RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10448
(1001 letters)
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 445 bits (1146), Expect = e-140
Identities = 258/726 (35%), Positives = 360/726 (49%), Gaps = 152/726 (20%)
Query: 191 KKKSKGRGKTKTKE-------LQEDEDGASGSKPRRYTPPPEKPTTDLRKKYEKQPPFLD 243
K K +GR +K E L+E+EDG GS R P +R
Sbjct: 123 KAKGRGRHASKLTEEEEDEEYLKEEEDGLGGSGGTRLLVQPSCIKGKMRD---------- 172
Query: 244 DTGMQLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLV 303
YQL G+NWL + I+ ILADEMGLGKT+QTI+ L L + GP +V
Sbjct: 173 --------YQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMV 224
Query: 304 SAPLSTIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSST 363
AP ST+ NW E + P V + G+ + R R+ + G
Sbjct: 225 VAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQRE------ELLVAG---------- 268
Query: 364 VKFHVLLTSYELITNDVALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLLLTG 423
KF V +TS+E+ + L W +++DEAHR+K+ S K + +S +LL+TG
Sbjct: 269 -KFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRLLITG 327
Query: 424 TPLQNNLEELFHLLNFLTPEKFNDLTSFQAEFADISKEEQ---VKRLHDLLGPHMLRRLK 480
TPLQNNL EL+ LLNFL PE F+ +F F + +Q V++LH +L P +LRRLK
Sbjct: 328 TPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLK 387
Query: 481 ADVLKNMPSKSEFIVRVELSPMQKKYYKYILTRNFEALNPKGGGQQVSLLNIMMDLKKCC 540
+DV K +P K E I++V +S MQK+YYK +L ++ + +N GG++ LLNI M L+KCC
Sbjct: 388 SDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVN--AGGERKRLLNIAMQLRKCC 445
Query: 541 NHPYLFPAAAEEAPVQGGQYEIQALTRAAGKLVLLSKMLKKLKEDGHRYGIKPEWLIANR 600
NHPYLF A P G++ L +GK+VLL K+L KLKE R I
Sbjct: 446 NHPYLFQGAEPGPPYTTGEH----LVENSGKMVLLDKLLPKLKERDSRVLI--------- 492
Query: 601 VINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNMTKMLDILEDYLDG 660
F MT++LDILEDYL
Sbjct: 493 -------------------------------------------FSQMTRLLDILEDYLMY 509
Query: 661 EGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVIIYDSDW 720
GY+Y RIDGN G R SID FN PG+ +FVFLLSTR+GGLGINLATAD VI+YDSDW
Sbjct: 510 RGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILYDSDW 569
Query: 721 NPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKVMI 780
NP Q D+QA RAHRIGQ+ +V +
Sbjct: 570 NP----QV---------------------------------DLQAQDRAHRIGQKKEVQV 592
Query: 781 YRFVTRNSVEERVTQVAKRKMMLTHLVVRPGMGGKQANFTKQELDDILRFGTEELFKEEE 840
+RF T ++EE+V + A +K+ L LV++ G +Q K EL ++R+G E +F ++
Sbjct: 593 FRFCTEYTIEEKVIERAYKKLALDALVIQQGRLAEQKTVNKDELLQMVRYGAEMVFSSKD 652
Query: 841 EQPENTEIIKQEAENQDPAYWVKLLRHHYEQHQEDVSRTLGKGKRVRKQTDDENDDDDFD 900
+ +I + A+ ++ L ++ ED ++ + DD + DFD
Sbjct: 653 STITDEDIDRIIAKGEEAT---AELDAKMKKFTEDA---------IKFKMDDTAELYDFD 700
Query: 901 EKNDGD 906
+++D D
Sbjct: 701 DEDDKD 706
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 295 bits (758), Expect = 2e-92
Identities = 138/317 (43%), Positives = 180/317 (56%), Gaps = 38/317 (11%)
Query: 252 YQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHC-KGPFLVSAPLSTI 310
YQLEG+NWL + ILADEMGLGKT+QTI L + KEG +GP LV PLST+
Sbjct: 1 YQLEGVNWLISLESNGLGGILADEMGLGKTLQTIALLATYLKEGKDRRGPTLVVCPLSTL 60
Query: 311 INWEREFETWAPDFYVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKFHVLL 370
NW EFE WAP VV Y GD R LR DT + V++
Sbjct: 61 HNWLNEFEKWAPALRVVVYHGDGRERSKLRQSMAKRLDT----------------YDVVI 104
Query: 371 TSYELITND---VALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLLLTGTPLQ 427
T+YE++ D ++LL +EW +V+DEAHRLK+++SK +K L +N+LLLTGTP+Q
