RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14030
(63 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 = 93.0 bits (232), Expect = 7e-25
Identities = 29/50 (58%), Positives = 35/50 (70%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLLTGIER 53
GTT GA DP+ IAD+ +YD+WLHVDAA+GG L + RHL GIER
Sbjct: 157 GTTDTGAIDPLEEIADLAEKYDLWLHVDAAYGGFLLPFPEPRHLDFGIER 206
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 90.1 bits (224), Expect = 1e-23
Identities = 29/50 (58%), Positives = 36/50 (72%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLLTGIER 53
GTT GAFDP+ + DIC +YD+WLHVDAA+ G A + + RH L GIER
Sbjct: 203 GTTGSGAFDPLQELGDICNKYDLWLHVDAAYAGSAFICPEFRHWLFGIER 252
>gnl|CDD|163511 TIGR03799, NOD_PanD_pyr, putative pyridoxal-dependent aspartate
1-decarboxylase. This enzyme is proposed here to be a
form of aspartate 1-decarboxylase, pyridoxal-dependent,
that represents a non-orthologous displacement to the
more widely distributed pyruvoyl-dependent form
(TIGR00223). Aspartate 1-decarboxylase makes
beta-alanine, used usually in pathothenate biosynthesis,
by decarboxylation from asparatate. A number of species
with the PanB and PanC enzymes, however, lack PanD. This
protein family occurs in a number of Proteobacteria that
lack PanD. This enzyme family appears to be a
pyridoxal-dependent enzyme (see pfam00282). The family
was identified by Partial Phylogenetic Profiling;
members in Geobacter sulfurreducens, G. metallireducens,
and Pseudoalteromonas atlantica are clustered with the
genes for PanB and PanC. We suggest the gene symbol panP
(panthothenate biosynthesis enzyme, Pyridoxal-dependent)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 522
Score = 75.1 bits (185), Expect = 4e-18
Identities = 28/50 (56%), Positives = 32/50 (64%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLLTGIER 53
GTT G DP+ +ADI E HVDAAWGG L+S +RHLL GIER
Sbjct: 274 GTTETGNIDPLDEMADIAQELGCHFHVDAAWGGATLLSNTYRHLLKGIER 323
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 70.9 bits (174), Expect = 2e-16
Identities = 23/51 (45%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLLT-GIER 53
GTT G+ D I +ADI EY +WLHVDAA+GG L + G+E
Sbjct: 216 GTTDTGSIDDIEELADIAEEYGIWLHVDAAFGGFLLPFLEPDGRWDFGLEG 266
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 59.9 bits (146), Expect = 1e-12
Identities = 19/33 (57%), Positives = 24/33 (72%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGG 36
GTT LG DPIP ++ I E ++LHVDAA+GG
Sbjct: 160 GTTELGQVDPIPELSKIALENGIFLHVDAAFGG 192
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 54.5 bits (131), Expect = 1e-10
Identities = 20/49 (40%), Positives = 28/49 (57%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLLTGIE 52
GTT A DP+ + I MW HVDAA+ G A + ++RH + G+E
Sbjct: 248 GTTSSTAVDPLLELGKIAKSNGMWFHVDAAYAGSACICPEYRHYIDGVE 296
>gnl|CDD|234361 TIGR03812, tyr_de_CO2_Arch, tyrosine decarboxylase MnfA. Members
of this protein family are the archaeal form, MnfA, of
tyrosine decarboxylase, and are involved in methanofuran
biosynthesis. Members show clear homology to the
Enterococcus form, Tdc, that is involved in tyrosine
decarboxylation for resistance to acidic conditions
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 373
Score = 53.5 bits (129), Expect = 2e-10
Identities = 17/33 (51%), Positives = 22/33 (66%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGG 36
GTT LG D I ++ I E ++LHVDAA+GG
Sbjct: 162 GTTELGQIDDIEELSKIALENGIYLHVDAAFGG 194
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 48.6 bits (115), Expect = 1e-08
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLLTGIE 52
GTT A DP+ + +I +Y +WLHVDAA+ G A + ++R + GIE
Sbjct: 296 GTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIE 344
>gnl|CDD|99742 cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold
type I) of pyridoxal phosphate (PLP)-dependent enzymes.
