RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13512
(170 letters)
>gnl|CDD|236653 PRK10137, PRK10137, alpha-glucosidase; Provisional.
Length = 786
Score = 31.3 bits (71), Expect = 0.22
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 13/67 (19%)
Query: 47 SFLETSGPLNDTYLPL---------YETDAGRRVYDATLASVRENFPQYVEEIEGTADGA 97
S LET ++ L L E G+ + D T+A +P Y +I T DG
Sbjct: 146 SLLETK-ITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIA---GEYPDYQRKISATRDGL 201
Query: 98 KVPFHKL 104
KV F K+
Sbjct: 202 KVTFGKV 208
Score = 30.1 bits (68), Expect = 0.51
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 12 SVRENFPQYVEEIEGTADGAKVPFHKGRTFSGIIKS 47
++ +P Y +I T DG KV F K R ++ S
Sbjct: 182 TIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTS 217
>gnl|CDD|235796 PRK06406, PRK06406, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 771
Score = 30.6 bits (69), Expect = 0.42
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 29 DGAKVPFHKGRTFSGIIKSFLETSGPLNDTYLPLYETDAGRRVYDATLASVRENFPQYVE 88
DG VPF K + I K+ L + + D + +++ VE
Sbjct: 11 DGTVVPFDKKKIAMAIYKAMLSVKN---------GSMEDAEELTDKVVERLKKYERPTVE 61
Query: 89 EIEGTAD 95
+I+ +
Sbjct: 62 QIQDIVE 68
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 28.4 bits (63), Expect = 2.1
Identities = 22/112 (19%), Positives = 46/112 (41%), Gaps = 14/112 (12%)
Query: 29 DGAKVPFHKGRTFSGIIKSFLETSGPLNDTYLP--LYET--DAGRRVYDATLASVRENFP 84
+G VPF++ R F + +F +T + + LP L + +V + + E
Sbjct: 15 NGMFVPFNQNRIFQALEAAFRDTRSLEDHSPLPEDLESSIRSITHQVVKEVVQKITEGQV 74
Query: 85 QYVEEIEGTADGAKVPFHKLFLLHMDDITPNVV----HRKSAVEGTVGCSSV 132
VE I+ + +L++ + D+ + + RK+ + + SV
Sbjct: 75 VTVERIQDMVE------SQLYVNGLQDVARDYIVYRDDRKAHRKKSWQSLSV 120
>gnl|CDD|198190 cd09937, SH2_csk_like, Src homology 2 (SH2) domain found in
Carboxyl-Terminal Src Kinase (Csk). Both the C-terminal
Src kinase (CSK) and CSK-homologous kinase (CHK) are
members of the CSK-family of protein tyrosine kinases.
These proteins suppress activity of Src-family kinases
(SFK) by selectively phosphorylating the conserved
C-terminal tail regulatory tyrosine by a similar
mechanism. CHK is also capable of inhibiting SFKs by a
non-catalytic mechanism that involves binding of CHK to
SFKs to form stable protein complexes. The
unphosphorylated form of SFKs is inhibited by CSK and
CHK by a two-step mechanism. The first step involves the
formation of a complex of SFKs with CSK/CHK with the
SFKs in the complex are inactive. The second step,
involves the phosphorylation of the C-terminal tail
tyrosine of SFKs, which then dissociates and adopt an
inactive conformation. The structural basis of how the
phosphorylated SFKs dissociate from CSK/CHK to adopt the
inactive conformation is not known. The inactive
conformation of SFKs is stabilized by two intramolecular
inhibitory interactions: (a) the pYT:SH2 interaction in
which the phosphorylated C-terminal tail tyrosine (YT)
binds to the SH2 domain, and (b) the linker:SH3
interaction of which the SH2-kinase domain linker binds
to the SH3 domain. SFKs are activated by multiple
mechanisms including binding of the ligands to the SH2
and SH3 domains to displace the two inhibitory
intramolecular interactions, autophosphorylation, and
dephosphorylation of YT. By selective phosphorylation
and the non-catalytic inhibitory mechanism CSK and CHK
are able to inhibit the active forms of SFKs. CSK and
CHK are regulated by phosphorylation and inter-domain
interactions. They both contain SH3, SH2, and kinase
domains separated by the SH3-SH2 connector and SH2
kinase linker, intervening segments separating the three
domains. They lack a conserved tyrosine phosphorylation
site in the kinase domain and the C-terminal tail
regulatory tyrosine phosphorylation site. The CSK SH2
domain is crucial for stabilizing the kinase domain in
the active conformation. A disulfide bond here regulates
CSK kinase activity. The subcellular localization and
activity of CSK are regulated by its SH2 domain. In
general SH2 domains are involved in signal transduction.