Sbjct: 105 TTYEVLRKDKKLLSLLNKVEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQ 164
Query: 428 NNLEELFHLLNFLTPEKFNDLTSFQAEF-------------ADISKEEQVKRLHDLLGPH 474
NNLEEL+ LLNFL P F F+ F +E + RLH LL P
Sbjct: 165 NNLEELWALLNFLRPGPFGSFKVFEEWFNIPIANTADNKNKNLEKGKEGINRLHKLLKPF 224
Query: 475 MLRRLKADVLKNMPSKSEFIVRVELSPMQKKYYKYILTRNFEALNP-----KGGGQQVSL 529
+LRR K DV K++P K+E ++ LS Q+K YK +LT+ AL+ + SL
Sbjct: 225 LLRRTKDDVEKSLPPKTEHVLYCNLSDEQRKLYKKLLTKRRLALSFAVEGGEKNVGIASL 284
Query: 530 LNIMMDLKKCCNHPYLF 546
LN++M L+K CNHPYLF
Sbjct: 285 LNLIMQLRKICNHPYLF 301
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 291 bits (745), Expect = 2e-84
Identities = 217/863 (25%), Positives = 336/863 (38%), Gaps = 148/863 (17%)
Query: 18 EHRRYDRDREEEKKEKEEARIYGQMARQILLALFLGTGDRYLQTSSPKSPSQNLD--FTS 75
D + K E I + L G R L +Q +
Sbjct: 103 RVLIADEVGLGDLKTIEAGAI-------LKELLLRGEIKRVLILVPKTLRAQWVVELLEK 155
Query: 76 FLEVYHPQLLKSYMKKMNNDFTEPPALEEPLDEEDKRMARLNRHNINDEELEKKYYRY-- 133
F + + P E L +A+ + + LE ++
Sbjct: 156 FNIRLAVLDKEGLRYLLKQYDAYNPFSTEDLVLISLDLAKRSDSKRREALLEAEWGERDL 215
Query: 134 -GIKPEWLIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNKK 192
I + + K + Y + + + D + L + E ++
Sbjct: 216 LVIDEAHNLGSSEGTRKLAPLETLEYELLKQLAEKIPSKLLDLKVLL--LSATPEQLKEE 273
Query: 193 KSKGRGKTKTKELQEDEDGASGSKPRRYTPPPEKPTTDLRKKYEKQPPFLDD-------- 244
R + D R + D K+ + +D
Sbjct: 274 DLFARLRLLDPLRLADLSQILEKFVRETLKLSARDLKDELKELLAELRLSEDLLNAPEPV 333
Query: 245 -TGMQLHAYQLEGINWLR---YSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHC-KG 299
+L YQLEG+NWL S ILAD+MGLGKT+QTI L SL + G
Sbjct: 334 DLSAELRPYQLEGVNWLSELLRSNLLGG--ILADDMGLGKTVQTIALLLSLLESIKVYLG 391
Query: 300 PFLVSAPLSTIINWEREFETWAPDF-YVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCR 358
P L+ P S + NW+REFE +APD V+ Y G+K R+ + D
Sbjct: 392 PALIVVPASLLSNWKREFEKFAPDLRLVLVYHGEKSELDKKRE---ALRDLLKLH----- 443
Query: 359 IRSSTVKFHVLLTSYELITN---DVALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSI 415
+ F V++T+YEL+ D L IEW +V+DEAHR+K++QS K L
Sbjct: 444 ---LVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQFLKA 500
Query: 416 QNKLLLTGTPLQNNLEELFHLLN-FLTPEKFN-DLTSFQAEFADI-----------SKEE 462
N+L LTGTPL+N L EL+ LL FL P F F ++E
Sbjct: 501 LNRLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEAREL 560
Query: 463 QVKRLHDLLGPHMLRRLKAD--VLKNMPSKSEFIVRVELSPMQKKYYKYILTRNFEALN- 519
++ L LL P +LRR K D VLK +P K E ++ ELS Q++ Y+ +L +
Sbjct: 561 GIELLRKLLSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQL 620
Query: 520 -----------PKGGGQQVSLLNIMMDLKKCCNHPYLFPAAAEEAPVQGGQYEIQALTRA 568
+ G ++++L ++ L++ CNHP L +G + +
Sbjct: 621 LEDLEKADSDENRIGDSELNILALLTRLRQICNHPALVD--------EGLEATFDRIVLL 672
Query: 569 AGKLVLLSKMLKKLKEDGHRYGIKPEWLIANRVINSKTLRDGSTIYLVKWRDLPYDKATW 628
+ + K L + K + + ++ K L +G
Sbjct: 673 LREDKDFDYLKKPLIQLS-----KGKLQALDELLLDKLLEEGHYH--------------- 712
Query: 629 EDENEDIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPG 688
+ + F T +LD+LEDYL G KY R+DG+ RQE IDRFNA
Sbjct: 713 -----------KVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNAD- 760
Query: 689 ASQFVFLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATAD 748
+ VFLLS ++GGLG +NL AD
Sbjct: 761 EEEKVFLLSLKAGGLG-------------------------------------LNLTGAD 783
Query: 749 TVIIYDSDWNPHNDIQAFSRAHRIGQQNKVMIYRFVTRNSVEERVTQVAKRKMMLTHLVV 808
TVI++D WNP ++QA RAHRIGQ+ V +YR +TR ++EE++ ++ ++K L ++
