RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5269
(190 letters)
>gnl|CDD|221257 pfam11838, DUF3358, Domain of unknown function (DUF3358). This
domain is functionally uncharacterized. This domain is
found in eukaryotes and bacteria. This domain is found
to the C-terminus of an aminopeptidase domain.
Length = 323
Score = 67.7 bits (166), Expect = 1e-13
Identities = 29/98 (29%), Positives = 44/98 (44%), Gaps = 5/98 (5%)
Query: 60 FYQFGVQILKPAGQSLGWEPKANENHLNTLLRSLIISRLGVYGDPDTLTLARAKFEAHVK 119
+F ++ P + LGWE +H LLR+L++S G + + A +F A +
Sbjct: 101 LKKFVRKLAAPLLEKLGWEFGPGSDHQLQLLRALLLSLAGGDEE--VVAAALDRFRALLD 158
Query: 120 GT---AILPADLRSPVYRAAIAGGSEATYQQLLKVIHN 154
G A + DLR V+ A A G Y Q+L N
Sbjct: 159 GDKSLAAIDPDLRWSVFAALAANGGAKEYDQILAEYKN 196
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 34.5 bits (79), Expect = 0.021
Identities = 24/100 (24%), Positives = 31/100 (31%), Gaps = 13/100 (13%)
Query: 91 RSLIISRLGVYGDPDTLTLARAKFEAHVKGTA--ILPADLRSPVYRAAIAGGSEATYQQL 148
R + GD + A + A +LP L AA AG T
Sbjct: 268 RLRVGGTDEEGGDDPSDPEREDLVIAELLRVARALLPG-LADAGIEAAWAGLRPPTTPDG 326
Query: 149 L----------KVIHNYGHGGYGVTTAPGTSRYAVQLVTR 178
L + GHGG+G T AP R L+
Sbjct: 327 LPVIGRAAPLPNLYVATGHGGHGFTLAPALGRLLADLILG 366
>gnl|CDD|233338 TIGR01275, ACC_deam_rel, pyridoxal phosphate-dependent enzymes,
D-cysteine desulfhydrase family. This model represents
a family of pyridoxal phosphate-dependent enzymes
closely related to (and often designated as putative
examples of) 1-aminocyclopropane-1-carboxylate
deaminase. It appears that members of this family
include both D-cysteine desulfhydrase (EC 4.4.1.15) and
1-aminocyclopropane-1-carboxylate deaminase (EC
3.5.99.7).
Length = 318
Score = 29.0 bits (65), Expect = 1.3
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 136 AIAGGSEATYQQLLKVIHNYGHGGYGVTTAPGTSRYAVQLVTRA----LDPTSSLKS 188
AIA G E T ++ + +Y GYGV T+ G V+ V LDP + K+
Sbjct: 228 AIAEGLELTVSAVIPLWDDYFGPGYGVPTSEGME--IVKKVASLEGIILDPVYTGKA 282
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 28.5 bits (63), Expect = 2.0
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 123 ILPADLRSPVYRAAIAGG 140
I PADLR+ VYR++ AGG
Sbjct: 173 INPADLRTDVYRSSGAGG 190
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 28.8 bits (65), Expect = 2.3
Identities = 23/148 (15%), Positives = 45/148 (30%), Gaps = 23/148 (15%)
Query: 20 FERLPKYTSWLTSGLAERGLRQFRRIPVDL-----------LLSNTEYHHLFYQFGVQIL 68
F+ LPK T + +F + D L + + ++L
Sbjct: 266 FDYLPKNTLIVVDERVLEAAEEFEKEVADFYEARLSDGEYPPLPPEALYLSAEELF-ELL 324
Query: 69 KPAGQSLGWEPKANENHLNTLLRSLIISRLGVYGDPDTLTLARAKFEAHVKGTAILPADL 128
KP + + E ++ + L +G A K +G
Sbjct: 325 KPVPRISLFPEHLPELSAEEIINLDPLPDLAFFGQHKEPLDALRKEIERFRGG------- 377
Query: 129 RSPVYRAAIAGGSEATYQQLLKVIHNYG 156
Y+ I SE ++LL+++ +
Sbjct: 378 ----YKVIILAESEGRRERLLELLAEHD 401
>gnl|CDD|218204 pfam04672, Methyltransf_19, S-adenosyl methyltransferase. This
family contains a SAM (S-adenosyl methyltransferase)
domain, with a central beta sheet with 3 alpha-helices
on both sides. Crystal packing analysis of the structure
PDB:3GIW suggests that a monomer is the solution state
oligomeric form. An unidentified ligand (UNL, cyan) was
found at the putative active site surrounded by the
residues His57, His170, Phe171, Tyr216 and Met22. The
UNL is likely to be a phenylalanine or
phenylalanine-like molecule. (details derived from
TOPSAN).
