RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy445
(142 letters)
>gnl|CDD|216970 pfam02312, CBF_beta, Core binding factor beta subunit. Core
binding factor (CBF) is a heterodimeric transcription
factor essential for genetic regulation of hematopoiesis
and osteogenesis. The beta subunit enhances DNA-binding
ability of the alpha subunit in vitro, and has been show
to have a structure related to the OB fold.
Length = 170
Score = 149 bits (378), Expect = 5e-47
Identities = 60/94 (63%), Positives = 75/94 (79%), Gaps = 5/94 (5%)
Query: 39 MPRVVPDQKSKFESDELFRRLSRESEVRYTGFRDRPQEERQVRFQNGCREGHTEIAFIAT 98
MPRVVPDQ+SKFESDELFR+LSRESE++YTG+RDRP EER+ RFQN CREGH E++F+A+
Sbjct: 1 MPRVVPDQRSKFESDELFRKLSRESEIKYTGYRDRPAEERRDRFQNHCREGHAELSFVAS 60
Query: 99 GTNIQLVFNPSISANSYHMAPPSRECDFDKEHGK 132
GTN+QL FNP ++ + DFD+E GK
Sbjct: 61 GTNLQLQFNP--NSTIGNQ---KEYVDFDREPGK 89
>gnl|CDD|239811 cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal,
anticodon recognition domain of the type found in the
homodimeric non-discriminating (ND) Pyrococcus
kodakaraensis aspartyl-tRNA synthetase (AspRS). This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. P. kodakaraensis
AspRS is a class 2b aaRS. aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation the AA by ATP in the
presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose. P.
kodakaraensis ND-AspRS can charge both tRNAAsp and
tRNAAsn. Some of the enzymes in this group may be
discriminating, based on the presence of homologs of
asparaginyl-tRNA synthetase (AsnRS) in their completed
genomes.
Length = 108
Score = 28.4 bits (64), Expect = 0.55
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 42 VVPDQKSKFESDELFRRLSRESEVRYTG 69
P +K E + R+LSRES + TG
Sbjct: 45 TAPKKKVDKELFKTVRKLSRESVISVTG 72
>gnl|CDD|232792 TIGR00033, aroC, chorismate synthase. Homotetramer (noted in
E.coli) suggests reason for good conservation [Amino
acid biosynthesis, Aromatic amino acid family].
Length = 351
Score = 28.1 bits (63), Expect = 1.4
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 12/64 (18%)
Query: 53 DELFRRLSRESEVRYTGFRDRPQEERQVRFQNGCREGHTEIAFIATGTNIQL-VFNPSIS 111
+L RR R R T R +E +V +G EG T TG I L + N +
Sbjct: 34 PDLDRR--RPGYSRGTRMR---KENDEVEILSGVFEGKT------TGAPIALMIRNKDVR 82
Query: 112 ANSY 115
++ Y
Sbjct: 83 SSDY 86
>gnl|CDD|143530 cd07155, NR_DBD_ER_like, DNA-binding domain of estrogen receptor
(ER) and estrogen related receptors (ERR) is composed of
two C4-type zinc fingers. DNA-binding domains of
estrogen receptor (ER) and estrogen related receptors
(ERR) are composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
co-ordinates a single zinc atom. ER and ERR interact
with the palindromic inverted repeat,
5'GGTCAnnnTGACC-3', upstream of the target gene and
modulate the rate of transcriptional initiation. ERR and
ER are closely related and share sequence similarity,
target genes, co-regulators and promoters. While ER is
activated by endogenous estrogen, ERR lacks the ability
to bind to estrogen. Estrogen receptor mediates the
biological effects of hormone estrogen by the binding of
the receptor dimer to estrogen response element of
target genes. However, ERRs seem to interfere with the
classic ER-mediated estrogen responsive signaling by
targeting the same set of genes. ERRs and ERs exhibit
the common modular structure with other nuclear
receptors. They have a central highly conserved DNA
binding domain (DBD), a non-conserved N-terminal domain,
a flexible hinge and a C-terminal ligand binding domain
(LBD).
Length = 75
Score = 26.3 bits (58), Expect = 2.1
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 106 FNPSISANSYHMAPPSRECDFDKEHGKSV 134
F +I N + P + EC+ DK+ KS
Sbjct: 25 FKRTIQGNLGYSCPSTSECEVDKKRRKSC 53
>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
Provisional.
