RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5921
(1200 letters)
>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 = 754 bits (1949), Expect = 0.0
Identities = 285/451 (63%), Positives = 353/451 (78%), Gaps = 4/451 (0%)
Query: 623 GSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQS 682
GSQFRVES++LRL++ N++ SPS +Q A RA E LPL++EPES Y+DP+IVLDFQS
Sbjct: 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQS 60
Query: 683 LYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQK--LTISPSGVA 740
LYPS++IAYNYC+STCLGRVE L F F + L + L L K +TISP+GV
Sbjct: 61 LYPSIMIAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLPPPPLDLLLLKDDVTISPNGVM 120
Query: 741 FVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYT 800
FV KS+R GILPKML+EILDTR+MVK++MK+YK + LQR+L ARQL LKL+ANVTYGYT
Sbjct: 121 FVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDDKKLQRILDARQLALKLLANVTYGYT 180
Query: 801 AANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQ 860
AA+FSGRMPCVE+ DS+V GRETL++AIE + +T KW +VVYGDTDS+FVL PG+TK+
Sbjct: 181 AASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLFVLLPGRTKE 240
Query: 861 EAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGI 920
EAF+IGKEIA VT NP+P+KLKFEKVY PC+L TKKRYVGY YE+ DQ +P ++AKGI
Sbjct: 241 EAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGI 300
Query: 921 ETVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEYRG 980
ETVRRDGCPAV KIL+KSL +LFETKDLS VK Y+++Q+SK++ GR+S+QD FAKE R
Sbjct: 301 ETVRRDGCPAVQKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRL 360
Query: 981 QAGYKPGACVPALSL-ARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQ 1039
YK GA +PA ++ A + + DPRAEP+ ERVPYV+V G PG LI LV SP E L
Sbjct: 361 GT-YKEGATLPAGAIVALRRMEKDPRAEPQYGERVPYVVVRGEPGSRLIDLVVSPEEFLA 419
Query: 1040 DSSLRLNSEYYITRVIIPPLERCFLLLGTPV 1070
D SLRL++EYYIT+ IIP L+R F L+G V
Sbjct: 420 DPSLRLDAEYYITKQIIPALDRLFNLVGVDV 450
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 355 bits (913), Expect = e-107
Identities = 210/696 (30%), Positives = 332/696 (47%), Gaps = 82/696 (11%)
Query: 384 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTK 443
L VLA +I +S PD D + I Y + E + + + I E V
Sbjct: 154 LRVLAFDIETLSEPGKFPDGEKDPIIMISYAI-----EAEGGLIEVFIYTSGEGFSVE-- 206
Query: 444 PIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRI 503
V +E EL F+E +R++DPD+++GY + W YL ER LG+ L L R
Sbjct: 207 -----VVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPL--RLGRD 259
Query: 504 TEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRH-EVNLQSYTFENIMYHVLHER----I 558
+ R Q+ GR+ I+L+ LR +NL+SY+ E + +L E I
Sbjct: 260 -----GSELRVRKSGFSSQV-GRLHIDLYPALRRRPLNLKSYSLEAVSEALLGEGKREDI 313
Query: 559 PLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQ-LDFIGRTSEMARLFGIQFY 617
P S + + W + + Y + ++ I + + E++R+ G+
Sbjct: 314 PYDSMEEIWPDWADS-----KLRLLLYNLSDADLVLRILLKNELLPLLIELSRVSGLPLD 368
Query: 618 EVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIV 677
+V GS RVE ++LR ++ + P+ ++R R L+LEPE LY + ++V
Sbjct: 369 DVTRAGSGARVEGLLLREAKRRGELI--PNKEERPE-RKKYKGGLVLEPEPGLYEN-VLV 424
Query: 678 LDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPS 737
LDF SLYPS+II YN T + SP
Sbjct: 425 LDFSSLYPSIIIKYNISPDTLVEEDC---------------------------SDDYSPP 457
Query: 738 GVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTY 797
GV G LP++L+E+LD R +K+ MK+ K + +++L RQL LK++AN Y
Sbjct: 458 GVGHGFCKREKGFLPEILEELLDRRDEIKKKMKKEKDPS-ERKLLDGRQLALKVLANSFY 516
Query: 798 GYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGK 857
GY + S R C+E +SV + GRE L++ E + RV+YGDTDS+FV PG
Sbjct: 517 GYLGYSNS-RFYCIECAESVTAFGREILRETKELAE---EMGLRVIYGDTDSLFVTLPGA 572
Query: 858 TKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQT-KKRYVGYMYETADQDKPIYE 916
T +EA +IG+E+ V P+ ++L+ EKVY+ +L T KKRY G +D E
Sbjct: 573 TYEEAIKIGEELVEEVNERLPSGIELEVEKVYKRFLLPTAKKRYAG-----LLEDGDKIE 627
Query: 917 AKGIETVRRDGCPAVSKILKKSLCLLFETKDLS-VVKEYVEKQFSKIISGRISVQDMTFA 975
KG+ETVRRD V + ++ L +L +D+ + +YV K+ +G + ++ + +
Sbjct: 628 VKGLETVRRDWPELVKEFQREVLEVLLSGRDVEEALAKYVRDVIEKLRNGEVPIEKLVIS 687
Query: 976 KEY-RGQAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSP 1034
K R + YK A P + +A + L + +R+PYVIV G G + + P
Sbjct: 688 KRLTRPLSEYK--ANKPHVVVAAR--LRKRGINVKPGDRIPYVIVKG-KGKLVERAE--P 740
Query: 1035 YELLQDSSLRLNSEYYITRVIIPPLERCFLLLGTPV 1070
EL+ + + ++ EYYIT+ ++P LER +G
Sbjct: 741 PELVDEENSPIDYEYYITKQLLPALERILEPIGGNF 776
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 358 bits (921), Expect = e-106
Identities = 236/778 (30%), Positives = 378/778 (48%), Gaps = 96/778 (12%)
Query: 452 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEV----- 506
EKEL + E V DPD L GY I YLL R L LN + L RI
Sbjct: 329 TEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIK 388
Query: 507 EKRNSSRD--EVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIP--LHS 562
+ + SS+ ++ ++ + GRI ++ L+R + L+SY+ + + L E+ +S
Sbjct: 389 DSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYS 448
Query: 563 W--KLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVL 620
L E R + + + L +RL+++L I EMAR+ G +L
Sbjct: 449 IISDLQNGSPETRRRIAVYCLKDAILP-----LRLLDKLLLIYNYVEMARVTGTPIGWLL 503
Query: 621 SRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDF 680
+RG Q +V S +LR + N+V + E +LEP+ Y +PI LDF
Sbjct: 504 TRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEG-ATVLEPKKGFYDEPIATLDF 562
Query: 681 QSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTI-SPSGV 739
SLYPS++IA+N C+ST + + + + +P+G
Sbjct: 563 ASLYPSIMIAHNLCYSTLVPPNDA---------------------NNYPEDTYVTTPTGD 601
Query: 740 AFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGY 799
FV K +R GILP +++E++ R K+ MK+ K + L++VL+ RQL LK+ AN YGY
Sbjct: 602 KFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK-DPLLKKVLNGRQLALKISANSVYGY 660
Query: 800 TAANFSGRMPCVEVGDSVVSKGRETLQKAIETV------NNTSKWQCRVVYGDTDSMFVL 853
T A G++PC+EV S+ S GR+ + K E V N K V+YGDTDS+ V
Sbjct: 661 TGAQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVK 720
Query: 854 APGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQTKKRYVGYMYETADQ-DK 912
QEA ++GKE A ++ P+KL+FEKVY P +L KKRY G +Y ++ DK
Sbjct: 721 FGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNKKRYAGLLYTNPEKYDK 780
Query: 913 PIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDM 972
+ KGIETVRRD C V ++++ L + KD+ E+ + + S ++ RI + +
Sbjct: 781 --IDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLL 838
Query: 973 TFAKEYRGQAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVK 1032
K G+ Y+ + + LA++ DP + P V +RV YVIV GA G P + +
Sbjct: 839 VITKSL-GKDDYE--GRLAHVELAKKLRQRDPGSAPNVGDRVSYVIVKGAKGAPQYERAE 895
Query: 1033 SPYELLQDSSLRLNSEYYITRVIIPPLERCFLLLGTPVLPWYKNLPRKL-------HVYL 1085
P +L ++++ ++++YY+ + I PL R F V+ N P L H+ +
Sbjct: 896 DPLYVL-ENNIPIDTQYYLDQ-IKNPLLRIF----EGVM---DN-PDSLFSGEHTRHITI 945
Query: 1086 PSV----LNERKKKSTISQYFASVNCVCCNQMTQNNKG-VCDACL--NQTQLLGTCLYYK 1138
S L++ KK + C+ C + +G +CD C + + G K
Sbjct: 946 SSSSKGGLSKFVKK--------QLQCLGCK--SVIKEGALCDNCNQNKEPSIYGK----K 991
Query: 1139 IQAWQRSQDQVNKV---CTTCVGRSTSND--CISLDCPVLYRKTQITRDLDQLSYVLS 1191
+ + + + +++ C C G S + C + DCP+ YR+ ++ +DL +L +LS
Sbjct: 992 LAKRRHKEAEYSQLWTQCQRCQG-SLHQEVICTNRDCPIFYRRKKVQKDLAELQELLS 1048
>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 = 302 bits (776), Expect = 8e-92
Identities = 153/459 (33%), Positives = 244/459 (53%), Gaps = 41/459 (8%)
Query: 623 GSQFRVESIMLRLSRLNNFVAVSP---SIKQRAHMRAPESLP--LILEPESRLYTDPIIV 677
