RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1361
(1274 letters)
>gnl|CDD|99915 cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily catalytic
domain. Three DNA-dependent DNA polymerases type B
(alpha, delta, and epsilon) have been identified as
essential for nuclear DNA replication in eukaryotes. DNA
polymerase (Pol) alpha is almost exclusively required for
the initiation of DNA replication and the priming of
Okazaki fragments during elongation. In most organisms no
specific repair role, other than check point control, has
been assigned to this enzyme. Pol alpha contains both
polymerase and exonuclease domains, but lacks exonuclease
activity suggesting that the exonuclease domain may be
for structural purposes only.
Length = 400
Score = 655 bits (1693), Expect = 0.0
Identities = 251/411 (61%), Positives = 305/411 (74%), Gaps = 11/411 (2%)
Query: 619 KGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT 678
K +KKA Y+GGLVLEPKKG YDKFI+L+DFNSLYPSIIQEYNICFTT+ D D
Sbjct: 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEE 60
Query: 679 LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSM 738
LP + GILP I+KLVE RRQVK LMK D Q DIRQ ALKLTANSM
Sbjct: 61 PP--LPPSDQEKGILPRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSM 117
Query: 739 YGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYD 798
YGCLGF SRF+A+PLAAL+T+KGREIL TK LVE +N EVIYGDTDS+MI+ DY+
Sbjct: 118 YGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVIYGDTDSIMINTGTTDYE 177
Query: 799 SVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKG 858
K+GN+IK E NK YK+LE+DIDGV+K +LLLKKKKYAAL + GK +E+KG
Sbjct: 178 EAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVDDDKGK--LKKEVKG 235
Query: 859 VDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLT 918
+D+VRRDW L+ E G +V+ QIL ++S +D ++NIHE+++KI DL NG +PL
Sbjct: 236 LDIVRRDWCPLSKEIGNYVLDQILSDKSR-----EDIVENIHEYLRKINEDLRNGKIPLE 290
Query: 919 LLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQR 978
ITKQLTK PEEY D+K+LPHVQVALR+N +K+K GDTI YIIC+DG+S++ R
Sbjct: 291 KFIITKQLTKNPEEYPDKKSLPHVQVALRMNKRG-RKVKAGDTIPYIICKDGSSKSLADR 349
Query: 979 AYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDAVRIAECLGLD 1029
AY+ +E+K N LKID+ YYLSQQI P ++RL EPIEGTDAVR+AECLGLD
Sbjct: 350 AYHPDEVKKNENLKIDIEYYLSQQILPPISRLCEPIEGTDAVRLAECLGLD 400
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.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 = 1172
Score = 521 bits (1344), Expect = e-164
Identities = 265/454 (58%), Positives = 340/454 (74%), Gaps = 13/454 (2%)
Query: 561 RITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ-YGKNKKEGEETGEANKGK 619
+ITN+ GN++SRTLMGGRSERNEFLLLHAF+E +Y++PDKQ + K +K G+E E + K
Sbjct: 730 QITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQKLGDEDEEIDGYK 789
Query: 620 GRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTL 679
KKAAY+GGLVLEPK G YDK+++LMDFNSLYPSIIQE+NICFTT+ Q D L
Sbjct: 790 KGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQ----QKVDEDEL 845
Query: 680 CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMY 739
E LP+ +++ GILP E++KLVE R++VK LMKQ +L+ DL +QYDIRQKALKLTANSMY
Sbjct: 846 PE-LPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMY 903
Query: 740 GCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDS 799
GCLG+ SRF+A+PLAALVTAKGREIL +T+ LVE +N EVIYGDTDS+MI+ Y+
Sbjct: 904 GCLGYSKSRFYAKPLAALVTAKGREILEHTRQLVEEMNLEVIYGDTDSIMINTPGTKYEE 963
Query: 800 VFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGV 859
VFKIG + KSE NKLYK LELDIDGV+K +LLLKKKKYAA+ + S+G QE+KG+
Sbjct: 964 VFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTTKQEVKGL 1023
Query: 860 DVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTL 919
D+VRRDWS LA E GK V+ IL ++ +++ ++ + E ++KI ++ NG VPL
Sbjct: 1024 DIVRRDWSPLAKETGKKVLDTILSDK-----DVEEAVEEVQEVLEKIGKNVLNGEVPLEK 1078
Query: 920 LEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRA 979
I KQLT+ P++Y D +LPHV VALR+N +K+K GD +SY+IC+DG + +A QRA
Sbjct: 1079 FVINKQLTRDPKDYPDGASLPHVHVALRINARGGRKVKAGDVVSYVICKDGGNLSARQRA 1138
Query: 980 YNIEELKNNSK-LKIDVNYYLSQQIHPVVTRLLE 1012
Y +EEL+ L D YYL QIHPVV R+LE
Sbjct: 1139 YALEELQRKHNNLIYDTQYYLEHQIHPVVLRILE 1172
Score = 226 bits (577), Expect = 3e-60
Identities = 145/499 (29%), Positives = 221/499 (44%), Gaps = 49/499 (9%)
Query: 84 VYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEK----HDKR 139
+YE+V E+EY++RV ++ DD D G+GYVEDGRE F D+ + + K+ K+
Sbjct: 8 IYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDKDDGSAAEAKK 67
Query: 140 KKNKNIQNPNAKGDIQKLLANMPVKKKKKEEVQLNNDDVLADLLSEVNTTIAPTLKLNTK 199
K +N + +I+ + KKKK + L D +L D+L E+N T K+
Sbjct: 68 KDKENHKKVTKPNNIKAVRIACAPKKKKDRKKSLGKDGLLGDILQELNKTETAQRKI--T 125
Query: 200 TNEIVIPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMN 259
+ +PK + +P + +FS I K+ P+ ++ V +
Sbjct: 126 PRLVSVPKLKFSSPADVPAINDFS----NHHPAVVDIVKKAIPVSTRYLLEKILIPVPLK 181
Query: 260 VAEQSKEEPVDDGLWEQMQIDDWDNSQQTQDVLPEQAKVELQIEAIESQSIE-------- 311
AE + V ++++ +D D E + S
Sbjct: 182 RAEFAG-GDVQMEGDPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWD 240
Query: 312 -EKVDVTNVESVSSAVELSTSPPPQVV-EKKEHKCAEWEAIQTEPSTSEPQVHSRTADDS 369
E V + + +T + V E+ W+ I E + E V+ D+
Sbjct: 241 YESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNG----DN 296
Query: 370 LPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIY 429
L + F+ DA+ED ++ G V LFG+ + H S CV V+ I+R ++
Sbjct: 297 FDLVYLA--DRQVFQFYWDAYEDPAEKLGVVLLFGR-----DVDHVSPCVQVKGINRDLF 349
Query: 430 LLPRSEHLK------TKEPVSIAQVYSEFD-QIATQYKILDFKSRKIEKKYAFNLPG--V 480
LPR + T+ +++ Y EF ++A YK F+++ I KKY F P
Sbjct: 350 FLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPDIDA 409
Query: 481 PDLSEYLEVRYS-----AKCPALPSDLSGDTFSHVFGTKSSFLENLLLERKIKGPSWLEF 535
P SEYLEV Y A ALPSDL G TF HVFG+ + LE LL RKIKGP WL
Sbjct: 410 PYSSEYLEVTYELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAV 469
Query: 536 --PEAEKFPSRISWCKYEV 552
P+ ++P R SWCKYE
Sbjct: 470 KGPDELEYP-RRSWCKYEG 487
Score = 35.4 bits (81), Expect = 0.26
Identities = 34/147 (23%), Positives = 54/147 (36%), Gaps = 25/147 (17%)
Query: 619 KGRKKAAYSGGLVLEP--KKGFYD--KFIILMDFN--SLYPSIIQEYNICFTTIPVRMLQ 672
R Y GG V P +KG ++++DF+ SL PSII+ + R
Sbjct: 478 PRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFA 537
Query: 673 DSDITTLCEYLPEH-----------------QVDTGILPSEIKKLVESRRQVKALMKQ-P 714
D H G PS ++ L R +K M +
Sbjct: 538 -LDKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVK 596
Query: 715 NLSSDLLMQYDIRQKALKLTANSMYGC 741
+ D ++ +D +Q+ALK+ AN +
Sbjct: 597 KIDPDEIVGHDYQQRALKVLANRINDL 623
>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B. This region of DNA
polymerase B appears to consist of more than one
structural domain, possibly including elongation,
DNA-binding and dNTP binding activities.