Length = 308
Score = 27.4 bits (61), Expect = 2.5
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 15/74 (20%)
Query: 48 SKFESDELFRRLSRESEVRYTGFRDRPQEERQVRFQN--GCREGHT-EIAFIATGTNIQL 104
SKF DE R++ E+ + GF R+ N G REGH +A +A N QL
Sbjct: 143 SKFLFDEYVRQILPEANSQICGF----------RYFNVYGPREGHKGSMASVAFHLNNQL 192
Query: 105 VF--NPSISANSYH 116
NP + S +
Sbjct: 193 NNGENPKLFEGSEN 206
>gnl|CDD|227504 COG5177, COG5177, Uncharacterized conserved protein [Function
unknown].
Length = 769
Score = 27.4 bits (60), Expect = 2.9
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 41 RVVPDQKSKFESDELFRRLSRESEVR-YTGFRDRPQEERQ 79
V D++S + +E F LS E E R FRD +E+R+
Sbjct: 425 EVAGDEESAIDDNEGFEELSPEEEERQLREFRDMEKEDRE 464
>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed.
Length = 790
Score = 27.4 bits (60), Expect = 3.6
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 15/84 (17%)
Query: 53 DELFRRLSRESEVRYTGFRDRPQEERQVRFQNGCREGHTEIAFIATGTNIQLVFNPSISA 112
D+ F E+RY+ R+ R F E HT +A G +
Sbjct: 643 DDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEELHT---LVAEGVVV---------- 689
Query: 113 NSYHMAPPSRECDFDKEHGKSVSR 136
++ +PP ++ +FD +GK +SR
Sbjct: 690 --HNCSPPFKQAEFDILYGKGISR 711
>gnl|CDD|236476 PRK09354, recA, recombinase A; Provisional.
Length = 349
Score = 26.3 bits (59), Expect = 7.0
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 117 MAPPSRECDFDKEHGKSVSRFN 138
+APP ++ +FD +G+ +SR
Sbjct: 252 VAPPFKQAEFDIMYGEGISREG 273
>gnl|CDD|215755 pfam00154, RecA, recA bacterial DNA recombination protein. RecA is
a DNA-dependent ATPase and functions in DNA repair
systems. RecA protein catalyzes an ATP-dependent DNA
strand-exchange reaction that is the central step in the
repair of dsDNA breaks by homologous recombination.
Length = 322
Score = 26.1 bits (58), Expect = 7.6
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 117 MAPPSRECDFDKEHGKSVSRF 137
+APP ++ +FD +G+ +S+
Sbjct: 244 VAPPFKQAEFDIMYGEGISKE 264
>gnl|CDD|238566 cd01146, FhuD, Fe3+-siderophore binding domain FhuD. These
proteins have been shown to function as initial
receptors in ABC transport of Fe3+-siderophores in many
eubacterial species. They belong to the TroA-like
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
A typical TroA-like protein is comprised of two
globular subdomains connected by a long alpha helix and
binds its specific ligands in the cleft between these
domains.
Length = 256
Score = 25.7 bits (57), Expect = 8.2
Identities = 3/31 (9%), Positives = 11/31 (35%)
Query: 29 EQPKPRFIFKMPRVVPDQKSKFESDELFRRL 59
+ +F + +++ L++ L
Sbjct: 196 AKADADVLFVFTYEDEELAQALQANPLWQNL 226
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to a
dsDNA region. ATP is hydrolyzed in the process. Part of
the SOS respones, it is regulated by LexA via
autocatalytic cleavage [DNA metabolism, DNA replication,
recombination, and repair].
Length = 321
Score = 25.8 bits (57), Expect = 9.0
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 118 APPSRECDFDKEHGKSVSR 136
APP +E +FD +G+ +S+
Sbjct: 248 APPFKEAEFDILYGEGISK 266
>gnl|CDD|149180 pfam07960, CBP4, CBP4. The CBP4 in S. cerevisiae is essential
for the expression and activity of ubiquinol-cytochrome
c reductase. This family appears to be fungal specific.
Length = 128
Score = 25.4 bits (56), Expect = 9.5
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 54 ELFRRLSRESEVRYTGFRDRPQEERQ 79
EL R + E RY RD Q+E
Sbjct: 35 ELIARYNPELRKRYEEERDLRQQEFD 60
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
0.320 0.136 0.405
Gapped
Lambda K H
0.267 0.0644 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,208,586
Number of extensions: 627199
Number of successful extensions: 457
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 20
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
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 (24.8 bits)