G Q RV S++LR ++ NF+ R E +LEP+ Y +P++V
Sbjct: 1 GQQIRVFSLLLREAKERNFILPDKFELRSLSRQVNIKKEGYQGATVLEPKKGFYNNPVLV 60
Query: 678 LDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPS 737
LDF SLYPS+I A+N C+ T L V+ + ++ L +
Sbjct: 61 LDFASLYPSIIQAHNLCYET-LVDVDA-------EAPKLAAERNLEVLHI-----VVGSL 107
Query: 738 GVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTY 797
FV K +R GILP +L+++L R K+ MKE K L+ +L +QL LK+ AN Y
Sbjct: 108 RERFVKKGVRKGILPVLLRDLLAKRKEKKKLMKESKDPEELRTLLDKQQLALKVTANSVY 167
Query: 798 GYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGK 857
G+T A +GR+PC+ + +SV + GRE ++K V + +V+YGDTDS+FV PG
Sbjct: 168 GFTGAA-NGRLPCLPIAESVTAIGREMIEKTKRYVEELLNYGFKVIYGDTDSVFVKFPGV 226
Query: 858 TKQEAFEIGKEIANVVTNNNPT-PVKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYE 916
+EA ++GKE+A VT+ P+KL+FEKVY+P +L +KKRY G Y+ +
Sbjct: 227 DIEEAKKLGKELAKHVTSELFFKPIKLEFEKVYKPLLLISKKRYAGLKYD--GKGDI--- 281
Query: 917 AKGIETVRRDGCPAVSKILKKSLCLLFETKDLS--------VVKEYVEKQFSKIISGRIS 968
KG++ VRRD C V ++++K L LL + KD+ V+ E ++ K++ ++
Sbjct: 282 -KGVDLVRRDWCEFVKEVIRKVLDLLLKDKDVEDAAPSLKIVIIEILKSLTDKLVQNKVP 340
Query: 969 VQDMTFAKEY-RGQAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAP---G 1024
++D+ KE + + YK P +++A + P V +R+PYVIV G G
Sbjct: 341 LEDLVITKELSKPPSEYK-KKNPPHVTVALRLKKRGNEEAPEVGDRIPYVIVKGPFHAKG 399
Query: 1025 LPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLERCF 1063
+L + P +L++ L +++EYY+ ++PP+ER F
Sbjct: 400 ALPYELAEDPEYVLEN--LPIDAEYYLDNQLVPPVERIF 436
>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 = 272 bits (697), Expect = 1e-81
Identities = 134/408 (32%), Positives = 212/408 (51%), Gaps = 33/408 (8%)
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
++EP Y PI LDF SLYPS+++A+N C++T L +
Sbjct: 8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNT------------------A 49
Query: 723 RSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVL 782
+ L +P+G FV S+R G+LP++L+E+L R K+ +KE + + VL
Sbjct: 50 KKLPPED--YIKTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEET-DPFKKAVL 106
Query: 783 HARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETV------NNTS 836
RQL LK+ AN YG+T A G++PC+E+ SV S GR+ ++K + V N
Sbjct: 107 DGRQLALKISANSVYGFTGAT-VGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTKANGY 165
Query: 837 KWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQT 896
+V+YGDTDS+ V +EA ++GKE A V+ P+KL+FEKVY P +L
Sbjct: 166 SHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLIN 225
Query: 897 KKRYVGYMYETADQ-DKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYV 955
KKRY G ++ D+ DK + KGIETVRRD C V +++ L + +D+ E+V
Sbjct: 226 KKRYAGLLWTNPDKHDK--MDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFV 283
Query: 956 EKQFSKIISGRISVQDMTFAKEYRGQAGYKPGACVPALSLARQWVLTDPRAEPRVSERVP 1015
+ S ++ +I + + K + + LA + DP + P V +RVP
Sbjct: 284 KGVISDLLQNKIDISLLVITKAL-TKTADDYAGKQAHVELAERMRKRDPGSAPNVGDRVP 342
Query: 1016 YVIVSGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLERCF 1063
YVI+ GA G + + P +L++ ++ ++++YY+ + PL R F
Sbjct: 343 YVIIKGAKGAKAYEKAEDPIYVLEN-NIPIDTQYYLENQLSKPLLRIF 389
>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 = 261 bits (670), Expect = 9e-79
Identities = 126/404 (31%), Positives = 179/404 (44%), Gaps = 88/404 (21%)
Query: 661 PLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNV 720
+ +P LY + +IVLDF+SLYPS+II YN +T +G E D G
Sbjct: 6 GYVFDPIPGLY-ENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVG------ 58
Query: 721 SIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQR 780
F R G+LP++L+E+L+ R K+ MK K +
Sbjct: 59 --------------------FRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERV 98
Query: 781 VLHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQC 840
+ RQ LK++AN YGY A F R EV S+ S GRE +Q I V
Sbjct: 99 LYDNRQQALKVLANSFYGYLGAKFF-RFYDPEVAASITSFGREIIQDTIALVEEHGA--- 154
Query: 841 RVVYGDTDSMFVLAPG-KTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQTKKR 899
RV+YGDTDS+FV P TK++A + G+EI + + + ++L+FEKVY P L KKR
Sbjct: 155 RVIYGDTDSIFVSLPKMGTKEDAIKEGREILQELADEHL--LELEFEKVYLPFFLGKKKR 212
Query: 900 YVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQF 959
Y G QD+ + KG+ET RRD P V K K+ L L+ E + E V++
Sbjct: 213 YAGLDIWK-GQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEEERK---VEAVKEYI 268
Query: 960 SKIISGRISVQDMTFAKEYRGQAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIV 1019
++ ++V YV+
Sbjct: 269 DEL-------------------------------------------------DKVKYVVT 279
Query: 1020 SGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLERCF 1063
G G+P + P E L D R++ EYY+ R++ PPLER F
Sbjct: 280 RGGKGVPDYERADPPLEDL-DKRHRIDYEYYLERLLQPPLERIF 322
>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 = 263 bits (674), Expect = 2e-77
Identities = 145/492 (29%), Positives = 243/492 (49%), Gaps = 39/492 (7%)
Query: 384 LTVLAVEIHAISRALLKPDP--AYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVR 441
L +L+ +I + PD DE+ I + + + + +G E+
Sbjct: 3 LKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGDKKGANRRILFTLGTCKEIDG-- 60
Query: 442 TKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 501
I+++ +NEKEL F E ++++DPDI+ G+ I Y++ R L ++ ++
Sbjct: 61 ---IEVYEFNNEKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIG 117
Query: 502 R------ITEVEKRNSSRD-EVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL 554
R I + S+ + + ++ + GR+VI+L+RL ++++ L SY + + ++L
Sbjct: 118 RLKIGLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLL 177
Query: 555 H-ERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFG 613
E+ L + + + + + + + ++L +L+ I E+AR+ G
Sbjct: 178 GKEKDDLPYKDIPELYNGNYEERDE--LLRYCIQDAVLTLKLFNKLNVIPLIIELARIAG 235
Query: 614 IQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSI----KQRAHMRAPESLP--LILEPE 667
I L GSQ RVES++LR ++ NN++ S + ++ +LEP+
Sbjct: 236 IPLRRTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKVKYEGGKVLEPK 295
Query: 668 SRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKK 727
Y +P++VLDF SLYPS+IIA+N C+ST +G E + I
Sbjct: 296 KGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGE-----------VVIKGDLIIPEDL 344
Query: 728 LQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLH-ARQ 786
L K + FV K+IR GILPK+L+++LD R +K+ MK+ K + + L +RQ
Sbjct: 345 LTIK-YEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQ 403
Query: 787 LGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETV--NNTSKWQCRVVY 844
L LKL AN YGY S R+PC + SV + GRE L+K E + N K +V+Y
Sbjct: 404 LALKLTANSVYGYLGFTNS-RLPCKPLAASVTALGREILEKTKELIEENGYPKPGFKVIY 462
Query: 845 GDTDSMFVLAPG 856
GDTDS+FV PG
Sbjct: 463 GDTDSIFVTKPG 474
>gnl|CDD|99821 cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' exonuclease domain
of eukaryotic DNA polymerase zeta, a family-B DNA
polymerase. The 3'-5' exonuclease domain of eukaryotic
DNA polymerase zeta. DNA polymerase zeta is a family-B
DNA polymerase which is distantly related to DNA
polymerase delta. It plays a major role in translesion
replication and the production of either spontaneous or
induced mutations. In addition, DNA polymerase 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. The
catalytic subunit contains both polymerase and 3'-5'
exonuclease domains, but only exhibits polymerase
activity. The DnaQ-like 3'-5' exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, without the four conserved acidic residues that
are crucial for metal binding and catalysis.
