RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3865
(107 letters)
>gnl|CDD|216993 pfam02359, CDC48_N, Cell division protein 48 (CDC48), N-terminal
domain. This domain has a double psi-beta barrel fold
and includes VCP-like ATPase and N-ethylmaleimide
sensitive fusion protein N-terminal domains. Both the
VAT and NSF N-terminal functional domains consist of
two structural domains of which this is at the
N-terminus. The VAT-N domain found in AAA ATPases
pfam00004 is a substrate 185-residue recognition
domain.
Length = 84
Score = 65.7 bits (161), Expect = 1e-15
Identities = 30/80 (37%), Positives = 38/80 (47%), Gaps = 4/80 (5%)
Query: 8 RGDTVLLRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTC--PDEKIRMNR 65
D + RG R MDEL LF GD V ++GKRR +V IV IRM+
Sbjct: 7 PNDRDVGRGIARLSPKDMDELGLFPGDIVEIKGKRR--TVAIVWPARPEDEGPGIIRMDG 64
Query: 66 VMRNNLRVRLSDVVSLVPCP 85
V R N V + D V++ P
Sbjct: 65 VQRKNAGVSIGDEVTVRPAE 84
>gnl|CDD|215012 smart01073, CDC48_N, Cell division protein 48 (CDC48) N-terminal
domain. This domain has a double psi-beta barrel fold
and includes VCP-like ATPase and N-ethylmaleimide
sensitive fusion protein N-terminal domains. Both the
VAT and NSF N-terminal functional domains consist of
two structural domains of which this is at the
N-terminus. The VAT-N domain found in AAA ATPases is a
substrate 185-residue recognition domain.
Length = 82
Score = 59.5 bits (145), Expect = 3e-13
Identities = 29/72 (40%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 14 LRGKRRKESAKMDELNLFRGDTVLLRGKRRKESVCIVLSDDTC-PDEKIRMNRVMRNNLR 72
RG R MDEL LF GD VL+ GKRR V IV P IR++ V R N
Sbjct: 13 GRGIARLSPEDMDELGLFPGDYVLITGKRRT--VAIVWPAYPEDPGGIIRIDGVQRKNAG 70
Query: 73 VRLSDVVSLVPC 84
V + D V++
Sbjct: 71 VSIGDTVTVRKA 82
>gnl|CDD|213016 cd12140, SH3_Amphiphysin_I, Src Homology 3 domain of Amphiphysin
I. Amphiphysins function primarily in endocytosis and
other membrane remodeling events. They exist in several
isoforms and mammals possess two amphiphysin proteins
from distinct genes. Amphiphysin I proteins, enriched
in the brain and nervous system, contain domains that
bind clathrin, Adaptor Protein complex 2 (AP2),
dynamin, and synaptojanin. They function in synaptic
vesicle endocytosis. Human autoantibodies to
amphiphysin I hinder GABAergic signaling and contribute
to the pathogenesis of paraneoplastic stiff-person
syndrome. Amphiphysins contain an N-terminal BAR domain
with an additional N-terminal amphipathic helix (an
N-BAR), a variable central domain, and a C-terminal SH3
domain. The SH3 domain of amphiphysins bind
proline-rich motifs present in binding partners such as
dynamin, synaptojanin, and nsP3. It also belongs to a
subset of SH3 domains that bind ubiquitin in a site
that overlaps with the peptide binding site. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 72
Score = 27.2 bits (60), Expect = 0.76
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 21 ESAKMDELNLFRGDTVLL 38
E+A DEL L RGD VL+
Sbjct: 12 EAANSDELELKRGDIVLV 29
>gnl|CDD|221615 pfam12514, DUF3718, Protein of unknown function (DUF3718). This
domain family is found in bacteria and viruses, and is
approximately 70 amino acids in length. There is a
single completely conserved residue C that may be
functionally important.
Length = 69
Score = 25.7 bits (57), Expect = 2.1
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 47 VCI-VLSDDTCPDEKIRMNRVMRNNLRVRLSDVVSLVPCPG 86
+C V SDD KIR+ + ++ R++ + + C G
Sbjct: 1 ICKAVASDD-----KIRLRKTLKEY-RIKKRRIAPGLVCNG 35
>gnl|CDD|233291 TIGR01143, murF,
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine
ligase. This family consists of the strictly bacterial
MurF gene of peptidoglycan biosynthesis. This enzyme is
almost always
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,
6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a
few species, MurE adds lysine rather than
diaminopimelate. This enzyme acts on the product from
MurE activity, and so is also subfamily rather than
equivalog. Staphylococcus aureus is an example of
species in this MurF protein would differ [Cell
envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 417
Score = 26.1 bits (58), Expect = 4.5
Identities = 9/26 (34%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 3 ELNLFRGDTVLLRGKRRKESAKMDEL 28
+ L +GD VL++G R S K++++
Sbjct: 391 KTLLRKGDVVLVKGSR---SVKLEKV 413
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 25.2 bits (55), Expect = 9.5
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 76 SDVVSLVPCPGIVYGKRIHVLPIDDS 101
SD +L+ P +G R+H +P DS
Sbjct: 174 SDRHALIVPPSTGHGNRVHPMPFPDS 199
>gnl|CDD|238413 cd00798, INT_XerDC, XerD and XerC integrases, DNA
breaking-rejoining enzymes, N- and C-terminal domains.
XerD-like integrases are involved in the site-specific
integration and excision of lysogenic bacteriophage
genomes, transposition of conjugative transposons,
termination of chromosomal replication, and stable
plasmid inheritance. They share the same fold in their
catalytic domain containing six conserved active site
residues and the overall reaction mechanism with the DNA
breaking-rejoining enzyme superfamily. In Escherichia
coli, the Xer site-specific recombination system acts to
convert dimeric chromosomes, which are formed by
homologous recombination to monomers. Two related
recombinases, XerC and XerD, bind cooperatively to a
recombination site present in the E. coli chromosome.
Each recombinase catalyzes the exchange of one pair of
DNA strand in a reaction that proceeds through a
Holliday junction intermediate. These enzymes can bridge
two different and well-separated DNA sequences called
arm- and core-sites. The C-terminal domain binds,
cleaves and re-ligates DNA strands at the core-sites,
while the N-terminal domain is largely responsible for
high-affinity binding to the arm-type sites.
Length = 284
Score = 24.9 bits (55), Expect = 9.6
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 16 GKRRKE--SAKMDELNLFRGDTVLLRGKRRKE 45
G R E K+ +++L RG + +RGK KE
Sbjct: 140 GLRVSELVGLKLSDVDLSRG-LIRVRGKGNKE 170
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
0.324 0.142 0.413
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,428,076
Number of extensions: 460677
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 379
Number of HSP's successfully gapped: 15
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)