RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12448
(168 letters)
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 201 bits (514), Expect = 1e-60
Identities = 78/152 (51%), Positives = 104/152 (68%), Gaps = 8/152 (5%)
Query: 2 KAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESILLRGDHTRTKIVSTSR 61
+AEDP+YVLENN+PID+ YYL+ Q+ PL+RIF ++ + L G+HTR +S+S
Sbjct: 893 RAEDPLYVLENNIPIDTQYYLD-QIKNPLLRIFEGVMDNP--DSLFSGEHTRHITISSSS 949
Query: 62 VGALSMFVQKKQTCIGCKVVLHDTSLSNALCNFC-LAKEKQYYEAENDKYQQLEKKFCQL 120
G LS FV+K+ C+GCK V+ + ALC+ C KE Y + K + E ++ QL
Sbjct: 950 KGGLSKFVKKQLQCLGCKSVIKE----GALCDNCNQNKEPSIYGKKLAKRRHKEAEYSQL 1005
Query: 121 WTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQ 152
WTQCQ CQGSLH++VICT+RDCPIFY RKKVQ
Sbjct: 1006 WTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQ 1037
>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 = 84.4 bits (209), Expect = 3e-22
Identities = 32/75 (42%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 75 CIGCKVVLHDTSLSNALCNFCLAKEKQYYEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQ 134
C+ C L + + LC CL + + ++LE++F +LWT CQ CQGSLHE+
Sbjct: 1 CLVCGKKLKEGE--SPLCKNCLRNPQASLYKLLSRLRELERRFSRLWTICQRCQGSLHEE 58
Query: 135 VICTSRDCPIFYMRK 149
V+C SRDCP+FY R
Sbjct: 59 VLCDSRDCPVFYKRV 73
>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 = 87.3 bits (217), Expect = 6e-21
Identities = 32/38 (84%), Positives = 35/38 (92%)
Query: 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPIL 38
KAEDPIYVLENN+PID+ YYLENQLSKPL+RIF PIL
Sbjct: 356 EKAEDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPIL 393
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 55.9 bits (135), Expect = 9e-10
Identities = 21/46 (45%), Positives = 24/46 (52%)
Query: 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESIL 46
+AE P V E N PID YY+ QL L RI PI G+ AE
Sbjct: 736 ERAEPPELVDEENSPIDYEYYITKQLLPALERILEPIGGNFAELKG 781
>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 = 52.7 bits (127), Expect = 1e-08
Identities = 24/44 (54%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 2 KAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESI 45
AEDP YVLEN +PID+ YYL+NQL P+ RIF I S
Sbjct: 405 LAEDPEYVLEN-LPIDAEYYLDNQLVPPVERIFEAIFFGDVISW 447
>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 = 40.0 bits (94), Expect = 2e-04
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 3 AEDPIYVLENNVPIDSNYYLENQLSKPLIRIFS 35
A+ P+ L+ ID YYLE L PL RIF
Sbjct: 291 ADPPLEDLDKRHRIDYEYYLERLLQPPLERIFE 323
>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 = 34.6 bits (79), Expect = 0.021
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 3 AEDPIYVLENNVPIDSNYYLENQLSKPLIRIF 34
A + + NN+ D+ YYLE+Q+ ++RI
Sbjct: 1140 ALEELQRKHNNLIYDTQYYLEHQIHPVVLRIL 1171
>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 = 33.3 bits (77), Expect = 0.042
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 10 LENNVPIDSNYYLENQLSKPLIRIFSPILG 39
N+ ID YYL Q+ P+ R+ PI G
Sbjct: 358 KNENLKIDIEYYLSQQILPPISRLCEPIEG 387
>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 = 30.6 bits (70), Expect = 0.36
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 16 IDSNYYLENQLSKPLIRIFSPI 37
+D+ YY+ Q+ L R+F+ +
Sbjct: 425 LDAEYYITKQIIPALDRLFNLV 446
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 28.6 bits (64), Expect = 1.7
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 56 IVSTSR-----VGALSMFVQKKQTCIGCKVVLHDTSLS 88
IVS+S V LS FV K+Q GC V+LH+ + S
Sbjct: 120 IVSSSVGPEYYVNILS-FVDKEQLEPGCSVLLHNKTHS 156
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 28.7 bits (65), Expect = 1.8
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 13 NVPIDSNYYLENQLSKPLIRIFSPILGDKAESI 45
PID +YY+E QL RI P GD ++
Sbjct: 747 KSPIDYDYYIEKQLQPVADRIL-PFFGDDFATL 778
>gnl|CDD|167678 PRK04021, PRK04021, hypothetical protein; Reviewed.
Length = 92
Score = 27.1 bits (60), Expect = 1.9
Identities = 12/34 (35%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 22 LENQLSKPLIRIFSPILGDKAESILLRGDHTRTK 55
++ + +K L++ FS +LG AE ++RG+ +R K
Sbjct: 43 VKGKANKELVKFFSKLLG--AEVEIIRGETSREK 74
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 28.4 bits (64), Expect = 2.1
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 10 LENNVPIDSNY----YLENQLSKPLIRIFSPIL 38
+E N I SN YL ++L + RIFS +L
Sbjct: 174 IEQNSSIRSNIRSNKYLVSELINSMARIFSILL 206
>gnl|CDD|233139 TIGR00814, stp, serine transporter. The Hydroxy/Aromatic Amino
Acid Permease (HAAAP) Family- serine/threonine subfamily
(TC 2.A.42.2) The HAAAP family includes well
characterized aromatic amino acid:H+ symport permeases
and hydroxy amino acid permeases. This subfamily is
specific for hydroxy amino acid transporters and
includes the serine permease, SdaC, of E. coli, and the
threonine permease, TdcC, of E. coli.//added GO terms,
none avaialbelf or ser/thr specifically [SS 2/6/05]
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 397
Score = 28.1 bits (63), Expect = 2.3
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPIL 38
+ + + E N+ I S YL N + I PI+
Sbjct: 252 LSPAEAVAAKEQNISILS--YLANHFNAAWISYAGPIV 287
>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 = 27.7 bits (62), Expect = 3.5
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 2 KAEDPIYVLENNVPIDSNYYLENQLSKPLIRI 33
+A V E + D+ YY++NQ+ ++RI
Sbjct: 329 RAYPYDMVDEKH-KYDAEYYIDNQVLPAVLRI 359
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 26.8 bits (60), Expect = 5.6
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 101 QYYEAENDKYQQLEK------KFCQLWTQCQTCQG 129
Q +E +ND Y K K+ LW QC+ C G
Sbjct: 12 QIFEIDNDSYMYDTKYSWNTQKYKHLWVQCENCYG 46
>gnl|CDD|239502 cd03408, Band_7_5, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and are known to interact
with a variety of proteins. Stomatin interacts with and
regulates members of the degenerin/epithelia Na+ channel
family in mechanosensory cells of Caenorhabditis elegans
and vertebrate neurons and participates in trafficking
of Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome.
Length = 207
Score = 26.5 bits (59), Expect = 6.0
Identities = 9/40 (22%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 1 MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGD 40
+K DP+ + N V + L K L + L
Sbjct: 109 LKVTDPVLFVTNIVG-TRGLFTVEDLEKSLRALIVAALSS 147
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
0.322 0.134 0.411
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,775,952
Number of extensions: 643972
Number of successful extensions: 528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 521
Number of HSP's successfully gapped: 30
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
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 (21.9 bits)
S2: 55 (25.1 bits)