RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12449
(102 letters)
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 98.6 bits (246), Expect = 1e-25
Identities = 33/48 (68%), Positives = 40/48 (83%)
Query: 51 QLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFG 98
QLWTQCQ CQGSLH++VICT+RDCPIFY RKKVQ +L +++ RFG
Sbjct: 1004 QLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051
Score = 80.5 bits (199), Expect = 4e-19
Identities = 32/45 (71%), Positives = 37/45 (82%), Gaps = 3/45 (6%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQV-GKLPC 50
KE+K+ D KKVL+GRQLALKISANSVYG+TGAQV G+LPC
Sbjct: 629 KEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPC 671
Score = 33.1 bits (76), Expect = 0.014
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 9/37 (24%)
Query: 1 MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSV 37
MVKFGT +++EAM L G++ A +IS +
Sbjct: 718 MVKFGTDDIQEAMDL---------GKEAAERISKKFL 745
>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 = 96.2 bits (240), Expect = 5e-25
Identities = 36/44 (81%), Positives = 37/44 (84%), Gaps = 2/44 (4%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
K+LKE D FKK VLDGRQLALKISANSVYGFTGA VGKLPC
Sbjct: 92 KDLKEET--DPFKKAVLDGRQLALKISANSVYGFTGATVGKLPC 133
Score = 30.3 bits (69), Expect = 0.14
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 1 MVKFGTKELKEAMTL 15
MVKFG +++EAM L
Sbjct: 180 MVKFGVSDVEEAMKL 194
>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 = 63.6 bits (155), Expect = 5e-15
Identities = 22/30 (73%), Positives = 25/30 (83%)
Query: 52 LWTQCQTCQGSLHEQVICTSRDCPIFYMRK 81
LWT CQ CQGSLHE+V+C SRDCP+FY R
Sbjct: 44 LWTICQRCQGSLHEEVLCDSRDCPVFYKRV 73
>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 = 68.1 bits (167), Expect = 6e-15
Identities = 28/58 (48%), Positives = 37/58 (63%), Gaps = 3/58 (5%)
Query: 7 KELKEAMT--LDEFKKK-VLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
KE K+ M D + + +LD +QLALK++ANSVYGFTGA G+LPC + T G
Sbjct: 133 KEKKKLMKESKDPEELRTLLDKQQLALKVTANSVYGFTGAANGRLPCLPIAESVTAIG 190
>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 = 57.2 bits (138), Expect = 4e-11
Identities = 23/44 (52%), Positives = 30/44 (68%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
K +K+ E KK+LD RQLALK++ANSVYG+ G +LPC
Sbjct: 383 KLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPC 426
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 54.7 bits (132), Expect = 4e-10
Identities = 20/44 (45%), Positives = 29/44 (65%), Gaps = 2/44 (4%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
K++K+ D ++K+LDGRQLALK+ ANS YG+ G + C
Sbjct: 487 KKMKKE--KDPSERKLLDGRQLALKVLANSFYGYLGYSNSRFYC 528
>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 = 50.1 bits (120), Expect = 1e-08
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQ 51
K+ +A L ++ + D RQ ALK+ ANS YG+ GA+ +
Sbjct: 84 KKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDP 128
>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 = 46.4 bits (111), Expect = 2e-07
Identities = 23/51 (45%), Positives = 32/51 (62%), Gaps = 5/51 (9%)
Query: 1 MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQV-GKLPC 50
MVK K+ K+ L +++LD RQLALK+ AN YG+T A G++PC
Sbjct: 144 MVKKAMKKYKDDKKL----QRILDARQLALKLLANVTYGYTAASFSGRMPC 190
>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 = 40.4 bits (95), Expect = 4e-05
Identities = 15/36 (41%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTG 42
+++K+ + + K+LD RQ A+KI ANS YG+ G
Sbjct: 85 EKMKKLDP-ESEEYKLLDERQRAIKILANSFYGYMG 119
>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 = 40.3 bits (95), Expect = 5e-05
Identities = 18/35 (51%), Positives = 25/35 (71%), Gaps = 2/35 (5%)
Query: 7 KELKEAM--TLDEFKKKVLDGRQLALKISANSVYG 39
+++K+ M D KK LD RQLALK++ANS+YG
Sbjct: 85 RQVKKLMKSEKDPDKKAQLDIRQLALKLTANSMYG 119
>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 = 39.3 bits (91), Expect = 1e-04
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 7 KELKEAMTLDEFKKKVL--DGRQLALKISANSVYGFTGAQVGKLPCQ 51
KE+K+ M D L D RQ ALK++ANS+YG G + +
Sbjct: 870 KEVKKLMKQDLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAK 916
>gnl|CDD|132858 cd07219, Pat_PNPLA1, Patatin-like phospholipase domain containing
protein 1. Members of this family share a patatin
domain, initially discovered in potato tubers. Some
members of PNPLA1 subfamily do not have the lipase
consensus sequence Gly-X-Ser-X-Gly which is essential
for hydrolase activity. This family includes PNPLA1
from Homo sapiens and Gallus gallus. Currently, there is
no literature available on the physiological role,
structure, or enzymatic activity of PNPLA1. It is
expressed in various human tissues in low mRNA levels.
Length = 382
Score = 37.6 bits (87), Expect = 4e-04
Identities = 19/41 (46%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 39 GFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCP-IFY 78
GFTG Q PC WT T +Q IC RDCP IF+
Sbjct: 173 GFTGMQ----PCSFWTDSITISTFSGQQDIC-PRDCPAIFH 208
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed.