Length = 458
Score = 400 bits (1031), Expect = e-128
Identities = 164/477 (34%), Positives = 235/477 (49%), Gaps = 43/477 (9%)
Query: 577 GRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKK 636
G+ R LLL E++++LPDK ++ + KK Y G VLEPKK
Sbjct: 1 GQQIRVFSLLLREAKERNFILPDKFELRSLS---------RQVNIKKEGYQGATVLEPKK 51
Query: 637 GFYDKFIILMDFNSLYPSIIQEYNICFTTI--PVRMLQDSDITTLCEYLPEHQVDT---- 690
GFY+ ++++DF SLYPSIIQ +N+C+ T+ E L
Sbjct: 52 GFYNNPVLVLDFASLYPSIIQAHNLCYETLVDVDAEAPKLAAERNLEVLHIVVGSLRERF 111
Query: 691 -------GILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 743
GILP ++ L+ R++ K LMK+ +L D +Q ALK+TANS+YG G
Sbjct: 112 VKKGVRKGILPVLLRDLLAKRKEKKKLMKESKDPEELRTLLDKQQLALKVTANSVYGFTG 171
Query: 744 FPNSRFFAQPLAALVTAKGREILLNTKSLVENL---NYEVIYGDTDSLMISCNVNDYDSV 800
N R P+A VTA GRE++ TK VE L ++VIYGDTDS+ + D +
Sbjct: 172 AANGRLPCLPIAESVTAIGREMIEKTKRYVEELLNYGFKVIYGDTDSVFVKFPGVDIEEA 231
Query: 801 FKIGNQIKSECNK--LYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKG 858
K+G ++ +K ++L+ + VYK +LL+ KK+YA L +GK +IKG
Sbjct: 232 KKLGKELAKHVTSELFFKPIKLEFEKVYKPLLLISKKRYAGL----KYDGKG----DIKG 283
Query: 859 VDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQN-IHEHMKKIRTDLDNGFVPL 917
VD+VRRDW + E + V+ +L ++ L+ I E +K + L VPL
Sbjct: 284 VDLVRRDWCEFVKEVIRKVLDLLLKDK--DVEDAAPSLKIVIIEILKSLTDKLVQNKVPL 341
Query: 918 TLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQ-GDTISYIICEDGTSEAAT 976
L ITK+L+K P EY K PHV VALRL +++ + GD I Y+I + G A
Sbjct: 342 EDLVITKELSKPPSEYKK-KNPPHVTVALRLKKRGNEEAPEVGDRIPYVIVK-GPFHAKG 399
Query: 977 QRAYNIEELKN--NSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDAVRIAECLGLDTS 1031
Y + E L ID YYL Q+ P V R+ E I D + + L L
Sbjct: 400 ALPYELAEDPEYVLENLPIDAEYYLDNQLVPPVERIFEAIFFGDVISWEKLLELFGK 456
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 335 bits (862), Expect = 1e-99
Identities = 156/472 (33%), Positives = 230/472 (48%), Gaps = 44/472 (9%)
Query: 563 TNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRK 622
+ V G L G R E LLL + ++P NK + +
Sbjct: 360 SRVSGLPLDDVTRAGSGARVEGLLLREAKRRGELIP-----------------NKEERPE 402
Query: 623 KAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEY 682
+ Y GGLVLEP+ G Y+ ++++DF+SLYPSII +YNI T+ D +
Sbjct: 403 RKKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDCSDDYSPPGVGH 461
Query: 683 LPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCL 742
+ + G LP +++L++ R ++K MK+ D RQ ALK+ ANS YG L
Sbjct: 462 GFC-KREKGFLPEILEELLDRRDEIKKKMKKE-KDPSERKLLDGRQLALKVLANSFYGYL 519
Query: 743 GFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFK 802
G+ NSRF+ A VTA GREIL TK L E + VIYGDTDSL ++ Y+ K
Sbjct: 520 GYSNSRFYCIECAESVTAFGREILRETKELAEEMGLRVIYGDTDSLFVTLPGATYEEAIK 579
Query: 803 IGNQIKSECN-KLYKQLELDIDGVYKYMLLL-KKKKYAALSISKLSNGKMICSQEIKGVD 860
IG ++ E N +L +EL+++ VYK LL KK+YA L K+ E+KG++
Sbjct: 580 IGEELVEEVNERLPSGIELEVEKVYKRFLLPTAKKRYAGLLE---DGDKI----EVKGLE 632
Query: 861 VVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLL 920
VRRDW +L E + V+ +L + + ++++ E ++ ++ L
Sbjct: 633 TVRRDWPELVKEFQREVLEVLLSGRDVEEALA-KYVRDVIEKLRNGEVPIE-------KL 684
Query: 921 EITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAY 980
I+K+LT+ EY + PHV VA RL +K GD I Y+I +RA
Sbjct: 685 VISKRLTRPLSEY--KANKPHVVVAARL-RKRGINVKPGDRIPYVIV--KGKGKLVERAE 739
Query: 981 NIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDAVRIAEC-LGLDTS 1031
E + ID YY+++Q+ P + R+LEPI G A E GL S
Sbjct: 740 PPELVDEE-NSPIDYEYYITKQLLPALERILEPIGGNFAELKGEDQTGLFDS 790
>gnl|CDD|99912 cd00145, POLBc, DNA polymerase type-B family catalytic domain.
DNA-directed DNA polymerases elongate DNA by adding
nucleotide triphosphate (dNTP) residues to the 5'-end of
the growing chain of DNA. DNA-directed DNA polymerases
are multifunctional with both synthetic (polymerase) and
degradative modes (exonucleases) and play roles in the
processes of DNA replication, repair, and recombination.
DNA-dependent DNA polymerases can be classified in six
main groups based upon their phylogenetic relationships
with E. coli polymerase I (class A), E. coli polymerase
II (class B), E. coli polymerase III (class C),
euryarchaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB, and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family B
DNA polymerases include E. coli DNA polymerase II, some
eubacterial phage DNA polymerases, nuclear replicative
DNA polymerases (alpha, delta, epsilon, and zeta), and
eukaryotic viral and plasmid-borne enzymes. DNA
polymerase is made up of distinct domains and
sub-domains. The polymerase domain of DNA polymerase
type B (Pol domain) is responsible for the
template-directed polymerization of dNTPs onto the
growing primer strand of duplex DNA that is usually
magnesium dependent. In general, the architecture of the
Pol domain has been likened to a right hand with
fingers, thumb, and palm sub-domains with a deep groove
to accommodate the nucleic acid substrate. There are a
few conserved motifs in the Pol domain of family B DNA
polymerases. The conserved aspartic acid residues in the
DTDS motifs of the palm sub-domain is crucial for
binding to divalent metal ion and is suggested to be
important for polymerase catalysis.
Length = 323
Score = 238 bits (609), Expect = 2e-70
Identities = 96/268 (35%), Positives = 141/268 (52%), Gaps = 6/268 (2%)
Query: 624 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYL 683
Y GG V +P G Y+ +I++DF SLYPSII YN+ TT+ + +
Sbjct: 1 EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGF 59
Query: 684 PEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 743
+ G+LP +++L+ R + K MK L+ + + YD RQ+ALK+ ANS YG LG
Sbjct: 60 RSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLG 119
Query: 744 FPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVN-DYDSVFK 802
RF+ +AA +T+ GREI+ +T +LVE VIYGDTDS+ +S + K
Sbjct: 120 AKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYGDTDSIFVSLPKMGTKEDAIK 179
Query: 803 IGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVV 862
G +I + LEL+ + VY L KKK+YA L I K G+ +IKG++
Sbjct: 180 EGREI-LQELADEHLLELEFEKVYLPFFLGKKKRYAGLDIWK---GQDEGKIDIKGLETR 235
Query: 863 RRDWSQLASEAGKFVISQILDEQSYTDY 890
RRD L + K V+ IL+E+ +
Sbjct: 236 RRDSPPLVKKFQKEVLELILEEERKVEA 263
Score = 35.0 bits (81), Expect = 0.22
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 960 DTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLE 1012
D + Y++ G +RA E + + +ID YYL + + P + R+ E
Sbjct: 272 DKVKYVVTRGGKGVPDYERADPPLEDLDK-RHRIDYEYYLERLLQPPLERIFE 323
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 250 bits (641), Expect = 8e-70
Identities = 130/475 (27%), Positives = 203/475 (42%), Gaps = 106/475 (22%)
Query: 576 GGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPK 635
GG E L L H YV P+ GE GEA GG V++ K
Sbjct: 369 GGSVAAFEHLYLPRAHRAGYVAPNL--------GERPGEA----------SPGGYVMDSK 410
Query: 636 KGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQV------- 688
G YD ++L DF SLYPSII+ +NI + V L E V
Sbjct: 411 PGLYDSVLVL-DFKSLYPSIIRTFNIDPDGL-VEGLAQPP---------EESVAGFLGAR 459
Query: 689 ---DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFP 745
+ LP +++L E R + K M +P +A+K+ N+ YG LG
Sbjct: 460 FSREKHFLPEIVERLWEGRDEAKREMNKP------------LSQAIKIIMNAFYGVLGSS 507
Query: 746 NSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNV-NDYDSVFKIG 804
RFF LA+ +T +G EI+ T+ L+E Y+VIYGDTDS + +D + KIG
Sbjct: 508 GCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGDTDSTFVWLGGAHDEEDAAKIG 567
Query: 805 NQIKSECNKLYKQ-----------LELDIDGVYK--YMLLLK------KKKYAALSISKL 845
+ E N+ +++ LEL+ + Y+ +M ++ KK+YA L
Sbjct: 568 RALVQEINQWWQEHLQQEFGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGD 627
Query: 846 SNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKK 905
+G+++ KG++ VR DW+ LA E + + +I + Y DY +++
Sbjct: 628 GDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRGEPYVDY------------VRE 671
Query: 906 IRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSK-----KLKQGD 960
+ L G + L K+L + +EY R PHV+ A + K + + G
Sbjct: 672 VIDKLRAGELD-EKLVYRKRLRRPLDEYQ-RNVPPHVRAARLADEMGYKVGRPLQYQNGG 729
Query: 961 TISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIE 1015
I Y+I +G +++ ID +YY+ +Q+ PV R+L
Sbjct: 730 KIGYVITVNGPEPLEYRKS------------PIDYDYYIEKQLQPVADRILPFFG 772
>gnl|CDD|99919 cd05536, POLBc_B3, DNA polymerase type-B B3 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
members of the archaea also possess multiple family B DNA
polymerases (B1, B2 and B3). So far there is no specific
function(s) has been assigned for different members of
the archaea type B DNA polymerases. Phylogenetic analyses
of eubacterial, archaeal, and eukaryotic family B DNA
polymerases are support independent gene duplications
during the evolution of archaeal and eukaryotic family B
DNA polymerases. Structural comparison of the
thermostable DNA polymerase type B to its mesostable
homolog suggests several adaptations to high temperature
such as shorter loops, disulfide bridges, and increasing
electrostatic interaction at subdomain interfaces.