Length = 231
Score = 222 bits (569), Expect = 3e-66
Identities = 89/229 (38%), Positives = 137/229 (59%), Gaps = 14/229 (6%)
Query: 383 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLY--TCPPEEDR-KVGIILI---GQESE 436
+LT+L++E+H +R L PDP +D + AIFY + P D KVG+I++ +
Sbjct: 3 HLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNAS 62
Query: 437 LPEVRTKPIQMH--FVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLG- 493
+R+ + V +E ELF I+ VR++DPDIL GYEI+ SWGYL+ER LG
Sbjct: 63 NGRIRSGLSGIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGI 122
Query: 494 LNLNQELSRI--TEVEKRNSSRDEVKNTQ---LQMPGRIVINLWRLLRHEVNLQSYTFEN 548
+L E+SR+ K DE T +++ GR ++N+WRL+R E+ L +YT EN
Sbjct: 123 DDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLEN 182
Query: 549 IMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIE 597
++YHVLH+RIPL+S K LT W++ + +W +E+YL RV + +++
Sbjct: 183 VVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEILD 231
>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 = 190 bits (485), Expect = 9e-53
Identities = 109/409 (26%), Positives = 185/409 (45%), Gaps = 49/409 (11%)
Query: 662 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVS 721
L+LEP+ LY I++LDF SLYPS+I YN CF+T + P
Sbjct: 12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPPL-------- 63
Query: 722 IRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRV 781
GILP++++++++ R VK+ MK + + +
Sbjct: 64 --------------------PPSDQEKGILPRIIRKLVERRRQVKKLMKS-EKDPDKKAQ 102
Query: 782 LHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCR 841
L RQL LKL AN YG ++S R + + SKGRE LQK + V +
Sbjct: 103 LDIRQLALKLTANSMYGCLGFSYS-RFYAKPLAALITSKGREILQKTKDLVEKMN---LE 158
Query: 842 VVYGDTDSMFVLAPGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQTKKRYV 901
V+YGDTDS+ + +EA ++G +I V N + +++ + V++ +L KK+Y
Sbjct: 159 VIYGDTDSIMINTGTTDYEEAKKLGNKIKKEV-NKSYKKLEIDIDGVFKRLLLLKKKKYA 217
Query: 902 GYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKD----LSVVKEYVEK 957
D+ K E KG++ VRRD CP +I L + K + + EY+ K
Sbjct: 218 ALKVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVENIHEYLRK 277
Query: 958 QFSKIISGRISVQDMTFAKEYRGQAG-----YKPGACVPALSLARQWVLTDPRAEPRVSE 1012
+ +G+I ++ K Q Y +P + +A + + + + +
Sbjct: 278 INEDLRNGKIPLEKFIITK----QLTKNPEEYPDKKSLPHVQVALR--MNKRGRKVKAGD 331
Query: 1013 RVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLER 1061
+PY+I L P E+ ++ +L+++ EYY+++ I+PP+ R
Sbjct: 332 TIPYIICKDGSSKSLADRAYHPDEVKKNENLKIDIEYYLSQQILPPISR 380
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 195 bits (497), Expect = 2e-51
Identities = 150/709 (21%), Positives = 261/709 (36%), Gaps = 165/709 (23%)
Query: 415 LYTCPPEEDRKVGIILIGQESELPEVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIG 474
L C R V I++G + + +V++EK L F + DPD++IG
Sbjct: 175 LEGCG---QRPV--IMLGPPNG-----EALDFLEYVADEKALLEKFNAWFAEHDPDVIIG 224
Query: 475 YEIETLSWGYLLERGYVLGLNLNQELSR-ITEVEKRNSSRDEVKNTQLQMPGRIVINLWR 533
+ + L ER G+ L L R +E+E R +PGR+V++
Sbjct: 225 WNVVQFDLRLLQERAERYGIPLR--LGRDGSELEWREHPFRSGYGF-ASVPGRLVLDGID 281
Query: 534 LLRHEV-NLQSYTFENIMYHVLHE----RIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIR 588
L+ S++ E + +L E P + + + Y ++
Sbjct: 282 ALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPA-----LARYNLK 336
Query: 589 ----VTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV 644
VT I + L F+ E A + G+ V GS E + L + +VA
Sbjct: 337 DCELVTRIFEKTKLLPFL---LERATVTGLPLDRV--GGSVAAFEHLYLPRAHRAGYVA- 390
Query: 645 SPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRV 702
P++ + R E+ P +++ + LY D ++VLDF+SLYPS+I +N G V
Sbjct: 391 -PNLGE----RPGEASPGGYVMDSKPGLY-DSVLVLDFKSLYPSIIRTFNIDP---DGLV 441
Query: 703 EHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTR 762
E L + G F S LP++++ + + R
Sbjct: 442 EGLAQPPE---ESVA-----------------GFLGARF---SREKHFLPEIVERLWEGR 478
Query: 763 LMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGR 822
K+ M + S A +K+I N YG ++ R + S+ +G
Sbjct: 479 DEAKREMNKPLSQA------------IKIIMNAFYGVLGSSGC-RFFDPRLASSITMRGH 525
Query: 823 ETLQKAIETVNNTSKWQCRVVYGDTDSMFV-LAPGKTKQEAFEIGKEIANVVTNNNPTPV 881
E +++ E + +V+YGDTDS FV L +++A +IG+ + + +
Sbjct: 526 EIMKQTRELIEAQGY---QVIYGDTDSTFVWLGGAHDEEDAAKIGRALVQEINQWWQEHL 582
Query: 882 K----------LKFEKVYQPCILQT--------KKRYVGYMYETADQDKPIYEAKGIETV 923
+ L+FEK Y+ + T KKRY G + E + ++ KG+ETV
Sbjct: 583 QQEFGLESALELEFEKHYRRFFMPTIRGAEEGSKKRYAGLIQEGDGDGRIVF--KGLETV 640
Query: 924 RRDGCPAVSKILKKSLCLLFETKDLSV-VKEYVEKQ----------FSKIISGRIS---- 968
R D P + ++ +F + V+E ++K + K + +
Sbjct: 641 RTDWTPLAKEFQQELYERIFRGEPYVDYVREVIDKLRAGELDEKLVYRKRLRRPLDEYQR 700
Query: 969 -----VQDMTFAKEYRGQAG----YKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIV 1019
V+ A E + G Y+ G ++ YVI
Sbjct: 701 NVPPHVRAARLADEMGYKVGRPLQYQNGG------------------------KIGYVIT 736
Query: 1020 SGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLERCFLLLGT 1068
P P E + ++ +YYI + + P +R G
Sbjct: 737 VNGPE---------PLEYRKS---PIDYDYYIEKQLQPVADRILPFFGD 773
>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 = 193 bits (492), Expect = 5e-50
Identities = 164/716 (22%), Positives = 290/716 (40%), Gaps = 84/716 (11%)
Query: 372 LNEVTSHVENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILI 431
LN E + + P+P YD + C D K
Sbjct: 516 LNPSIIRNEIVSIPDTLH--REFALDKPPPEPPYDVHPCVGTRPKDCSFPLDLK------ 567
Query: 432 GQESELPEVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYV 491
E P KP + ++ E+ L F+ V++ DPD ++G++ + + L R
Sbjct: 568 ---GEFPGK--KPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRIND 622
Query: 492 LGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMY 551
L + ++ R+ K E + GR++ ++ + + +SY ++
Sbjct: 623 LKIPTWSKIGRLRRSPKFGRRFGE------RTCGRMICDVEISAKELIRCKSYDLSELVQ 676
Query: 552 HVLH-ERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMAR 610
+L ER + + + E + Y +EH I++++ +L+ + ++
Sbjct: 677 QILKTERKVIPIDNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVLPLALQITN 733
Query: 611 LFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAH---------------MR 655
+ G L G R E ++L NN++ I ++ +
Sbjct: 734 IAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQKLGDEDEEIDGYKKGKK 793
Query: 656 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGC 715
A + L+LEP+ LY ++++DF SLYPS+I +N CF+T
Sbjct: 794 AAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTT------------------ 835
Query: 716 IDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSN 775
+QQK+ D + GILP+ L+++++ R VK+ MK+ N
Sbjct: 836 ------------VQQKVDEDELP-ELPDSELEMGILPRELRKLVERRKEVKKLMKQ-DLN 881
Query: 776 AALQRVLHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNT 835
L+ RQ LKL AN YG + S R + V +KGRE L+ + V
Sbjct: 882 PDLRLQYDIRQKALKLTANSMYGCLGYSKS-RFYAKPLAALVTAKGREILEHTRQLV--- 937
Query: 836 SKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQ 895
+ V+YGDTDS+ + PG +E F+IGKE + V ++L + V++ +L
Sbjct: 938 EEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYK-LLELDIDGVFKRLLLL 996
Query: 896 TKKRYVGYMYETADQDKPIY--EAKGIETVRRDGCPAVSKILKKSLCLLFETKD----LS 949
KK+Y E E KG++ VRRD P + KK L + KD +
Sbjct: 997 KKKKYAAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVE 1056