Length = 787
Score = 33.1 bits (76), Expect = 0.012
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPC 50
K+ K+ LDE ++ D Q ALK+ N+ YG GA+ KL
Sbjct: 491 KKAKDP-NLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYR 533
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 31.5 bits (72), Expect = 0.057
Identities = 18/36 (50%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 7 KELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTG 42
K LKEA + E K + D Q KI ANSVYG G
Sbjct: 641 KLLKEATSSVE--KAIYDSMQYTYKIVANSVYGLMG 674
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 29.1 bits (66), Expect = 0.32
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 16 DEFKKKVLDGRQLALKISANSVYGFTGA 43
DE K+++ A+KI N+ YG G+
Sbjct: 479 DEAKREMNKPLSQAIKIIMNAFYGVLGS 506
>gnl|CDD|200533 cd11272, Sema_plexin_A2, The Sema domain, a protein interacting
module, of Plexin A2. Plexin A2 serves as a receptor
for class 6 semaphorins. Interactions between Plexin A2,
A4 and semaphorins 6A and 6B control the
lamina-restricted projection of hippocampal mossy
fibers. Sema6B also repels the growth of mossy fibers in
a Plexin A4 dependent manner. Plexin A2 does not
suppress Sema6B function. In addition, studies have
shown that Plexin A2 may be related to anxiety and other
psychiatric disorders. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 515
Score = 29.1 bits (65), Expect = 0.37
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 14/60 (23%)
Query: 26 RQLALKISANSVYGFTGAQVGKLP---CQLWTQCQTCQGS---------LHEQVICTSRD 73
R +A I +Y + QV ++P C+ +T C C S LH +C+ RD
Sbjct: 447 RDMAFSIDHKYLYVMSERQVSRVPVESCEQYTTCGECLSSGDPHCGWCALHN--MCSRRD 504
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 28.1 bits (63), Expect = 0.74
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQ 44
LK + E + + + Q+A KI NS+YG G +
Sbjct: 518 TLTKSSLKALLEECEKEIALCNTIQMARKILINSLYGALGNE 559
>gnl|CDD|224475 COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport
and metabolism].
Length = 342
Score = 26.9 bits (60), Expect = 1.9
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 2 VKFGTKELKEAMTLDEFKKKVLDGRQ 27
+K G L+ M+ + K + G+
Sbjct: 88 LKAGEYRLRPGMSAADILKLLESGKS 113
>gnl|CDD|153433 cd08010, yceG_like, proteins similar to Escherichia coli yceG.
The gene product of Escherichia coli yceG has been
erroneously annotated as an aminodeoxychorismate lyase.
Its overexpression has been reported to cause abnormal
biofilm architecture, and it has been reported to be
part of a putative five-gene operon. It might function
as a periplasmic solute-binding protein. The family
also includes Streptomyces caeruleus NovB, an
uncharacterized member of the novobiocin biosynthetic
gene cluster.
Length = 245
Score = 26.4 bits (59), Expect = 2.6
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQLALKI 32
K G EL M+L E +++ G+ +K+
Sbjct: 2 KAGEYELSPGMSLAEILERLTSGKSAQVKV 31
>gnl|CDD|215244 PLN02445, PLN02445, anthranilate synthase component I.
Length = 523
Score = 26.2 bits (58), Expect = 3.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 3 KFGTKELKEAMTLDEFKKKVLDGRQ 27
+FG K MT +E+K VL ++
Sbjct: 223 QFGPSLEKSNMTSEEYKNAVLQAKE 247
>gnl|CDD|215444 PLN02830, PLN02830, UDP-sugar pyrophosphorylase.
Length = 615
Score = 25.8 bits (57), Expect = 4.2
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 12 AMTLDEFKKKVLDGRQLALKISANSVYGFTGAQV 45
A+T E KKKV G +KIS S GA +
Sbjct: 511 ALTFSELKKKVAPGS---VKISQRSTLVLEGADI 541
>gnl|CDD|217147 pfam02618, YceG, YceG-like family. This family of proteins is
found in bacteria. Proteins in this family are
typically between 332 and 389 amino acids in length.
This family was previously incorrectly annotated and
names as aminodeoxychorismate lyase. The structure of
Escherichia coli yceG was solved by X-ray
crystallography.
Length = 291
Score = 25.6 bits (57), Expect = 4.9
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 2 VKFGTKELKEAMTLDEFKKKVLDGRQLALKI 32
+K G ELK M+ E +K++ G+ + K+
Sbjct: 43 LKAGEYELKPGMSAAEILEKLVSGKVVQYKV 73
>gnl|CDD|240283 PTZ00127, PTZ00127, cytochrome c oxidase assembly protein;
Provisional.
Length = 403
Score = 25.0 bits (55), Expect = 8.6
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 7 KELKEAMTLDEFKK 20
K++ MTL+EFKK
Sbjct: 126 KQVHYGMTLEEFKK 139
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 24.9 bits (55), Expect = 10.0
Identities = 5/24 (20%), Positives = 15/24 (62%)
Query: 1 MVKFGTKELKEAMTLDEFKKKVLD 24
+V+ + +++MTL+E +++
Sbjct: 555 VVRRRGGKQQKSMTLEELVEELKK 578
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
0.324 0.136 0.420
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: 4,919,818
Number of extensions: 372759
Number of successful extensions: 534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 534
Number of HSP's successfully gapped: 34
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)