Length = 371
Score = 232 bits (593), Expect = 2e-67
Identities = 137/390 (35%), Positives = 209/390 (53%), Gaps = 33/390 (8%)
Query: 625 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP 684
+Y GG+VLEP+KG ++ I+++DF+SLYPSI+ +YNI T+ +D D+ +
Sbjct: 3 SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCEDCDVEPQVGHKF 61
Query: 685 EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGF 744
G +PS ++ L+E RR++K MK+ + S+ D RQ+A+K+ ANS YG +G+
Sbjct: 62 RKDPP-GFIPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGW 120
Query: 745 PNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLM--ISCNVNDYDSVFK 802
N+R++ + A VTA GRE + T + E ++VIYGDTDSL I V K
Sbjct: 121 ANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYGDTDSLFVKIDGADAVKKKVKK 180
Query: 803 IGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVV 862
+ I E LEL+I+ YK + KK+YA L +GK+ + G++VV
Sbjct: 181 LLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGKID----VVGLEVV 227
Query: 863 RRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEI 922
RRDWS++A E V+ IL E +++ ++ + E ++K++ G VP L I
Sbjct: 228 RRDWSEIAKETQARVLEAILKEG-----DVEEAVKIVKEVIEKLK----RGEVPPEKLVI 278
Query: 923 TKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNI 982
KQLTK EY + PHV A +L K++ G I Y+I + S + RAY
Sbjct: 279 WKQLTKDLSEY--KATGPHVAAAKKLAKRGY-KVRPGTKIGYVIVKG--SGKISDRAYPY 333
Query: 983 EELKNNSKLKIDVNYYLSQQIHPVVTRLLE 1012
+ + K K D YY+ Q+ P V R+LE
Sbjct: 334 DMVD--EKHKYDAEYYIDNQVLPAVLRILE 361
>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta subfamily catalytic
domain. Three DNA-dependent DNA polymerases type B
(alpha, delta, and epsilon) have been identified as
essential for nuclear DNA replication in eukaryotes.
Presently, no direct data is available regarding the
strand specificity of DNA polymerase during DNA
replication in vivo. However, mutation analysis supports
the hypothesis that DNA polymerase delta is the enzyme
responsible for both elongation and maturation of Okazaki
fragments on the lagging strand.
Length = 393
Score = 226 bits (579), Expect = 2e-65
Identities = 129/408 (31%), Positives = 212/408 (51%), Gaps = 37/408 (9%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI----PVRMLQDSDITTL-- 679
Y G V+EP KG+YD I +DF SLYPSI+ +N+C+TT+ + L D
Sbjct: 3 YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLPPEDYIKTPN 62
Query: 680 CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMY 739
+Y + V G+LP +++L+ +R++ K +K+ D RQ ALK++ANS+Y
Sbjct: 63 GDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVY 121
Query: 740 GCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENL---------NYEVIYGDTDSLMI 790
G G + +++ VT+ GR+++ TK LVE + +VIYGDTDS+M+
Sbjct: 122 GFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTKANGYSHDAKVIYGDTDSVMV 181
Query: 791 SCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLKKKKYAALSISKLSN-G 848
V+D + K+G + +K + K ++L+ + VY LL+ KK+YA L +
Sbjct: 182 KFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNPDKHD 241
Query: 849 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 908
KM KG++ VRRD L + +++IL E+ ++ E +K + +
Sbjct: 242 KMDT----KGIETVRRDNCLLVQNVVETCLNKILIERD---------VEGAIEFVKGVIS 288
Query: 909 DLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTN-SKKLKQGDTISYIIC 967
DL + ++LL ITK LTK ++Y ++A HV++A R+ + GD + Y+I
Sbjct: 289 DLLQNKIDISLLVITKALTKTADDYAGKQA--HVELAERMRKRDPGSAPNVGDRVPYVII 346
Query: 968 EDGTSEAATQRAYN-IEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPI 1014
+ A ++A + I L+NN + ID YYL Q+ + R+ EPI
Sbjct: 347 KGAKGAKAYEKAEDPIYVLENN--IPIDTQYYLENQLSKPLLRIFEPI 392
>gnl|CDD|214691 smart00486, POLBc, DNA polymerase type-B family. DNA polymerase
alpha, delta, epsilon and zeta chain (eukaryota), DNA
polymerases in archaea, DNA polymerase II in e. coli,
mitochondrial DNA polymerases and and virus DNA
polymerases.
Length = 474
Score = 217 bits (555), Expect = 2e-61
Identities = 104/256 (40%), Positives = 143/256 (55%), Gaps = 28/256 (10%)
Query: 558 EKIRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANK 617
I + + G L RTL G R E LLL + +Y+LP K+ + ++
Sbjct: 226 LIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKE--------LYDFKGSE 277
Query: 618 GKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVR-------M 670
+KK Y GG VLEPKKGFYD ++++DFNSLYPSII +N+C++T+
Sbjct: 278 PDLKKKVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGEVVIKGD 337
Query: 671 LQDSDITTLCEY-------LPEHQVDTGILPSEIKKLVESRRQVKALMKQ-PNLSSDLLM 722
L + +Y + + GILP +KKL++ R+++K LMK+ + S +L
Sbjct: 338 LIIPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKK 397
Query: 723 QYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNY---- 778
D RQ ALKLTANS+YG LGF NSR +PLAA VTA GREIL TK L+E Y
Sbjct: 398 LLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPKPG 457
Query: 779 -EVIYGDTDSLMISCN 793
+VIYGDTDS+ ++
Sbjct: 458 FKVIYGDTDSIFVTKP 473
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 205 bits (523), Expect = 8e-54
Identities = 134/433 (30%), Positives = 212/433 (48%), Gaps = 69/433 (15%)
Query: 616 NKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 675
G + Y G VLEPKKGFYD+ I +DF SLYPSI+ +N+C++T ++ +D
Sbjct: 530 KYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYST----LVPPND 585
Query: 676 ITTLCE----------YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYD 725
E + +V GILP +++L+ +R++ K MK L +
Sbjct: 586 ANNYPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK-DPLLKKVLN 644
Query: 726 IRQKALKLTANSMYGCLGFPNSRFFAQP---LAALVTAKGREILLNTKSLVENL------ 776
RQ ALK++ANS+YG G P ++ +T+ GR+++ TK LVE
Sbjct: 645 GRQLALKISANSVYGYTGAQVGGQL--PCLEVSTSITSFGRQMIDKTKELVEKHYTKANG 702
Query: 777 ---NYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLL 832
+ VIYGDTDS+M+ +D +G + +K + K ++L+ + VY LL+
Sbjct: 703 YKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLM 762
Query: 833 KKKKYAALSISKLSN-GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYS 891
KK+YA L + K+ C KG++ VRRD L + + V+++IL E+
Sbjct: 763 NKKRYAGLLYTNPEKYDKIDC----KGIETVRRDNCLLVQQMVETVLNKILIEKD----- 813
Query: 892 LDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNT 951
+++ E K +DL + ++LL ITK L K ++Y R L HV++A
Sbjct: 814 ----VESAIEFTKGKISDLLQNRIDISLLVITKSLGK--DDYEGR--LAHVELA------ 859
Query: 952 NSKKLKQ---------GDTISYIICEDGTSEAATQRAYN-IEELKNNSKLKIDVNYYLSQ 1001
KKL+Q GD +SY+I + +RA + + L+NN + ID YYL
Sbjct: 860 --KKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAEDPLYVLENN--IPIDTQYYL-D 914
Query: 1002 QIHPVVTRLLEPI 1014
QI + R+ E +
Sbjct: 915 QIKNPLLRIFEGV 927
>gnl|CDD|99920 cd05537, POLBc_Pol_II, DNA polymerase type-II subfamily catalytic
domain. Bacteria contain five DNA polymerases (I, II,
III, IV and V). DNA polymerase II (Pol II) is a prototype
for the B-family of polymerases. The role of Pol II in a
variety of cellular activities, such as repair of DNA
damaged by UV irradiation or oxidation has been proven by
genetic studies. DNA polymerase III is the main enzyme
responsible for replication of the bacterial chromosome;
however, In vivo studies have also shown that Pol II is
able to participate in chromosomal DNA replication with
larger role in lagging-strand replication.
