 100 GEKIPRIQTFHSFCASILRKHGE--VVGLPTDFAILDSAESRTIIKQLLK---DLQIDDK 154
G P +Q H+ SILRK GE + A+L E R ++K+LL+ L+ +
Sbjct: 453 GNTAPYVQYAHARICSILRKAGEDELDLSTEADALLTELEERELVKKLLEFPEVLEEAAE 512
Query: 155 DYDPH 159
+ +PH
Sbjct: 513 ELEPH 517
>gnl|CDD|37246 KOG2035, KOG2035, KOG2035, Replication factor C, subunit RFC3
[Energy production and conversion, Replication,
recombination and repair].
Length = 351
Score = 30.3 bits (68), Expect = 1.9
Identities = 29/132 (21%), Positives = 55/132 (41%), Gaps = 23/132 (17%)
Query: 32 AQQTHAVTIPDDTPLLILAG-AGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQE 90
A +++ D P L++ G +G GK T ++ +L + + KI TFT +
Sbjct: 22 ANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMC-LLRELYGVGVEKLKIETRTFTTPS--- 77
Query: 91 MKNRLACYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQLLKDLQ 150
+K+ I T S H E+ P+D D + ++K++ + Q
Sbjct: 78 ---------KKKL-EISTVSS------NYHLEIT--PSDAGNYDRVVIQELLKEVAQTQQ 119
Query: 151 IDDKDYDPHEVI 162
I+ + P +V+
Sbjct: 120 IETQGQRPFKVV 131
>gnl|CDD|147737 pfam05746, DALR_1, DALR anticodon binding domain. This all alpha
helical domain is the anticodon binding domain in
Arginyl and glycyl tRNA synthetase. This domain is known
as the DALR domain after characteristic conserved amino
acids.
Length = 117
Score = 29.9 bits (68), Expect = 2.1
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 110 HSFCASILRKHGE-VVGLPTDFAILDSAESRTIIKQLLK 147
H+ SILRK GE + L D +L E + ++K LL+
Sbjct: 5 HARICSILRKAGELGINLDIDALLLLEEEEKELLKALLQ 43
>gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 29.6 bits (66), Expect = 3.3
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 41 PDDTPLLILAGAGTGKTTVLIARMLHLICHK 71
P P+LI+ GTGK L AR++H + +
Sbjct: 99 PSGLPVLIIGETGTGKE--LFARLIHALSAR 127
>gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication,
recombination and repair].
Length = 1100
Score = 29.2 bits (65), Expect = 3.9
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 20 PSCVPNYLKGLNAQQTHAV--TIPDDTPLLILAGAGTGKTTVL--IARMLHLICHKEIPP 75
P L LN Q A+ + + LIL GTGKTT + + ++L +
Sbjct: 660 PKIKKIILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVAL------G 713
Query: 76 SKILAMTFTNQAIQEMKNRLA 96
K+L ++T+ A+ + +L
Sbjct: 714 KKVLLTSYTHSAVDNILIKLK 734
>gnl|CDD|28927 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 = 28.9 bits (64), Expect = 4.3
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 46 LLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMT--FTNQAIQEMKNRLACYL 99
+L+ A G+GKT + +L L+ + +LA T NQ + +K +
Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGI 58
>gnl|CDD|30845 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 29.0 bits (65), Expect = 4.3
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 36 HAVTIPDDTPLLILAGAGTGKTTVLIA--RMLHLIC---HKEIPPSKILAMTFTNQAI 88
AV + P + GK +L+A R+++L H PS+++ M+F NQA+
Sbjct: 310 LAVEKREVRPQVDEYELPDGKRIILLAEGRLVNLAAATGH----PSEVMDMSFANQAL 363
>gnl|CDD|33289 COG3486, IucD, Lysine/ornithine N-monooxygenase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 436
Score = 28.7 bits (64), Expect = 5.7
Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 18/83 (21%)
Query: 608 VEGERRLAYVGITRAKKKC--HLFYTINRRTHD---FTRVERYQPSQVSQFLLELYDPSH 662
+ +R + +G ++ + L + + + TR + P S+F LE + P
Sbjct: 184 LLQKRSVTVIGSGQSAAEIFLDLLNSQPPQDYQLNWITRSSGFLPMDYSKFGLEYFSPE- 242
Query: 663 TQEIIYDDIYGTFSEHWNQIPEP 685
+++++ +P
Sbjct: 243 ------------YTDYFYGLPPE 253
>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
transporters homologous to the Drosophila white gene,
which acts as a dimeric importer for eye pigment
precursors. The eye pigmentation of Drosophila is
developed from the synthesis and deposition in the
cells of red pigments, which are synthesized from
guanine, and brown pigments, which are synthesized from
tryptophan. The pigment precursors are encoded by the
white, brown, and scarlet genes, respectively.