PLP combines with an alpha-amino acid to form a compound
called a Schiff base or aldimine intermediate, which
depending on the reaction, is the substrate in four
kinds of reactions (1) transamination (movement of amino
groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
Structure and sequence analysis has revealed that the
PLP dependent enzymes can be classified into four major
groups of different evolutionary origin: aspartate
aminotransferase superfamily (fold type I), tryptophan
synthase beta superfamily (fold type II), alanine
racemase superfamily (fold type III), and D-amino acid
superfamily (fold type IV) and Glycogen phophorylase
family (fold type V).
Length = 170
Score = 38.9 bits (91), Expect = 2e-05
Identities = 17/36 (47%), Positives = 19/36 (52%)
Query: 3 PGTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGA 38
P TT G P+ I I EY + L VDAA GGA
Sbjct: 100 PNTTSGGVLVPLKEIRKIAKEYGILLLVDAASAGGA 135
>gnl|CDD|224029 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 37.5 bits (88), Expect = 1e-04
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDAA 33
G PI I +IC E + HVDA
Sbjct: 155 GTIQPIAEIGEICKERGILFHVDAV 179
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase [DNA metabolism,
Restriction/modification].
Length = 353
Score = 36.7 bits (85), Expect = 2e-04
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 8 LGAFDPIPAIADICAEYDMWLHVDAAWGGGAL---VSRKHRHLLT 49
G+ PI IA++ ++ + HVDAA G + +S L++
Sbjct: 151 TGSIQPIREIAEVLEAHEAFFHVDAAQVVGKITVDLSADRIDLIS 195
>gnl|CDD|215829 pfam00266, Aminotran_5, Aminotransferase class-V. This domain is
found in amino transferases, and other enzymes including
cysteine desulphurase EC:4.4.1.-.
Length = 370
Score = 36.1 bits (84), Expect = 3e-04
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 3 PGTTVLGAFDPIPAIADICAEYDMWLHVDAA 33
+ V G +P+ I + EY + VDAA
Sbjct: 147 HVSNVTGTVNPVEEIGKLAHEYGALVVVDAA 177
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 35.2 bits (81), Expect = 6e-04
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 12 DPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLL 48
D + IA ICAEYD+ V+ A+G + S K+ HL+
Sbjct: 172 DRVKEIAKICAEYDVPHLVNGAYG---IQSEKYIHLI 205
>gnl|CDD|130848 TIGR01788, Glu-decarb-GAD, glutamate decarboxylase. This model
represents the pyridoxal phosphate-dependent glutamate
(alpha) decarboxylase found in bacteria (low and hi-GC
gram positive, proteobacteria and cyanobacteria),
plants, fungi and at least one archaon (Methanosarcina).
The product of the enzyme is gamma-aminobutyrate (GABA).
Length = 431
Score = 34.7 bits (80), Expect = 0.001
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 6/39 (15%)
Query: 4 GTTVLGAFDPIPAIADICAEY------DMWLHVDAAWGG 36
GTT G ++ + A+ D EY D+ +HVDAA GG
Sbjct: 195 GTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGG 233
>gnl|CDD|131061 TIGR02006, IscS, cysteine desulfurase IscS. This model represents
IscS, one of several cysteine desulfurases from a larger
protein family designated (misleadingly, in this case)
class V aminotransferases. IscS is one of at least 6
enzymes characteristic of the IscSUA-hscAB-fsx system of
iron-sulfur cluster assembly. Scoring almost as well as
proteobacterial sequences included in the model are
mitochondrial cysteine desulfurases, apparently from an
analogous system in eukaryotes. The sulfur, taken from
cysteine, may be used in other systems as well, such as
tRNA base modification and biosynthesis of other
cofactors [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Protein synthesis, tRNA and rRNA
base modification].
Length = 402
Score = 34.0 bits (78), Expect = 0.002
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 8 LGAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
+G I AI +IC E ++ HVDAA G +
Sbjct: 155 IGVIQDIAAIGEICRERKVFFHVDAAQSVGKI 186
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 33.7 bits (78), Expect = 0.002
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
G P+P + D+ +Y L VD A G
Sbjct: 146 GDIAPLPELVDLAKKYGAILFVDEAHSVGVY 176
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 33.1 bits (76), Expect = 0.003
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 4 GTTVLGAFDPIPAIADICAEY---DMWLHVDAAWGGGAL 39
GTT+ GA D I I +I + D ++H DAA G L
Sbjct: 169 GTTMTGAIDNIKEIQEILKKIGIDDYYIHADAALSGMIL 207
>gnl|CDD|211833 TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium
transferase. In the archaea and eukaryotes, the
conversion of the mischarged serine to selenocysteine
(Sec) on its tRNA is accomplished in two steps. This
enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase,
acts second, after a phosphophorylation step catalyzed
by a homolog of the bacterial SelA protein [Protein
synthesis, tRNA aminoacylation].