Length = 371
Score = 177 bits (451), Expect = 1e-48
Identities = 112/422 (26%), Positives = 188/422 (44%), Gaps = 89/422 (21%)
Query: 628 GGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQ 687
GG V++ K G Y ++L DF SLYPSII+ + I P+ +++ PE
Sbjct: 5 GGYVMDSKPGLYKNVLVL-DFKSLYPSIIRTFLI----DPLGLIEGLKAPD-----PEDL 54
Query: 688 V----------DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANS 737
+ + ILP I +L +R + K + + A+K+ NS
Sbjct: 55 IPGFLGARFSREKHILPDLIARLWAARDEAK-------REKNAPLSQ-----AIKIIMNS 102
Query: 738 MYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVN-D 796
YG LG RFF LA+ +T +G EI+ T++ +E Y+VIYGDTDS + D
Sbjct: 103 FYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEELD 162
Query: 797 YDSVFKIGNQIKSECNKLYKQ-----------LELDIDGVYK--YMLLLK------KKKY 837
IG ++ S+ N+ + Q LE++ + Y +M ++ KK+Y
Sbjct: 163 AAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRY 222
Query: 838 AALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQ 897
A L ++G KG++ VR DW+ LA + K + ++ +++ Y +
Sbjct: 223 AGLKS---TDGGD--ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGF------- 270
Query: 898 NIHEHMKKIRT-DLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKL 956
I E ++++ +LD LL K+L + EYT + PHVQ A RL + +++L
Sbjct: 271 -IKETVEELLAGELDE------LLVYRKRLRRPLSEYT-KNVPPHVQAA-RLADQINREL 321
Query: 957 ---KQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEP 1013
+Q I Y+I +G E R +D +Y+ +Q+ P+ +L
Sbjct: 322 GRPRQYQWIEYVITVNG-PEPLEYR-----------TSPLDYQHYIDKQLKPIADSILPF 369
Query: 1014 IE 1015
+
Sbjct: 370 LG 371
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed.
Length = 787
Score = 173 bits (440), Expect = 2e-44
Identities = 118/415 (28%), Positives = 189/415 (45%), Gaps = 40/415 (9%)
Query: 605 NKKEGEET-GEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICF 663
K++ E K K Y GGLV +P G + + ++DF SLYPSII ++N+
Sbjct: 385 WKEDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSP 443
Query: 664 TTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQ--VKALMKQPNLSSDLL 721
T+ + + + E D L S + L+ R K K PNL +
Sbjct: 444 ETVRIPECKCHYDDEVPELGHSVCDDRPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERR 503
Query: 722 MQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVI 781
YD+ Q+ALK+ N+ YG G N + + +A +TA GREILL+TK E L +V+
Sbjct: 504 AWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEELGLKVL 563
Query: 782 YGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLK-KKKYAAL 840
YGDTDSL + +S+ ++ +I+ ++L++D Y ++ KK Y
Sbjct: 564 YGDTDSLFVWG--PTKESLEELIKEIEERTG-----IDLEVDKTYDWVAFSGLKKNY--- 613
Query: 841 SISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDE-QSYTDYSLDDRLQNI 899
L +GK+ +IKG+ +R+ + E + V+ ++L +S D ++ I
Sbjct: 614 -FGVLKDGKV----KIKGIVAKKRNTPEFVKELQREVL-EVLKSIRSPED--VEKVKDEI 665
Query: 900 HEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQG 959
+ +K+ L PL L I +L+K +EYT HV+ AL+L + ++ G
Sbjct: 666 EDVLKRYYEKLRAKDYPLDELAIRVRLSKPLDEYTKNTP-QHVKAALQLRDYG-VEVSPG 723
Query: 960 DTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPI 1014
D ISY+ +D Q A + E IDV Y+ + LE I
Sbjct: 724 DIISYVKVDDKRGVKPVQLA-KLSE--------IDVEKYIEL-----LRSALEQI 764
>gnl|CDD|99917 cd05534, POLBc_zeta, DNA polymerase type-B zeta subfamily catalytic
domain. DNA polymerase (Pol) zeta is a member of the
eukaryotic B-family of DNA polymerases and distantly
related to DNA Pol delta. Pol zeta plays a major role in
translesion replication and the production of either
spontaneous or induced mutations. Apart from its role in
translesion replication, Pol zeta also appears to be
involved in somatic hypermutability in B lymphocytes, an
important element for the production of high affinity
antibodies in response to an antigen.
Length = 451
Score = 162 bits (413), Expect = 9e-43
Identities = 106/433 (24%), Positives = 178/433 (41%), Gaps = 67/433 (15%)
Query: 630 LVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI----------------------- 666
LV+EP+ GFY +I++DF SLYPSI+ YN C++T
Sbjct: 40 LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLP 99
Query: 667 ---PVRMLQDSDITTL---CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDL 720
+L D+T ++ + V GILP +++++++R VK MK+ L
Sbjct: 100 PPPLDLLLLKDDVTISPNGVMFVKKS-VRKGILPKMLEEILDTRIMVKKAMKKYKDDKKL 158
Query: 721 LMQYDIRQKALKLTANSMYGCLG------FPNSRFFAQPLAALVTAKGREILLNTKSLVE 774
D RQ ALKL AN YG P +A + GRE L L+E
Sbjct: 159 QRILDARQLALKLLANVTYGYTAASFSGRMPCVE-----IADSIVQTGRETLERAIELIE 213
Query: 775 NLNY---EVIYGDTDSLMISC---NVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYK 827
+ +V+YGDTDSL + + FKIG +I ++L + VY
Sbjct: 214 STPKWGAKVVYGDTDSLFVLLPGRTKEE---AFKIGKEIAEAVTAANPSPIKLKFEKVYH 270
Query: 828 YMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSY 887
+L+ KK+Y + + KG++ VRRD + + + + + +
Sbjct: 271 PCVLVTKKRYVGYKYESPDQTEPTF--DAKGIETVRRDGCPAVQKILEKSLRILFETKD- 327
Query: 888 TDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALP-HVQVAL 946
L + ++++ + L G V + K++ Y + LP VAL
Sbjct: 328 --------LSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRL--GTYKEGATLPAGAIVAL 377
Query: 947 R-LNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHP 1005
R + + + G+ + Y++ + EE + L++D YY+++QI P
Sbjct: 378 RRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLRLDAEYYITKQIIP 437
Query: 1006 VVTRLLEPIEGTD 1018
+ RL + G D
Sbjct: 438 ALDRLFNLV-GVD 449
>gnl|CDD|99913 cd05530, POLBc_B1, DNA polymerase type-B B1 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
archaeal members also possess multiple family B DNA
polymerases (B1, B2 and B3). So far there is no specific
function(s) has been assigned for different members of
the archaea type B DNA polymerases. Phylogenetic
analyses of eubacterial, archaeal, and eukaryotic family
B DNA polymerases are support independent gene
duplications during the evolution of archaeal and
eukaryotic family B DNA polymerases.