Query: 950 VVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAGYKPGACVPALSLARQWVLTDPRAEP 1008
V+E +EK +++G + ++ K+ R Y GA +P + +A + +
Sbjct: 1057 EVQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDGASLPHVHVAL-RINARGGRKV 1115
Query: 1009 RVSERVPYVIVSGAPGLPLIKLVKSPYELL-QDSSLRLNSEYYITRVIIPPLERCF 1063
+ + V YVI L + + EL + ++L +++YY+ I P + R
Sbjct: 1116 KAGDVVSYVICKDGGNLSARQRAYALEELQRKHNNLIYDTQYYLEHQIHPVVLRIL 1171
Score = 43.9 bits (103), Expect = 6e-04
Identities = 77/409 (18%), Positives = 130/409 (31%), Gaps = 44/409 (10%)
Query: 419 PPEEDRKVGIILIGQESELPEVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIE 478
E R V + + V + VS E + F + + Q D D+ I +
Sbjct: 243 SEPEARVVTWKKPDKPTTGSYVES-------VSEEISMIKRFWDVIDQEDTDVEITVNGD 295
Query: 479 TLSWGYLLER--------GYVLGLNLNQELSRITEVEKRNSSRDEVKNTQ-----LQMPG 525
YL +R Y + S +VK L G
Sbjct: 296 NFDLVYLADRQVFQFYWDAYEDPAEKLGVVLLFGRDVDHVSPCVQVKGINRDLFFLPREG 355
Query: 526 RIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHY 585
+I +L ++ R +NL Y E + L + K + +E Y
Sbjct: 356 KIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPDIDAPYSSEY 415
Query: 586 LIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV- 644
L VT +F + + L G F+ V + ++LR + ++AV
Sbjct: 416 L-EVT----YELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVK 470
Query: 645 SPSIK-QRAHMRAPESLPLILEPESRLYTD----PIIVLDF--QSLYPSVIIAYNYCFST 697
P + P D P++VLDF +SL PS+I
Sbjct: 471 GPDELEYPRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPD 530
Query: 698 CLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQE 757
L R L P +V + + P + G P ++++
Sbjct: 531 TLHREFAL----DKPPPEPPYDVHPCVGTRPKD--CSFPLDLKGEFP----GKKPSLVED 580
Query: 758 ILDTRLMVKQSMKEYKSNAALQRVLH-ARQLGLKLIANVTYGYTAANFS 805
+ R ++K+ M + K + V H +Q LK++AN +S
Sbjct: 581 LATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWS 629
>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 = 149 bits (377), Expect = 7e-39
Identities = 111/409 (27%), Positives = 185/409 (45%), Gaps = 67/409 (16%)
Query: 662 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVS 721
++LEPE L+ + I+VLDF SLYPS++I YN T + GC D +V
Sbjct: 8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVRE------------GCEDCDVE 54
Query: 722 IRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRV 781
G F K G +P +L+++L+ R +K+ MK+ + ++
Sbjct: 55 P-------------QVGHKF-RKDPP-GFIPSVLEDLLEERRRIKEKMKKLDPESEEYKL 99
Query: 782 LHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCR 841
L RQ +K++AN YGY + R C E ++V + GRE ++ I+ +
Sbjct: 100 LDERQRAIKILANSFYGYMGWA-NARWYCKECAEAVTAWGREYIKTTIKIAEEKG---FK 155
Query: 842 VVYGDTDSMFVLAPG--KTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQTKKR 899
V+YGDTDS+FV G K++ ++ K I N P++L+ EK Y+ TKKR
Sbjct: 156 VIYGDTDSLFVKIDGADAVKKKVKKLLKYI------NEELPLELEIEKFYKRGFFVTKKR 209
Query: 900 YVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQF 959
Y G +D I + G+E VRRD + + L + + D+ + V++
Sbjct: 210 YAGL-----TEDGKI-DVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVI 263
Query: 960 SKIISGRISVQDMTFAK-------EYRGQAGYKPGACVPALSLARQWVLTDPRAEPRVSE 1012
K+ G + + + K EY+ + A LA++ + R
Sbjct: 264 EKLKRGEVPPEKLVIWKQLTKDLSEYKATGPH----VAAAKKLAKRGY------KVRPGT 313
Query: 1013 RVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLER 1061
++ YVIV G G I PY+++ + + ++EYYI ++P + R
Sbjct: 314 KIGYVIVKG-SG--KISDRAYPYDMVDEKH-KYDAEYYIDNQVLPAVLR 358
>gnl|CDD|176646 cd05160, DEDDy_DNA_polB_exo, DEDDy 3'-5' exonuclease domain of
family-B DNA polymerases. The 3'-5' exonuclease domain
of family-B DNA polymerases. This domain has a
fundamental role in reducing polymerase errors and is
involved in proofreading activity. Family-B DNA
polymerases contain an N-terminal DEDDy DnaQ-like
exonuclease domain in the same polypeptide chain as the
polymerase domain, similar to family-A DNA polymerases.
This domain contains three sequence motifs termed ExoI,
ExoII and ExoIII, with a specific YX(3)D pattern at
ExoIII. These motifs are clustered around the active
site and contain four conserved acidic residues that
serve as ligands for the two metal ions required for
catalysis. The exonuclease domain of family B polymerase
also contains a beta hairpin structure that plays an
important role in active site switching in the event of
nucleotide misincorporation. Members include Escherichia
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. Nuclear DNA polymerases alpha and
zeta lack the four conserved acidic metal-binding
residues. Family-B DNA polymerases are predominantly
involved in DNA replication and DNA repair.
Length = 199
Score = 107 bits (268), Expect = 4e-26
Identities = 47/198 (23%), Positives = 83/198 (41%), Gaps = 12/198 (6%)
Query: 400 KPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMHFVSNEKELFSI 459
P+P D + I Y KV +L I++ + ++EKEL
Sbjct: 14 GPEPDRDPIICITYADSFD----GVKVVFLLKTSTVGDDIEFIDGIEVEYFADEKELLKR 69
Query: 460 FIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNT 519
F + +R++DPDIL GY I+ YLL+R LG+ L + R + EK + S + +
Sbjct: 70 FFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIA-- 127
Query: 520 QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKW 579
+ GR+V +L + + L+SYT + + +L E +
Sbjct: 128 ---VKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDG---EIIEDAEWEEDPE 181
Query: 580 MTVEHYLIRVTGIIRLIE 597
+E+ L ++++E
Sbjct: 182 RLIEYNLKDAELTLQILE 199
>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 = 98.1 bits (245), Expect = 1e-21
Identities = 105/437 (24%), Positives = 163/437 (37%), Gaps = 111/437 (25%)
Query: 670 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQ 729
LY + ++VLDF+SLYPS+I + LG +E L D
Sbjct: 15 LYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKAPDP------------------- 51
Query: 730 QKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGL 789
+ L G F S ILP ++ + R K+ NA L + +
Sbjct: 52 EDLIPGFLGARF---SREKHILPDLIARLWAARDEAKRE-----KNAPLSQAI------- 96
Query: 790 KLIANVTYGYTAAN----FSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKW----QCR 841
K+I N YG + F R+ S+ +G E +++ T W +
Sbjct: 97 KIIMNSFYGVLGSTGCRFFDPRLA-----SSITLRGHEIMKQ-------TRAWIEQQGYQ 144
Query: 842 VVYGDTDSMFV-LAPGKTKQEAFEIGKEIANVVTNNNPTPVK----------LKFEKVYQ 890
V+YGDTDS FV L EA IGKE+A+ + +K ++FE Y
Sbjct: 145 VIYGDTDSTFVWLGEELDAAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYS 204
Query: 891 PCILQT--------KKRYVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLL 942
+ T KKRY G + KG+ETVR D P + K+ +
Sbjct: 205 RFFMPTIRGSDEGSKKRYAGLK---STDGGDELVFKGLETVRSDWTPLARQFQKELYERV 261
Query: 943 FETKDLSV-VKEYVEKQFSKIISGRISVQDMTFAKEYRGQAG-Y--KPGACVPALSLARQ 998
F + +KE VE+ +++G + + + K R Y V A LA Q
Sbjct: 262 FNDEPYEGFIKETVEE----LLAGELDEL-LVYRKRLRRPLSEYTKNVPPHVQAARLADQ 316
Query: 999 WVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPP 1058
+ PR + + YVI P E L+ + L+ ++YI + + P
Sbjct: 317 --INRELGRPRQYQWIEYVITVNGP------------EPLEYRTSPLDYQHYIDKQLKPI 362
Query: 1059 LERCFLLLGTPVLPWYK 1075
+ +LP+
Sbjct: 363 AD--------SILPFLG 371
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed.
