RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7603
(130 letters)
>gnl|CDD|216893 pfam02135, zf-TAZ, TAZ zinc finger. The TAZ2 domain of CBP binds
to other transcription factors such as the p53 tumour
suppressor protein, E1A oncoprotein, MyoD, and GATA-1.
The zinc coordinating motif that is necessary for
binding to target DNA sequences consists of HCCC.
Length = 74
Score = 29.6 bits (67), Expect = 0.12
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 50 EEIVQHMIDCIKEVNNVVEIPATTTRILLNHFK 82
+++++HM C + + + L+ H K
Sbjct: 32 KKLLKHMDSCKRRKCLYGGCL--SCKQLIKHAK 62
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 28.6 bits (65), Expect = 0.94
Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 15/80 (18%)
Query: 48 ST-EEIVQ-----HMIDC--------IKEVNNV-VEIPATTTRILLNHFKWDKEKLMERY 92
+T EE+ + H++D I+ V V E+ A LL + K D
Sbjct: 261 ATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLLDEPRIE 320
Query: 93 YDGDQESSTLDYSASTSSGL 112
+ + SA T GL
Sbjct: 321 RLEEGYPEAVFVSAKTGEGL 340
>gnl|CDD|221341 pfam11959, DUF3473, Domain of unknown function (DUF3473). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and archaea. This domain is
about 130 amino acids in length. This domain is found
associated with pfam01522. This domain has two
completely conserved residues (P and H) that may be
functionally important.
Length = 133
Score = 27.2 bits (61), Expect = 1.7
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 59 CIKEVNNVVEIPATTTRILLNHF 81
+ +VE P TTT + +
Sbjct: 22 RPETGGGLVEFPVTTTPLGGRNL 44
>gnl|CDD|223254 COG0176, MipB, Transaldolase [Carbohydrate transport and
metabolism].
Length = 239
Score = 27.2 bits (61), Expect = 2.1
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 43 VFEVLS--TEEIVQ---HMIDCIKEVNNVVEIPATT 73
V EVLS E +++ + I V V++IPAT
Sbjct: 67 VDEVLSFDAEAMIEEARRLAKLIDNVGIVIKIPATW 102
>gnl|CDD|235958 PRK07194, fliG, flagellar motor switch protein G; Reviewed.
Length = 334
Score = 26.5 bits (59), Expect = 4.0
Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 32/86 (37%)
Query: 32 PKDRQNDVEEFVFEVLSTEEIVQHMID--------CIKE-----------VNNVVEIPAT 72
P+DRQ+D+ ++ + +++ + ++D C+ V +I
Sbjct: 152 PEDRQDDI---LYRIAQLDDVDRDVVDELDELIERCLAVLSEQSHTKVIGVKQAADI--- 205
Query: 73 TTRILLNHFKWDKEKLME--RYYDGD 96
+N F D+++LME + +D +
Sbjct: 206 -----INRFPGDRQQLMEMLKEHDEE 226
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 26.8 bits (60), Expect = 4.2
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 32 PKDRQNDVEEFVFEVLSTEEIVQHMIDCIKEVNNVVEI-PATTTRILLNHFKWDKEKLME 90
P+ ++ ++E E EE V+ +I+ I+E+ V +I P + +K++ ++
Sbjct: 742 PEPDESKIDE---EAELAEEYVKRLIEDIREILKVAKIKPKKVYIYVAPDWKYEVLEIAA 798
Query: 91 RYYD 94
D
Sbjct: 799 ENGD 802
>gnl|CDD|236008 PRK07390, PRK07390, NAD(P)H-quinone oxidoreductase subunit F;
Validated.
Length = 613
Score = 26.8 bits (60), Expect = 4.3
Identities = 10/17 (58%), Positives = 10/17 (58%)
Query: 101 TLDYSASTSSGLVFSAV 117
L YS S GLVF AV
Sbjct: 311 ALSYSTSAYLGLVFIAV 327
>gnl|CDD|131015 TIGR01960, ndhF3_CO2, NAD(P)H dehydrogenase, subunit NdhF3 family.
This family represents a subfamily of NAD(P)H
dehydrogenase subunit 5, or ndhF. It is restricted to
two paralogs in each completed cyanobacterial genome, in
which several subtypes of ndhF are found. Included in
this family is NdhF3, shown to play a role in
high-affinity CO2 uptake in Synechococcus sp. PCC7002.
In all cases, neighboring genes include a paralog of
ndhD but do include other NAD(P)H dehydrogenase
subunits. Instead, genes related to C02 uptake tend to
be found nearby.
Length = 606
Score = 26.6 bits (59), Expect = 4.5
Identities = 12/28 (42%), Positives = 12/28 (42%)
Query: 101 TLDYSASTSSGLVFSAVDFGSGGSWFEF 128
L YS S GLVF AV G G
Sbjct: 311 ALSYSVSAYMGLVFIAVGLGQGDLALLL 338
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 26.0 bits (57), Expect = 6.6
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 41 EFVFEVLSTEEIVQHMIDCIKEVNNVVEIPA 71
E VF +S EE + + I+ +++ A
Sbjct: 402 EIVFNYMSHEEDWREFREAIRVTREILKQKA 432
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 25.7 bits (57), Expect = 7.9
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 37 NDVEEFVFEV-LSTEEIVQHMIDCIKEVNNVVE 68
N ++ + E+ LS EE Q ++ +++VN ++E
Sbjct: 132 NKIDRLILELKLSPEEAYQRLLRIVEDVNAIIE 164
>gnl|CDD|232817 TIGR00081, purC, phosphoribosylaminoimidazole-succinocarboxamide
synthase. Alternate name: SAICAR synthetase purine de
novo biosynthesis. E.coli example noted as homotrimer.
Check length. Longer versions may be multifunctional
enzymes [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 237
Score = 25.8 bits (57), Expect = 8.0
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 18 SDDIGYAMEVENQNPKDRQ----NDVEEFVFEVLSTEEIVQHMIDCIKE 62
DDI A + E ++ + + F+FE L I H ID I++
Sbjct: 31 RDDIS-AFDGEKKDQIPGKGRLNTKISAFIFEKLEEAGIPTHYIDLIED 78
>gnl|CDD|220058 pfam08885, GSCFA, GSCFA family. This family of proteins are
functionally uncharacterized. They have been named GSCFA
after a highly conserved N-terminal motif in the
alignment. Distant similarity to the pfam00657 lipases
suggests these proteins are likely to be enzymes.
Length = 251
Score = 25.6 bits (57), Expect = 8.6
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 38 DVEEFVFEVLSTEEIVQHM---IDCIKEVN 64
D E F LS EEIV+ + I +K +N
Sbjct: 136 DKELHEFRNLSVEEIVEDLRAIIALLKAIN 165
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
0.311 0.129 0.365
Gapped
Lambda K H
0.267 0.0631 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,419,577
Number of extensions: 553122
Number of successful extensions: 478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 478
Number of HSP's successfully gapped: 28
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.4 bits)