Length = 372
Score = 147 bits (372), Expect = 4e-38
Identities = 100/352 (28%), Positives = 163/352 (46%), Gaps = 31/352 (8%)
Query: 619 KGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT 678
KG+K Y G +VLEP G + ++++DF SLYPSII+ +N+ + T V T
Sbjct: 9 KGKK---YRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET--VNCPHCECKTN 62
Query: 679 LCEYLPEHQVDT---GILPSEIKKLVESRRQV-KALMKQPNLSSDLLMQYDIRQKALKLT 734
+ H V GI I L + R ++ K K +L ++ YD+ Q A+K+
Sbjct: 63 EVPEVG-HWVCKKRPGITSQIIGLLRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVF 121
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNV 794
N+ YG G N + P+A TA GR I+ +T L +V+YGDTDSL +
Sbjct: 122 INASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGLKVLYGDTDSLFLWNPP 181
Query: 795 NDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKK-YAALSISKLSNGKMICS 853
+ ++ + ++ +L L+L++D Y+Y++ KK Y + +G +
Sbjct: 182 QE-----QLEDLVEWVEKEL--GLDLELDKEYRYVVFSGLKKNY----LGVTKDGSV--- 227
Query: 854 QEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNG 913
+IKG+ +R+ + E VI + S D+ + I + +K + L
Sbjct: 228 -DIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEDFE--KAREKIRDIVKGVYKRLKKK 284
Query: 914 FVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYI 965
L L L+K PEEYT HV+ A +L + ++ GD ISY+
Sbjct: 285 EYTLDQLAFKVMLSKPPEEYTKNTP-QHVKAARQLEKY-GRNVEAGDIISYV 334
>gnl|CDD|99914 cd05531, POLBc_B2, DNA polymerase type-B B2 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
archaeal members also possess multiple family B DNA
polymerases (B1, B2 and B3). So far there is no specific
function(s) has been assigned for different members of
the archaea type B DNA polymerases. Phylogenetic analyses
of eubacterial, archaeal, and eukaryotic family B DNA
polymerases are support independent gene duplications
during the evolution of archaeal and eukaryotic family B
DNA polymerases.
Length = 352
Score = 140 bits (355), Expect = 4e-36
Identities = 95/391 (24%), Positives = 166/391 (42%), Gaps = 56/391 (14%)
Query: 624 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYL 683
A GGLV +P+ G Y+ + DF+S+YPSII +YNI TI R + D L +
Sbjct: 3 LADRGGLVFQPEPGLYENVAQI-DFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRI 61
Query: 684 PEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 743
G LP ++ L+E R + K L K+ + Y RQKALK + +G LG
Sbjct: 62 CLK--RRGFLPEVLEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLG 112
Query: 744 FPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKI 803
+ N++F + +TA GR+ILL K + E + + V++G DSL I D + +
Sbjct: 113 YKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWIQGR-GDIEEL--- 168
Query: 804 GNQIKSECNKLYKQ--LELDIDGVYKYMLLLKKKKYAALS---ISKLSNGKMICSQEIKG 858
++ ++ + L ++G Y +++ L ++ +LS+G+M ++G
Sbjct: 169 -------AREIEERTGIPLKLEGHYDWIVFLPERDGLGAPNRYFGRLSDGEMK----VRG 217
Query: 859 VDVVRRDWSQLASEAGKFVISQILDE-QSYTDY--SLDDRLQNIHEHMKKIRTDLDNGFV 915
+++ RRD + + + IL ++ + ++ L +++++R
Sbjct: 218 IELRRRDTPPFVKKFQEEAL-DILASAKTPEELLKLREEALDLFRRYLQRLR------EG 270
Query: 916 PLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAA 975
L L I K+++K EY + AL+ + G I YI+ +
Sbjct: 271 DLEDLIIEKKISKRSSEYKVLAST-----ALKALRAKGVSVVPGMKIEYIVRDGKRPVPD 325
Query: 976 TQRAYNIEELKNNSKLKIDVNYYLSQQIHPV 1006
N E D YY
Sbjct: 326 ---LGNDEG--------YDTKYYRELLERAA 345
>gnl|CDD|220087 pfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc finger. The DNA
Polymerase alpha zinc finger domain adopts an
alpha-helix-like structure, followed by three turns, all
of which involve proline. The resulting motif is a
helix-turn-helix motif, in contrast to other zinc finger
domains, which show anti-parallel sheet and helix
conformation. Zinc binding occurs due to the presence of
four cysteine residues positioned to bind the metal
centre in a tetrahedral coordination geometry. Function
of this domain is uncertain: it has been proposed that
the zinc finger motif may be an essential part of the DNA
binding domain.
Length = 187
Score = 127 bits (322), Expect = 1e-33
Identities = 53/188 (28%), Positives = 82/188 (43%), Gaps = 15/188 (7%)
Query: 1055 EEVKYQFCDKFEFTCMNPSCKQVNTVEAPTRLSTHGVVFVLDECINPECKVPPYTYLPHL 1114
+ +++ C + + C PSC E S V +C C L +
Sbjct: 7 DSERFRDCARLKLKC--PSCGTEFPFEGIFASSGERVTPSGLQCSK--CNAL--IPLLQI 60
Query: 1115 INKLSQDMNKYIVKYYEGWLKCEDPGCSDLTRRCPLGLKTRLCTTCHKYKLHRVYTELQL 1174
+N+L + +I YYEGWL C+DP C + TR+ + K R K K+ Y++ QL
Sbjct: 61 VNQLELAIRAHIKLYYEGWLVCDDPTCGNRTRQLSVYGK-RCLNPGCKGKMRYEYSDKQL 119
Query: 1175 YQQLSFFHYICDITKALTKSDTPSIKFDSETY--------MGYCKMKQHVERFLESSAYN 1226
Y QL +F + D+ KA ++ P K + Y +K V+++L S Y
Sbjct: 120 YNQLLYFQSLFDVDKAKKENLKPQEKESLKKVLALAEQNRERYKTLKGTVDKYLSKSGYR 179
Query: 1227 IVDLKKLF 1234
VDL LF
Sbjct: 180 KVDLGSLF 187
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 107 bits (269), Expect = 2e-23
Identities = 81/331 (24%), Positives = 134/331 (40%), Gaps = 71/331 (21%)
Query: 622 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD------ 675
K Y GG V PK+ +D +++ D+NSLYP++ N+ T+ V ++ + +
Sbjct: 526 NKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETL-VGVVVNDNRLEAEI 584
Query: 676 --------------ITTLCEYLPEHQVDT---------GILPSEIKKLVESRRQVKALMK 712
I CE V GI+P +K +E R + K L+K
Sbjct: 585 NKQELRRKYPYPRYIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLK 644
Query: 713 QPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSL 772
+ S + + YD Q K+ ANS+YG +GF NS ++ A TA GR ++ S+
Sbjct: 645 EATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSV 703
Query: 773 VEN--------------------------------------LNYEVIYGDTDSLMISCNV 794
+ + +YGDTDS+ + N
Sbjct: 704 LNGSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVFLEINT 763
Query: 795 NDYDSVFKIGNQIKSECNK--LYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMIC 852
D D KI +++ N+ L+ +++ + VYK +++ KKKY L S +
Sbjct: 764 KDVDKSIKIAKELERIINEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVP 823
Query: 853 SQEIKGVDVVRRDWSQLASEAGKFVISQILD 883
+ KG RRD S+ K +++LD
Sbjct: 824 ERVNKGTSETRRDVSKFHKYMIKIYKTRLLD 854
>gnl|CDD|99921 cd05538, POLBc_Pol_II_B, DNA polymerase type-II B subfamily catalytic
domain. Bacteria contain five DNA polymerases (I, II,
III, IV and V). DNA polymerase II (Pol II) is a prototype
for the B-family of polymerases. The role of Pol II in a
variety of cellular activities, such as repair of DNA
damaged by UV irradiation or oxidation has been proved by
genetic studies. DNA polymerase III is the main enzyme
responsible for replication of the bacterial chromosome;
however, In vivo studies have also shown that Pol II is
able to participate in chromosomal DNA replication with
larger role in lagging-strand replication.