Length = 444
Score = 33.1 bits (76), Expect = 0.004
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 12 DPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRHLL 48
D I IA ICA YD+ V+ A+G L S K+ L+
Sbjct: 222 DDIEEIAKICANYDIPHIVNNAYG---LQSNKYMELI 255
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 32.6 bits (75), Expect = 0.005
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
G P+P + ++ +Y L+VD A G L
Sbjct: 185 GDIAPLPELVELAEKYGALLYVDEAHAVGVL 215
>gnl|CDD|129937 TIGR00858, bioF, 8-amino-7-oxononanoate synthase.
7-keto-8-aminopelargonic acid synthetase is an alternate
name. This model represents 8-amino-7-oxononanoate
synthase, the BioF protein of biotin biosynthesis. This
model is based on a careful phylogenetic analysis to
separate members of this family from
2-amino-3-ketobutyrate and other related pyridoxal
phosphate-dependent enzymes. In several species,
including Staphylococcus and Coxiella, a candidate
8-amino-7-oxononanoate synthase is confirmed by location
in the midst of a biotin biosynthesis operon but scores
below the trusted cutoff of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 360
Score = 30.7 bits (70), Expect = 0.025
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 13 PIPAIADICAEYDMWLHVDAAWGGGAL 39
P+P + + Y WL VD A G G L
Sbjct: 164 PLPQLVALAERYGAWLMVDDAHGTGVL 190
>gnl|CDD|184450 PRK14012, PRK14012, cysteine desulfurase; Provisional.
Length = 404
Score = 30.3 bits (69), Expect = 0.034
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 8 LGAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
+G I AI +IC E + HVDAA G +
Sbjct: 157 IGVIQDIAAIGEICRERGIIFHVDAAQSVGKV 188
>gnl|CDD|99739 cd00615, Orn_deC_like, Ornithine decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD corresponds to ornithine decarboxylase (ODC),
arginine decarboxylase (ADC) and lysine decarboxylase
(LDC). ODC is a dodecamer composed of six homodimers and
catalyzes the decarboxylation of tryptophan. ADC
catalyzes the decarboxylation of arginine and LDC
catalyzes the decarboxylation of lysine. Members of this
family are widely found in all three forms of life.
Length = 294
Score = 29.9 bits (68), Expect = 0.050
Identities = 5/20 (25%), Positives = 8/20 (40%)
Query: 17 IADICAEYDMWLHVDAAWGG 36
I + + + VD A G
Sbjct: 175 IVEEAHHRGLPVLVDEAHGA 194
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 29.2 bits (66), Expect = 0.088
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 7 VLGAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
V G +P+ IA++ E+ + VDAA G L
Sbjct: 174 VTGTVNPVKEIAELAHEHGALVLVDAAQAAGHL 206
>gnl|CDD|235655 PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed.
Length = 385
Score = 28.6 bits (65), Expect = 0.14
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 13 PIPAIADICAEYDMWLHVDAAWGGGAL 39
P+ + + + WL VD A G G L
Sbjct: 186 PLAELVALARRHGAWLLVDEAHGTGVL 212
>gnl|CDD|163523 TIGR03811, tyr_de_CO2_Ent, tyrosine decarboxylase, Enterococcus
type. This model represents tyrosine decarboxylases in
the family of the Enterococcus faecalis enzyme Tdc.
These enzymes often are encoded next to
tyrosine/tyramine antiporter, together comprising a
system in which tyrosine decarboxylation can protect
against exposure to acid conditions. This clade differs
from the archaeal tyrosine decarboxylases associated
with methanofuran biosynthesis [Cellular processes,
Adaptations to atypical conditions].
Length = 608
Score = 27.9 bits (62), Expect = 0.25
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 5/38 (13%)
Query: 4 GTTVLGAFDPIPAIADICAEYD-----MWLHVDAAWGG 36
G+T GA D I I + + +LHVDAA+GG
Sbjct: 287 GSTEEGAVDGIDKIVALRNKLMKEGIYFYLHVDAAYGG 324
>gnl|CDD|178257 PLN02651, PLN02651, cysteine desulfurase.
