RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5925
(696 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 = 250 bits (641), Expect = 8e-76
Identities = 92/153 (60%), Positives = 117/153 (76%), Gaps = 2/153 (1%)
Query: 525 GSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQS 584
GSQFRVES++LRL++ N++ SPS +Q A RA E LPL++EPES Y+DP+IVLDFQS
Sbjct: 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQS 60
Query: 585 LYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQ--NLTISPSGVA 642
LYPS++IAYNYC+STCLGRVE L F F + L + L L ++TISP+GV
Sbjct: 61 LYPSIMIAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLPPPPLDLLLLKDDVTISPNGVM 120
Query: 643 FVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 675
FV KS+R GILPKML+EILDTR+MVK++MK+YK
Sbjct: 121 FVKKSVRKGILPKMLEEILDTRIMVKKAMKKYK 153
Score = 95.4 bits (238), Expect = 8e-21
Identities = 44/99 (44%), Positives = 58/99 (58%), Gaps = 9/99 (9%)
Query: 70 ESSLERSMKPDD--RPSPTRKNKSTRSSFDS---DMFPSSSSRDRLYTDPIIVLDFQSLY 124
ES L R KP++ PSP+R+ + + + + M P S Y+DP+IVLDFQSLY
Sbjct: 7 ESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPES----GFYSDPVIVLDFQSLY 62
Query: 125 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIASRESNQ 163
PS++IAYNYC+STCLGRVE L F F +
Sbjct: 63 PSIMIAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLPPP 101
>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 = 205 bits (525), Expect = 7e-62
Identities = 94/265 (35%), Positives = 138/265 (52%), Gaps = 45/265 (16%)
Query: 244 YLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLY--TCPPEEDR-KVGIILIGQESELPE 300
+LT+L++E+H +R L PDP +D + AIFY + P D KVG+I+
Sbjct: 3 HLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVII--------- 53
Query: 301 VRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFS 360
V K S L G +E V +E ELF
Sbjct: 54 ----------VDELKSNASNGRIR------SGLSGIPVE-----------VVESELELFE 86
Query: 361 IFIENVRQWDPDILIGYEIETLSWGYLLERGYVLG-LNLNQELSRI--TEVEKRNSSRDE 417
I+ VR++DPDIL GYEI+ SWGYL+ER LG +L E+SR+ K DE
Sbjct: 87 ELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDE 146
Query: 418 VKNTQ---LQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEH 474
T +++ GR ++N+WRL+R E+ L +YT EN++YHVLH+RIPL+S K LT W++
Sbjct: 147 WGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKS 206
Query: 475 RTHLYKWMTVEHYLIRVTGIIRLIE 499
+ +W +E+YL RV + +++
Sbjct: 207 GSASERWRVLEYYLKRVRLNLEILD 231
>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 = 182 bits (463), Expect = 2e-50
Identities = 103/359 (28%), Positives = 178/359 (49%), Gaps = 29/359 (8%)
Query: 348 ERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSR--- 404
E + +NEKEL F E ++++DPDI+ G+ I Y++ R L ++ ++ R
Sbjct: 62 EVYEFNNEKELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKI 121
Query: 405 ---ITEVEKRNSSRD-EVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLH-ER 459
I + S+ + + ++ + GR+VI+L+RL ++++ L SY + + ++L E+
Sbjct: 122 GLRIPNKKPLFGSKSFGLSDIKVYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEK 181
Query: 460 IPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFY 519
L + + + + + + + ++L +L+ I E+AR+ GI
Sbjct: 182 DDLPYKDIPELYNGNYEERDE--LLRYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPLR 239
Query: 520 EVLSRGSQFRVESIMLRLSRLNNFVAVSPSI----KQRAHMRAPESLP--LILEPESRLY 573
L GSQ RVES++LR ++ NN++ S + ++ +LEP+ Y
Sbjct: 240 RTLYYGSQIRVESLLLREAKKNNYILPSKELYDFKGSEPDLKKKVKYEGGKVLEPKKGFY 299
Query: 574 TDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQN 633
+P++VLDF SLYPS+IIA+N C+ST +G E V DL
Sbjct: 300 DNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGE--VVIKGDLIIPEDLLTIK--------- 348
Query: 634 LTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNLTMLNSMLLI 692
+ FV K+IR GILPK+L+++LD R +K+ MK+ K ES +L+S L
Sbjct: 349 -YEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEK-DESEELKKLLDSRQLA 405
Score = 52.9 bits (127), Expect = 3e-07
Identities = 20/34 (58%), Positives = 27/34 (79%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVE 143
Y +P++VLDF SLYPS+IIA+N C+ST +G E
Sbjct: 298 FYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGVGE 331
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 156 bits (395), Expect = 1e-39
Identities = 107/409 (26%), Positives = 172/409 (42%), Gaps = 65/409 (15%)
Query: 282 EEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETF 341
+ + L +E P +R + +E F + DP I+I Y IE