Evidence from genetic and biochemical studies suggest
that the White and Brown proteins function as
heterodimers to import guanine, while the White and
Scarlet proteins function to import tryptophan.
However, a recent study also suggests that White may be
involved in the transport of a metabolite, such as
3-hydroxykynurenine, across intracellular membranes.
Mammalian ABC transporters belonging to the White
subfamily (ABCG1, ABCG5, and ABCG8) have been shown to
be involved in the regulation of lipid-trafficking
mechanisms in macrophages, hepatocytes, and intestinal
mucosa cells. ABCG1 (ABC8), the human homolog of the
Drosophila white gene is induced in monocyte-derived
macrophages during cholesterol influx mediated by
acetylated low-density lipoprotein. It is possible
that human ABCG1 forms heterodimers with several
heterologous partners..
Length = 226
Score = 28.7 bits (64), Expect = 5.8
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 19 VPSCVPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVL--IARMLH 66
V N+ K ++ + + IL +G+GKTT+L I+ +
Sbjct: 9 VGLKAKNWNKYARILNDVSLHVESGQVMAILGSSGSGKTTLLDAISGRVE 58
>gnl|CDD|31309 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 28.4 bits (62), Expect = 6.6
Identities = 20/117 (17%), Positives = 41/117 (35%), Gaps = 10/117 (8%)
Query: 557 LRENLGSFIPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAY 616
+R L +++ T+ +G E D + +S L+ E G+ R
Sbjct: 661 IRRLLNEAGKG---VEVGTVDGFQGREKDVIILS-----LVRSNDDKGEIGFLGDPRRLN 712
Query: 617 VGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLELYDPSHTQEIIYDDIYG 673
V +TRAK+K + + T + + + + + + L + D
Sbjct: 713 VALTRAKRKLIVVG--SSSTLESDPLYKRLINDLKRKGLLAELNLLDLRLTDLDDES 767
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the
ATP synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor
Rho.
Length = 213
Score = 28.6 bits (65), Expect = 6.6
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 46 LLILAGAGTGKTTVL--IAR 63
+ I G+GTGKT +L IAR
Sbjct: 18 IGIFGGSGTGKTVLLGMIAR 37
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the
zinc-dependent alcohol dehydrogenases (ADH) of the
medium chain alcohol dehydrogenase/reductase family
(MDR), tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic
domain. Unlike ADH, where NAD(P)(H) acts as a cofactor,
NADH in FDH is a tightly bound redox cofactor (similar
to nicotinamide proteins). The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 345
Score = 28.4 bits (64), Expect = 7.0
Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 1/13 (7%)
Query: 12 HILKGDFVPSCVP 24
HILKGD VP+ P
Sbjct: 43 HILKGD-VPTVTP 54
>gnl|CDD|147761 pfam05785, CNF1, Rho-activating domain of cytotoxic necrotizing
factor. This family consists of several bacterial
cytotoxic necrotizing factor proteins as well as related
dermonecrotic toxin (DNT) from Bordetella species.
Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of
rabbit skin and re-organisation of the actin
cytoskeleton in cultured cells. Bordetella dermonecrotic
toxin (DNT) stimulates the assembly of actin stress
fibres and focal adhesions by deamidating or
polyaminating Gln63 of the small GTPase Rho. DNT is an
A-B toxin which is composed of an N-terminal
receptor-binding (B) domain and a C-terminal
enzymatically active (A) domain.
Length = 281
Score = 28.1 bits (63), Expect = 7.5
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 23 VPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTV 59
V N +G N + +P+ PL+I +GA +G TTV
Sbjct: 101 VSNGARGTNGIKIALSEVPEGKPLIITSGALSGCTTV 137
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.136 0.409
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,468,239
Number of extensions: 455795
Number of successful extensions: 1334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1305
Number of HSP's successfully gapped: 39
Length of query: 685
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 585
Effective length of database: 4,102,837
Effective search space: 2400159645
Effective search space used: 2400159645
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 (21.8 bits)
S2: 61 (27.3 bits)