Sbjct: 784 TVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEEKILELQEKKQELLDSLI 843
Query: 809 RPGMGGKQANFTKQELDDILRFG 831
+ + + ++L D+ G
Sbjct: 844 DAEGEKELSKLSIEDLLDLFSLG 866
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 97.2 bits (242), Expect = 7e-23
Identities = 52/211 (24%), Positives = 75/211 (35%), Gaps = 36/211 (17%)
Query: 248 QLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPL 307
L YQ E I L D ILA G GKT+ + K G G LV P
Sbjct: 8 PLRPYQKEAIEALLSGLR---DVILAAPTGSGKTLAALLPALEALKRGK-GGRVLVLVPT 63
Query: 308 -STIINWEREFETWAPDFY--VVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTV 364
W E + P VV G R LR ++ S
Sbjct: 64 RELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLR-----------------KLESG-- 104
Query: 365 KFHVLLTSYELITNDVA--LLGSIEWAVLVVDEAHRLKSN----QSKFFKFLSGYSIQNK 418
K +L+T+ + + + L ++++DEAHRL Q + L ++Q
Sbjct: 105 KTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQ-L 163
Query: 419 LLLTGTP---LQNNLEELFHLLNFLTPEKFN 446
LLL+ TP ++N LE + F+
Sbjct: 164 LLLSATPPEEIENLLELFLNDPVFIDVGFTP 194
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 92.7 bits (231), Expect = 8e-23
Identities = 29/85 (34%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 652 DILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATAD 711
+ L + L G K R+ G ++ R+E +D+FN + L++T G++L D
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNN---GKIKVLVATDVAERGLDLPGVD 57
Query: 712 TVIIYDSDWNPHNDIQAFSRAHRIG 736
VIIYD W+P + IQ RA R G
Sbjct: 58 LVIIYDLPWSPASYIQRIGRAGRAG 82
>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 = 93.5 bits (233), Expect = 2e-22
Identities = 33/101 (32%), Positives = 47/101 (46%), Gaps = 3/101 (2%)
Query: 644 FYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGL 703
F KMLD L + L G K + G+ + R+E + F + V L++T
Sbjct: 34 FCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREG---EIVVLVATDVIAR 90
Query: 704 GINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINL 744
GI+L VI YD W+P + +Q RA R GQ+ I L
Sbjct: 91 GIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 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 = 90.7 bits (226), Expect = 4e-22
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 656 DYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVII 715
L G K R+ G ++ R+E ++ F + L++T G GI+L + VI
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNG---KSKVLVATDVAGRGIDLPDVNLVIN 57
Query: 716 YDSDWNPHNDIQAFSRAHRIG 736
YD WNP + IQ RA R G
Sbjct: 58 YDLPWNPASYIQRIGRAGRAG 78
>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 = 84.7 bits (210), Expect = 4e-19
Identities = 32/164 (19%), Positives = 55/164 (33%), Gaps = 28/164 (17%)
Query: 269 DTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLSTIINWEREFETWAPDFY--V 326
D +LA G GKT+ + + L G LV AP + N E V
Sbjct: 2 DVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGEGIKV 60
Query: 327 VTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKFHVLLTSYELITNDVAL--LG 384
+G + + K +++ + + +++ L
Sbjct: 61 GYLIGGTSIKQQEKLLSG--------------------KTDIVVGTPGRLLDELERLKLS 100
Query: 385 SIEWAVLVVDEAHRLKSNQSKFF---KFLSGYSIQNKLLLTGTP 425
+ +L++DEAHRL + L + LLL+ TP
Sbjct: 101 LKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|148208 pfam06465, DUF1087, Domain of Unknown Function (DUF1087). Members
of this family are found in various chromatin
remodelling factors and transposases. Their exact
function is, as yet, unknown.