Sbjct: 135 DIGSIHSLFLEHREDVRPPLRVLAFDIE-TLSEPGKFPDGEK-----DPIIMISYAIEAE 188
Query: 342 SWGYLL---------ERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGY 392
+ V +E EL F+E +R++DPD+++GY + W YL ER
Sbjct: 189 GGLIEVFIYTSGEGFSVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAE 248
Query: 393 VLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRH-EVNLQSYTFENI 451
LG+ L L R + R Q+ GR+ I+L+ LR +NL+SY+ E +
Sbjct: 249 RLGIPL--RLGRD-----GSELRVRKSGFSSQV-GRLHIDLYPALRRRPLNLKSYSLEAV 300
Query: 452 MYHVLHER----IPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQ-LDFIGR 506
+L E IP S + + W + + Y + ++ I + +
Sbjct: 301 SEALLGEGKREDIPYDSMEEIWPDWADS-----KLRLLLYNLSDADLVLRILLKNELLPL 355
Query: 507 TSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLIL 566
E++R+ G+ +V GS RVE ++LR ++ + P+ ++R R L+L
Sbjct: 356 LIELSRVSGLPLDDVTRAGSGARVEGLLLREAKRRGELI--PNKEERPE-RKKYKGGLVL 412
Query: 567 EPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRS 626
EPE LY + ++VLDF SLYPS+II YN T +
Sbjct: 413 EPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDC--------------------- 450
Query: 627 LKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 675
+ SP GV G LP++L+E+LD R +K+ MK+ K
Sbjct: 451 ------SDDYSPPGVGHGFCKREKGFLPEILEELLDRRDEIKKKMKKEK 493
Score = 50.5 bits (121), Expect = 2e-06
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIASRE 160
LY + ++VLDF SLYPS+II YN T + S RE
Sbjct: 418 LYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDCSDDYSPPGVGHGFCKRE 467
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 151 bits (384), Expect = 6e-38
Identities = 96/334 (28%), Positives = 153/334 (45%), Gaps = 39/334 (11%)
Query: 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEV----- 408
EKEL + E V DPD L GY I YLL R L LN + L RI
Sbjct: 329 TEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIK 388
Query: 409 EKRNSSRD--EVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIP--LHS 464
+ + SS+ ++ ++ + GRI ++ L+R + L+SY+ + + L E+ +S
Sbjct: 389 DSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYS 448
Query: 465 W--KLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVL 522
L E R + + + L +RL+++L I EMAR+ G +L
Sbjct: 449 IISDLQNGSPETRRRIAVYCLKDAILP-----LRLLDKLLLIYNYVEMARVTGTPIGWLL 503
Query: 523 SRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDF 582
+RG Q +V S +LR + N+V + E +LEP+ Y +PI LDF
Sbjct: 504 TRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEG-ATVLEPKKGFYDEPIATLDF 562
Query: 583 QSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTI-SPSGV 641
SLYPS++IA+N C+ST + + ++ + +P+G
Sbjct: 563 ASLYPSIMIAHNLCYSTLVPPNDA---------------------NNYPEDTYVTTPTGD 601
Query: 642 AFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 675
FV K +R GILP +++E++ R K+ MK+ K
Sbjct: 602 KFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK 635
Score = 53.9 bits (130), Expect = 2e-07
Identities = 17/29 (58%), Positives = 23/29 (79%)
Query: 111 YTDPIIVLDFQSLYPSVIIAYNYCFSTCL 139
Y +PI LDF SLYPS++IA+N C+ST +
Sbjct: 553 YDEPIATLDFASLYPSIMIAHNLCYSTLV 581
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 104 bits (262), Expect = 4e-23
Identities = 87/375 (23%), Positives = 148/375 (39%), Gaps = 63/375 (16%)
Query: 311 VSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWD 370
SN+ EL+S +E Q P I++G + +L +V++EK L F + D
Sbjct: 164 TSNKGELYSIGLEGCGQ-RPVIMLG-PPNGEALDFL---EYVADEKALLEKFNAWFAEHD 218
Query: 371 PDILIGYEIETLSWGYLLERGYVLGLNLNQELSR-ITEVEKRNSSRDEVKNTQLQMPGRI 429
PD++IG+ + L ER G+ L L R +E+E R +PGR+
Sbjct: 219 PDVIIGWNVVQFDLRLLQERAERYGIPLR--LGRDGSELEWREHPFRSGYGF-ASVPGRL 275
Query: 430 VINLWRLLRHEV-NLQSYTFENIMYHVLHE----RIPLHSWKLLTCWWEHRTHLYKWMTV 484
V++ L+ S++ E + +L E P + + +
Sbjct: 276 VLDGIDALKSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPA-----L 330
Query: 485 EHYLIR----VTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRL 540
Y ++ VT I + L F+ E A + G+ V GS E + L +
Sbjct: 331 ARYNLKDCELVTRIFEKTKLLPFL---LERATVTGLPLDRV--GGSVAAFEHLYLPRAHR 385
Query: 541 NNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFS 598
+VA P++ + R E+ P +++ + LY D ++VLDF+SLYPS+I +N
Sbjct: 386 AGYVA--PNLGE----RPGEASPGGYVMDSKPGLY-DSVLVLDFKSLYPSIIRTFNIDP- 437
Query: 599 TCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQ 658
G VE L + G F S LP++++
Sbjct: 438 --DGLVEGLAQPPE---ESVA-----------------GFLGARF---SREKHFLPEIVE 472
Query: 659 EILDTRLMVKQSMKE 673
