RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15711
(248 letters)
>gnl|CDD|238160 cd00257, Fascin, Fascin-like domain; members include
actin-bundling/crosslinking proteins facsin,
histoactophilin and singed; identified in sea urchin,
Drosophila, Xenopus, rodents, and humans; The
fascin-like domain adopts a beta-trefoil topology and
contains an internal threefold repeat; the fascin
subgroup contains four copies of the domain;
Structurally similar to fibroblast growth factor (FGF).
Length = 119
Score = 32.2 bits (74), Expect = 0.074
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 215 GKWGLKGEGDRFIGTKKPKHLFSGKRGIGKT 245
GKW L+ E R++G L + +G
Sbjct: 84 GKWALRAENGRYLGGDGSGTLKASSETVGPD 114
>gnl|CDD|224878 COG1967, COG1967, Predicted membrane protein [Function unknown].
Length = 271
Score = 28.8 bits (65), Expect = 2.4
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 61 KLGIFYFSLHKLDELEKEEAQREEAGYYAV 90
KL I L+ LDELE++ + E +
Sbjct: 223 KLAILLGVLYLLDELEEDGEEEENYIKLVI 252
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 28.8 bits (65), Expect = 2.9
Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 227 IGTKK--PKHLFSGKRGIGKT 245
+ + + P +LF+G RG GKT
Sbjct: 32 LISNRIAPAYLFTGPRGTGKT 52
>gnl|CDD|238844 cd01709, RT_like_1, RT_like_1: A subfamily of reverse
transcriptases (RTs). An RT gene is usually indicative
of a mobile element such as a retrotransposon or
retrovirus. RTs occur in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 346
Score = 28.4 bits (64), Expect = 3.7
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 94 EYDQTMIE--IKELAKQIRDKKSIM 116
E DQ+ ++ I EL KQ+ KS++
Sbjct: 194 EIDQSQVDAHIDELRKQLDACKSVL 218
>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 = 28.5 bits (63), Expect = 4.0
Identities = 24/89 (26%), Positives = 31/89 (34%), Gaps = 16/89 (17%)
Query: 111 DKKSIMRQDALLIKQSTKPRLPRTALSKNREGVEARASRSRGRSVEGPGGKRQRLDSEGN 170
D S + +D+ T R P + S R G S SR RS G +R R
Sbjct: 297 DDGSAISEDSAGGSHHTMRRPPHST-SGERRGRRRNRSESRSRSRSRSGSRRYR------ 349
Query: 171 AVTVSKSRARSDSKVTPRDQSGLRDPQVL 199
+ R R P +S R VL
Sbjct: 350 -----RRRGRG----VPGRRSESRQDTVL 369
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 28.3 bits (64), Expect = 4.8
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 235 LFSGKRGIGKT 245
LFSG RG+GKT
Sbjct: 42 LFSGTRGVGKT 52
>gnl|CDD|213990 cd07435, PHP_PolIIIA_POLC, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III at
PolC gene. DNA polymerase III alphas (PolIIIAs) that
contain a PHP domain have been classified into four
basic groups based on phylogenetic and domain structural
analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group
is distinct from the other three and is clustered
together. The PHP (also called histidinol
phosphatase-2/HIS2) domain is associated with several
types of DNA polymerases, such as PolIIIA and family X
DNA polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. DNA polymerase III
holoenzyme is one of the five eubacterial DNA
polymerases that are responsible for the replication of
the DNA duplex. The alpha subunit of DNA polymerase III
core enzyme catalyzes the reaction for polymerizing both
DNA strands. PolC PHP is located in different location
compare to dnaE1, 2, and 3. The PHP domain has four
conserved sequence motifs and and contains an invariant
histidine that is involved in metal ion coordination.The
PHP domain of PolC is structurally homologous to other
members of the PHP family that have a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel. PHP domains found
in dnaEs of thermophilic origin exhibit 3'-5'
exonuclease activity. In contrast, PolC PHP lacks
detectable nuclease activity.
Length = 268
Score = 27.8 bits (63), Expect = 4.9
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 128 KPRLPRTALSKNREG 142
PR+P++ L K REG
Sbjct: 101 VPRIPKSELEKYREG 115
>gnl|CDD|200222 TIGR02965, xanthine_xdhB, xanthine dehydrogenase, molybdopterin
binding subunit. Members of the protein family are the
molybdopterin-containing large subunit (or, in,
eukaryotes, the molybdopterin-binding domain) of
xanthine dehydrogenase, and enzyme that reduces the
purine pool by catabolizing xanthine to urate. This
model is based primarily on bacterial sequences; it does
not manage to include all eukaryotic xanthine
dehydrogenases and thereby discriminate them from the
closely related enzyme aldehyde dehydrogenase [Purines,
pyrimidines, nucleosides, and nucleotides, Other].
Length = 758
Score = 28.1 bits (63), Expect = 5.3
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 47 AGYYAVPKIEYDQTKL---GIFYFS 68
G+Y PKI +D+ K +YF+
Sbjct: 580 TGFYKTPKIHWDRAKGRGRPFYYFA 604
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 27.9 bits (63), Expect = 5.4
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 235 LFSGKRGIGKT 245
LFSG RG GKT
Sbjct: 40 LFSGPRGTGKT 50
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit
[Transcription].
