RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13908
(149 letters)
>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 205
Score = 62.3 bits (152), Expect = 9e-13
Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 18/141 (12%)
Query: 1 MVRKLKYHEQKLLKKVDFISWEADNNLHEVKIMRRFGIQKRQDYTTYNKLS--RLIRTLA 58
M R ++KL +++ F W + E K+ + G + KLS L
Sbjct: 1 MARYPG-PKKKLSRRLGFNPWLKERLCKERKLPYKPGQHG---QERWKKLSDYGLQLREK 56
Query: 59 QKIKDLDPKDPFRVESSAKLLEKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNK 118
QK++ F + L G ++ + + +RRL V+YR
Sbjct: 57 QKLR------AFYGVLEKQFRRYLKEAGRLKGV------TGLNLLALLERRLDNVVYRLG 104
Query: 119 MVQQLRLATQFIEQAHVRVGP 139
+ R A Q + H+ V
Sbjct: 105 FAKTRRQARQLVSHGHILVNG 125
>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
Length = 194
Score = 52.4 bits (126), Expect = 3e-09
Identities = 34/115 (29%), Positives = 65/115 (56%), Gaps = 3/115 (2%)
Query: 29 EVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGL 87
E+K++ +G++ KR+ + LSR IR A+ + LD K+P R+ LL ++ GL
Sbjct: 29 ELKLVGEYGLRNKRELWRVQYALSR-IRNAARMLLTLDEKNPRRIFEGEALLRRMNRYGL 87
Query: 88 I-RTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPEL 141
+ ++ L+ +T +F +RRL +++++ M + + A I Q H+RVG ++
Sbjct: 88 LDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQI 142
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
Length = 181
Score = 47.8 bits (114), Expect = 2e-07
Identities = 31/115 (26%), Positives = 62/115 (53%), Gaps = 3/115 (2%)
Query: 29 EVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGL 87
E+K+ +G++ KR+ + L++ IR A+++ LD KDP R+ LL +++ +GL
Sbjct: 27 ELKLCGEYGLKNKREIWRVQYTLAK-IRKAARELLTLDEKDPKRLFEGEALLRRMHRLGL 85
Query: 88 I-RTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVGPEL 141
+ + L+ +T +RRL +++ + + + A I Q H+RVG ++
Sbjct: 86 LDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQI 140
>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
type)/S9(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S9 as well as archaeal
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 162
Score = 44.3 bits (105), Expect = 2e-06
Identities = 26/119 (21%), Positives = 57/119 (47%), Gaps = 3/119 (2%)
Query: 21 WEADNNLHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLE 80
W + E+K++ ++G++ +++ R R A+++ LD D R+ +LL
Sbjct: 18 WIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD--DEQRLFEGNQLLR 75
Query: 81 KLYLMGLI-RTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVG 138
+L +G++ L++ +T F +RRL +++ + + + A Q I H+ V
Sbjct: 76 RLVRLGILDEENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHIAVD 134
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
Length = 177
Score = 36.4 bits (85), Expect = 0.002
Identities = 29/119 (24%), Positives = 61/119 (51%), Gaps = 4/119 (3%)
Query: 21 WEADNNLHEVKIMRRFGIQ-KRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLL 79
W+ + E +++ ++G++ KR+ + + L + R A+ + L P++ R + +LL
Sbjct: 18 WQKERIAEERELLGKYGLRNKRELWKAQSILRK-YRRQARSLLALPPEE--RAKEEEQLL 74
Query: 80 EKLYLMGLIRTKWDLENCNKVTASSFCKRRLPVVMYRNKMVQQLRLATQFIEQAHVRVG 138
KL G+++ L++ +T +RRL ++YR + + + A QFI H+ V
Sbjct: 75 GKLKRYGILKENATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVN 133
>gnl|CDD|143944 pfam00178, Ets, Ets-domain.
Length = 85
Score = 30.4 bits (69), Expect = 0.085
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 17 DFISWEADNN-----LHEVKIMRRFGIQKRQDYTTYNKLSRLIRTLAQK 60
DFI W + + ++ R +GI+K + Y+KLSR +R +K
Sbjct: 19 DFIRWTGRDKGEFKLVDPEEVARLWGIRKNKPNMNYDKLSRALRYYYKK 67
>gnl|CDD|197710 smart00413, ETS, erythroblast transformation specific domain.
variation of the helix-turn-helix motif.
Length = 87
Score = 29.2 bits (66), Expect = 0.25
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 7/50 (14%)
Query: 17 DFISWEADNNLHEVKIM------RRFGIQKRQDYTTYNKLSRLIRTLAQK 60
D I W D + E K++ R +G +K + Y KLSR +R +K
Sbjct: 19 DIIKWT-DRDEGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYYKK 67
>gnl|CDD|201819 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases, a
yeast protein containing a pseudouridine synthetase and
a deaminase domain, bacterial tyrosyl-tRNA synthetases,
and a number of uncharacterized, small proteins that may
be involved in translation regulation. The S4 domain
probably mediates binding to RNA.
Length = 48
Score = 27.4 bits (62), Expect = 0.50
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRV 137
RL V+ R + A Q I HVRV
Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHVRV 30
>gnl|CDD|184523 PRK14125, PRK14125, cell division suppressor protein YneA;
Provisional.