+ + R K+ M +
Sbjct: 473 RLWEGRDEAKREMNK 487
Score = 44.5 bits (106), Expect = 2e-04
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIAS 158
LY D ++VLDF+SLYPS+I +N G VE L +A
Sbjct: 413 LY-DSVLVLDFKSLYPSIIRTFNIDP---DGLVEGLAQPPE---ESVAG 454
>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 = 100 bits (252), Expect = 2e-22
Identities = 53/170 (31%), Positives = 79/170 (46%), Gaps = 20/170 (11%)
Query: 525 GSQFRVESIMLRLSRLNNFVAVSP---SIKQRAHMRAPESLP--LILEPESRLYTDPIIV 579
G Q RV S++LR ++ NF+ R E +LEP+ Y +P++V
Sbjct: 1 GQQIRVFSLLLREAKERNFILPDKFELRSLSRQVNIKKEGYQGATVLEPKKGFYNNPVLV 60
Query: 580 LDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPS 639
LDF SLYPS+I A+N C+ T L V+ + ++ L +
Sbjct: 61 LDFASLYPSIIQAHNLCYET-LVDVDA-------EAPKLAAERNLEVLHI-----VVGSL 107
Query: 640 GVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRNLTMLNSM 689
FV K +R GILP +L+++L R K+ MKE K E L T+L+
Sbjct: 108 RERFVKKGVRKGILPVLLRDLLAKRKEKKKLMKESKDPEEL--RTLLDKQ 155
Score = 58.1 bits (141), Expect = 7e-09
Identities = 16/28 (57%), Positives = 22/28 (78%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFST 137
Y +P++VLDF SLYPS+I A+N C+ T
Sbjct: 53 FYNNPVLVLDFASLYPSIIQAHNLCYET 80
>gnl|CDD|222444 pfam13901, DUF4206, Domain of unknown function (DUF4206). This is
a family of cysteine-rich proteins. Many members also
carry a pleckstrin-homology domain, pfam00169.
Length = 202
Score = 92.3 bits (230), Expect = 2e-21
Identities = 28/56 (50%), Positives = 39/56 (69%)
Query: 1 LCLARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQLPCKRCIRMRIRR 56
LC +GFICE C+++EVIFP+Q + RC CGA FH +C+ PC +C R+R R+
Sbjct: 147 LCTGKGFICEFCDNDEVIFPFQTDTTSRCEGCGAVFHKECYESSPCPKCARLRRRK 202
>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 = 90.1 bits (224), Expect = 1e-20
Identities = 38/148 (25%), Positives = 68/148 (45%), Gaps = 8/148 (5%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
++EKEL F + +R++DPDIL GY I+ YLL+R LG+ L + R + EK
Sbjct: 60 FADEKELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKS 119
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471
+ S + + + GR+V +L + + L+SYT + + +L E
Sbjct: 120 SGSTERIA-----VKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDG---EII 171
Query: 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIE 499
+ +E+ L ++++E
Sbjct: 172 EDAEWEEDPERLIEYNLKDAELTLQILE 199
>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 = 85.1 bits (211), Expect = 5e-18
Identities = 37/121 (30%), Positives = 53/121 (43%), Gaps = 27/121 (22%)
Query: 563 PLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNV 622
+ +P LY + +IVLDF+SLYPS+II YN +T +G E D G
Sbjct: 6 GYVFDPIPGLY-ENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVG------ 58
Query: 623 SIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKFSESLRN 682
F R G+LP++L+E+L+ R K+ MK K + R
Sbjct: 59 --------------------FRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERV 98
Query: 683 L 683
L
Sbjct: 99 L 99
Score = 58.5 bits (142), Expect = 4e-09
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 109 RLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFG 154
+ +IVLDF+SLYPS+II YN +T +G E D G
Sbjct: 13 PGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVG 58
>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 = 81.5 bits (202), Expect = 2e-16
Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 20/111 (18%)
Query: 565 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 624
++EP Y PI LDF SLYPS+++A+N C++T L +
Sbjct: 8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNT------------------A 49
Query: 625 RSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 675
+ L +P+G FV S+R G+LP++L+E+L R K+ +KE
Sbjct: 50 KKLPPED--YIKTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEET 98
Score = 54.2 bits (131), Expect = 1e-07
Identities = 16/29 (55%), Positives = 22/29 (75%)
Query: 111 YTDPIIVLDFQSLYPSVIIAYNYCFSTCL 139
Y PI LDF SLYPS+++A+N C++T L
Sbjct: 16 YDVPIATLDFASLYPSIMMAHNLCYTTLL 44
>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 = 72.2 bits (178), Expect = 2e-13
Identities = 31/110 (28%), Positives = 47/110 (42%), Gaps = 28/110 (25%)
Query: 564 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVS 623
L+LEP+ LY I++LDF SLYPS+I YN CF+T + P
Sbjct: 12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPP--------- 62
Query: 624 IRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKE 673