Length = 347
Score = 92.9 bits (231), Expect = 4e-20
Identities = 94/397 (23%), Positives = 144/397 (36%), Gaps = 61/397 (15%)
Query: 625 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP 684
+ GG G I+ D SLYPSI+ Y IC P R DS
Sbjct: 2 KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRIC----PAR---DS---------- 43
Query: 685 EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGF 744
GI + +K LVE R K + + + +Q A K+ NS YG LG
Sbjct: 44 -----LGIFLALLKYLVELRLAAKESARAAARPA-ERDAFKAKQAAFKVLINSFYGYLGT 97
Query: 745 PNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIG 804
F AA VT GRE+L + + DTD + +
Sbjct: 98 GLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFI--PPNGVDTEDEE 155
Query: 805 NQIKSECNK-LYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVR 863
++ E + L K + ++ DG Y+ M K K YA L +GK+I +KG
Sbjct: 156 EELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLD----YDGKLI----VKGSAFRS 207
Query: 864 RDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEIT 923
R E F+ L +H+ + L + +P++ L T
Sbjct: 208 RGIEPFLRE---FLR-------EAVRLLLQGDGAGVHDLYEDYLRRLRSHELPISDLART 257
Query: 924 KQLTKAPEEYTD----RKALPHV--QVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQ 977
+ L ++PEEY K P ++AL GD ++Y + GT + +
Sbjct: 258 ETLKESPEEYLQKVRAGKRNPAAAYEIALARPREWRA----GDRVTYYV--SGTGKGVSV 311
Query: 978 RAYNIEELKNNSKLKIDVN--YYLSQQIHPVVTRLLE 1012
N + + D N +Y +++ + RLL
Sbjct: 312 YE-NCRLVADYDPAHPDENTGFYA-ERLLQLAARLLP 346
>gnl|CDD|221491 pfam12254, DNA_pol_alpha_N, DNA polymerase alpha subunit p180 N
terminal. This domain family is found in eukaryotes,
and is approximately 70 amino acids in length. The
family is found in association with pfam00136,
pfam08996, pfam03104. This family is the N terminal of
DNA polymerase alpha subunit p180 protein. The N
terminal contains the catalytic region of the alpha
subunit.
Length = 67
Score = 68.8 bits (169), Expect = 2e-14
Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 3/67 (4%)
Query: 61 FQKLKDLKGQGVKHKYEFTADE--NVYEEVSEKEYTERVLKR-QEDDWIDDDGGDGYVED 117
KL+ + G K E+ +E ++Y+EV E+EY + V +R DD+I DD G+GYV+D
Sbjct: 1 LAKLRAAREGGKKRLDEYEVEEEKDIYDEVDEEEYRKIVRQRLLNDDFIVDDDGEGYVDD 60
Query: 118 GREIFDD 124
GRE +DD
Sbjct: 61 GREEWDD 67
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 64.3 bits (157), Expect = 3e-10
Identities = 72/297 (24%), Positives = 106/297 (35%), Gaps = 88/297 (29%)
Query: 617 KGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNI-------CFTTIPV- 668
+ K KK Y+G V EP G Y +++ D SLYPSII++ NI F PV
Sbjct: 368 ENKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVH 426
Query: 669 -----------------------------------------------RMLQDSDITTLCE 681
+ML L +
Sbjct: 427 EYINKTAPRPSDEYSCSPNGWMYRKDIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIK 486
Query: 682 YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLM---------QYDIRQKALK 732
+ E D+ P ++ + + KA +K SS + + Q A K
Sbjct: 487 TILEDLNDSVDTPIDVDYYFDFSDEFKAELKTLTKSSLKALLEECEKEIALCNTIQMARK 546
Query: 733 LTANSMYGCLGFPNSRFFAQPLAALVTAKGR----------EILLNTKSLVENLNYEVIY 782
+ NS+YG LG + R++ A +T G+ LN E+ +Y VIY
Sbjct: 547 ILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDEDY-VIY 605
Query: 783 GDTDSLMISCNVND-----YDSVFKIGNQIKSECNKLYKQ-LELDIDGVY----KYM 829
GDTDS I N++ + FK N +K K+ +E ID Y +YM
Sbjct: 606 GDTDS--IYVNLDPLVEKVGEDKFKDTNHWVDFLDKFCKERMEPYIDSSYRELCEYM 660
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit;
Provisional.
Length = 1545
Score = 56.0 bits (135), Expect = 1e-07
Identities = 52/214 (24%), Positives = 75/214 (35%), Gaps = 46/214 (21%)
Query: 612 TGEANKGKGRKKAAYSGGLVLEPKKGF-----YDKFIILMDFNSLYPSIIQEYNIC---- 662
E R+K GG V P G Y + +DF SLYPS + + NI
Sbjct: 619 MPEKYARDCRQKIKLKGGYVFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAI 678
Query: 663 ----------------FTTIPVRMLQDSDITTLCEYLPE------HQVDTGILPSEIKKL 700
+ I + + + T+ PE T S +
Sbjct: 679 VDPDCTARVRGWVVFDWKKIDRGFGKATLMYTILRTKPEEPSWRRFTTYTT---SSLNHY 735
Query: 701 VESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAA-LVT 759
+ R + K MKQ L ++ Q +K+ ANS YG A L+T
Sbjct: 736 LSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYGV---------APHACQHLIT 785
Query: 760 AKGR-EILLNTKSLVENLNYEVIYGDTDSLMISC 792
GR +I L + + + V YGDTDS+M
Sbjct: 786 TLGRHKIKLVEEFIKKEPGMTVNYGDTDSVMFQL 819
>gnl|CDD|99918 cd05535, POLBc_epsilon, DNA polymerase type-B epsilon subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase (Pol) epsilon has been proposed to play a
role in elongation of the leading strand during DNA
replication. Pol epsilon might also have a role in DNA
repair. The structure of pol epsilon is characteristic
of this family with the exception that it contains a
large c-terminal domain with an unclear function.
Phylogenetic analyses indicate that Pol epsilon is the
ortholog to the archaeal Pol B3 rather than to Pol
alpha, delta, or zeta. This might be because pol epsilon
is ancestral to both archaea and eukaryotes DNA
polymerases type B.
Length = 621
Score = 37.3 bits (87), Expect = 0.065
Identities = 49/221 (22%), Positives = 84/221 (38%), Gaps = 65/221 (29%)
Query: 696 EIKKLV-ESRRQVKALMKQPNL-----SSDLLMQYDIRQKALKLTANSMYGCLGFPNSRF 749
E K L +++++A + + +++ YD Q A K NS YG + SR+
Sbjct: 237 EYKGLHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRW 296
Query: 750 FAQPLAALVTAKGREILLNTKSLVENL---------------------NYEVIYGDTDSL 788
++ +A +V G I+ + LVE + N+ + +
Sbjct: 297 YSMEMAGIVCYTGANIIQMARELVEQIGRPLELDTDGIWCILPKSFPENFTFKTKNGKKV 356
Query: 789 MIS--CNV----------ND-----YDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLL 831
IS C + ND D +SE + + ++DG YK M+L
Sbjct: 357 TISYPCVMLNHLVHKKFTNDQYQELVDPSTGTYE-TRSENS-----IFFEVDGPYKAMIL 410
Query: 832 --------LKKKKYAALSISKLSNGKMICSQEIKGVDVVRR 864
L KK+YA + +G + E+KG +V RR
Sbjct: 411 PASKEEGKLLKKRYAVFN----EDGSLA---ELKGFEVKRR 444
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 36.7 bits (85), Expect = 0.070
Identities = 39/214 (18%), Positives = 79/214 (36%), Gaps = 19/214 (8%)
Query: 130 PQKKEKHDKRKKNKNIQNPNAKGDIQKLLANMPVKKKKKEEVQLNNDDVLADLLSEVNTT 189
P K N + P++K K + + VK K ++ Q + + TT
Sbjct: 145 PVAPAASPALKPTANGKRPSSKP--PKSIMSPEVKVKSAKKTQDTSKE----------TT 192
Query: 190 IAPTLKLNTKTNEIVIPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKS 249
T + + P +++F K EKK +K + + E +S
Sbjct: 193 TEKT----EGKTSVKAASLKRNPPKKSNIMSSFFKKKTKEKKEKKEASESTVKEESEEES 248
Query: 250 NDSVMEVEMNVAEQSKEEPVDDGLWEQMQIDDWDNSQQTQDVLPEQAKVELQIEAIESQS 309
+ +E AE + + +D + + D+ ++T++ E+ K +++ +
Sbjct: 249 GKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKRK---RLKKMMEDE 305
Query: 310 IEEKVDVTNVESVSSAVELSTSPPPQVVEKKEHK 343
E++ ES E PP + +K+E K
Sbjct: 306 DEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEK 339
>gnl|CDD|164925 PHA02524, 43A, DNA polymerase subunit A; Provisional.
Length = 498
Score = 36.5 bits (84), Expect = 0.096
Identities = 31/110 (28%), Positives = 45/110 (40%), Gaps = 21/110 (19%)
Query: 619 KGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI-----PVRMLQD 673
K K ++ G V EP G Y ++ + D SLYPSI++ NI I P R+
Sbjct: 370 KASPKQSFPGAYVKEPVPGGY-RYGLSFDLTSLYPSILRLLNISPEMIAGMFSPARL--- 425
Query: 674 SDITTLCEYLPEHQVD------------TGILPSEIKKLVESRRQVKALM 711
D P Q G+LP+E +K+ R+ K +M
Sbjct: 426 EDYINKVAPKPSDQFSCAPNGMMYKKGVVGVLPNETEKVFLQRKSEKKMM 475
>gnl|CDD|235984 PRK07272, PRK07272, amidophosphoribosyltransferase; Provisional.