Length = 787
Score = 97.1 bits (242), Expect = 2e-20
Identities = 79/375 (21%), Positives = 146/375 (38%), Gaps = 71/375 (18%)
Query: 614 IQFYEVLSRG--SQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLY 671
++++E RG ++ E I+ V IK + + L+ +P ++
Sbjct: 371 LEYWEHRKRGWLIPWK-EDILRLDHE----VYKKAIIKGKKYRGG-----LVFQPPPGIF 420
Query: 672 TDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQK 731
+ + VLDF SLYPS+I+ +N T V + +L S+ +
Sbjct: 421 FN-VYVLDFASLYPSIIVKWNLSPET----VRIPECKCHYDDEVPELGHSVCDDR----- 470
Query: 732 LTISPSGVAFVDKSIRCGILPKMLQEIL-DTRLMVKQSMKEYKSNAALQR-VLHARQLGL 789
L +L +L D R+ + + + + +R Q L
Sbjct: 471 -----------------PGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRAL 513
Query: 790 KLIANVTYGYTAA-NFS-GRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDT 847
K+ N +YG A NF R+ E S+ + GRE L + T + +V+YGDT
Sbjct: 514 KVFLNASYGVFGAENFKLYRIEVAE---SITALGREIL---LSTKKKAEELGLKVLYGDT 567
Query: 848 DSMFVLAPGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQ-TKKRYVGYMYE 906
DS+FV P K E E+ + T + L+ +K Y KK Y G + +
Sbjct: 568 DSLFVWGPTKESLE------ELIKEIEER--TGIDLEVDKTYDWVAFSGLKKNYFGVLKD 619
Query: 907 TADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFET-------KDLSVVKEYVEKQF 959
K + KGI +R+ V ++ ++ L +L K +++ +++ +
Sbjct: 620 ----GK--VKIKGIVAKKRNTPEFVKELQREVLEVLKSIRSPEDVEKVKDEIEDVLKRYY 673
Query: 960 SKIISGRISVQDMTF 974
K+ + + ++
Sbjct: 674 EKLRAKDYPLDELAI 688
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 90.9 bits (226), Expect = 2e-18
Identities = 86/322 (26%), Positives = 148/322 (45%), Gaps = 62/322 (19%)
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ P+ +++ + +++ D+ SLYP+V I N T +G V V+D+ I+ +
Sbjct: 535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVV----VNDNRLEAEIN-KQEL 589
Query: 723 RSLKKLQQKLTI-----SP---SGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKS 774
R + + + SP S +A D+ I GI+PK+L+ L+ R K+ +KE S
Sbjct: 590 RRKYPYPRYIYVHCEPRSPDLVSEIAVFDRRIE-GIIPKLLKTFLEERARYKKLLKEATS 648
Query: 775 NAALQRVLH-ARQLGLKLIANVTYG----YTAANFS----------GRMPCVEVGDSVV- 818
++++ ++ + Q K++AN YG +A +S GR ++ +SV+
Sbjct: 649 --SVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRN-MIKYLNSVLN 705
Query: 819 ----SKGRETLQK-----------AIETVNNTSKWQC-----RVVYGDTDSMFVLAPGKT 858
G+ L +I+T +T+ R VYGDTDS+F+ K
Sbjct: 706 GSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVFLEINTKD 765
Query: 859 KQEAFEIGKEIANVVTNNN--PTPVKLKFEKVYQPCILQTKKRYVGYMY--ETADQDKPI 914
++ +I KE+ ++ N K++FE VY+ I+Q+KK+Y Y + D P
Sbjct: 766 VDKSIKIAKELERII-NEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPE 824
Query: 915 YEAKGIETVRRDGCPAVSKILK 936
KG RRD VSK K
Sbjct: 825 RVNKGTSETRRD----VSKFHK 842
>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 = 84.3 bits (209), Expect = 4e-17
Identities = 77/306 (25%), Positives = 126/306 (41%), Gaps = 69/306 (22%)
Query: 662 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVS 721
L+ +PE LY + + +DF S+YPS+I+ YN T ++ + +
Sbjct: 9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPET---------INCRCCECRDHVYLG 58
Query: 722 IRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRV 781
R K R G LP++L+ +L+ RL K+ KE
Sbjct: 59 HRICLK-------------------RRGFLPEVLEPLLERRLEYKRLKKEED-------P 92
Query: 782 LHARQLGLKLIANVTYGYTA---ANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKW 838
RQ LK I ++GY A F GR +EV +++ + GR+ L +A E +
Sbjct: 93 YAGRQKALKWILVTSFGYLGYKNAKF-GR---IEVHEAITAYGRKILLRAKEI---AEEM 145
Query: 839 QCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQ-PCILQTK 897
RV++G DS+++ G ++ A EI + T + LK E Y L +
Sbjct: 146 GFRVLHGIVDSLWIQGRGDIEELAREIEER----------TGIPLKLEGHYDWIVFLPER 195
Query: 898 ------KRYVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVV 951
RY G + + + +GIE RRD P V K +++L +L K +
Sbjct: 196 DGLGAPNRYFGRLSDGE------MKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEEL 249
Query: 952 KEYVEK 957
+ E+
Sbjct: 250 LKLREE 255
>gnl|CDD|217371 pfam03104, DNA_pol_B_exo1, DNA polymerase family B, exonuclease
domain. This domain has 3' to 5' exonuclease activity
and adopts a ribonuclease H type fold.
Length = 254
Score = 79.0 bits (195), Expect = 5e-16
Identities = 46/178 (25%), Positives = 78/178 (43%), Gaps = 21/178 (11%)
Query: 384 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTK 443
L VL+ +I S P+ D + I LY + + + + + +
Sbjct: 86 LRVLSFDIECTSLKGKFPENEKDPIIQISCMLYREGEPDPIEDKLFTLKSCALIEI---- 141
Query: 444 PIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL--- 500
+++ +EKEL F E +RQ+DPDI+ GY + W Y+L R +LGL + E
Sbjct: 142 GGEVYIFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKILGLKMTPEYGVR 201
Query: 501 ---------SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENI 549
V N SR++VK + GRI ++L+R+++ + L SY +
Sbjct: 202 SSKIGRLKRGGFPRVFSGNGSREKVK-----ISGRIHLDLYRVIKRDSKLGSYKLNAV 254
>gnl|CDD|99820 cd05777, DNA_polB_delta_exo, DEDDy 3'-5' exonuclease domain of
eukaryotic DNA polymerase delta, a family-B DNA
polymerase. The 3'-5' exonuclease domain of eukaryotic
DNA polymerase delta. DNA polymerase delta is a family-B
DNA polymerase with a catalytic subunit that contains a
DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one
of the three DNA-dependent type B DNA polymerases (alpha
and epsilon are the other two) that have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase delta is the enzyme responsible for both
elongation and maturation of Okazaki fragments on the
lagging strand. It is also implicated in mismatch repair
(MMR) and base excision repair (BER). The catalytic
subunit displays both polymerase and 3'-5' exonuclease
activities. The exonuclease domain contains three
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues necessary for metal binding
and catalysis. The exonuclease domain of family B
polymerase also contains a beta hairpin structure that
plays an important role in active site switching in the
event of nucleotide misincorporation.