GILP++++++++ R VK+ MK
Sbjct: 63 -------------------LPPSDQEKGILPRIIRKLVERRRQVKKLMKS 93
Score = 54.5 bits (132), Expect = 9e-08
Identities = 18/43 (41%), Positives = 23/43 (53%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFP 152
LY I++LDF SLYPS+I YN CF+T + P
Sbjct: 20 LYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEEPP 62
>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 = 68.6 bits (168), Expect = 8e-13
Identities = 46/207 (22%), Positives = 77/207 (37%), Gaps = 38/207 (18%)
Query: 245 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTK 304
L VL+ +I S P+ D + I LY + + + + + +
Sbjct: 86 LRVLSFDIECTSLKGKFPENEKDPIIQISCMLYREGEPDPIEDKLFTLKSCALIEI---- 141
Query: 305 PIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIE 364
++ +EKEL F E +RQ+DPDI+ GY + F W Y+L R
Sbjct: 142 GGEVYIFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNR--------------- 186
Query: 365 NVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQ 424
+ L E G + V N SR++VK
Sbjct: 187 --------------AKILGLKMTPEYGVRSSKIGRLKRGGFPRVFSGNGSREKVK----- 227
Query: 425 MPGRIVINLWRLLRHEVNLQSYTFENI 451
+ GRI ++L+R+++ + L SY +
Sbjct: 228 ISGRIHLDLYRVIKRDSKLGSYKLNAV 254
>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 = 70.1 bits (171), Expect = 3e-12
Identities = 71/343 (20%), Positives = 139/343 (40%), Gaps = 58/343 (16%)
Query: 346 LLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRI 405
L+E + E+ L F+ V++ DPD ++G++ + + L R L + ++ R+
Sbjct: 577 LVEDL--ATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRL 634
Query: 406 TEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLH-ERIPLHS 464
K E + GR++ ++ + + +SY ++ +L ER +
Sbjct: 635 RRSPKFGRRFGE------RTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPI 688
Query: 465 WKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSR 524
+ + E + Y +EH I++++ +L+ + ++ + G L
Sbjct: 689 DNINNMYSESSSLTY---LLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMG 745
Query: 525 GSQFRVESIMLRLSRLNNFVAVSPSIKQRAH---------------MRAPESLPLILEPE 569
G R E ++L NN++ I ++ +A + L+LEP+
Sbjct: 746 GRSERNEFLLLHAFYENNYIVPDKQIFRKQQKLGDEDEEIDGYKKGKKAAYAGGLVLEPK 805
Query: 570 SRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKK 629
LY ++++DF SLYPS+I +N CF+T V+ D P
Sbjct: 806 VGLYDKYVLLMDFNSLYPSIIQEFNICFTT----VQQKVDEDELP--------------- 846
Query: 630 LQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMK 672
D + GILP+ L+++++ R VK+ MK
Sbjct: 847 ------------ELPDSELEMGILPRELRKLVERRKEVKKLMK 877
Score = 36.6 bits (84), Expect = 0.051
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFST 137
LY ++++DF SLYPS+I +N CF+T
Sbjct: 808 LYDKYVLLMDFNSLYPSIIQEFNICFTT 835
>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 = 65.7 bits (161), Expect = 6e-12
Identities = 33/114 (28%), Positives = 56/114 (49%), Gaps = 11/114 (9%)
Query: 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNS 413
E+EL + + V++ DPDI+ GY I YLLER L LN L RI +++
Sbjct: 70 TEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRI--KNIKST 127
Query: 414 SRDEVK---------NTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHE 458
+D ++ + GRI +L ++++ + L+SY+ ++ H L E
Sbjct: 128 IKDTTFSSKQMGTRETKEINIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGE 181
>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 = 60.4 bits (147), Expect = 2e-10
Identities = 33/122 (27%), Positives = 56/122 (45%), Gaps = 21/122 (17%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
V EKE+ FIE V++ DPD++ Y + + YL +R LG+ L+ R
Sbjct: 53 VKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDL---------GR 103
Query: 412 NSSRDEVK----NTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL--------HER 459
+ S +++ N ++ GRI ++L+ + R +NL YT E + + E
Sbjct: 104 DGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEE 163
Query: 460 IP 461
I
Sbjct: 164 IA 165
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 58.2 bits (141), Expect = 1e-08
Identities = 76/403 (18%), Positives = 148/403 (36%), Gaps = 63/403 (15%)
Query: 295 ESELPEVRTKPIQMNFV----SNEKELFSTFIENVRQWD-------PDIL--IGYEIETF 341
E P+ +++ + S + + + +V +WD +IL + Y
Sbjct: 118 EDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVY----- 172
Query: 342 SWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVLGLNLNQ 400
F E+E+ +I + P I G+ +E Y++ R +LG +
