RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11311
(499 letters)
>gnl|CDD|197698 smart00396, ZnF_UBR1, Putative zinc finger in N-recognin, a
recognition component of the N-end rule pathway. Domain
is involved in recognition of N-end rule substrates in
yeast Ubr1p.
Length = 71
Score = 72.1 bits (177), Expect = 5e-16
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 62 KLCTYTITQKEFMNQHWYHCHTCKMIDGVGVCSVCAQ-VCHKNHDITYS-KFGNFFCDCG 119
+C Y T E + Y C TC + +CS C + CHK HD++ G+ CDCG
Sbjct: 1 DVCGYKFTGGEVI----YRCKTCGLDPTCVLCSDCFRPSCHKGHDVSLKTSRGSGICDCG 56
Query: 120 AKE 122
KE
Sbjct: 57 DKE 59
>gnl|CDD|216929 pfam02207, zf-UBR, Putative zinc finger in N-recognin (UBR box).
This region is found in E3 ubiquitin ligases that
recognise N-recognins.
Length = 71
Score = 65.9 bits (161), Expect = 1e-13
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 6/63 (9%)
Query: 62 KLCTYTITQKEFMNQHWYHCHTCKMIDGVGVCSVC-AQVCHKNHDITYSK-FGNFFCDCG 119
+C Y Q Y C TC + +C C + CHK HD+ CDCG
Sbjct: 1 SVCGYVFKSG----QPVYRCLTCSLDPTCVICYECFSISCHKGHDVVELFSKRGGCCDCG 56
Query: 120 AKE 122
E
Sbjct: 57 DPE 59
>gnl|CDD|216039 pfam00643, zf-B_box, B-box zinc finger.
Length = 42
Score = 30.1 bits (68), Expect = 0.21
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 4/29 (13%)
Query: 79 YHCHTCKMIDGVGVCSVCAQVCHKNHDIT 107
+C C+ + +C CA HK H +
Sbjct: 16 LYCEDCQQL----LCEECALSGHKGHTVV 40
>gnl|CDD|222668 pfam14309, DUF4378, Domain of unknown function (DUF4378).
Length = 160
Score = 30.3 bits (69), Expect = 1.2
Identities = 30/135 (22%), Positives = 55/135 (40%), Gaps = 14/135 (10%)
Query: 203 MSSASLSHQESSSMPSSLRQRSSFEPILSNSYHYMYDDNYYGYNQIKIENLREKLGPVSP 262
+S++ L E SS+ + S + L S ++ Y ++ KL
Sbjct: 10 LSASGLLRDEESSLS----RWHSSDCPLDPSLFDELENKYSESSKDTESRSDRKL----- 60
Query: 263 NIFDRIWEILPPILEVFKEMTPALKAGIAKTSPV----GVFDRVSHGLFQLQNMQHKFVE 318
+FD + EIL ILE + M P LK+ + P + + V + +L + + +
Sbjct: 61 -LFDCVNEILVEILEPYLSMKPWLKSVTLRIRPKPSGEQLLEEVWKEISRLLSSACEVED 119
Query: 319 NTDNLMVPVMGSQEG 333
D+L+ + S G
Sbjct: 120 ELDSLVDKDLSSGGG 134
>gnl|CDD|199864 cd06240, M14-like_1_3, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 274
Score = 29.6 bits (67), Expect = 3.0
Identities = 12/61 (19%), Positives = 18/61 (29%), Gaps = 8/61 (13%)
Query: 22 GESEAFPPPLDLDIEWNDDVTHDDDEDSAGDESDEDSLCNKLCTYTITQKEFMNQHWYHC 81
E P L + V HD++ D E + + E+ Q Y
Sbjct: 125 TPKEQRSPLPRL---YGKYVGHDNNRDGYMFSQKETTR-----NNRVLFLEWFPQIMYDL 176
Query: 82 H 82
H
Sbjct: 177 H 177
>gnl|CDD|240496 cd13738, SPRY_PRY_TRIM14, PRY/SPRY domain of tripartite
motif-binding protein 14 (TRIM14). This is a TRIM14
domain family contains residues in the N-terminus that
form a distinct PRY domain structure such that the B30.2
domain consists of PRY and SPRY subdomains. TRIM14
domains have yet to be characterized. These B30.2
domains are a more recent adaptation where the SPRY/PRY
combination is a possible component of immune defense.