Length = 484
Score = 35.8 bits (83), Expect = 0.15
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 15/80 (18%)
Query: 822 IDGVYKYMLLLKKKKYAA--------LSISKLSNGKMICSQEIKGVDVVRRDWSQLASEA 873
+ G + Y+LL + K AA LSI K+ NG + + E DVV +W + +
Sbjct: 165 VKGGFAYLLLTEDKLIAALDPNGFRPLSIGKMKNGAYVVASETCAFDVVGAEWVR-DVQP 223
Query: 874 GKFVISQILDE----QSYTD 889
G+ VI I DE SYT
Sbjct: 224 GEIVI--IDDEGIQYDSYTT 241
>gnl|CDD|189028 cd09858, PIN_MKT1, PIN domain of Mkt1: A global regulator of mRNAs
encoding mitochondrial proteins and eukaryotic homologs.
The Mkt1 gene product interacts with the Poly(A)-binding
protein associated factor, Pbp1, and is present at the 3'
end of RNA transcripts during translation. The Mkt1-Pbp1
complex is involved in the post-transcriptional
regulation of HO endonuclease expression. Mkt1 and
eukaryotic homologs are atypical members of the
structure-specific, 5' nuclease family. Conical members
of this family possess a PIN (PilT N terminus) domain
with a helical arch/clamp region/I domain (approximately
40 to 55 residues in MKT1 PIN domains) and inserted
within the PIN domain is a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Although Mkt1 appears to possess both a PIN and H3TH
domain, the Mkt1 PIN domain lacks several of the active
site residues necessary to bind essential divalent metal
ion cofactors (Mg2+/Mn2+) required for nuclease activity
in this family. Also, Mkt1 lacks the glycine-rich loop in
the H3TH domain which is proposed to facilitate duplex
DNA binding.
Length = 215
Score = 33.3 bits (77), Expect = 0.47
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 972 SEAATQRAYNIEELKNNSKLKIDVNYYLSQQIH 1004
E + + LKN +++ ID +YLS+ +
Sbjct: 11 FERGLVTSAPLSALKN-ARIGIDATHYLSRLLT 42
>gnl|CDD|234042 TIGR02870, spore_II_D, stage II sporulation protein D. Stage II
sporulation protein D (SpoIID) is a protein of the
endospore formation program in a number of lineages in
the Firmicutes (low-GC Gram-positive bacteria). It is
expressed in the mother cell compartment, under control
of Sigma-E. SpoIID, along with SpoIIM and SpoIIP, is one
of three major proteins involved in engulfment of the
forespore by the mother cell [Cellular processes,
Sporulation and germination].
Length = 338
Score = 33.2 bits (76), Expect = 0.77
Identities = 16/98 (16%), Positives = 43/98 (43%), Gaps = 15/98 (15%)
Query: 213 PTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKEEPVDDG 272
P + + E + P++K+P +K + ++V S E+ +
Sbjct: 18 PAIIVAGFGDPQNVTEENEKLAPVEKKPEKGVTNLKEEEVAIKVYR-----SNEDKI--- 69
Query: 273 LWEQMQIDDWDNSQQTQDVLPEQAKVELQIEAIESQSI 310
E++ ++++ + V+ + E +IEA+++Q++
Sbjct: 70 --EKVPLEEY-----VKGVVASEMPAEFEIEALKAQAV 100
>gnl|CDD|118064 pfam09528, Ehrlichia_rpt, Ehrlichia tandem repeat (Ehrlichia_rpt).
This entry represents 77 residues of an 80 amino acid
(240 nucleotide) tandem repeat, found in a variable
number of copies in an immunodominant outer membrane
protein of Ehrlichia chaffeensis, a tick-borne obligate
intracellular pathogen.
Length = 707
Score = 33.1 bits (74), Expect = 1.0
Identities = 45/209 (21%), Positives = 77/209 (36%), Gaps = 10/209 (4%)
Query: 163 VKKKKKEEVQLNNDDVLADLLSEVNTTIAPTLKLNTKTNEIVIPKEEPPAPTAKEYLAN- 221
+ K E++Q D + SEV ++ T K + E+ +P + +
Sbjct: 179 TAEVKAEDLQPAVDGSIEHSSSEVGEEVSKTEKEES-NPEVKAEDLQPAVDDDVAHHESE 237
Query: 222 -FSKPIKVEKKIEKP-IKKEPSPLKDEIKSNDSVMEVEMNVAEQSKEEPVDDGLWEQMQI 279
KP + K+ E P +K E + S E+E + E KEE + + E +Q
Sbjct: 238 VGDKPAETSKEEETPEVKAEDLQPAVDGSVEHSSSEIEEHQGETEKEEGIPESHAEDLQP 297
Query: 280 DDWDNSQQTQDVLPEQAKVELQIEAIESQSIEEKVDVTNVESVSSAVELSTSPPPQVVEK 339
D + E E ++ E + +V +++ + + P QVVE
Sbjct: 298 AVDDIVEHPSS---EPFVAEEEVSETEKEENNPEVLAEDLQDAADGESGVSDQPAQVVE- 353
Query: 340 KEHKCAEWEAIQTEPSTSEPQVHSRTADD 368
+ +E E Q E E S DD
Sbjct: 354 --ERESEIEEHQGETEKEEGIPESHAEDD 380
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 33.0 bits (75), Expect = 1.1
Identities = 23/111 (20%), Positives = 45/111 (40%), Gaps = 2/111 (1%)
Query: 101 QEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKKNKNIQNPNAKGDIQKLLAN 160
+E+D+I D G + RE + E+ + ++++ +N G +K
Sbjct: 282 REEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKL 341
Query: 161 MPVKKKKKEEVQLNNDDVLADLLSEVNTTIAPTLKLNTKTNEIVIPKEEPP 211
+K KK + ++D S+++ + +L K E KEEP
Sbjct: 342 KKLKGKKNGLDKDDSDSGDDSDDSDIDGEDSVSLVTAKKQKE--PKKEEPV 390
>gnl|CDD|222879 PHA02563, PHA02563, DNA polymerase; Provisional.
Length = 630
Score = 32.8 bits (75), Expect = 1.3
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 743 GFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 789
G N P+AA +TA+ R +L + L E IY DTDS+
Sbjct: 442 GEENKEPNYIPIAAFITARARSNLLSALQYLYEKF----IYCDTDSIH 485
>gnl|CDD|219668 pfam07964, Red1, Rec10 / Red1. Rec10 / Red1 is involved in meiotic
recombination and chromosome segregation during
homologous chromosome formation. This protein localises
to the synaptonemal complex in S. cerevisiae and the
analogous structures (linear elements) in S. pombe. This
family is currently only found in fungi.
Length = 706
Score = 32.9 bits (75), Expect = 1.3
Identities = 24/135 (17%), Positives = 42/135 (31%), Gaps = 11/135 (8%)
Query: 132 KKEKHDKRKKNKNIQNPNAKGDIQKLLANMPVKKKKKEEVQLNNDDVLADLLSEVNTTIA 191
KK K+ K KN + K Q L N K K+ V+ ++ ++
Sbjct: 464 KKVGKSKQTKLKNFKPVPNKSKKQ-LANNNSQNIKSKKVVKAKTNNKANLQDVGECSSPP 522
Query: 192 PTLKLN-----TKTNEIVIPKEE-----PPAPTAKEYLANFSKPIKVEKKIEKPIKKEPS 241
+ N T ++ + + P A K ++ K + S
Sbjct: 523 NNKEKNDKQTSTSSSVLKSDRSSIEVRNPNANVKKLEDTTYNAKFPTVSKNNAYTLVDIS 582
Query: 242 PLKDEIKSNDSVMEV 256
+D + S D V
Sbjct: 583 TSEDAVNSADDTRSV 597
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 32.9 bits (75), Expect = 1.4
Identities = 33/179 (18%), Positives = 59/179 (32%), Gaps = 22/179 (12%)
Query: 177 DVLADLLSEVNTTIAPTLKL--------------NTKTNEIVIPKEEPPAP-TAKEYLAN 221
++L DLL ++ + P L NEI K E +
Sbjct: 326 EILFDLLKDLKISDNPNDTLEILIIKLLALSELEEEDENEIKFKKIEENSIDNLDIKEKK 385
Query: 222 FSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKEEPVDDGLWEQMQIDD 281
+E K + +E KD N S + N+ S D+ L + +I +
Sbjct: 386 IENENDIEGKSDTKNLEEGFETKDNKNKNSSFINKTENILTNSP--LKDELLEKTTEIIN 443
Query: 282 WDNSQQTQDVLPEQAKVELQIEAIESQSIEEKVDVTNVESVSSAVELSTSPPPQVVEKK 340
+N Q+ E ++ I + E ++E ++ + S S P+ K
Sbjct: 444 IENPQE-----FEFGQIGNDIISTEIAQLDENQNLIDTGEFDLENNFSNSFNPENGNKI 497
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 32.3 bits (73), Expect = 2.1
Identities = 43/215 (20%), Positives = 79/215 (36%), Gaps = 22/215 (10%)
Query: 41 KMEGGRAKRQKIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYE----EVSEKEYTER 96
K+E R RQ+++K +K ++ K+ +G+ H +DE++ ++ +E E
Sbjct: 83 KLEEERRHRQRLEK-DKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPEN 141
Query: 97 VLKRQEDDWIDDDGGDGY----VEDGREIFDDD--------IEDVPQKKEKHDKRKKNKN 144
L EDD D D Y ++ + + D + + + EK D K
Sbjct: 142 ALPSDEDD---KDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKK 198
Query: 145 IQNPNAKGDIQKLLANMPVKKKKKEEVQLNNDDVLADLLSEVNTTIAPTLKLNTKTNEIV 204
+ P K +K K KKKE + + D ++A + +
Sbjct: 199 SKKPKKKEKKEK--EKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSG 256
Query: 205 IPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKE 239
+ P K K +KK ++ K+E
Sbjct: 257 TAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEE 291
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 32.0 bits (73), Expect = 2.7
Identities = 28/188 (14%), Positives = 68/188 (36%), Gaps = 12/188 (6%)
Query: 86 EEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKKNKNI 145
E +E E R L+ +E+ +++ GR F + + + +K K KN+
Sbjct: 389 ENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFK 448
Query: 146 QNPNAKGDIQKL------LANMPVKKKKKEEVQLNNDDVLADLLSEVNTTIAPTLKLNTK 199
+ + + + + + K K+ E ++ P LK +
Sbjct: 449 EKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEEN------PWLKTTSS 502
Query: 200 TNEIVIPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMN 259
+ ++ ++K A K +K K++ L D++ + ++++++
Sbjct: 503 VGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSIDLDDDLIDEEDSIKLDVD 562
Query: 260 VAEQSKEE 267
E +E
Sbjct: 563 DEEDEDDE 570
>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed.