Sbjct: 173 -------MPF-DTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAK 224
Query: 401 ELSRITEVEKRNSSRDE-VKNTQLQMPGRIVINLWRLLRH--EVNLQSYTFENIMYHVLH 457
LS +V++R + + G +++ L + N SY + I L
Sbjct: 225 RLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKFTFTNQPSYRLDYIAEVELG 284
Query: 458 ERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQ 517
++ +S + E Y +E+ +I V + RL ++ I MA I
Sbjct: 285 KKKLDYSDGPFKKFRETDHQKY----IEYNIIDVELVDRLDDKRKLIELVLSMAYYAKIN 340
Query: 518 FYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPI 577
F +V S + ++ S + + + ++H + + + EP Y +
Sbjct: 341 FEDVF---SPIKTWDAIIFNSLKEEKIVIP---ENKSHKKQKYAGAFVKEPVPGAY-RWV 393
Query: 578 IVLDFQSLYPSVIIAYNYCFSTCLG-----RVEHLGVSDSFPFGCIDLNVSIRSLKKLQQ 632
+ D SLYPS+I N T G V ++ + P + +
Sbjct: 394 VSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEY-INKTAPRPSDEYSC---------- 442
Query: 633 NLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 675
SP+G K IR G++P ++++ D R + K+ M +
Sbjct: 443 ----SPNG-WMYRKDIR-GVIPTEIKKVFDQRKIYKKKMLAAE 479
Score = 34.7 bits (80), Expect = 0.20
Identities = 28/115 (24%), Positives = 42/115 (36%), Gaps = 15/115 (13%)
Query: 235 EVTSHVENYYLTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQ 294
EVT+ EI AI+ YD + FY EE G +
Sbjct: 114 EVTAEDGFPDPEEAKYEIDAITH--------YDSIDDRFYVFDLGSVEEWDAKGDEV--- 162
Query: 295 ESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+ K + M F E+E+ +I + P I G+ +E F Y++ R
Sbjct: 163 ---PQEILDKVVYMPF-DTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINR 213
>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 = 50.8 bits (122), Expect = 4e-07
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 12/75 (16%)
Query: 329 DPDILIGY-----EIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLS 383
DP I+I ++E L +++++ F++ V+++DPDI++GY
Sbjct: 24 DPIIVISLATSNGDVEFILAEGL-------DDRKIIREFVKYVKEYDPDIIVGYNSNAFD 76
Query: 384 WGYLLERGYVLGLNL 398
W YL+ER VLG+ L
Sbjct: 77 WPYLVERARVLGVKL 91
Score = 47.3 bits (113), Expect = 5e-06
Identities = 14/37 (37%), Positives = 27/37 (72%)
Query: 313 NEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
+++++ F++ V+++DPDI++GY F W YL+ER
Sbjct: 47 DDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVER 83
>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 = 44.9 bits (107), Expect = 5e-05
Identities = 21/107 (19%), Positives = 44/107 (41%)
Query: 350 HFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVE 409
NE+ L + F+ +++ DPD+L+G+++E LL R L + + R+
Sbjct: 77 RIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSV 136
Query: 410 KRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL 456
+ GR++ + + + + +SY + VL
Sbjct: 137 WPKKKGGGKFGERELTAGRLLCDTYLSAKELIRCKSYDLTELSQQVL 183
Score = 36.8 bits (86), Expect = 0.019
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 310 FVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSI 361
NE+ L + F+ +++ DPD+L+G+++E F LL R I
Sbjct: 78 IFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRI 129
>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 = 45.0 bits (107), Expect = 8e-05
Identities = 18/31 (58%), Positives = 25/31 (80%), Gaps = 1/31 (3%)
Query: 564 LILEPESRLYTDPIIVLDFQSLYPSVIIAYN 594
++LEPE L+ + I+VLDF SLYPS++I YN
Sbjct: 8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN 37
Score = 38.5 bits (90), Expect = 0.010
Identities = 13/18 (72%), Positives = 16/18 (88%)
Query: 115 IIVLDFQSLYPSVIIAYN 132
I+VLDF SLYPS++I YN
Sbjct: 20 IVVLDFSSLYPSIMIKYN 37
>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 = 43.7 bits (104), Expect = 1e-04
Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 7/101 (6%)
Query: 350 HFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVE 409
+ ++EK L I Q+DPDI+IG+ + L R GL L L R
Sbjct: 46 EWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLR--LGRGGSPL 103
Query: 410 KRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFEN 450
S + L +PGR+V++ L+ +Y FE+
Sbjct: 104 NWRQSGKPGQGF-LSLPGRVVLDGIDALKT----ATYHFES 139
Score = 43.3 bits (103), Expect = 1e-04
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 282 EEDRKVGIILIGQESELPEVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETF 341
E +V +++G + P + + ++EK L I Q+DPDI+IG+ + F
Sbjct: 26 EGQERV--LMVGDPED-----DAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINF 78
Query: 342 SWGYLLER 349
L R
Sbjct: 79 DLRLLQRR 86
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed.