Length = 364
Score = 27.3 bits (61), Expect = 0.36
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDAA 33
G P+ I ++C E + H DAA
Sbjct: 152 GVIQPVEEIGELCREKKVLFHTDAA 176
>gnl|CDD|130884 TIGR01825, gly_Cac_T_rel, pyridoxal phosphate-dependent
acyltransferase, putative. This model represents an
enzyme subfamily related to three known enzymes; it
appears closest to glycine C-acteyltransferase, shows no
overlap with it in species distribution, and may share
that function. The three closely related enzymes are
glycine C-acetyltransferase (2-amino-3-ketobutyrate
coenzyme A ligase), 5-aminolevulinic acid synthase, and
8-amino-7-oxononanoate synthase. All transfer the
R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from
coenzyme A to an amino acid (Gly, Gly, Ala,
respectively), with release of CO2 for the latter two
reactions.
Length = 385
Score = 27.1 bits (60), Expect = 0.44
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
G P+P I ++ Y +VD A G G +
Sbjct: 177 GDVAPLPEIVELAERYGAVTYVDDAHGSGVM 207
>gnl|CDD|223153 COG0075, COG0075, Serine-pyruvate aminotransferase/archaeal
aspartate aminotransferase [Amino acid transport and
metabolism].
Length = 383
Score = 26.4 bits (59), Expect = 0.88
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDA 32
G +P+ IA E+ L VDA
Sbjct: 145 GVLNPLKEIAKAAKEHGALLIVDA 168
>gnl|CDD|225395 COG2839, COG2839, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 160
Score = 26.2 bits (58), Expect = 0.95
Identities = 13/59 (22%), Positives = 19/59 (32%), Gaps = 14/59 (23%)
Query: 7 VLGAFDPIPA--------IADICAEY----DMWLHVDAAWGG--GALVSRKHRHLLTGI 51
++G F +P I E D L V A G G LV + ++
Sbjct: 91 IIGIFISLPPFGIILGPFIGAFVGELIERRDFLLAVKAGLGSLVGFLVGSIAQAVIILF 149
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 25.9 bits (57), Expect = 1.2
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 3 PGTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGG 37
PGT G + + + D A + + A+WGGG
Sbjct: 132 PGTD--GPPETMEEVLDFAAAIGYPVIIKASWGGG 164
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 25.8 bits (57), Expect = 1.5
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
+ V G PI I ++ E ++ +DAA G +
Sbjct: 146 ASNVTGTILPIEEIGELAQENGIFFILDAAQTAGVI 181
>gnl|CDD|132444 TIGR03403, nifS_epsilon, cysteine desulfurase, NifS family, epsilon
proteobacteria type. Members of this family are the
NifS-like cysteine desulfurase of the epsilon division
of the Proteobacteria, similar to the NifS protein of
nitrogen-fixing bacteria. Like NifS, and unlike IscS,
this protein is found as part of a system of just two
proteins, a cysteine desulfurase and a scaffold, for
iron-sulfur cluster biosynthesis. This protein is called
NifS by Olsen, et al. (PMID:11123951), so we use this
designation.
Length = 382
Score = 25.6 bits (56), Expect = 1.5
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDA 32
G PI I +IC E + H DA
Sbjct: 154 GMIFPIKEIGEICKERGVLFHTDA 177
>gnl|CDD|223476 COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme
apparently involved in regulation of cell wall
biogenesis [Cell envelope biogenesis, outer membrane].
Length = 374
Score = 25.7 bits (57), Expect = 1.7
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 13 PIPAIADICAEYDMWLHVDAAWGGGA 38
+ AI + + + + DAA GA
Sbjct: 137 DMDAIMALAKRHGLPVIEDAAQAHGA 162
>gnl|CDD|99744 cd06451, AGAT_like, Alanine-glyoxylate aminotransferase (AGAT)
family. This family belongs to pyridoxal phosphate
(PLP)-dependent aspartate aminotransferase superfamily
(fold I). The major groups in this CD correspond to
alanine-glyoxylate aminotransferase (AGAT),
serine-glyoxylate aminotransferase (SGAT), and
3-hydroxykynurenine transaminase (HKT). AGAT is a
homodimeric protein, which catalyses the transamination
of glyoxylate to glycine, and SGAT converts serine and
glyoxylate to hydroxypyruvate and glycine. HKT catalyzes
the PLP-dependent transamination of 3-hydroxykynurenine,
a potentially toxic metabolite of the kynurenine
pathway.