Length = 66
Score = 79.1 bits (195), Expect = 3e-18
Identities = 38/68 (55%), Positives = 47/68 (69%), Gaps = 4/68 (5%)
Query: 833 EELFKEEEEQPENTEIIKQEAENQDPAYWVKLLRHHYEQHQEDVSRTLGKGKRVRKQ--T 890
E+L KEEEE TEIIK+ AE+ DP YW KLL+HHYEQ + + + LGKGKR RKQ
Sbjct: 1 EQLLKEEEEAE--TEIIKEAAESDDPDYWEKLLKHHYEQLRAEEEKALGKGKRSRKQVNY 58
Query: 891 DDENDDDD 898
+E+D D
Sbjct: 59 AEEDDIDG 66
>gnl|CDD|219716 pfam08074, CHDCT2, CHDCT2 (NUC038) domain. The CHDCT2 C-terminal
domain is found in PHD/RING finger and chromo
domain-associated CHD-like helicases.
Length = 174
Score = 75.7 bits (186), Expect = 1e-15
Identities = 32/45 (71%), Positives = 41/45 (91%)
Query: 939 EVLNQLEELLSDMKSDVSRLPATLARIPPVAQRLHMSERSILSRL 983
+VLNQL+ELLSDMK+DV+RLP+TL+++ PV +RL MSER ILSRL
Sbjct: 130 KVLNQLDELLSDMKADVNRLPSTLSQLAPVTERLQMSERQILSRL 174
>gnl|CDD|214605 smart00298, CHROMO, Chromatin organization modifier domain.
Length = 55
Score = 50.3 bits (121), Expect = 4e-08
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 144 RVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNKKKS 194
++++ + + G YLVKW+ Y + TWE E E++ + ++ Y KK+
Sbjct: 6 KILDHRWKKKGELEYLVKWKGYSYSEDTWEPE-ENLLNCSKKLDNYKKKER 55
Score = 47.2 bits (113), Expect = 4e-07
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 600 RVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFY 645
++++ + + G YLVKW+ Y + TWE E E++ + ++ Y
Sbjct: 6 KILDHRWKKKGELEYLVKWKGYSYSEDTWEPE-ENLLNCSKKLDNY 50
>gnl|CDD|215889 pfam00385, Chromo, Chromo (CHRromatin Organisation MOdifier)
domain.
Length = 52
Score = 48.7 bits (117), Expect = 1e-07
Identities = 16/36 (44%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 144 RVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDI 179
R+++ + + G+ YLVKW+ PYD+ATWE E E++
Sbjct: 4 RILDHRLRKGGNKEYLVKWKGYPYDEATWEPE-ENL 38
Score = 48.7 bits (117), Expect = 1e-07
Identities = 16/36 (44%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 600 RVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDI 635
R+++ + + G+ YLVKW+ PYD+ATWE E E++
Sbjct: 4 RILDHRLRKGGNKEYLVKWKGYPYDEATWEPE-ENL 38
>gnl|CDD|237991 cd00024, CHROMO, Chromatin organization modifier (chromo) domain is
a conserved region of around 50 amino acids found in a
variety of chromosomal proteins, which appear to play a
role in the functional organization of the eukaryotic
nucleus. Experimental evidence implicates the chromo
domain in the binding activity of these proteins to
methylated histone tails and maybe RNA. May occur as
single instance, in a tandem arrangement or followd by a
related "chromo shadow" domain.
