RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10208
(143 letters)
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 61.5 bits (150), Expect = 5e-12
Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 8/99 (8%)
Query: 3 YVNTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIAL---GSDVFH--IYRLSSGLNKR 57
Y I++ KY+ + +R+ G + G P S++ S Y LS LN+R
Sbjct: 246 YGEHIDRIVDLAKYLAELIRADPGFELLGEPNLSLVCFRLKPSVKLDELNYDLSDRLNER 305
Query: 58 G-WNTNSLQF--PVGIHICITHMHTQPGVADKFISDVRE 93
G W+ + P + +T+ T AD + D+
Sbjct: 306 GGWHVPATTLGGPNVLRFVVTNPLTTRDDADALLEDIER 344
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 37.7 bits (88), Expect = 0.001
Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 3/89 (3%)
Query: 10 IIETVKYIEKELRSMDGLFIFGTPATSVIA--LGSDVFHIYRLSSGLNKRGWNTNSLQFP 67
+E +Y+ +EL + + P ++A L D + LS L++RGW + P
Sbjct: 347 TLELARYLAEELEKLGDFELVNEPELPIVAFRLKDDEDTLADLSERLDRRGWQVPAQLLP 406
Query: 68 VGIHICITHMHTQPGVADKFISDVREELA 96
G+ I + H KFI
Sbjct: 407 KGLAI-VFGTHVTGRQGLKFIVANLLITD 434
>gnl|CDD|128385 smart00071, Galanin, Galanin. Galanin is a neuropeptide that
controls various biological activities: it regulates
the release growth hormone, inhibits the release of
insulin and somatostatin, contracts smooth muscle of
the gastrointestinal and genitourinary tract and may be
involved in the control of adrenal secretion.
Length = 103
Score = 27.1 bits (60), Expect = 1.7
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 56 KRGWNTNSLQFPVGIHICITH--MHTQPGVADK 86
KRGW NS + +G H H H + G+ K
Sbjct: 11 KRGWTLNSAGYLLGPHAIDNHRSFHDKHGLTGK 43
>gnl|CDD|216340 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
Length = 217
Score = 27.9 bits (63), Expect = 1.7
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 90 DVREELAIIMQNPGLQLEGVMAM 112
++ + PGL+LEG+M
Sbjct: 130 ELPALAEALAALPGLRLEGLMTH 152
>gnl|CDD|143511 cd07376, PLPDE_III_DSD_D-TA_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes Similar to D-Serine Dehydratase
and D-Threonine Aldolase. This family includes
eukaryotic D-serine dehydratases (DSD), cryptic DSDs
from bacteria, D-threonine aldolases (D-TA), low
specificity D-TAs, and similar uncharacterized proteins.
DSD catalyzes the dehydration of D-serine to
aminoacrylate, which is rapidly hydrolyzed to pyruvate
and ammonia. D-TA reversibly catalyzes the aldol
cleavage of D-threonine into glycine and acetaldehyde,
and the synthesis of D-threonine from glycine and
acetaldehyde. Members of this family are fold type III
PLP-dependent enzymes, similar to bacterial alanine
racemase (AR), which contains an N-terminal PLP-binding
TIM barrel domain and a C-terminal beta-sandwich domain.
AR exists as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Based on similarity to AR, it is possible
members of this family also form dimers in solution.
Length = 345
Score = 27.4 bits (61), Expect = 2.8
Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 7/47 (14%)
Query: 82 GVADKFISDVREELAIIMQN---PGLQLEGVMAMYGKSHSIPDRSII 125
GV + LA+ PGL+L GVMA G +
Sbjct: 126 GVRP----EEAAALALADAVQASPGLRLAGVMAYEGHIYGAGGAREG 168
>gnl|CDD|223425 COG0348, NapH, Polyferredoxin [Energy production and conversion].
Length = 386
Score = 27.4 bits (61), Expect = 3.0
Identities = 7/51 (13%), Positives = 13/51 (25%)
Query: 1 MSYVNTTRSIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDVFHIYRLS 51
M N +I ++ M A + ++RL
Sbjct: 261 MLKFNLPFGLIAYSTFMALPTIGMSACLRPRLCAYGGVLQLVSPLGLFRLK 311
>gnl|CDD|216234 pfam00998, RdRP_3, Viral RNA dependent RNA polymerase. This
family includes viral RNA dependent RNA polymerase
enzymes from hepatitis C virus and various plant
viruses.
Length = 486
Score = 26.8 bits (60), Expect = 4.4
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 1 MSYVNTTRSIIETVKYIE 18
S VN R ++E V +
Sbjct: 32 NSLVNLRRGLVERVFKVT 49
>gnl|CDD|234602 PRK00055, PRK00055, ribonuclease Z; Reviewed.