Length = 356
Score = 25.7 bits (57), Expect = 1.7
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 4 GTTVLGAFDPIPAIADICAEYDMWLHVDA 32
T G +P+ I + ++D L VDA
Sbjct: 133 NETSTGVLNPLEGIGALAKKHDALLIVDA 161
>gnl|CDD|236670 PRK10307, PRK10307, putative glycosyl transferase; Provisional.
Length = 412
Score = 25.3 bits (56), Expect = 2.0
Identities = 15/32 (46%), Positives = 16/32 (50%), Gaps = 5/32 (15%)
Query: 27 WLH-----VDAAWGGGALVSRKHRHLLTGIER 53
WLH VDAA+G G L K L T ER
Sbjct: 135 WLHIQDYEVDAAFGLGLLKGGKVARLATAFER 166
>gnl|CDD|236707 PRK10522, PRK10522, multidrug transporter membrane
component/ATP-binding component; Provisional.
Length = 547
Score = 25.3 bits (56), Expect = 2.0
Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 27 WLHVDAAWGGGALVSRKHRHL 47
W+ V WGG LV+R ++H+
Sbjct: 156 WMAV-TIWGGFVLVARVYKHM 175
>gnl|CDD|224919 COG2008, GLY1, Threonine aldolase [Amino acid transport and
metabolism].
Length = 342
Score = 25.3 bits (56), Expect = 2.3
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 11 FDPIPAIADICAEYDMWLHVDAAWGGGALVS 41
D + AI+ +C E+ + LH+D A ALV+
Sbjct: 149 LDELEAISAVCKEHGLPLHMDGARLANALVA 179
>gnl|CDD|99746 cd06453, SufS_like, Cysteine desulfurase (SufS)-like. This family
belongs to the pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). The
major groups in this CD correspond to cysteine
desulfurase (SufS) and selenocysteine lyase. SufS
catalyzes the removal of elemental sulfur and selenium
atoms from L-cysteine, L-cystine, L-selenocysteine, and
L-selenocystine to produce L-alanine; and selenocysteine
lyase catalyzes the decomposition of L-selenocysteine.
Length = 373
Score = 25.1 bits (56), Expect = 2.4
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 6 TVLGAFDPIPAIADICAEYDMWLHVDAA 33
VLG +P+ I +I E + + VD A
Sbjct: 150 NVLGTINPVKEIGEIAHEAGVPVLVDGA 177
>gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this
protein family are NifS, one of several related families
of cysteine desulfurase involved in iron-sulfur (FeS)
cluster biosynthesis. NifS is part of the NIF system,
usually associated with other nif genes involved in
nitrogenase expression and nitrogen fixation. The
protein family is given a fairly broad interpretation
here. It includes a clade nearly always found in
extended nitrogen fixation genomic regions, plus a
second clade more closely related to the first than to
IscS and also part of NifS-like/NifU-like systems. This
model does not extend to a more distantly clade found in
the epsilon proteobacteria such as Helicobacter pylori,
also named NifS in the literature, built instead in
TIGR03403.
Length = 379
Score = 24.9 bits (55), Expect = 2.6
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 9 GAFDPIPAIADICAEYDMWLHVDA 32
G PI I +I E H DA
Sbjct: 150 GTIFPIEEIGEIAKERGALFHTDA 173
>gnl|CDD|216261 pfam01041, DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS aminotransferase
family. The members of this family are probably all
pyridoxal-phosphate-dependent aminotransferase enzymes
with a variety of molecular functions. The family
includes StsA, StsC and StsS. The aminotransferase
activity was demonstrated for purified StsC protein as
the L-glutamine:scyllo-inosose aminotransferase
EC:2.6.1.50, which catalyzes the first amino transfer in
the biosynthesis of the streptidine subunit of
streptomycin.
Length = 362
Score = 24.9 bits (55), Expect = 2.6
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 8 LGAFDPIPAIADICAEYDMWLHVDAAWGGGA 38
G + AI I AE+ + + DAA GA
Sbjct: 122 YGQPADMDAIRAIAAEHGLPVIEDAAHAHGA 152
>gnl|CDD|215528 PLN02977, PLN02977, glutathione synthetase.
Length = 478
Score = 25.0 bits (55), Expect = 3.0
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 9/33 (27%)
Query: 35 GGGALVSRKHRHLLTGIER---------PQNRS 58
G +LVS+ HR LL+ R P+N +
Sbjct: 155 GLSSLVSQLHRSLLSRYGRVLGLDPERVPENPA 187
>gnl|CDD|180866 PRK07179, PRK07179, hypothetical protein; Provisional.