Length = 55
Score = 44.2 bits (105), Expect = 5e-06
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 137 PEWLIANRVINSKTLRDGSTI-YLVKWRDLPYDKATWEDENEDIPGLKESIEFYNKK 192
E+ + ++++ + +DG YLVKW+ Y + TWE E E++ KE I+ + KK
Sbjct: 1 EEYEVE-KILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPE-ENLEDCKELIDEFKKK 55
Score = 42.6 bits (101), Expect = 2e-05
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 593 PEWLIANRVINSKTLRDGSTI-YLVKWRDLPYDKATWEDENEDIPGLKESIEF 644
E+ + ++++ + +DG YLVKW+ Y + TWE E + EF
Sbjct: 1 EEYEVE-KILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEENLEDCKELIDEF 52
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 48.7 bits (117), Expect = 2e-05
Identities = 33/107 (30%), Positives = 49/107 (45%), Gaps = 22/107 (20%)
Query: 387 EWAVLVVDEAHRL------KSNQSKFFKFLSGYSIQNKLLLTGTPLQNNLEELFHLLNFL 440
EW +LVVDEAH L S + + + L+ I LLLT TP Q E F L L
Sbjct: 272 EWDLLVVDEAHHLVWSEEAPSREYQVVEQLAE-VIPGVLLLTATPEQLGQESHFARLRLL 330
Query: 441 TPEKFNDLTSFQAE---FADISK------------EEQVKRLHDLLG 472
P++F+D +F E + ++ ++ + L +LLG
Sbjct: 331 DPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLG 377
Score = 30.6 bits (70), Expect = 5.0
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 272 LADEMGLGKTI 282
LADE+GLGKTI
Sbjct: 174 LADEVGLGKTI 184
>gnl|CDD|219039 pfam06461, DUF1086, Domain of Unknown Function (DUF1086). This
family consists of several eukaryotic domains of unknown
function which are present in chromodomain helicase DNA
binding proteins. This domain is often found in
conjunction with pfam00176, pfam00271, pfam06465,
pfam00385 and pfam00628.
Length = 158
Score = 42.3 bits (99), Expect = 3e-04
Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 5/50 (10%)
Query: 892 DENDDDDFDEKNDGDLTGRRSAKKKEMSKQERDRPLPPLLARVGGNIEVL 941
E D+D+DEK T RR +K+ ++ + LPPL+A VGG IEVL
Sbjct: 5 REEGDEDYDEKPR---TVRRPYRKR--ARDNSEEKLPPLMAGVGGQIEVL 49
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 34.7 bits (80), Expect = 0.24
Identities = 25/142 (17%), Positives = 51/142 (35%), Gaps = 23/142 (16%)
Query: 365 KFHVLLTSYELITNDVALLGSI--EWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLL-L 421
V + + + + L + E+ +++ DE H L + + + L S L L
Sbjct: 122 PAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAP--SYRRILELLSAAYPRLGL 179
Query: 422 TGTP---LQNNLEELFHLL---------------NFLTPEKFNDLTSFQAEFADISKEEQ 463
T TP + +LF L+ +L P K+ ++ E + ++
Sbjct: 180 TATPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKE 239
Query: 464 VKRLHDLLGPHMLRRLKADVLK 485
R +LL R + + +
Sbjct: 240 SARFRELLRARGTLRAENEARR 261
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 32.2 bits (74), Expect = 0.30
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 388 WAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLL-LTGTP 425
V+++DEAH S+ ++ + LL LT TP
Sbjct: 62 ALVIIIDEAHH--SSAKTKYRKILEKFKPAFLLGLTATP 98
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 32.6 bits (75), Expect = 0.31
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 11/51 (21%)
Query: 390 VLVVDEAHRLKSNQSKFFKFL---SGYSIQNKLLLTGTPLQNNLEELFHLL 437
+L++DEA L + + L S IQ ++L GTP EL LL
Sbjct: 82 LLIIDEAQHLSLEALEELRDLYDLSEKGIQ--VILVGTP------ELRKLL 124
>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 = 33.6 bits (77), Expect = 0.59
Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 9/98 (9%)
Query: 639 KESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLST 698
I F ++++ L + L G+K + G++ R ++++F + L++T
Sbjct: 274 GRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFK---DGELRVLVAT 330
Query: 699 RSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIG 736
G+++ VI YD +P + + HRIG
Sbjct: 331 DVAARGLDIPDVSHVINYDLPLDPEDYV------HRIG 362
>gnl|CDD|198461 cd10470, FAM20B_C, C-terminal putative kinase domain of FAM20B
xylose kinase. Experiments with human FAM20B suggest
that it is a xylose kinase that participates in
proteoglycan production. It may regulate the number of
glycosaminoglycan chains by phosphorylating the xylose
residue in the glycosaminoglycan-protein linkage region
of proteoglycans. The C-terminal domain of FAM20B is a
putative kinase domain, based on mutagenesis of the
C-terminal domain of Drosophila Four-Jointed, a related
Golgi kinase. This subfamily belongs to the FAM20_C
(also known as DUF1193) domain family.