Length = 103
Score = 28.5 bits (64), Expect = 0.57
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 6 KYHEQKLLKKVDFISWEADNN 26
+Y + + K +FI W D N
Sbjct: 53 QYAGKHHMAKNEFIEWVEDVN 73
>gnl|CDD|223383 COG0306, PitA, Phosphate/sulphate permeases [Inorganic ion
transport and metabolism].
Length = 326
Score = 28.3 bits (64), Expect = 1.3
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 52 RLIRTLAQKIKDLDPKDPFRVESSA 76
R+I T+ +KI +L P F + S+
Sbjct: 232 RVIETVGKKITELTPSRGFSAQLSS 256
>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain
surface is populated by conserved, charged residues that
define a likely RNA-binding site; Found in stress
proteins, ribosomal proteins and tRNA synthetases; This
may imply a hitherto unrecognized functional similarity
between these three protein classes.
Length = 70
Score = 26.4 bits (59), Expect = 1.7
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 108 RRLPVVMYRNKMVQQLRLATQFIEQAHVRV 137
RL ++ R + A Q I+ HV V
Sbjct: 1 MRLDKILARLGLAPSRSEARQLIKHGHVLV 30
>gnl|CDD|237881 PRK14985, PRK14985, maltodextrin phosphorylase; Provisional.
Length = 798
Score = 27.7 bits (62), Expect = 2.6
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 110 LPVVMYRNKMVQQLRL 125
LPVV YRN + Q LRL
Sbjct: 207 LPVVGYRNGVAQPLRL 222
>gnl|CDD|173735 cd07831, STKc_MOK, Catalytic domain of the Serine/Threonine
Kinase, MAPK/MAK/MRK Overlapping Kinase.
Serine/Threonine Kinases (STKs), MAPK/MAK/MRK
Overlapping Kinase (MOK) subfamily, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The MOK subfamily is
part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. MOK, also called Renal tumor
antigen 1 (RAGE-1), is widely expressed and is enriched
in testis, kidney, lung, and brain. It is expressed in
approximately 50% of renal cell carcinomas (RCC) and is
a potential target for immunotherapy. MOK is stabilized
by its association with the HSP90 molecular chaperone.
It is induced by the transcription factor Cdx2 and may
be involved in regulating intestinal epithelial
development and differentiation.
Length = 282
Score = 27.2 bits (61), Expect = 2.9
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 6 KYHEQKLLKKVDFISWEADNNLHEVKIMRR 35
KY+ K +KK F S E NNL E++ +RR
Sbjct: 25 KYYAIKCMKK-HFKSLEQVNNLREIQALRR 53
>gnl|CDD|111791 pfam02942, Flu_B_NS1, Influenza B non-structural protein (NS1).
A specific region of the influenza B virus NS1 protein,
which includes part of its effector domain, blocks the
covalent linkage of ISG15 to its target proteins both
in vitro and in infected cells. Of the several hundred
proteins induced by interferon (IFN) alpha/beta, the
ubiquitin-like ISG15 protein is one of the most
predominant. Influenza A virus employs a different
strategy: its NS1 protein does not bind the ISG15
protein, but little or no ISG15 protein is produced
during infection.
Length = 247
Score = 27.3 bits (60), Expect = 3.2
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 34 RRFGIQKRQDYTTYNKLSRLIRTLAQKIKDLDPKDPFRVESSAKLLEKLYLMGL 87
R Q+ DY ++L+RL R L +IK + +P ES LE+ +G+
Sbjct: 32 ERLSWQRALDYPGQDRLNRLKRKLESRIKTHNKSEP---ESKRMSLEERKAIGV 82
>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7.
LARP7 is a component of the 7SK snRNP, a key factor in
the regulation of RNA polymerase II transcription. 7SK
functionality is dependent on the presence of LARP7,
which is thought to stabilize the 7SK RNA by
interacting with its 3' end. The release of 7SK RNA
from P-TEFb/HEXIM/7SK complexes activates the
cyclin-dependent kinase P-TEFb, which in turn
phosphorylates the C-terminal domain of RNA pol II and
mediates a transition into productive transcription
elongation.
Length = 82
Score = 25.3 bits (55), Expect = 6.0
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 14 KKVDFISWEADNNLHEVKIMRRFGIQKRQDY------TTYNKLSRL 53
K+VDF W D NLH+ + +R + R Y ++NK+ +L
Sbjct: 11 KQVDF--WFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKL 54
>gnl|CDD|180732 PRK06853, PRK06853, indolepyruvate oxidoreductase subunit beta;
Reviewed.
Length = 197
Score = 26.0 bits (58), Expect = 8.4
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 132 QAHVRVGPELEGDMIE 147
+HVR G E+ +I
Sbjct: 50 VSHVRFGDEVYSPLIP 65
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 25.5 bits (56), Expect = 10.0
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 105 FCKRRLPVVMYRNKMVQQLRLATQFIEQA 133
RR+P++ Y NKM L I Q
Sbjct: 100 IKHRRIPILFYANKMDLPDALTAVKITQL 128
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 0.136 0.394
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,592,289
Number of extensions: 672096
Number of successful extensions: 638
Number of sequences better than 10.0: 1
Number of HSP's gapped: 634
Number of HSP's successfully gapped: 40
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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: 54 (24.5 bits)