RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17723
(145 letters)
>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 = 42.5 bits (100), Expect = 2e-06
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 40 CKACDRDTSAGEMIQCGKCVRYLHPACLDLPGEMLPHMKLYDWQCSDCKSC 90
C C + GE++ C C R+ H ACL P E + +W C +CK
Sbjct: 2 CAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPE-GEWYCPECKPK 51
Score = 37.5 bits (87), Expect = 1e-04
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 90 CVACEKAQDDDKMLFCDLCDRGYHNYCIGLDKIPTV 125
C C K DD ++L CD CDR +H C+G P
Sbjct: 2 CAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEE 37
>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 = 37.2 bits (86), Expect = 2e-04
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 2/48 (4%)
Query: 40 CKACDRDTSAGEMIQCGKCVRYLHPACLDLPGEMLPHMKLYDWQCSDC 87
C C + GE++QC C R+ H CL P W C C
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLL--EEEPDGKWYCPKC 47
Score = 34.5 bits (79), Expect = 0.001
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 90 CVACEKAQDDDKMLFCDLCDRGYHNYCIGLDKIP 123
C C K D ++L CD CDR YH C+G +
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLE 35
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 31.5 bits (71), Expect = 0.13
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 76 HMKLYDWQCSDCKSCVACEKAQDDDK--MLFCDLCDRGYHNYCIGLDKIP 123
H++ + C C +++ ++FCD C+ H C G+ +P
Sbjct: 182 HVEPIEPSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLP 231
>gnl|CDD|234043 TIGR02871, spore_ylbJ, sporulation integral membrane protein YlbJ.
Members of this protein family are found exclusively in
Firmicutes (low-GC Gram-positive bacterial) and are
known from studies in Bacillus subtilis to be part of
the sigma-E regulon. Mutation leads to a sporulation
defect, confirming that members of this protein family,
YlbJ, are sporulation proteins. This protein appears to
be universal among endospore-forming bacteria, but is
encoded by a pair ORFs distant from eash other in
Symbiobacterium thermophilum IAM14863 [Cellular
processes, Sporulation and germination].
Length = 362
Score = 29.6 bits (67), Expect = 0.51
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 124 TVGLVFTLKKKKNKKKKKKKKK 145
T+GL+ K++ +K KKKK
Sbjct: 154 TMGLILRFYKRRKRKILSKKKK 175
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 28.6 bits (64), Expect = 1.2
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 130 TLKKKKNKKKKKKKKK 145
+K KK KKKKKKKKK
Sbjct: 272 MVKFKKPKKKKKKKKK 287
Score = 27.0 bits (60), Expect = 4.7
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 124 TVGLVFTLKKKKNKKKKKKKKK 145
V + KK K KKKKKKK++
Sbjct: 268 DVSEMVKFKKPKKKKKKKKKRR 289
>gnl|CDD|219901 pfam08555, DUF1754, Eukaryotic family of unknown function
(DUF1754). This is a eukaryotic protein family of
unknown function.
Length = 90
Score = 27.0 bits (60), Expect = 1.8
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 131 LKKKKNKKKKKKKKK 145
LK KK KKKKKKK
Sbjct: 12 LKGKKIDVKKKKKKK 26
>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
protein DltB. Members of this protein family are DltB,
part of a four-gene operon for D-alanyl-lipoteichoic
acid biosynthesis that is present in the vast majority
of low-GC Gram-positive organisms. This protein may be
involved in transport of D-alanine across the plasma
membrane [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 380
Score = 27.5 bits (62), Expect = 2.6
Identities = 9/23 (39%), Positives = 11/23 (47%), Gaps = 3/23 (13%)
Query: 125 VGLVFT---LKKKKNKKKKKKKK 144
+ L T +K K KK KK K
Sbjct: 333 LLLALTDAWQRKSKKYKKNKKNK 355
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 27.6 bits (62), Expect = 2.8
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 132 KKKKNKKKKKKKKK 145
KK+K K+K K KK+
Sbjct: 402 KKEKEKEKPKVKKR 415
Score = 27.2 bits (61), Expect = 3.2
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 132 KKKKNKKKKKKKKK 145
+KK K+K+K K K
Sbjct: 400 AEKKEKEKEKPKVK 413
Score = 26.8 bits (60), Expect = 5.3
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 130 TLKKKKNKKKKKKKKK 145
L K+ KK+K+K+K
Sbjct: 395 VLAKRAEKKEKEKEKP 410
Score = 26.4 bits (59), Expect = 5.5
Identities = 6/14 (42%), Positives = 11/14 (78%)
Query: 132 KKKKNKKKKKKKKK 145
K+ + K+K+K+K K
Sbjct: 398 KRAEKKEKEKEKPK 411
>gnl|CDD|240380 PTZ00362, PTZ00362, hypothetical protein; Provisional.
