RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2616
(82 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 = 54.9 bits (133), Expect = 1e-10
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 25 QVAPKIKERMMKSGSMMITYQPIHALPNFFRLVLQNSALDHSDMDYFIDEIERL 78
++ + +R+ + G + + PN R V+ N D D +++IER
Sbjct: 293 ELNYDLSDRLNERGGWHVPATTLGG-PNVLRFVVTNPLTTRDDADALLEDIERA 345
>gnl|CDD|234652 PRK00128, ipk, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase;
Provisional.
Length = 286
Score = 24.7 bits (55), Expect = 5.3
Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 3/16 (18%)
Query: 29 KIKERMMKSG---SMM 41
KIKERM+K G ++M
Sbjct: 230 KIKERMLKFGADGALM 245
>gnl|CDD|165303 PHA03002, PHA03002, Hypothetical protein; Provisional.
Length = 679
Score = 24.7 bits (54), Expect = 6.0
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 51 PNFFRLVLQNSALDHSDMDYFIDE 74
N +L+++N+ L D++Y I E
Sbjct: 103 INVIKLMIENNLLTIDDIEYIISE 126
>gnl|CDD|234570 PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.
Length = 911
Score = 24.7 bits (55), Expect = 6.4
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 57 VLQNSALDHSDM--DYFIDEIERLGHDL 82
V + L + D ++ E+ LG +L
Sbjct: 267 VTREVLLLQRWVALDLYLKELHALGSEL 294
>gnl|CDD|237314 PRK13238, tnaA, tryptophanase/L-cysteine desulfhydrase,
PLP-dependent; Provisional.
Length = 460
Score = 24.8 bits (55), Expect = 6.9
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 33 RMMKSGSMMITYQP-----IHALPNFFRLVLQNSALDHSDMDYFIDEIERL 78
R ++ GS+++ P + A RL + S MDY + ++ +
Sbjct: 380 RGVEIGSLLLGRDPKTGEQLPAPAELLRLAIPRRVYTQSHMDYVAEALKAV 430
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 287
Score = 24.5 bits (54), Expect = 7.7
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 14/67 (20%)
Query: 17 NSNSSSSLQVAPKIKERMMKSGSMMITYQPIHALPNFF-------RLVLQNSALDHSDMD 69
S S V P K+++ K G + +T + FF LVLQ L
Sbjct: 171 GSRGS----VLPLFKKQIKKGGPLTVTDPDMT---RFFMTIPEAVDLVLQACILGDGGGI 223
Query: 70 YFIDEIE 76
+ +D
Sbjct: 224 FLLDMGP 230
>gnl|CDD|221344 pfam11964, DUF3478, Protein of unknown function (DUF3478). This
family of proteins is functionally uncharacterized.
This protein is found in bacteria and archaea. Proteins
in this family are typically between 120 to 132 amino
acids in length. This protein has a single completely
conserved residue A that may be functionally important.
Length = 118
Score = 24.1 bits (53), Expect = 8.4
Identities = 9/36 (25%), Positives = 12/36 (33%), Gaps = 2/36 (5%)
Query: 41 MITYQPIHALPNFFRLVLQNSALDHSDMDYFIDEIE 76
MI P N + L H D + I +E
Sbjct: 1 MIEIIPTPD-DNVLAFKVSG-KLTHEDYEVLIPALE 34
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 0.130 0.359
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,004,179
Number of extensions: 298909
Number of successful extensions: 300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 299
Number of HSP's successfully gapped: 10
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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 (21.7 bits)
S2: 53 (24.1 bits)