RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9533
(73 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 33.6 bits (78), Expect = 8e-04
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 3 FVWFQNRRAKWRK 15
VWFQNRRAKW++
Sbjct: 45 KVWFQNRRAKWKR 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 29.9 bits (68), Expect = 0.021
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 4 VWFQNRRAKWRKKE 17
+WFQNRRAK ++ E
Sbjct: 46 IWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 28.8 bits (65), Expect = 0.064
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 4 VWFQNRRAKWR 14
VWFQNRRAKW+
Sbjct: 47 VWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 26.2 bits (58), Expect = 1.3
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 4 VWFQNRRAKWRKKEHTKK 21
+WFQN+RAK +KK K
Sbjct: 97 IWFQNKRAKEKKKRSGKV 114
>gnl|CDD|215441 PLN02825, PLN02825, amino-acid N-acetyltransferase.
Length = 515
Score = 25.9 bits (57), Expect = 1.8
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 35 CSGDPIPAEELKRKERARRQKKLMKSL 61
CS + +P KR +R K MK L
Sbjct: 488 CSIESLPEARRKRINLSRGSKYYMKKL 514
>gnl|CDD|224235 COG1316, LytR, Transcriptional regulator [Transcription].
Length = 307
Score = 25.5 bits (56), Expect = 2.3
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 49 ERARRQKKLMKSLERQVGPLTT 70
RA RQ+++M +L ++ +
Sbjct: 197 GRAARQREVMTALANKMLSPNS 218
>gnl|CDD|129050 smart00814, Alpha_TIF, Alpha trans-inducing protein (Alpha-TIF).
Alpha-TIF (VP16) from Herpes Simplex virus is an
essential tegument protein involved in the
transcriptional activation of viral immediate early (IE)
promoters (alpha genes) during the lytic phase of viral
infection. VP16 associates with cellular transcription
factors to enhance transcription rates, including the
general transcription factor TFIIB and the
transcriptional coactivator PC4. The N-terminal residues
of VP16 confer specificity for the IE genes, while the
C-terminal residues are responsible for transcriptional
activation. Within the C-terminal region are two
activation regions that can independently and
cooperatively activate transcription. VP16 forms a
transcriptional regulatory complex with two cellular
proteins, the POU-domain transcription factor Oct-1 and
the cell-proliferation factor HCF-1. VP16 is an
alpha/beta protein with an unusual fold. Other
transcription factors may have a similar topology.
Length = 356
Score = 25.0 bits (55), Expect = 3.4
Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 11/53 (20%)
Query: 31 HPVTCS-------GDPIPAEELKRKERARRQKKL----MKSLERQVGPLTTPI 72
PV + G P+ A EL+ RR+ L +E PL P
Sbjct: 244 QPVLFNHGVVILEGRPLTAAELREVNYRRRELGLPLIRCGLVEEPGSPLVQPP 296
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 24.9 bits (54), Expect = 3.9
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 1/51 (1%)
Query: 22 GPGRPAHNAHPVTCSGDP-IPAEELKRKERARRQKKLMKSLERQVGPLTTP 71
G P A G E RK R RR + ++ E P+ P
Sbjct: 481 GAETPVVAAAAAQAPGVVAADGERAPRKRRRRRNGRPVEGAEPVSTPVPAP 531
>gnl|CDD|234372 TIGR03843, TIGR03843, conserved hypothetical protein. This model
represents a protein family largely restricted to the
Actinobacteria (high-GC Gram-positives), although it is
also found in the Chloroflexi. Distant similarity to the
phosphatidylinositol 3- and 4-kinase is suggested by the
matching of some members to pfam00454.
Length = 253
Score = 24.9 bits (55), Expect = 3.9
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 37 GDPIPAEELKRKERARRQKKLMKSLERQVGPLTTP 71
G+P+PAE L R R L L R++ L TP
Sbjct: 187 GEPLPAELLADLARLRDD--LDGDLGRELAELLTP 219
>gnl|CDD|212550 cd11712, GINS_A_psf2, Alpha-helical domain of GINS complex
protein Psf2 (partner of Sld5 2). Psf2 is a component
of GINS tetrameric protein complex and has been found
to play important roles in normal eye development in
Xenopus laevis. GINS is a complex of four subunits
(Sld5, Psf1, Psf2 and Psf3) that is involved in both
initiation and elongation stages of eukaryotic
chromosome replication. Besides being essential for the
maintenance of genomic integrity, GINS plays a central
role in coordinating DNA replication with cell cycle
checkpoints and is involved in cell growth. The
eukaryotic GINS subunits are homologous and homologs
are also found in the archaea; the complex is not found
in bacteria. The four subunits of the complex consist
of two domains each, termed the alpha-helical (A) and
beta-strand (B) domains. The A and B domains of
Sld5/Psf1 are permuted with respect to Psf1/Psf3.