It belongs to Class IV TRIM protein family which has
members involved in antiviral immunity at various levels
of interferon signaling cascade.
Length = 173
Score = 29.1 bits (65), Expect = 4.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 252 NLREKLGPVSPNIFDRIWEIL 272
NL LGP P FD++W++L
Sbjct: 24 NLLGILGPCPPQRFDKLWQVL 44
>gnl|CDD|176134 cd08443, PBP2_CysB, The C-terminal substrate domain of LysR-type
transcriptional regulator CysB contains type 2
periplasmic binding fold. CysB is a transcriptional
activator of genes involved in sulfate and thiosulfate
transport, sulfate reduction, and cysteine synthesis. In
Escherichia coli, the regulation of transcription in
response to sulfur source is attributed to two
transcriptional regulators, CysB and Cbl. CysB, in
association with Cbl, downregulates the expression of
ssuEADCB operon which is required for the utilization of
sulfur from aliphatic sulfonates, in the presence of
cysteine. Also, Cbl and CysB together directly function
as transcriptional activators of tauABCD genes, which
are required for utilization of taurine as sulfur source
for growth. Like many other members of the LTTR family,
CysB is composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The structural topology of
this substrate-binding domain is most similar to that of
the type 2 periplasmic binding proteins (PBP2), which
are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 198
Score = 28.7 bits (64), Expect = 5.9
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 271 ILPPILEVFKEMTPALKAGIAKTSPVGVFDRVSHGL 306
+LPP+++ F E P + + + SP + + VS GL
Sbjct: 14 VLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGL 49
>gnl|CDD|237988 cd00021, BBOX, B-Box-type zinc finger; zinc binding domain
(CHC3H2); often present in combination with other
motifs, like RING zinc finger, NHL motif, coiled-coil or
RFP domain in functionally unrelated proteins, most
likely mediating protein-protein interaction.
Length = 39
Score = 25.7 bits (57), Expect = 8.0
Identities = 6/26 (23%), Positives = 9/26 (34%), Gaps = 4/26 (15%)
Query: 79 YHCHTCKMIDGVGVCSVCAQVCHKNH 104
C T + + +C C H H
Sbjct: 13 LFCETDRAL----LCVDCDLSVHSGH 34
>gnl|CDD|197662 smart00336, BBOX, B-Box-type zinc finger.
Length = 42
Score = 25.4 bits (56), Expect = 8.5
Identities = 6/26 (23%), Positives = 11/26 (42%), Gaps = 4/26 (15%)
Query: 79 YHCHTCKMIDGVGVCSVCAQVCHKNH 104
+ C C + +C C + H+ H
Sbjct: 16 FFCEECGAL----LCRTCDEAEHRGH 37
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 28.5 bits (64), Expect = 9.5
Identities = 10/36 (27%), Positives = 15/36 (41%)
Query: 23 ESEAFPPPLDLDIEWNDDVTHDDDEDSAGDESDEDS 58
+ D D E +V D+D D G+ D +S
Sbjct: 88 AEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVES 123
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
0.317 0.131 0.387
Gapped
Lambda K H
0.267 0.0666 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,176,015
Number of extensions: 2257823
Number of successful extensions: 2231
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2222
Number of HSP's successfully gapped: 19
Length of query: 499
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 398
Effective length of database: 6,457,848
Effective search space: 2570223504
Effective search space used: 2570223504
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: 61 (27.4 bits)