Length = 479
Score = 27.0 bits (60), Expect = 4.3
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 128 VFTLKKKKNKKKKKKKKK 145
VF + KKK KKKKK K+
Sbjct: 4 VFNIFKKKKKKKKKASKE 21
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 26.2 bits (58), Expect = 5.5
Identities = 11/13 (84%), Positives = 11/13 (84%)
Query: 133 KKKNKKKKKKKKK 145
KKK KKKKKKK K
Sbjct: 92 KKKQKKKKKKKAK 104
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 26.2 bits (58), Expect = 6.1
Identities = 28/78 (35%), Positives = 33/78 (42%), Gaps = 19/78 (24%)
Query: 79 LYDWQCSDCKSCVACEKAQDDDKMLFCDLCDRGYHNYCIGLDKI---PTVGLVFTLK--- 132
+ W C CV EKA + K C +C + Y D + PT V LK
Sbjct: 125 VALWPCG----CVFSEKALKEVKSKVCPVCGKPYSEE----DVVPLNPTEEEVELLKARL 176
Query: 133 -----KKKNKKKKKKKKK 145
KKK KKKKKK KK
Sbjct: 177 EEERAKKKKKKKKKKTKK 194
>gnl|CDD|221445 pfam12157, DUF3591, Protein of unknown function (DUF3591). This
domain is found in eukaryotes and is typically between
445 to 462 amino acids in length. Most members are
annotated as being transcription initiation factor TFIID
subunit 1, and this region is the conserved central
portion of these proteins.
Length = 457
Score = 26.5 bits (59), Expect = 6.3
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 119 LDKIPTVGLVFTLKKKKNKKKKKKKKK 145
L+ P + +VF+ K K KKK K K
Sbjct: 60 LNFRPGLQIVFS-KLKHRKKKHDKGKD 85
>gnl|CDD|223982 COG1054, COG1054, Predicted sulfurtransferase [General function
prediction only].
Length = 308
Score = 26.5 bits (59), Expect = 6.3
Identities = 7/35 (20%), Positives = 8/35 (22%)
Query: 34 VPESDKCKACDRDTSAGEMIQCGKCVRYLHPACLD 68
+ C C I C C C D
Sbjct: 240 EGDHTPCDNCRNPLCNLLFISCEYCEGKYCGCCSD 274
>gnl|CDD|220692 pfam10324, 7TM_GPCR_Srw, Serpentine type 7TM GPCR chemoreceptor
Srw. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srw is a solo family
amongst the superfamilies of chemoreceptors.
Chemoperception is one of the central senses of soil
nematodes like C. elegans which are otherwise 'blind'
and 'deaf'. The genes encoding Srw do not appear to be
under as strong an adaptive evolutionary pressure as
those of Srz.
Length = 317
Score = 26.4 bits (59), Expect = 6.5
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 116 CIGLDKIPTVGLVFTLKK-KKNKKKKKKKKK 145
CI L I T+ L+ L+K KK++K
Sbjct: 205 CI-LLPILTILLIIELRKAKKSRKNLSSSSN 234
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 26.1 bits (58), Expect = 7.4
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 132 KKKKNKKKKKKKKK 145
KKKK KKK KK+KK
Sbjct: 397 KKKKRKKKGKKRKK 410
>gnl|CDD|232990 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. Every known example of the
phenylalanyl-tRNA synthetase, except the monomeric form
of mitochondrial, is an alpha 2 beta 2 heterotetramer.
The beta subunits break into two subfamilies that are
considerably different in sequence, length, and pattern
of gaps. This model represents the subfamily that
includes the beta subunit from Bacteria other than
spirochetes, as well as a chloroplast-encoded form from
Porphyra purpurea. The chloroplast-derived sequence is
considerably shorter at the amino end, however, so This
model was built in fragment mode [Protein synthesis,
tRNA aminoacylation].
Length = 797
Score = 26.1 bits (58), Expect = 9.2
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 117 IGLDKIPTVGLVFTLKKKKNKKKKKKKKK 145
G D IP L + K KN + +K
Sbjct: 470 YGYDNIPAEPLSVSSKLNKNNENYLLLRK 498
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 26.1 bits (58), Expect = 9.2
Identities = 12/14 (85%), Positives = 13/14 (92%)
Query: 131 LKKKKNKKKKKKKK 144
LK+KK KKKKKKKK
Sbjct: 434 LKEKKRKKKKKKKK 447
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
0.321 0.137 0.448
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,915,441
Number of extensions: 565804
Number of successful extensions: 1816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1716
Number of HSP's successfully gapped: 120
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (21.8 bits)
S2: 54 (24.6 bits)