Length = 230
Score = 67.2 bits (165), Expect = 3e-12
Identities = 49/192 (25%), Positives = 81/192 (42%), Gaps = 36/192 (18%)
Query: 384 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRT- 442
L +L+ +I R + P+P D V I ++ E E P +R
Sbjct: 7 LRILSFDIECAGRKGVFPEPEKDPVIQI--------------ANVVTRQGEGE-PFIRNI 51
Query: 443 ------KPI---QMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLG 493
PI Q+ E+EL + + V++ DPDI+ GY I YLLER L
Sbjct: 52 FTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALK 111
Query: 494 LNLNQELSRITEVEKRNSSRDEVK---------NTQLQMPGRIVINLWRLLRHEVNLQSY 544
LN L RI +++ +D ++ + GRI +L ++++ + L+SY
Sbjct: 112 LNTFPFLGRI--KNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVIQRDYKLRSY 169
Query: 545 TFENIMYHVLHE 556
+ ++ H L E
Sbjct: 170 SLNSVSAHFLGE 181
>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 = 66.2 bits (162), Expect = 3e-11
Identities = 62/248 (25%), Positives = 107/248 (43%), Gaps = 51/248 (20%)
Query: 662 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVS 721
++LEP ++ + ++VLDF SLYPS+I +N + T V+
Sbjct: 17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET----------------------VN 53
Query: 722 IRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRV 781
+ K P +V K GI +++ + D R+ + + + KS R
Sbjct: 54 CPHCEC---KTNEVPEVGHWVCKKRP-GITSQIIGLLRDLRVKIYKKKAKDKSLDEEMRQ 109
Query: 782 LH-ARQLGLKLIANVTYG-YTAANFSGRMPCVEVGDSVVSKGR----ETLQKAIETVNNT 835
+ Q +K+ N +YG + A NF + C V +S + GR T++KA E
Sbjct: 110 WYDVVQSAMKVFINASYGVFGAENFP--LYCPPVAESTTALGRYIITSTIKKAREL---- 163
Query: 836 SKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIANVVTNNNPTPVKLKFEKVYQPCILQ 895
+V+YGDTDS+F+ P + + E ++ V + L+ +K Y+ +
Sbjct: 164 ---GLKVLYGDTDSLFLWNPPQEQLE------DLVEWVEKE--LGLDLELDKEYRYVVFS 212
Query: 896 T-KKRYVG 902
KK Y+G
Sbjct: 213 GLKKNYLG 220
>gnl|CDD|222632 pfam14260, zf-C4pol, C4-type zinc-finger of DNA polymerase delta. In
fission yeast this zinc-finger domain appears is the
region of Pol3 that binds directly to the B-subunit,
Cdc1. Pol delta is a hetero-tetrameric enzyme comprising
four evolutionarily well-conserved proteins: the
catalytic subunit Pol3 and three smaller subunits Cdc1,
Cdc27 and Cdm1.
Length = 73
Score = 59.3 bits (144), Expect = 4e-11
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 1107 CVCCNQMTQNNKG-VCDACLNQTQLLGTCLYYKIQAWQRSQDQVNKVCTTCVGRS-TSND 1164
C+ C + + + +C CL Q L +++ +R ++ +C C G
Sbjct: 1 CLVCGKKLKEGESPLCKNCLRNPQASLYKLLSRLRELERRFSRLWTICQRCQGSLHEEVL 60
Query: 1165 CISLDCPVLYRKT 1177
C S DCPV Y++
Sbjct: 61 CDSRDCPVFYKRV 73
>gnl|CDD|99823 cd05780, DNA_polB_Kod1_like_exo, DEDDy 3'-5' exonuclease domain of
Pyrococcus kodakaraensis Kod1 and similar archaeal
family-B DNA polymerases. The 3'-5' exonuclease domain
of archaeal family-B DNA polymerases with similarity to
Pyrococcus kodakaraensis Kod1, including polymerases
from Desulfurococcus (D. Tok Pol) and Thermococcus
gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are
thermostable enzymes that exhibit both polymerase and
3'-5' exonuclease activities. They are family-B DNA
polymerases. Their amino termini harbor a DEDDy-type
DnaQ-like 3'-5' exonuclease domain that contains three
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. These motifs are
clustered around the active site and are involved in
metal binding and catalysis. The exonuclease domain of
family B polymerases contains a beta hairpin structure
that plays an important role in active site switching in
the event of nucleotide misincorporation. Members of
this subfamily show similarity to eukaryotic DNA
polymerases involved in DNA replication. Some archaea
possess multiple family-B DNA polymerases. Phylogenetic
analyses of eubacterial, archaeal, and eukaryotic
family-B DNA polymerases support independent gene
duplications during the evolution of archaeal and
eukaryotic family-B DNA polymerases.
Length = 195
Score = 62.8 bits (153), Expect = 6e-11
Identities = 41/171 (23%), Positives = 72/171 (42%), Gaps = 36/171 (21%)
Query: 401 PDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMHFVSNEKELFSIF 460
P+P D + I + D ++ ++ +LP V V EKE+ F
Sbjct: 19 PNPEKDPIIMISFA--------DEGGNKVITWKKFDLPFVEV-------VKTEKEMIKRF 63
Query: 461 IENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVK--- 517
IE V++ DPD++ Y + + YL +R LG+ L+ R+ S +++
Sbjct: 64 IEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDL---------GRDGSEIKIQRGG 114
Query: 518 -NTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL--------HERIP 559
N ++ GRI ++L+ + R +NL YT E + + E I
Sbjct: 115 FNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIA 165
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 65.9 bits (161), Expect = 1e-10
Identities = 87/414 (21%), Positives = 153/414 (36%), Gaps = 52/414 (12%)
Query: 374 EVTSHVENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQ 433
EVT+ EI AI+ YD + FY EE G +
Sbjct: 114 EVTAEDGFPDPEEAKYEIDAITH--------YDSIDDRFYVFDLGSVEEWDAKGDEV--- 162
Query: 434 ESELPEVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+ K + M F E+E+ +I + P I G+ +E Y++ R +L
Sbjct: 163 ---PQEILDKVVYMPF-DTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNIL 218
Query: 493 GLNLNQELSRITEVEKRNSSRDE-VKNTQLQMPGRIVINLWRLLRH--EVNLQSYTFENI 549
G + LS +V++R + + G +++ L + N SY + I
Sbjct: 219 GEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKFTFTNQPSYRLDYI 278
Query: 550 MYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMA 609
L ++ +S + E Y +E+ +I V + RL ++ I MA
Sbjct: 279 AEVELGKKKLDYSDGPFKKFRETDHQKY----IEYNIIDVELVDRLDDKRKLIELVLSMA 334
Query: 610 RLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESR 669
I F +V S + ++ S + + + ++H + + + EP
Sbjct: 335 YYAKINFEDVFS---PIKTWDAIIFNSLKEEKIVIP---ENKSHKKQKYAGAFVKEPVPG 388
Query: 670 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLG-----RVEHLGVSDSFPFGCIDLNVSIRS 724
Y ++ D SLYPS+I N T G V ++ + P + + S
Sbjct: 389 AY-RWVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEY-INKTAPRPSDEYSCS--- 443
Query: 725 LKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAAL 778
P+G K IR G++P ++++ D R + K+ M + NA L
Sbjct: 444 -----------PNG-WMYRKDIR-GVIPTEIKKVFDQRKIYKKKMLAAERNAEL 484
Score = 34.3 bits (79), Expect = 0.48
Identities = 40/177 (22%), Positives = 70/177 (39%), Gaps = 38/177 (21%)
Query: 842 VVYGDTDSMFVLAP------------------------GKTKQEAF-EIG-KEIANVVTN 875
V+YGDTDS++V K + E + + +E+ + N
Sbjct: 603 VIYGDTDSIYVNLDPLVEKVGEDKFKDTNHWVDFLDKFCKERMEPYIDSSYRELCEYM-N 661
Query: 876 NNPTPVKLKFEKVYQPCILQTKKRYVGYMY--ETADQDKPIYEAKGIETVRRDGCPAVSK 933
N + + E + P KKRY ++ E +P + GIET R AV K
Sbjct: 662 NYEHLMFMDREAIAGPGFWTAKKRYALNVWDSEGTRYAEPKLKIMGIETQRSSTPKAVQK 721
Query: 934 ILKKSLCLLFETKDLSVVKEY--VEKQFSKI----ISGRISVQDMTFAKEYRGQAGY 984
LK+++ + + + S+ + EK+F K+ I+ S ++ +Y G
Sbjct: 722 ALKEAIRRILQEGEESLQEYIKEFEKEFRKLDYEEIAFVSSANNIA---KYSDDKGI 775
>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 = 57.9 bits (140), Expect = 1e-08
Identities = 67/289 (23%), Positives = 116/289 (40%), Gaps = 38/289 (13%)
Query: 749 GILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLH-ARQLGLKLIANVTYGYTAA---NF 804
GI +L+ +++ RL K+S + A +R A+Q K++ N YGY F
Sbjct: 45 GIFLALLKYLVELRLAAKESARAAARPA--ERDAFKAKQAAFKVLINSFYGYLGTGLHAF 102
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
S E V GRE L+ I + + V DTD ++ + P E E
Sbjct: 103 SD----PEAAAEVTRLGRELLKLMIRWL---RRRGATPVEVDTDGIYFIPPNGVDTEDEE 155
Query: 865 IGKEIANVVTNNNPTPVKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
+E+ +++ P + ++F+ Y+ K Y Y+ K I KG
Sbjct: 156 --EELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLDYD----GKLI--VKGSAFRS 207
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDM-------TFAKE 977
R P + + L++++ LL + D + V + E ++ S + + D+ +E
Sbjct: 208 RGIEPFLREFLREAVRLLLQ-GDGAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEE 266
Query: 978 YRG--QAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPG 1024
Y +AG + A ++LAR E R +RV Y + G
Sbjct: 267 YLQKVRAGKRNPAAAYEIALAR-------PREWRAGDRVTYYVSGTGKG 308
>gnl|CDD|99827 cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of
Escherichia coli DNA polymerase II and similar bacterial
family-B DNA polymerases. The 3'-5' exonuclease domain
of Escherichia coli DNA polymerase II (Pol II) and
similar bacterial proteins. Pol II is a family-B DNA
polymerase. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are clustered around the active site and are
involved in metal binding and catalysis. The exonuclease
domain has a fundamental role in the proofreading
activity of polII. It contains a beta hairpin structure
that plays an important role in active site switching in
the event of a nucleotide misincorporation. Pol II is
involved in a variety of cellular activities, such as
the repair of DNA damaged by UV irradiation or
oxidation. It plays a pivotal role in
replication-restart, a process that bypasses DNA damage
in an error-free manner. Pol II is also involved in
lagging strand synthesis.