Length = 206
Score = 31.6 bits (72), Expect = 1.3
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 611 STIYLVKWRDLPYD-------KATWEDENEDIPGLKESIEFYNMTKMLDILE----DYLD 659
L K R P+ A WE + + +K+ + + ++LD+++ D+L
Sbjct: 40 DVWPLQKHRH-PWQRTYKENKLARWETDEDYCDKVKKKSPYDSGPRLLDLIDTAIFDFLI 98
Query: 660 GEG--YKYERIDGN 671
G G + YE +
Sbjct: 99 GNGDRHHYETFQDD 112
>gnl|CDD|227311 COG4977, COG4977, Transcriptional regulator containing an amidase
domain and an AraC-type DNA-binding HTH domain
[Transcription].
Length = 328
Score = 31.9 bits (73), Expect = 1.5
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 921 QERDRPLPPLLARVGGNIEVLNQLEELLSDMKSDVSRLPATLARIPPVAQRLHMSERSIL 980
DR PLL R+G L + EL M++++ P +L + A R +S R L
Sbjct: 202 SGGDRQRLPLLGRLGHRDPRLLRAIEL---MEANLEE-PLSLEEL---ADRAGLSRRQ-L 253
Query: 981 SRLAATSTSTNPS 993
RL +P+
Sbjct: 254 ERLFRAELGVSPA 266
>gnl|CDD|233752 TIGR02153, gatD_arch, glutamyl-tRNA(Gln) amidotransferase, subunit
D. This peptide is found only in the Archaea. It is
part of a heterodimer, with GatE (TIGR00134), that acts
as an amidotransferase on misacylated Glu-tRNA(Gln) to
produce Gln-tRNA(Gln). The analogous amidotransferase
found in bacteria is the GatABC system, although GatABC
homologs in the Archaea appear to act instead on
Asp-tRNA(Asn) [Protein synthesis, tRNA aminoacylation].
Length = 404
Score = 31.6 bits (72), Expect = 2.3
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 11/49 (22%)
Query: 830 FGTEELFKEEEEQPENTEIIKQEA--------ENQDPAYWVKLLRHHYE 870
F EEL PE EI +A EN P YW+K+ +
Sbjct: 89 FTAEELA---RAVPELLEIANIKARAVFNILSENMKPEYWIKIAEAVAK 134
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 31.3 bits (72), Expect = 2.9
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 14/72 (19%)
Query: 456 ADI-SKEEQVKRLHDLLGPH----------MLRRL-KADVLKNMPSKSEFIVRVELSPMQ 503
AD+ EE ++RL + LRR KA ++ +P S+F + ELS Q
Sbjct: 227 ADLPPAEENIERLKEEKYYIVVPTSAEAELALRRAAKAGLIDYIPGDSDFEILGELSEKQ 286
Query: 504 KKYYKYILTRNF 515
KK +YI R
Sbjct: 287 KKALEYI--REV 296
>gnl|CDD|226993 COG4646, COG4646, DNA methylase [Transcription / DNA replication,
recombination, and repair].