Length = 787
Score = 42.4 bits (100), Expect = 8e-04
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 516 IQFYEVLSRG--SQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLY 573
++++E RG ++ E I+ V IK + + L+ +P ++
Sbjct: 371 LEYWEHRKRGWLIPWK-EDILRLDHE----VYKKAIIKGKKYRGG-----LVFQPPPGIF 420
Query: 574 TDPIIVLDFQSLYPSVIIAYN 594
+ + VLDF SLYPS+I+ +N
Sbjct: 421 FN-VYVLDFASLYPSIIVKWN 440
Score = 33.5 bits (77), Expect = 0.41
Identities = 11/23 (47%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYN 132
++ + + VLDF SLYPS+I+ +N
Sbjct: 419 IFFN-VYVLDFASLYPSIIVKWN 440
>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 = 40.8 bits (96), Expect = 0.002
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 564 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFST 599
++LEP ++ + ++VLDF SLYPS+I +N + T
Sbjct: 17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET 51
Score = 35.8 bits (83), Expect = 0.069
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFST 137
++VLDF SLYPS+I +N + T
Sbjct: 29 VVVLDFASLYPSIIKVWNLSYET 51
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 38.8 bits (91), Expect = 0.010
Identities = 35/134 (26%), Positives = 65/134 (48%), Gaps = 17/134 (12%)
Query: 565 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 624
+ P+ +++ + +++ D+ SLYP+V I N T +G V V+D+ I+ +
Sbjct: 535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVV----VNDNRLEAEIN-KQEL 589
Query: 625 RSLKKLQQNLTI-----SP---SGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKF 676
R + + + SP S +A D+ I GI+PK+L+ L+ R K+ +KE
Sbjct: 590 RRKYPYPRYIYVHCEPRSPDLVSEIAVFDRRIE-GIIPKLLKTFLEERARYKKLLKE--- 645
Query: 677 SESLRNLTMLNSML 690
+ S + +SM
Sbjct: 646 ATSSVEKAIYDSMQ 659
Score = 30.8 bits (70), Expect = 3.0
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 107 RDRLYTDPIIVLDFQSLYPSVIIAYN 132
+ +++ + +++ D+ SLYP+V I N
Sbjct: 539 KQKMFDNNVLIFDYNSLYPNVCIFGN 564
>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 = 35.7 bits (83), Expect = 0.065
Identities = 26/99 (26%), Positives = 39/99 (39%), Gaps = 26/99 (26%)
Query: 572 LYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQ 631
LY + ++VLDF+SLYPS+I + LG +E L D
Sbjct: 15 LYKN-VLVLDFKSLYPSIIRTFLI---DPLGLIEGLKAPDP------------------- 51
Query: 632 QNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQS 670
++L G F S ILP ++ + R K+
Sbjct: 52 EDLIPGFLGARF---SREKHILPDLIARLWAARDEAKRE 87
Score = 34.6 bits (80), Expect = 0.15
Identities = 13/24 (54%), Positives = 19/24 (79%), Gaps = 1/24 (4%)
Query: 105 SSRDRLYTDPIIVLDFQSLYPSVI 128
S+ LY + ++VLDF+SLYPS+I
Sbjct: 10 DSKPGLYKN-VLVLDFKSLYPSII 32
>gnl|CDD|215738 pfam00130, C1_1, Phorbol esters/diacylglycerol binding domain (C1
domain). This domain is also known as the Protein
kinase C conserved region 1 (C1) domain.