Length = 270
Score = 26.7 bits (60), Expect = 5.0
Identities = 5/8 (62%), Positives = 6/8 (75%)
Query: 71 HICITHMH 78
I ITH+H
Sbjct: 56 KIFITHLH 63
>gnl|CDD|143489 cd06814, PLPDE_III_DSD_D-TA_like_3, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes Similar to D-Serine Dehydratase
and D-Threonine Aldolase, Unknown Group 3. This
subfamily is composed of uncharacterized bacterial
proteins with similarity to eukaryotic D-serine
dehydratases (DSD) and D-threonine aldolases (D-TA). DSD
catalyzes the dehydration of D-serine to aminoacrylate,
which is rapidly hydrolyzed to pyruvate and ammonia.
D-TA reversibly catalyzes the aldol cleavage of
D-threonine into glycine and acetaldehyde, and the
synthesis of D-threonine from glycine and acetaldehyde.
DSD and D-TA are fold type III PLP-dependent enzymes,
similar to bacterial alanine racemase (AR), which
contains an N-terminal PLP-binding TIM barrel domain and
a C-terminal beta-sandwich domain. AR exists as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. Based on
their similarity to AR, it is possible members of this
family also form dimers in solution.
Length = 379
Score = 26.1 bits (58), Expect = 8.0
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 2/30 (6%)
Query: 82 GVADKFISDVREELAIIMQNPGLQLEGVMA 111
G AD + + L I P L+ G+M
Sbjct: 148 GFADP--QTLPKALTAIDAPPRLRFSGLMG 175
>gnl|CDD|238373 cd00731, CheA_reg, CheA regulatory domain; CheA is a histidine
protein kinase present in bacteria and archea.
Activated by the chemotaxis receptor a histidine
phosphoryl group from CheA is passed directly to an
aspartate in the response regulator CheY. This
signalling mechanism is modulated by the methyl
accepting chemotaxis proteins (MCPs). MCPs form a
highly interconnected, tightly packed array within the
membrane that is organized, at least in part, through
interactions with CheW and CheA. The CheA regulatory
domain belongs to the family of CheW_like proteins and
has been proposed to mediate interaction with the
kinase regulator CheW.
Length = 132
Score = 25.2 bits (56), Expect = 8.9
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 9 SIIETVKYIEKELRSMDGLFIFGTPATSVIALGSDVFHIYRLSSGLNKRGWNTNSLQFPV 68
+++ETV+ K+++ +DG VI + ++ + RL N RG N + V
Sbjct: 22 AVVETVRIKPKDIKRVDG-------GKEVINVRGELLPLVRLGELFNVRGENEEPDEGVV 74
>gnl|CDD|226641 COG4172, COG4172, ABC-type uncharacterized transport system,
duplicated ATPase component [General function prediction
only].
Length = 534
Score = 26.1 bits (58), Expect = 9.2
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 18 EKELRSMDGL---FIFGTPATS---VIALGSDVFHIYRLSSGLNKRGW 59
E++LR + G IF P TS + +G + + RL GL++
Sbjct: 84 ERQLRGVRGNKIGMIFQEPMTSLNPLHTIGKQLAEVLRLHRGLSRAAA 131
>gnl|CDD|233963 TIGR02651, RNase_Z, ribonuclease Z. Processing of the 3-prime
end of tRNA precursors may be the result of
endonuclease or exonuclease activity, and differs in
different species. Member of this family are
ribonuclease Z, a tRNA 3-prime endonuclease that
processes tRNAs to prepare for addition of CCA. In
species where all tRNA sequences already have the CCA
tail, such as E. coli, the need for such an enzyme is
unclear. Protein similar to the E. coli enzyme, matched
by TIGR02649, are designated ribonuclease BN
[Transcription, RNA processing].
Length = 299
Score = 25.6 bits (57), Expect = 9.4
Identities = 5/8 (62%), Positives = 6/8 (75%)
Query: 71 HICITHMH 78
I ITH+H
Sbjct: 54 RIFITHLH 61
>gnl|CDD|184200 PRK13640, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 282
Score = 25.9 bits (57), Expect = 9.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 83 VADKFISDVREELAIIMQNPGLQLEG 108
+ K + D+RE++ I+ QNP Q G
Sbjct: 74 LTAKTVWDIREKVGIVFQNPDNQFVG 99
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
0.321 0.138 0.407
Gapped
Lambda K H
0.267 0.0842 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,374,737
Number of extensions: 650779
Number of successful extensions: 583
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 34
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (21.9 bits)
S2: 54 (24.4 bits)