Length = 193
Score = 49.9 bits (120), Expect = 1e-06
Identities = 32/128 (25%), Positives = 53/128 (41%), Gaps = 14/128 (10%)
Query: 421 EEDRKVGIILIGQESELPEVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETL 480
E +V +++G + P + + ++EK L I Q+DPDI+IG+ +
Sbjct: 26 EGQERV--LMVGDPED-----DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINF 78
Query: 481 SWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVN 540
L R GL L L R S + L +PGR+V++ L+
Sbjct: 79 DLRLLQRRAEAHGLPLR--LGRGGSPLNWRQSGKPGQGF-LSLPGRVVLDGIDALKT--- 132
Query: 541 LQSYTFEN 548
+Y FE+
Sbjct: 133 -ATYHFES 139
>gnl|CDD|99824 cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease domain of
Sulfurisphaera ohwakuensis DNA polymerase B3 and similar
archaeal family-B DNA polymerases. The 3'-5'
exonuclease domain of archaeal proteins with similarity
to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a
family-B DNA polymerase. Family-B DNA polymerases
contain an N-terminal DEDDy DnaQ-like exonuclease domain
in the same polypeptide chain as the polymerase domain,
similar to family-A DNA polymerases. B3 exhibits both
polymerase and 3'-5' exonuclease activities. This
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, with a specific YX(3)D pattern
at ExoIII. These motifs are clustered around the active
site and are involved in metal binding and catalysis.
The exonuclease domain of family B polymerases also
contains a beta hairpin structure that plays an
important role in active site switching in the event of
nucleotide misincorporation. Archaeal proteins that are
involved in DNA replication are similar to those from
eukaryotes. Some archaea possess multiple family-B DNA
polymerases. B3 is mainly found in crenarchaea.
Phylogenetic analyses of eubacterial, archaeal, and
eukaryotic family B-DNA polymerases support independent
gene duplications during the evolution of archaeal and
eukaryotic family-B DNA polymerases.
Length = 188
Score = 49.6 bits (119), Expect = 2e-06
Identities = 17/45 (37%), Positives = 31/45 (68%)
Query: 452 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNL 496
+++++ F++ V+++DPDI++GY W YL+ER VLG+ L
Sbjct: 47 DDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL 91
>gnl|CDD|99819 cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' exonuclease
domain of eukaryotic DNA polymerase alpha, a family-B
DNA polymerase. The 3'-5' exonuclease domain of
eukaryotic DNA polymerase alpha. DNA polymerase alpha
is a family-B DNA polymerase with a catalytic subunit
that contains a DnaQ-like 3'-5' exonuclease domain. It
is one of the three DNA-dependent type B DNA polymerases
(delta and epsilon are the other two) that have been
identified as essential for nuclear DNA replication in
eukaryotes. DNA polymerase alpha is almost exclusively
required for the initiation of DNA replication and the
priming of Okazaki fragments during elongation. It
associates with DNA primase and is the only enzyme able
to start DNA synthesis de novo. The catalytic subunit
contains both polymerase and 3'-5' exonuclease domains,
but only exhibits polymerase activity. The 3'-5'
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, without the four conserved
acidic residues that are crucial for metal binding and
catalysis. This explains why in most organisms, that no
specific repair role, other than check point control,
has been assigned to this enzyme. The exonuclease domain
may have a structural role.
Length = 234
Score = 45.7 bits (109), Expect = 5e-05
Identities = 21/107 (19%), Positives = 44/107 (41%)
Query: 448 HFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVE 507
NE+ L + F+ +++ DPD+L+G+++E LL R L + + R+
Sbjct: 77 RIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSV 136
Query: 508 KRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL 554
+ GR++ + + + + +SY + VL
Sbjct: 137 WPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYDLTELSQQVL 183
>gnl|CDD|99822 cd05779, DNA_polB_epsilon_exo, DEDDy 3'-5' exonuclease domain of
eukaryotic DNA polymerase epsilon, a family-B DNA
polymerase. The 3'-5' exonuclease domain of eukaryotic
DNA polymerase epsilon. DNA polymerase epsilon is a
family-B DNA polymerase with a catalytic subunit that
contains a DEDDy-type DnaQ-like 3'-5' exonuclease
domain. It is one of the three DNA-dependent type B DNA
polymerases (alpha and delta are the other two) that
have been identified as essential for nuclear DNA
replication in eukaryotes. DNA polymerase epsilon plays
a role in elongating the leading strand during DNA
replication. It is also involved in DNA repair. The
catalytic subunit contains both polymerase and 3'-5'
exonuclease activities. The N-terminal exonuclease
domain contains three sequence motifs termed ExoI, ExoII
and ExoIII, with a specific YX(3)D pattern at ExoIII.
These motifs are clustered around the active site and
are involved in metal binding and catalysis. DNA
polymerase epsilon also carries a unique large
C-terminal domain with an unknown function. Phylogenetic
analyses indicate that it is orthologous to the archaeal
DNA polymerase B3 rather than to the eukaryotic alpha,
delta, or zeta polymerases. The exonuclease domain of
family-B polymerases contains a beta hairpin structure
that plays an important role in active site switching in
the event of nucleotide misincorporation.
Length = 204
Score = 39.6 bits (93), Expect = 0.004
Identities = 32/128 (25%), Positives = 56/128 (43%), Gaps = 20/128 (15%)
Query: 384 LTVLAVEIHAISRALLKPDPAYDEVKAIFY------YLYTCPPEEDRKVGIILIGQESEL 437
VLA +I L PD D++ I Y YL +R++ + ++ E
Sbjct: 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIV-----NREI----VSEDIED 52
Query: 438 PEVRTKP-IQMHF----VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVL 492
E KP + F +EK L F E++R+ P I++ Y + W ++ R +
Sbjct: 53 FEYTPKPEYEGPFKVFNEPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH 112
Query: 493 GLNLNQEL 500
GL++ +E+
Sbjct: 113 GLSMEEEI 120
>gnl|CDD|99828 cd05785, DNA_polB_like2_exo, Uncharacterized bacterial subgroup of
the DEDDy 3'-5' exonuclease domain of family-B DNA
polymerases. A subfamily of the 3'-5' exonuclease
domain of family-B DNA polymerases. This subfamily is
composed of uncharacterized bacterial family-B DNA
polymerases. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are involved in metal binding and catalysis. The
exonuclease domain of family-B DNA polymerases has a
fundamental role in proofreading activity. It contains a
beta hairpin structure that plays an important role in
active site switching in the event of a nucleotide
misincorporation. Family-B DNA polymerases are
predominantly involved in DNA replication and DNA
repair.