Length = 53
Score = 31.7 bits (72), Expect = 0.094
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 9 CELCNSEEVIFPWQLSSVH-RCNQCGACFHTKCHSQLP 45
C+ C F W L +C+ CG H +CHS +P
Sbjct: 14 CDHCGE----FLWGLGKQGLKCSWCGLNVHKRCHSLVP 47
>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 = 35.0 bits (81), Expect = 0.13
Identities = 28/110 (25%), Positives = 46/110 (41%), Gaps = 29/110 (26%)
Query: 564 LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVS 623
L+ +PE LY + + +DF S+YPS+I+ YN T ++ + +
Sbjct: 9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPET---------INCRCCECRDHVYLG 58
Query: 624 IRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKE 673
R K R G LP++L+ +L+ RL K+ KE
Sbjct: 59 HRICLK-------------------RRGFLPEVLEPLLERRLEYKRLKKE 89
Score = 29.6 bits (67), Expect = 5.2
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 118 LDFQSLYPSVIIAYN 132
+DF S+YPS+I+ YN
Sbjct: 24 IDFSSMYPSIIVKYN 38
>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 = 34.3 bits (79), Expect = 0.14
Identities = 32/127 (25%), Positives = 53/127 (41%), Gaps = 13/127 (10%)
Query: 329 DPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLL 388
D I++ W +L + EKEL + +R+ DPD++ G+ I YL
Sbjct: 34 DRIIIVALRDNR-GWEEVLHAEDAA-EKELLEELVAIIRERDPDVIEGHNIFRFDLPYLR 91
Query: 389 ERGYVLGLNLNQELSRITEVEKRNSSRDEVKN-----TQLQMPGRIVINLWRL-LRHEV- 441
R G+ L + R + ++ SR + +PGR VI+ + L +V
Sbjct: 92 RRCRRHGVPL--AIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVS 149
Query: 442 --NLQSY 446
+L SY
Sbjct: 150 SRDLPSY 156
Score = 30.5 bits (69), Expect = 2.2
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 314 EKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
EKEL + +R+ DPD++ G+ I F YL R
Sbjct: 58 EKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRR 93
>gnl|CDD|197519 smart00109, C1, Protein kinase C conserved region 1 (C1) domains
(Cysteine-rich domains). Some bind phorbol esters and
diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Length = 50
Score = 30.5 bits (69), Expect = 0.22
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 2 CLARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQLP 45
+ C +C I+ + RC++C H KC ++P
Sbjct: 7 TFTKPTFCCVCRKS--IWGSFKQGL-RCSECKVKCHKKCADKVP 47
>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 = 33.0 bits (76), Expect = 0.29
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQEL 402
+EK L F E++R+ P I++ Y + W ++ R + GL++ +E+
Sbjct: 72 DEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEI 120
Score = 33.0 bits (76), Expect = 0.30
Identities = 34/128 (26%), Positives = 56/128 (43%), Gaps = 23/128 (17%)
Query: 245 LTVLAVEIHAISRALLKPDPAYDEVKAIFY------YLYTCPPEEDRKVGIILIGQESEL 298
VLA +I L PD D++ I Y YL +R++ + ++ E
Sbjct: 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIV-----NREI----VSEDIED 52
Query: 299 PEVRTKP-IQMNF----VSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER---H 350
E KP + F +EK L F E++R+ P I++ Y + F W ++ R H
Sbjct: 53 FEYTPKPEYEGPFKVFNEPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIH 112
Query: 351 FVSNEKEL 358
+S E+E+
Sbjct: 113 GLSMEEEI 120
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 34.0 bits (78), Expect = 0.31
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 426 PGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWK--LLTC-WWEH 474
G + LL +EN+ + HE H W L+T WW+
Sbjct: 282 WGLVTFREKYLLADPETATDSDYENVEEVIAHELA--HQWFGNLVTMKWWDD 331
>gnl|CDD|237996 cd00029, C1, Protein kinase C conserved region 1 (C1) .
Cysteine-rich zinc binding domain. Some members of this
domain family bind phorbol esters and diacylglycerol,
some are reported to bind RasGTP. May occur in tandem
arrangement. Diacylglycerol (DAG) is a second
messenger, released by activation of Phospholipase D.
Phorbol Esters (PE) can act as analogues of DAG and
mimic its downstream effects in, for example, tumor
promotion. Protein Kinases C are activated by DAG/PE,
this activation is mediated by their N-terminal
conserved region (C1). DAG/PE binding may be
phospholipid dependent. C1 domains may also mediate
DAG/PE signals in chimaerins (a family of Rac GTPase
activating proteins), RasGRPs (exchange factors for
Ras/Rap1), and Munc13 isoforms (scaffolding proteins
involved in exocytosis).
Length = 50
Score = 28.6 bits (64), Expect = 1.2
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 5 RGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHSQLP 45
+ C++C Q RC+ C H KC ++P
Sbjct: 10 KPTFCDVCRKSIWGLFKQ---GLRCSWCKVKCHKKCADKVP 47
>gnl|CDD|211404 cd11550, Serine_rich_NEDD9, Serine rich Four helix bundle domain of
CAS (Crk-Associated Substrate) scaffolding protein,
Neural precursor cell Expressed, Developmentally
Down-regulated 9; a protein interaction module. NEDD9
is also called human enhancer of filamentation 1 (HEF1)
or CAS-L (Crk-associated substrate in lymphocyte). It
was first described as a gene predominantly expressed in
early embryonic brain, and was also isolated from a
screen of human proteins that regulate filamentous
budding in yeast, and as a tyrosine phosphorylated
protein in lymphocytes. It promotes metastasis in
different solid tumors. NEDD9 localizes in focal
adhesions and associates with FAK and Abl kinase. It
also interacts with SMAD3 and the proteasomal machinery
which allows its rapid turnover; these interactions are
not shared by other CAS proteins. CAS proteins function
as molecular scaffolds to regulate protein complexes
that are involved in many cellular processes. They share
a common domain structure containing protein interaction
modules that enable their scaffolding function,
including an N-terminal SH3 domain, an unstructured
substrate domain that contains many YxxP motifs, a
serine-rich four-helix bundle, and a FAT-like C-terminal
domain. CAS proteins associate with the 14-3-3 family;
this interaction is regulated by integrin-mediated cell
adhesion. The serine rich four helix bundle domain of
BCAR1, another CAS protein, has been shown to bind
14-3-3 in a phosphorylation-dependent manner. This
domain is structurally similar to other helical bundles
found in cell adhesion components such as alpha-catenin,
vinculin, and FAK, and may bind other proteins in
addition to the 14-3-3 family.