Length = 268
Score = 27.3 bits (61), Expect = 4.6
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 103 DPDTLTLARAKFEAHVKG-TAILPADLRSP 131
DP LT ARA + +G T + AD+R P
Sbjct: 105 DPIVLTHARALLTSTPEGATDYIHADVRDP 134
>gnl|CDD|153343 cd07659, BAR_PICK1, The Bin/Amphiphysin/Rvs (BAR) domain of Protein
Interacting with C Kinase 1. The BAR domain of
Arfaptin-like proteins, also called the Arfaptin domain,
is a dimerization and lipid binding module that can
detect and drive membrane curvature. Protein Interacting
with C Kinase 1 (PICK1), also called Protein kinase
C-alpha-binding protein, is highly expressed in brain
and testes. PICK1 plays a key role in the trafficking of
AMPA receptors, which are critical for regulating
synaptic strength and may be important in cellular
processes involved in learning and memory. PICK1 is also
critical in the early stages of spermiogenesis. Mice
deficient in PICK1 are infertile and show
characteristics of the human disease globozoospermia
such as round-headed sperm, reduced sperm count, and
severely impaired sperm motility. PICK1 may also be
involved in the neuropathogenesis of schizophrenia.
PICK1 contains an N-terminal PDZ domain and a C-terminal
BAR domain. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
The BAR domain of PICK1 is necessary for its membrane
localization and activation.
Length = 215
Score = 26.5 bits (59), Expect = 7.4
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 21/65 (32%)
Query: 55 EYHHLFYQFGVQILKPAGQSLGWEPKANENHLNTLLRSLIISRLGVYGDPDT-LTLAR-- 111
E H +FG+++LK K + L T L I PDT LT+ +
Sbjct: 67 EAHRSIEKFGIELLKTL--------KPMLSDLGTYLNKAI---------PDTKLTIKKYA 109
Query: 112 -AKFE 115
KFE
Sbjct: 110 DVKFE 114
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized plasmamembrane
domains. Some PDZ domain containing proteins bind one or
more of this family. Now includes JAKs.
Length = 201
Score = 26.5 bits (59), Expect = 8.7
Identities = 20/95 (21%), Positives = 29/95 (30%), Gaps = 13/95 (13%)
Query: 40 RQFRRIPVDLLLSNTEYHHLFYQFGVQILKPAGQSLGWEPKANENHLNTLLRSLIISRLG 99
+ + P L T + L+ Q IL+ G P E L LL +L +
Sbjct: 79 KFYPPDPNQLKEDPTRLNLLYLQVRNDILE------GRLPCPEEEAL--LLAALALQAE- 129
Query: 100 VYGDPDTLTLARAKFEAHVKGTAILPADLRSPVYR 134
+GD D + LP L
Sbjct: 130 -FGDYDEELHDLRGELSL---KRFLPKQLLDSRKL 160
>gnl|CDD|173821 cd07497, Peptidases_S8_14, Peptidase S8 family domain,
uncharacterized subfamily 14. This family is a member
of the Peptidases S8 or Subtilases serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members have
been shown to bind up to 4 ions via binding sites with
different affinity. Some members of this clan contain
disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values.
Length = 311
Score = 26.7 bits (59), Expect = 9.0
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 154 NYGHGGYGVTTAPGTSRYAV 173
N G G YG TAPG + A+
Sbjct: 177 NGGPG-YGTITAPGAASLAI 195
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 26.6 bits (59), Expect = 9.2
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 123 ILPADLRSPVYRAAIAGG 140
I PADLR +R++ AGG
Sbjct: 218 INPADLRIDTFRSSGAGG 235
>gnl|CDD|188042 TIGR00333, nrdI, ribonucleoside-diphosphate reductase 2, operon
protein nrdI. Ribonucleotide reductases (RNRs) are
enzymes that provide the precursors of DNA synthesis.
The three characterized classes of RNRs differ by their
metal cofactor and their stable organic radical. The
exact function of nrdI within the ribonucleotide
reductases has not yet been fully characterised
[Purines, pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 127
Score = 26.0 bits (57), Expect = 10.0
Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 14/71 (19%)
Query: 41 QFRRIPVDLLLS---NTEYHHLFYQFGVQILKPAGQSLGWEPKA-----NENHLNTLLRS 92
Q RIPVD + Y + + G + G PK N+ H LLR
Sbjct: 20 QHIRIPVDETDRIHVDQPYVLICPTYTG------GGTAGAVPKQVISFLNKKHNRALLRG 73
Query: 93 LIISRLGVYGD 103
+I S +GD
Sbjct: 74 VIASGNKNFGD 84
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
0.320 0.137 0.404
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,919,870
Number of extensions: 938720
Number of successful extensions: 880
Number of sequences better than 10.0: 1
Number of HSP's gapped: 879
Number of HSP's successfully gapped: 21
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)