Length = 175
Score = 27.4 bits (61), Expect = 5.5
Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 17 KWGLKGEGDRFIEDRYKLDELEKEEAQREEAGYYAVPKIEYDQTKLGIFYFSLHKLDELE 76
KWGL+ Y LDE+++E E E D + G +LD E
Sbjct: 75 KWGLR--------SWYPLDEIDEEIQAMTEKKDIKAKDKEVDAFEEGD----EDELDYDE 122
Query: 77 -KEEAQREEAGYYAVPKIEYDQTMIEIKE 104
KEE + +E + D+ EI E
Sbjct: 123 DKEEEEDDEVDSLDDENDDEDEDDDEIVE 151
>gnl|CDD|216205 pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein.
Length = 346
Score = 27.7 bits (62), Expect = 6.5
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 152 GRSVEGPGGKRQRLDSEGNAVTVSKSRARSDSKVTPRDQSGLRDPQVLMKVKKIAHKAIA 211
G +EG G R R S + S+S +R S+ + R+ S R+ + A+A
Sbjct: 146 GFYIEGFRG-RSRSSSRSS----SRSNSRGPSRGSSRNNSRNRNSSSPDDLVAAVLAALA 200
Query: 212 KKV 214
K
Sbjct: 201 KLG 203
>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 27.8 bits (62), Expect = 7.4
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 17/70 (24%)
Query: 170 NAVTVSKSRARSDS-------KVTP------RDQSGLRDPQVLMKVKKIAHKAIAKKVGK 216
N + SKSRARS S K+T R Q+G Q +V+ I + K++ K
Sbjct: 16 NGRSRSKSRARSQSRGRGRSVKITVNSRNKGRRQNGRNKYQSNQRVRNI----VNKQLRK 71
Query: 217 WGLKGEGDRF 226
G+ G
Sbjct: 72 QGVTGPKPAI 81
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 27.8 bits (62), Expect = 7.7
Identities = 24/98 (24%), Positives = 36/98 (36%), Gaps = 10/98 (10%)
Query: 119 DALLIKQSTKPRLPRTALSKNREGVEARASRSRGRSVEGPGGKRQRLDSEGNAVTVSKSR 178
D LI PR G AR +G + GGKR+++ + N S R
Sbjct: 721 DFSLISSERAPR---------NVGKTAREKAKKGDA-GKKGGKRRQVGKKVNFEPDSAFR 770
Query: 179 ARSDSKVTPRDQSGLRDPQVLMKVKKIAHKAIAKKVGK 216
+K + + + K +KIA AK+ K
Sbjct: 771 GEKKAKPKAAKKDARKAKKPSAKTQKIAAATKAKRAAK 808
>gnl|CDD|119241 pfam10721, DUF2514, Protein of unknown function (DUF2514). This
family is conserved in bacteria and some viruses. The
function is not known.
Length = 162
Score = 26.6 bits (59), Expect = 8.4
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 1/68 (1%)
Query: 133 RTALSKNREGVEARASRSRGRS-VEGPGGKRQRLDSEGNAVTVSKSRARSDSKVTPRDQS 191
R ++N +A+ + R+ RL E + + +KS SD+ R ++
Sbjct: 58 RRQAAQNEAAKDAQEEAAAARADAADADAAAGRLRQEADKLAAAKSCPTSDTAAAARGKA 117
Query: 192 GLRDPQVL 199
R VL
Sbjct: 118 AARAAMVL 125
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 27.4 bits (61), Expect = 8.8
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 234 HLFSGKRGIGKT 245
+LF+G RG+GKT
Sbjct: 41 YLFTGTRGVGKT 52
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 27.3 bits (61), Expect = 8.8
Identities = 25/136 (18%), Positives = 41/136 (30%), Gaps = 6/136 (4%)
Query: 22 GEGDRFIEDRYKLDELEKEEAQREEAGYYAVPKIEYDQTKLGIFYFSLHKLDELEKEEAQ 81
E + E KL+E+ KE + E + ++E SL +L A
Sbjct: 501 EEKELLEELIEKLEEVRKELEEELEEVEKLLDEVELLTGANSGGKTSLLELKAQIVVLAH 560
Query: 82 REEAGYYAVPKIEYDQTMIEIKELAKQIRDKKSIMRQDALLIKQSTKPRLPRTALSKNRE 141
K+E + +K+ K+ K LP K +
Sbjct: 561 MGLPVPAEEAKVEAVDEVKFLKK--KKGILDAGAFESTL---KDKKNKVLPEAKKRKLKL 615
Query: 142 GVEARA-SRSRGRSVE 156
G E + G V+
Sbjct: 616 GDEVEVITGEPGAVVK 631
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 27.3 bits (60), Expect = 8.9
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 232 PKHLFSGKRGIGKT 245
P +LFSG RG+GKT
Sbjct: 39 PAYLFSGTRGVGKT 52
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 27.3 bits (61), Expect = 9.7
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 235 LFSGKRGIGKT 245
LFSG RG GKT
Sbjct: 41 LFSGPRGCGKT 51
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
0.313 0.132 0.366
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,648,138
Number of extensions: 1227164
Number of successful extensions: 1055
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1047
Number of HSP's successfully gapped: 61
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.2 bits)