Length = 119
Score = 24.5 bits (54), Expect = 5.0
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 34 TCSGDPIPAEELKR--KE-RARRQKKLMKSLERQVGPLTTPIL 73
S D A+E++ ++ R RQ KL LE+ +G
Sbjct: 47 VASDDIPDADEIRSLVEDIRDVRQAKLRSGLEKLLGSGEVHAK 89
>gnl|CDD|240447 cd13432, LDT_IgD_like_2, IgD-like repeat domain of mycobacterial
L,D-transpeptidases. Immunoglobulin-like domain found
in actinobacterial L,D-transpeptidases, including
Mycobacterium tuberculosis LdtMt2, which is a
non-classical transpeptidase that generates 3->3
transpeptide linkages. LdtMt2 is associated with
virulence and resistance to amoxicillin. This domain
may occur in a tandem-repeat arrangement and is found
N-terminal to the catalytic L,D-transpeptidase domain;
this model represents the repeat adjacent to the
catalytic domain.
Length = 99
Score = 24.0 bits (53), Expect = 5.3
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 4/23 (17%)
Query: 2 SFVWFQNRRAKWRKKE----HTK 20
++ W +R WR KE TK
Sbjct: 48 AWYWLSDREVHWRPKEYWPPGTK 70
>gnl|CDD|188428 TIGR03913, rad_SAM_trio, Y_X(10)_GDL-associated radical SAM
protein. This narrowly distributed protein family
contains an N-terminal radical SAM domain. It occurs in
Pseudomonas fluorescens Pf0-1, Ralstonia solanacearum,
and numerous species and strains of Burkholderia.
Members always occur next to a trio of three mutually
homologous genes, all of which contain the domain
pfam08898 as the whole of the protein (about 60 amino
acids) or as the C-terminal domain. The function is
unknown, but the fact that all phylogenetically
correlated proteins are mutually homologous with
prominent invariant motifs (an invariant tyrosine and a
GDL motif) and as small as 60 amino acids suggests that
post-translational modification of pfam08898
domain-containing proteins may be its function. This
view is supported by closer homology to the PqqE radical
SAM protein involved in PQQ biosynthesis from the PqqA
precursor peptide than to other characterized radical
SAM proteins [Unknown function, Enzymes of unknown
specificity].
Length = 477
Score = 24.5 bits (53), Expect = 5.7
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 35 CSGDPIPAEELKRKERARRQKKLMKSLER 63
C D A R++ RRQ LM +LE+
Sbjct: 448 CGADVAAAAAAHRQDAQRRQA-LMNTLEQ 475
>gnl|CDD|218010 pfam04293, SpoVR, SpoVR like protein. Bacillus subtilis stage V
sporulation protein R is involved in spore cortex
formation. Little is known about cortex biosynthesis,
except that it depends on several sigma E controlled
genes, including spoVR.
Length = 427
Score = 24.1 bits (53), Expect = 7.9
Identities = 13/56 (23%), Positives = 21/56 (37%)
Query: 1 MSFVWFQNRRAKWRKKEHTKKGPGRPAHNAHPVTCSGDPIPAEELKRKERARRQKK 56
M+ V R K +E + R + V IP + K +E R+K+
Sbjct: 163 MNHVDRYKRPIKLSLEEEKARQEEREEYLQSQVNDLWRTIPPQREKLEEERARRKR 218
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 24.1 bits (53), Expect = 8.0
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 41 PAEELKRKERARRQKKLMKSL 61
P E + + KK ++S+
Sbjct: 95 PTPEKIEADEEKAIKKRIQSI 115
>gnl|CDD|225944 COG3410, COG3410, Uncharacterized conserved protein [Function
unknown].
Length = 191
Score = 24.0 bits (52), Expect = 8.5
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 38 DPIPAEELKRKERARRQKKLMKSLERQVG 66
D +P +LK E A +K + S Q G
Sbjct: 11 DKMPPLDLKIFEDAGTKKAAICSKTEQYG 39
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 23.9 bits (52), Expect = 9.4
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 25 RPAHNAHPVTCSGDPIPAEELKRKERA 51
R H++H V G+ LK+K +A
Sbjct: 227 RLLHHSHVVQIKGESY---RLKQKRKA 250
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
0.318 0.132 0.416
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,797,770
Number of extensions: 279447
Number of successful extensions: 537
Number of sequences better than 10.0: 1
Number of HSP's gapped: 534
Number of HSP's successfully gapped: 36
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)