Length = 637
Score = 31.0 bits (70), Expect = 3.9
Identities = 28/143 (19%), Positives = 55/143 (38%), Gaps = 30/143 (20%)
Query: 420 LLTGTPLQNNLEELFHLLNFLTPEK---------------FNDLTSFQAEFADISKEEQV 464
L +GTP+ N L E+F + +L F D+T+ + E +K + V
Sbjct: 478 LASGTPITNTLGEMFSVQRYLGAGALYERGLHEFDAWASTFGDVTT-ELELQPSAKYKPV 536
Query: 465 KRLH---DLLGPHMLRRLKADVLKNMPSKSEFIVRVELSP-----------MQKKYYKYI 510
R ++ + R ADV+ + ++E++ K Y+Y+
Sbjct: 537 VRFACFVNVPELIAMFRSFADVVMPLDLRAEYVPVPARDTGARQIVTRKPGRAFKRYQYV 596
Query: 511 LTRNFEALNPKGGGQQVSLLNIM 533
L+ +A+ + G Q ++
Sbjct: 597 LSPRIKAMEEREGPAQPGDDILL 619
>gnl|CDD|233065 TIGR00634, recN, DNA repair protein RecN. All proteins in this
family for which functions are known are ATP binding
proteins involved in the initiation of recombination and
recombinational repair [DNA metabolism, DNA replication,
recombination, and repair].
Length = 563
Score = 30.9 bits (70), Expect = 3.9
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 6/72 (8%)
Query: 898 DFDEKNDGDLTGRRSAKKKEMSKQERDRPLPPLLARVGGN----IEVLNQLEELLSDMKS 953
D D + L G A+ S D L L +VG E +L+ L +++
Sbjct: 241 DVDVQEGSLLEGLGEAQLALAS--VIDGSLRELAEQVGNALTEVEEATRELQNYLDELEF 298
Query: 954 DVSRLPATLARI 965
D RL R+
Sbjct: 299 DPERLNEIEERL 310
>gnl|CDD|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2
and 3. This family of class II histone deacetylase
complex subunits HDA2 and HDA3 is found in fungi, The
member from S. pombe is referred to as Ccq1. These
proteins associate with HDA1 to generate the activity of
the HDA1 histone deacetylase complex. HDA1 interacts
with itself and with the HDA2-HDA3 subcomplex to form a
probable tetramer and these interactions are necessary
for catalytic activity. The HDA1 histone deacetylase
complex is responsible for the deacetylation of lysine
residues on the N-terminal part of the core histones
(H2A, H2B, H3 and H4). Histone deacetylation gives a tag
for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and
developmental events. HDA2 and HDA3 have a conserved
coiled-coil domain towards their C-terminus.
Length = 279
Score = 30.4 bits (69), Expect = 4.7
Identities = 33/144 (22%), Positives = 54/144 (37%), Gaps = 38/144 (26%)
Query: 649 KMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLA 708
K LD++E L G+G Y+R+ G S+ +E+ + G S L I+L
Sbjct: 124 KTLDLVEALLLGKGLNYKRLSGE---SLYEENHKVSDKKG-----------SLSLWIHLT 169
Query: 709 TADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDWNPHND-IQAFS 767
T+D + DS + D +I +D + I++
Sbjct: 170 TSDGLTNTDSSLLSNYKF---------------------DLIISFDPSLDTSLPSIESLR 208
Query: 768 RAHRIGQQNKVMIYRFVTRNSVEE 791
+R + N I R V NS+E
Sbjct: 209 TQNR--RGNLTPIIRLVVVNSIEH 230
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 29.9 bits (68), Expect = 7.6
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 390 VLVVDEAHRLKSNQSKFFKF 409
V++VDEAHRL + +F F
Sbjct: 82 VVIVDEAHRLWTKSDLYFNF 101
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 30.0 bits (68), Expect = 7.7
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 891 DDENDDDDFDEKNDGDLTGRRSAKKKEMSKQERDR 925
+D+ DDDD D+ +D R +++ + E R
Sbjct: 144 EDDEDDDDDDDDDDIATRERSLERRRRRREWEEKR 178
>gnl|CDD|130410 TIGR01343, hacA_fam, homoaconitate hydratase family protein. This
model represents a subfamily of proteins consisting of
aconitase, homoaconitase, 3-isopropylmalate dehydratase,
and uncharacterized proteins. The majority of the
members of this family have been designated as
3-isopropylmalate dehydratase large subunit (LeuC) in
microbial genome annotation, but the only characterized
member is Thermus thermophilus homoaconitase, an enzyme
of a non-aspartate pathway of Lys biosynthesis.