Length = 162
Score = 30.2 bits (68), Expect = 1.8
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 618 IDLNVSIRSLKKLQQNLTISPSGV-AFVDKSIRC-GILPKMLQEILDTRLMVKQSMKEY 674
+D + +I L +LQQ + S S + A V R + + + EI V+ S+ EY
Sbjct: 4 LDPDTAIERLYRLQQAVESSVSNLMALVSPDWRTYSFMERHINEIRTAVDRVELSLGEY 62
>gnl|CDD|183445 PRK12330, PRK12330, oxaloacetate decarboxylase; Provisional.
Length = 499
Score = 30.9 bits (70), Expect = 2.3
Identities = 12/15 (80%), Positives = 12/15 (80%)
Query: 258 ALLKPDPAYDEVKAI 272
ALLKP PAYD VK I
Sbjct: 179 ALLKPQPAYDIVKGI 193
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 27.5 bits (61), Expect = 2.8
Identities = 8/39 (20%), Positives = 12/39 (30%), Gaps = 13/39 (33%)
Query: 8 ICELCNS----EEVIFPWQLSSVHRCNQCGACFHTKCHS 42
C +C E++ C+ C FH C
Sbjct: 1 YCAVCGKVDDDGELLL---------CDGCDRWFHLACLG 30
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet
known if PHD fingers have a common molecular function.
Several reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is
a ubiquitin ligase have been refuted as these domains
were RING fingers misidentified as PHD fingers.
Length = 47
Score = 27.2 bits (60), Expect = 3.3
Identities = 6/35 (17%), Positives = 12/35 (34%), Gaps = 5/35 (14%)
Query: 8 ICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCHS 42
C +C + + +C+ C +H C
Sbjct: 1 YCSVCGKPDD-----GGELLQCDGCDRWYHQTCLG 30
>gnl|CDD|238567 cd01147, HemV-2, Metal binding protein HemV-2. These proteins are
predicted to function as initial receptors in ABC
transport of metal ions. They belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
A typical TroA protein is comprised of two globular
subdomains connected by a single helix and can bind the
metal ion in the cleft between these domains. In
addition, these proteins sometimes have a low complexity
region containing a metal-binding histidine-rich motif
(repetitive HDH sequence).
Length = 262
Score = 30.0 bits (68), Expect = 4.0
Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 4/50 (8%)
Query: 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELS 403
L + E + W+PD++ YL GY Q L
Sbjct: 196 GGGGLKEVSPEQILLWNPDVI----FLDTGSFYLSLEGYAKNRPFWQSLK 241
>gnl|CDD|220784 pfam10497, zf-4CXXC_R1, Zinc-finger domain of monoamine-oxidase A
repressor R1. R1 is a transcription factor repressor
that inhibits monoamine oxidase A gene expression. This
domain is a four-CXXC zinc finger putative DNA-binding
domain found at the C-terminal end of R1. The domain
carries 12 cysteines of which four pairs are of the
CXXC type.
Length = 105
Score = 28.2 bits (63), Expect = 5.7
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 27 HRCNQCGACFHTKCHSQLPCKRCIRMRIR 55
H+C Q T C + K C +R +
Sbjct: 11 HQCRQKTLDLKTSCKDKKKGKECHGVRGQ 39
>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 = 28.5 bits (64), Expect = 7.3
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 618 IDLNVSIRSLKKLQQNLTISPSGV-AFVDKSIRCGILPKMLQEILDTRLM---VKQSMKE 673
+DL+ ++ +L +LQQ + S S + +FV + R + I D R V++S++E
Sbjct: 1 LDLDSALETLARLQQKVESSVSSLMSFVSPNWRT--REHLEANINDIRRAVDRVEESLRE 58
Query: 674 Y-KFSESLR 681
+ +F+
Sbjct: 59 FLEFARGAV 67
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
0.323 0.138 0.422
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: 35,832,173
Number of extensions: 3567800
Number of successful extensions: 2703
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2668
Number of HSP's successfully gapped: 84
Length of query: 696
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 592
Effective length of database: 6,324,786
Effective search space: 3744273312
Effective search space used: 3744273312
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 62 (27.9 bits)