They typically bind pTyr-containing ligands via two
surface pockets, a pTyr and hydrophobic binding pocket,
allowing proteins with SH2 domains to localize to
tyrosine phosphorylated sites.
Length = 98
Score = 26.9 bits (60), Expect = 2.6
Identities = 10/27 (37%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 132 VCCNQKNEHYLGRYLKSDKHLDIKEER 158
V K EHY R + + L I EE
Sbjct: 43 VSFEGKVEHY--RVIYRNGKLTIDEEE 67
>gnl|CDD|235820 PRK06521, PRK06521, hydrogenase 4 subunit B; Validated.
Length = 667
Score = 27.5 bits (62), Expect = 4.0
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 86 YVEEIEGTADGAKVPFHKLFLLHM 109
Y E EG GA F+ LFL M
Sbjct: 103 YFREYEGKGPGAMGFFYNLFLASM 126
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 26.6 bits (59), Expect = 5.3
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 71 VYDATLASVRENFPQYVEEIEGTADGAKVP 100
VYD T + + P ++EE E + +VP
Sbjct: 82 VYDVTNMASFHSLPSWIEECEQHSLPNEVP 111
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 27.2 bits (61), Expect = 5.6
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 137 KNEHYL-GRYLKSDKHLDIKEERRSKDKS 164
N L G+YL K +++ ++RR+ +
Sbjct: 577 ANPESLTGQYLSGKKTIEVPKKRRAPNGK 605
>gnl|CDD|118064 pfam09528, Ehrlichia_rpt, Ehrlichia tandem repeat (Ehrlichia_rpt).
This entry represents 77 residues of an 80 amino acid
(240 nucleotide) tandem repeat, found in a variable
number of copies in an immunodominant outer membrane
protein of Ehrlichia chaffeensis, a tick-borne obligate
intracellular pathogen.
Length = 707
Score = 26.9 bits (58), Expect = 6.5
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 4/86 (4%)
Query: 50 ETSGPLNDTYLPLYETDAGRRVYDATLASVRENFPQYVEEIEGTADGAKVPFHKLFLL-H 108
E P D + ++ G +V + E P+ + + ADG +P + + + +
Sbjct: 558 EDLQPAVDGSVEHSSSEVGDKVCET---CEEEFTPEIKADSQPVADGEDIPINPMPCIDN 614
Query: 109 MDDITPNVVHRKSAVEGTVGCSSVCC 134
+D I H+ + +CC
Sbjct: 615 IDSIIIFHYHKDCKKGSAIFEDEMCC 640
>gnl|CDD|235992 PRK07328, PRK07328, histidinol-phosphatase; Provisional.
Length = 269
Score = 26.5 bits (59), Expect = 7.7
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 59 YLPLYETDAGRRVYDATLASVRENFPQYVEEIEGT 93
+LP+Y R D LA E P YV E+E
Sbjct: 40 HLPMYFLPPEWR--DPGLAMRLEELPFYVSEVERL 72
>gnl|CDD|131525 TIGR02472, sucr_P_syn_N, sucrose-phosphate synthase, putative,
glycosyltransferase domain. This family consists of the
N-terminal regions, or in some cases the entirety, of
bacterial proteins closely related to plant
sucrose-phosphate synthases (SPS). The C-terminal domain
(TIGR02471), found with most members of this family,
resembles both bona fide plant sucrose-phosphate
phosphatases (SPP) and the SPP-like domain of plant SPS.
At least two members of this family lack the SPP-like
domain, which may have binding or regulatory rather than
enzymatic activity by analogy to plant SPS. This enzyme
produces sucrose 6-phosphate and UDP from UDP-glucose
and D-fructose 6-phosphate, and may be encoded near the
gene for fructokinase.
Length = 439
Score = 26.6 bits (59), Expect = 8.7
Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 29/84 (34%)
Query: 69 RRVYDATLASVRENFPQYVEEIEGTADGAK---VPF-------HKLFLLHMDDIT----- 113
R + DA ++ P Y + IE A GA+ +PF +L ++D++
Sbjct: 53 RLIKDAKVS------PDYAQPIERIAPGARIVRLPFGPRRYLRKELLWPYLDELADNLLQ 106
Query: 114 --------PNVVHRKSAVEGTVGC 129
P+++H A G VG
Sbjct: 107 HLRQQGHLPDLIHAHYADAGYVGA 130
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
0.316 0.135 0.395
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,568,816
Number of extensions: 761048
Number of successful extensions: 623
Number of sequences better than 10.0: 1
Number of HSP's gapped: 623
Number of HSP's successfully gapped: 17
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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 (21.6 bits)
S2: 55 (25.0 bits)