Length = 207
Score = 35.5 bits (82), Expect = 0.10
Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 11/101 (10%)
Query: 453 EKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSS 512
EKEL + +R+ DPD++ G+ I YL R G+ L + R + ++ S
Sbjct: 58 EKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPL--AIGRDGSIPRQRPS 115
Query: 513 RDEVKN-----TQLQMPGRIVINLWRL-LRHEV---NLQSY 544
R + +PGR VI+ + L +V +L SY
Sbjct: 116 RFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSY 156
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 34.4 bits (79), Expect = 0.52
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 524 PGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWK--LLTC-WWEH 572
G + LL +EN+ + HE H W L+T WW+
Sbjct: 282 WGLVTFREKYLLADPETATDSDYENVEEVIAHELA--HQWFGNLVTMKWWDD 331
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 33.4 bits (76), Expect = 0.87
Identities = 36/146 (24%), Positives = 53/146 (36%), Gaps = 12/146 (8%)
Query: 205 AKPPTSKSVTRWLERKEAFKRNAGTRSSVSSRVEQKILENEQCSQKGIVDVKCFEESSAL 264
KP S++ +K+ K + SS R + E ++ K K E +
Sbjct: 721 PKPAEKDSLSA--PKKQTSKTASEKSSSKGKRKHKNDEEADKIESK-----KQRLEEKSS 773
Query: 265 ERSMKPDDRPSPTRKNKSTRSSFDS---DMFPSSSSRESNQSPPNKDSIHEAEITHPDCS 321
S + NK +R S + +M PS SS S+ SP + + D S
Sbjct: 774 SCSPSSSSSHHHSSSNKESRKSSRNKEEEMLPSPSSPLSSSSPKPEHPSRKRPRRQEDTS 833
Query: 322 KSSQIDFNPDLFKSFIRKQLETPKRR 347
SS F+ KS K T K R
Sbjct: 834 SSSG-PFSASSTKS-SSKSSSTSKHR 857
>gnl|CDD|133872 PHA00380, PHA00380, tail protein.
Length = 599
Score = 32.2 bits (73), Expect = 2.0
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 117 TDVTNILSQEPFYSNFKDITR--TEITNKFVHLEAAPVALLEEHRCLFSGLSEWRQRVCL 174
TDV I+S PF +++K TR T ++V+ + +E +F+G E R V +
Sbjct: 9 TDVR-IMSGVPFSNDYKH-TRWFTSKAEQYVYFNNKTR-VHQEAEVVFTGSKENRPYVTV 65
Query: 175 EVTGDATRNVNDIM 188
+V D + N M
Sbjct: 66 DVPIDDLYDANYFM 79
>gnl|CDD|220549 pfam10069, DICT, Sensory domain found in DIguanylate Cyclases &
Two-component systems. DICT is a sensory domain found
associated with GGDEF, EAL, HD-GYP STAS, and two
component systems. It assumes an alpha+beta fold with a
4-stranded beta-sheet and might have a role in light
response.
Length = 125
Score = 29.9 bits (68), Expect = 3.4
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 43 MISSSESYLFTQNKSYDSPTIVAKQTLLPLSGELEKQIISAKSSST 88
S Q SPT +K TLL LS +E + +++ S T
Sbjct: 2 NDPESPLLSLLQLLPGTSPTSYSKSTLLALSRAIEDRALASGISGT 47
>gnl|CDD|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal
transduction histidine kinase) [Signal transduction
mechanisms].
Length = 750
Score = 30.9 bits (70), Expect = 4.7
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 12/92 (13%)
Query: 437 LPEVRTKPIQMHFVSNEKELFSIFIENVRQWD----PDILIGYEIETLSWGYLLERGYVL 492
LP V Q+ ++F I N ++ PDI I E + W + + +
Sbjct: 627 LPVVAADATQL------GQVFQNLIANAIKFGGPENPDIEISAERQEDEWTFSVRDNGI- 679
Query: 493 GLNLNQELSRITEVEKRNSSRDEVKNTQLQMP 524
G++ RI + +R SRDE T L +
Sbjct: 680 GID-PAYFERIFVIFQRLHSRDEYLGTGLGLA 710
>gnl|CDD|236308 PRK08594, PRK08594, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 257
Score = 30.5 bits (69), Expect = 4.9
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 17/65 (26%)
Query: 31 ANKMEGRAENEHMISSSESYLFTQNKSYDSPTIVAKQTLLPLSGELEKQIISAKSSSTEG 90
ANK + E + +S + +L QN S S T VA+ AK TEG
Sbjct: 98 ANKED--LRGEFLETSRDGFLLAQNISAYSLTAVAR---------------EAKKLMTEG 140
Query: 91 SSVVT 95
S+VT
Sbjct: 141 GSIVT 145
>gnl|CDD|183445 PRK12330, PRK12330, oxaloacetate decarboxylase; Provisional.
Length = 499
Score = 30.9 bits (70), Expect = 5.0
Identities = 12/15 (80%), Positives = 12/15 (80%)
Query: 397 ALLKPDPAYDEVKAI 411
ALLKP PAYD VK I
Sbjct: 179 ALLKPQPAYDIVKGI 193
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 30.9 bits (70), Expect = 5.2
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 11/54 (20%)
Query: 274 PSPTRKNKSTRSSFDSDMFPSSSSRESNQSPPNKDSIHEAEITHPDCSKSSQID 327
P P K + S + + K++IH+ + P SKS+ ID
Sbjct: 391 PQPQPVAKLEQGSLLT----------AASPQTKKETIHQEVPS-PSLSKSAAID 433
>gnl|CDD|165176 PHA02831, PHA02831, EEV host range protein; Provisional.
Length = 268
Score = 30.3 bits (68), Expect = 5.6
Identities = 27/102 (26%), Positives = 45/102 (44%), Gaps = 17/102 (16%)
Query: 1023 PGLPLIKLVKSPYELLQDSSLR-LNSEYYITRVIIPPLERCFLLLGTPV------LPWYK 1075
P P+ KL++ Y LQ+ L ++Y ++ ++ F+LLG+ V WY
Sbjct: 131 PKYPVCKLIRCKYPALQNGFLNVFEKKFYYGDIVNFKCKKGFILLGSSVSTCDINSIWYP 190
Query: 1076 NLPR----KLH-----VYLPSVLNERKKKSTISQYFASVNCV 1108
+P+ K+H YL L+E ST + Y N +
Sbjct: 191 GIPKCVKDKVHNEIQPNYLFDDLDEDFNNST-TNYNMQQNII 231
>gnl|CDD|239586 cd03509, DesA_FADS-like, Fatty acid desaturase protein family
subgroup, a delta-12 acyl-lipid desaturase-like,
DesA-like, yet uncharacterized subgroup of membrane
fatty acid desaturase proteins found in alpha-, beta-,
and gamma-proteobacteria. Sequences of this domain
family appear to be structurally related to membrane
fatty acid desaturases and alkane hydroxylases. They all
share in common extensive hydrophobic regions that would
be capable of spanning the membrane bilayer at least
twice. Comparison of these sequences also reveals three
regions of conserved histidine cluster motifs that
contain eight histidine residues: HXXXH, HXXHH, and
HXXHH. These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within homologs, stearoyl
CoA desaturase and alkane hydroxylase.
Length = 288
Score = 30.0 bits (68), Expect = 6.7
Identities = 27/90 (30%), Positives = 32/90 (35%), Gaps = 29/90 (32%)
Query: 482 WGYLLERGYVLGLNLNQELSRI-TEVEKRNSSRDEVKNTQLQMPGRIVIN----LWRLLR 536
W YLL Y L++I T +E R R GR VIN RLL
Sbjct: 181 WAYLLAVYYPALS-----LAKIRTFLEHRAHERPR---------GRTVINEAGGPLRLL- 225
Query: 537 HEVNLQSYTFENIMYHVLHERIPLHSWKLL 566
F N HV+H +P W L
Sbjct: 226 ---------FLNNNLHVVHHDLPTLPWYDL 246
>gnl|CDD|204076 pfam08824, Serine_rich, Serine rich protein interaction domain.
This is a serine rich domain that is found in the
docking protein p130(cas) (Crk-associated substrate).
This domain folds into a four helix bundle which is
associated with protein-protein interactions.
Length = 159
Score = 29.3 bits (66), Expect = 8.0
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 15/83 (18%)
Query: 716 IDLNVSIRSLKKLQQKLTISPSGV-AFVDKSIRCGILPKMLQEILDTRLM---VKQSMKE 771
+DL+ ++ +L +LQQK+ S S + +FV + R + I D R V++S++E
Sbjct: 1 LDLDSALETLARLQQKVESSVSSLMSFVSPNWRT--REHLEANINDIRRAVDRVEESLRE 58
Query: 772 Y-------KSNA--ALQRVLHAR 785
+ NA R LHA+
Sbjct: 59 FLEFARGAVGNATQLTDRNLHAK 81
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 30.0 bits (67), Expect = 8.1
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 265 ERSMKPDDRPSPTRKNKSTRSSFDSDMF----PSSSSRESNQSPPNKD 308
+ + + +P P+ +N+S R+ S++ P +++R SPP D
Sbjct: 194 DAAAQRPPQPGPSGQNRSPRTPTLSNVRVLDAPVATNRGEAPSPPRTD 241
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
0.319 0.133 0.393
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 59,627,528
Number of extensions: 5839776
Number of successful extensions: 4421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4322
Number of HSP's successfully gapped: 57
Length of query: 1200
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1092
Effective length of database: 6,147,370
Effective search space: 6712928040
Effective search space used: 6712928040
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 (21.7 bits)
S2: 65 (29.0 bits)