Length = 925
Score = 30.8 bits (70), Expect = 5.9
Identities = 20/133 (15%), Positives = 49/133 (36%), Gaps = 4/133 (3%)
Query: 47 AKRQKIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWI 106
D N + ++L Q ++ + E + E E L +E +
Sbjct: 787 ITEILSDGINNSDINDRPQELIDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNL 846
Query: 107 DDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKKN--KNIQNPNAKGDIQKLLANMPVK 164
+ E + +++I+++ + K + + K + K + AK + KL+ +
Sbjct: 847 KQEIKLELSEI--QEAEEEIQNINENKNEFVEFKNDPKKLNKLIIAKDVLIKLVISSDEI 904
Query: 165 KKKKEEVQLNNDD 177
K+ ++ + D
Sbjct: 905 KQDEKTTKKKKKD 917
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 30.2 bits (68), Expect = 6.2
Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 5/91 (5%)
Query: 57 KFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWIDD-----DGG 111
KF + K +H+ + +++ E K+QE+ +D GG
Sbjct: 142 KFEKECRALSRKKSDDEHRKRSGKQKEKRRVEDSQKHKEDRRKKQEEKRRNDEDKRPGGG 201
Query: 112 DGYVEDGREIFDDDIEDVPQKKEKHDKRKKN 142
G + D ++++ HD ++
Sbjct: 202 GGSSGGQSGLSTKDEPPKEKRQKHHDPERRL 232
>gnl|CDD|236768 PRK10819, PRK10819, transport protein TonB; Provisional.
Length = 246
Score = 30.0 bits (68), Expect = 6.5
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 204 VIPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIK 248
IP+ AP KP K KP+KK K E+K
Sbjct: 80 PIPEPPKEAPVVIPKPE--PKPKPKPKPKPKPVKKVEEQPKREVK 122
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 30.6 bits (69), Expect = 6.9
Identities = 30/160 (18%), Positives = 50/160 (31%), Gaps = 7/160 (4%)
Query: 206 PKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSK 265
PKEEP KE P + EK+ EK K E ++E K + V + K
Sbjct: 124 PKEEPKDRKPKEEAKEKRPPKEKEKEKEK--KVEEPRDREEEKKRERVRA-----KSRPK 176
Query: 266 EEPVDDGLWEQMQIDDWDNSQQTQDVLPEQAKVELQIEAIESQSIEEKVDVTNVESVSSA 325
+ P ++ + + + +Q + E + + ++ D S
Sbjct: 177 KPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEE 236
Query: 326 VELSTSPPPQVVEKKEHKCAEWEAIQTEPSTSEPQVHSRT 365
E S K + P T E + T
Sbjct: 237 DESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTET 276
>gnl|CDD|215629 PLN03200, PLN03200, cellulose synthase-interactive protein;
Provisional.
Length = 2102
Score = 30.5 bits (69), Expect = 7.3
Identities = 32/121 (26%), Positives = 44/121 (36%), Gaps = 24/121 (19%)
Query: 168 KEEVQLNNDDVLADLLS---------EVNTTIAPTLKLNTKTNEIVIPKEEPPAPTAKEY 218
KEE Q VLAD+ S + I P +KL T E V A +
Sbjct: 622 KEETQEKAASVLADIFSSRQDLCESLATDEIINPCIKLLTNNTEAV-------ATQSARA 674
Query: 219 LANFSKPIKVEKKIEKPIKKEPSPLKDEIKSND-SVMEVEMNV-------AEQSKEEPVD 270
LA S+ IK +K+ + PL KS+ V E + E + E +
Sbjct: 675 LAALSRSIKENRKVSYAAEDAIKPLIKLAKSSSIEVAEQAVCALANLLSDPEVAAEALAE 734
Query: 271 D 271
D
Sbjct: 735 D 735
>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer
membranes [Cell envelope biogenesis, outer membrane].
Length = 244
Score = 29.8 bits (67), Expect = 7.9
Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 1/67 (1%)
Query: 202 EIVIPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVA 261
E + +PP KP + K +KP K +P P K + K V
Sbjct: 61 EPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKP-KPKPKPKPKVKPQPKPKK 119
Query: 262 EQSKEEP 268
SK
Sbjct: 120 PPSKTAA 126
>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid layers.
The innermost capsid (core) is made of VP2. The genomic
RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 30.3 bits (68), Expect = 7.9
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 5/84 (5%)
Query: 227 KVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKEEPVDDGLWEQMQIDDWDN-- 284
EK EK +K LK+++ + V NV KE+ + L ++
Sbjct: 17 MQEKDDEKQDQKNRMELKEKVLDKKEEV-VTDNVDSPVKEQSSQENLKIADEVKKSTKEE 75
Query: 285 SQQTQDVLPEQA--KVELQIEAIE 306
S+Q +VL + + E+Q E ++
Sbjct: 76 SKQLLEVLKTKEEHQKEIQYEILQ 99
>gnl|CDD|239062 cd02149, NfsB_like_nitroreductase, NAD(P)H:FMN oxidoreductase family.
This domain catalyzes the reduction of flavin,
nitrocompound, quinones and azo compounds using NADH or
NADPH as an electron donor. The enzyme is a homodimer,
and each monomer binds a FMN as co-factor. This family
includes FRase I in Vibrio fischeri, wihich reduces FMN
into FMNH2 as part of the bioluminescent reaction. The
family also includes oxygen-insensitive nitroreductases
that use NADH or NADPH as an electron donor in the ping
pong bi bi mechanism. This type of nitroreductase can be
used in cancer chemotherapy to activate a range of
prodrugs.
Length = 157
Score = 29.1 bits (66), Expect = 9.4
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 1013 PIEGTDAVRIAECLGLDTSLYRS 1035
PIEG D ++ E LGLD Y S
Sbjct: 110 PIEGFDPAKLDEILGLDEKGYGS 132
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 30.1 bits (68), Expect = 9.7
Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 6/105 (5%)
Query: 207 KEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKE 266
+E KE AN ++ K +K+ E ++ + PL+ EI + ME Q++E
Sbjct: 525 QENQTDEAPKENNANSAQARKDQKRREAELRTQTQPLRKEIARLEKEMEKLNAQLAQAEE 584
Query: 267 EPVDDGLWEQMQIDDWDNSQQTQDVLPEQAKVELQIEAIESQSIE 311
+ D L++Q + L +QA + +E E +E
Sbjct: 585 KLGDSELYDQ------SRKAELTACLQQQASAKSGLEECEMAWLE 623
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
0.315 0.133 0.381
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 63,834,348
Number of extensions: 6317069
Number of successful extensions: 4616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4465
Number of HSP's successfully gapped: 105
Length of query: 1274
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1166
Effective length of database: 6,147,370
Effective search space: 7167833420
Effective search space used: 7167833420
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: 42 (22.0 bits)
S2: 65 (28.8 bits)