Length = 412
Score = 29.7 bits (67), Expect = 8.6
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 467 LHDLLGPHMLRRLK---ADVLKNMPSKSEFIV-------RVELSPMQKKYYKYILTRNFE 516
+HD+ P +RRL+ D + + P + +V ++ + MQK +++ +
Sbjct: 30 VHDITAPLAIRRLEEYGIDKVFD-PERIVIVVDHVVPASTIKAAEMQKLAREFVKKTGIK 88
Query: 517 ALNPKGGG 524
G G
Sbjct: 89 HFFDVGEG 96
>gnl|CDD|221976 pfam13199, Glyco_hydro_66, Glycosyl hydrolase family 66. This
family is a set of glycosyl hydrolase enzymes including
cycloisomaltooligosaccharide glucanotransferase
(EC:2.4.1.-) and dextranase (EC:3.2.1.11) activities.
Length = 564
Score = 29.6 bits (67), Expect = 8.9
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 106 LDEEDKRMARLNRHNINDEELEKKYYRY---------GIKPEWL-IANRVINSKTLRD 153
+E +K + +LNR++IN + YR+ W IANR +++ T++
Sbjct: 115 PEEYEKEIDQLNRYHINGLQFYDWQYRHHKPLPGTVGQPAQSWKDIANRPVSTSTVKG 172
>gnl|CDD|235832 PRK06567, PRK06567, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase; Validated.
Length = 1028
Score = 29.9 bits (67), Expect = 9.2
Identities = 36/129 (27%), Positives = 56/129 (43%), Gaps = 25/129 (19%)
Query: 88 YMKKMNNDFTEPPALEEPLDEEDKRMA-------RLNRHNINDEELEKKYYRYGIKPEWL 140
Y KK +F + +E+ L EEDK +A +L + N+EEL K + + G
Sbjct: 572 YYKKQVEEFAKD-YIEKDLTEEDKEIAEEFIAHAKLFKEAKNNEELRKVFNKLG------ 624
Query: 141 IANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLK---------ESIEFYNK 191
V L+D S Y + +L Y A D E++ L+ ES+EF N+
Sbjct: 625 -GATVYYRGRLQD-SPAYKLNHEELIYALALGVDFKENMQPLRINVDKYGHVESVEFENR 682
Query: 192 KKSKGRGKT 200
+ + KT
Sbjct: 683 NRHCEQSKT 691
>gnl|CDD|221849 pfam12912, N_NLPC_P60, NLPC_P60 stabilising domain, N term. This
domain, at the N-terminus, appears to be the stabilising
domain for the structure PDB:3m1u, which is a
four-domain protein. The next domain is an SH3b1, the
third an SH3b2 and the last, the C-terminal region, the
catalytic domain of the cysteine-peptidase type, ie
family NLPC_P60, pfam00877 (details derived from
TOPSAN).
Length = 125
Score = 28.2 bits (63), Expect = 9.4
Identities = 21/117 (17%), Positives = 32/117 (27%), Gaps = 17/117 (14%)
Query: 46 ILLALFLGTGDRYLQTSSPKSPSQNLDFTSFLEVYHPQLLKSYMKKMNNDFTEPPALEEP 105
+ L LF G + K P Q + L PQ L Y A +
Sbjct: 6 LSLLLFTGCSTKTPPPPPVKQPVQPGEIAD-LSR-LPQDLTVYADSAGAQPLLDQARQAA 63
Query: 106 LDEE---------DKRMARLNRHNINDEELEKKYYRYGIKPEWLIANRVINSKTLRD 153
LDEE R ++ +R + + N ++ D
Sbjct: 64 LDEEYLKRFFAPWHSTKPSFPRKDV------FWIFRKYNRKKGYGENLQPWPQSWFD 114
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 29.4 bits (66), Expect = 9.8
Identities = 26/111 (23%), Positives = 50/111 (45%), Gaps = 3/111 (2%)
Query: 640 ESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTR 699
++I + N + +D L + + + G++ R + F + G+++ L++T
Sbjct: 269 QAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRS-GSTRV--LITTD 325
Query: 700 SGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTV 750
GI++ VI YD +P N I R+ R G++ IN T D +
Sbjct: 326 LLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDI 376
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.134 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: 52,901,248
Number of extensions: 5429169
Number of successful extensions: 6271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6208
Number of HSP's successfully gapped: 78
Length of query: 1001
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 895
Effective length of database: 6,236,078
Effective search space: 5581289810
Effective search space used: 5581289810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 64 (28.3 bits)