RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3948
(143 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 31.6 bits (72), Expect = 0.013
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 63 HMRKHTGVKPLKCSSCNYSCST 84
HMR HTG KP KC C S S+
Sbjct: 5 HMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|238703 cd01412, SIRT5_Af1_CobB, SIRT5_Af1_CobB: Eukaryotic, archaeal and
prokaryotic group (class3) which includes human sirtuin
SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli
CobB; and are members of the SIR2 family of proteins,
silent information regulator 2 (Sir2) enzymes which
catalyze NAD+-dependent protein/histone deacetylation.
Sir2 proteins have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
CobB is a bacterial sirtuin that deacetylates acetyl-CoA
synthetase at an active site lysine to stimulate its
enzymatic activity. .
Length = 224
Score = 29.1 bits (66), Expect = 0.69
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 8 LKCTFCNIIF-NKLQDEELIMTHCKSCKKPKRPD 40
++C+ C + N + E + C C RP
Sbjct: 110 VRCSSCGYVGENNEEIPEEELPRCPKCGGLLRPG 143
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 25.8 bits (57), Expect = 1.4
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 74 KCSSCNYSCSTKSALSVHQKRH 95
KC C S S KS L H + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|223435 COG0358, DnaG, DNA primase (bacterial type) [DNA replication,
recombination, and repair].
Length = 568
Score = 27.8 bits (62), Expect = 2.1
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 38 RPDKSYNYACFICTYHTRKHGDMIGHMRKHTGV 70
P+K + Y CF C GD I + + G+
Sbjct: 50 SPEKGF-YHCFGCG----AGGDAIKFLMELLGL 77
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 2.5
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 73 LKCSSCNYSCSTKSALSVHQKRH 95
+C C +KSAL H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 23.6 bits (51), Expect = 9.9
Identities = 7/23 (30%), Positives = 9/23 (39%)
Query: 45 YACFICTYHTRKHGDMIGHMRKH 67
Y C C + + HMR H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|236254 PRK08384, PRK08384, thiamine biosynthesis protein ThiI;
Provisional.
Length = 381
Score = 26.8 bits (59), Expect = 4.1
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 14 NIIFNKLQDEELIMTHCKSCKKPKRPDKSYNYACFICTYHTRKHGDMI 61
+I K Q+ E I+ K KK NY C C + KH D I
Sbjct: 239 ELIVVKPQERERIIQKLKELKKE-------NYTCVFCKFMMVKHADRI 279
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 26.5 bits (58), Expect = 6.6
Identities = 22/101 (21%), Positives = 34/101 (33%), Gaps = 22/101 (21%)
Query: 7 ILKCTFCNIIF------------NKLQDEELIMTHCKSCKKPKRPDKSYNYACFICTYHT 54
I +C+FC L++E C SC + + C C H
Sbjct: 142 IFQCSFCQDFLCEDDQFEHQASCQVLENENF---KCMSCNRLGQYSCLRCKVCC-CNDHV 197
Query: 55 RKHGDMIGHMRKHTGVKPLKCSSCNYSCSTKSALSVHQKRH 95
R+ G K+ K L C C Y + LS+ + +
Sbjct: 198 RRKG------FKYDKDKNLPCPKCGYPTTETKDLSMSTRSY 232
>gnl|CDD|236282 PRK08535, PRK08535, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 310
Score = 26.4 bits (59), Expect = 6.7
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 18 NKLQDEELIMTHCKS 32
+++D ++IMTHC S
Sbjct: 116 KRIRDGDVIMTHCNS 130
>gnl|CDD|188057 TIGR00511, ribulose_e2b2, ribose-1,5-bisphosphate isomerase, e2b2
family. The delineation of this family was based
originally, in part, on a discussion and
neighbor-joining phylogenetic study by Kyrpides and
Woese of archaeal and other proteins homologous to the
alpha, beta, and delta subunits of eukaryotic initiation
factor 2B (eIF-2B), a five-subunit molecule that
catalyzes GTP recycling for eIF-2. Recently, Sato, et
al. assigned the function ribulose-1,5 bisphosphate
isomerase [Energy metabolism, Other].
Length = 301
Score = 26.2 bits (58), Expect = 6.9
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 18 NKLQDEELIMTHCKS 32
+++D ++IMTHC S
Sbjct: 111 KRIRDGDVIMTHCNS 125
>gnl|CDD|140327 PTZ00306, PTZ00306, NADH-dependent fumarate reductase; Provisional.
Length = 1167
Score = 26.3 bits (58), Expect = 7.0
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 3 VDHTILKCTFCNIIFNKLQDEELIMTHCK 31
+ TI++ T + I KL IMT
Sbjct: 542 IGFTIMR-TLEDHIRTKLSGRVTIMTETT 569
>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH. The
fifth LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated
protein-protein interactions. PINCH comprises an array
of five LIM domains that interact with integrin-linked
kinase (ILK), Nck2 (also called Nckbeta or Grb4) and
other interaction partners. These interactions are
essential for triggering the FA assembly and for
relaying diverse mechanical and biochemical signals
between Cell-extracellular matrix and the actin
cytoskeleton. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 24.2 bits (53), Expect = 8.6
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 58 GDMIGHMRKHTGVKPLKCSSCNYSCSTKS 86
GD++ + K V CS C+ + KS
Sbjct: 10 GDVVSALNKTWCVDHFSCSFCDTKLTLKS 38
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
0.328 0.137 0.438
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,779,764
Number of extensions: 554321
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 677
Number of HSP's successfully gapped: 45
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.4 bits)