Length = 407
Score = 25.0 bits (55), Expect = 3.1
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 8 LGAFDPIPAIADICAEYDMWLHVD 31
G P+ I DI E+ L VD
Sbjct: 194 TGTIAPLADIVDIAEEFGCVLVVD 217
>gnl|CDD|235893 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
Provisional.
Length = 397
Score = 24.8 bits (55), Expect = 3.6
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 13 PIPAIADICAEYDMWLHVDAAWGGG 37
P+P I D+ +YD + VD + G
Sbjct: 192 PLPEICDLADKYDALVMVDDSHAVG 216
>gnl|CDD|200432 TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.
This clade of aminotransferases is a member of the
pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family
is named after the instance in Leptospira interrogans
serovar Lai, str. 56601, where it is the 31st gene in
the 91-gene lipopolysaccharide biosynthesis locus.
Members of this family are generally found within a
subcluster of seven or more genes including an
epimerase/dehydratase, four genes homologous to the
elements of the neuraminic (sialic) acid biosynthesis
cluster (NeuABCD) and a nucleotidyl transferase.
Together it is very likely that these enzymes direct the
biosynthesis of a nine-carbon sugar analogous to
CMP-neuraminic acid. These seven genes form the core of
the cassette, although they are often accompanied by
additional genes that may further modify the product
sugar.
Length = 359
Score = 24.0 bits (53), Expect = 5.4
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 14 IPAIADICAEYDMWLHVDAAWGGGALVSRKH 44
+ I +IC E+++ + DAA G+ KH
Sbjct: 150 MDEIMEICDEWNLPVVEDAAESLGSFYKGKH 180
>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
(AHBA_syn). AHBA_syn family belongs to pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The members of this CD are
involved in various biosynthetic pathways for secondary
metabolites. Some well studied proteins in this CD are
AHBA_synthase, protein product of pleiotropic regulatory
gene degT, Arnb aminotransferase and pilin
glycosylation protein. The prototype of this family, the
AHBA_synthase, is a dimeric PLP dependent enzyme.
AHBA_syn is the terminal enzyme of
3-amino-5-hydroxybenzoic acid (AHBA) formation which is
involved in the biosynthesis of ansamycin antibiotics,
including rifamycin B. Some members of this CD are
involved in 4-amino-6-deoxy-monosaccharide D-perosamine
synthesis. Perosamine is an important element in the
glycosylation of several cell products, such as
antibiotics and lipopolysaccharides of gram-positive and
gram-negative bacteria. The pilin glycosylation protein
encoded by gene pglA, is a galactosyltransferase
involved in pilin glycosylation. Additionally, this CD
consists of ArnB (PmrH) aminotransferase, a
4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
enzyme. This CD also consists of several predicted
pyridoxal phosphate-dependent enzymes apparently
involved in regulation of cell wall biogenesis. The
catalytic lysine which is present in all characterized
PLP dependent enzymes is replaced by histidine in some
members of this CD.
Length = 352
Score = 24.0 bits (53), Expect = 5.9
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 13 PIPAIADICAEYDMWLHVDAA 33
+ AI I + + + DAA
Sbjct: 121 DMDAIMAIAKRHGLPVIEDAA 141
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 24.2 bits (53), Expect = 6.2
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 16 AIADICAEYDMWLHVDAAWGG 36
AI ++ E+D+ + D +
Sbjct: 187 AIVELAREHDIIIISDEIYEE 207
>gnl|CDD|184076 PRK13479, PRK13479, 2-aminoethylphosphonate--pyruvate transaminase;
Provisional.
Length = 368
Score = 23.7 bits (52), Expect = 6.7
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 6 TVLGAFDPIPAIADICAEYDMWLHVDAAWGGGAL 39
T G +P+ IA + + L VDA GA+
Sbjct: 142 TTTGILNPLDEIAAVAKRHGKRLIVDAMSSFGAI 175
>gnl|CDD|236421 PRK09231, PRK09231, fumarate reductase flavoprotein subunit;
Validated.
Length = 582
Score = 23.8 bits (52), Expect = 7.8
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 12 DPIPAIADICAEYDMWLHVDAAWGGGALVSRKH 44
+P IA I Y M H AA GG A V++ H
Sbjct: 27 NPNLKIALISKVYPMRSHTVAAEGGSAAVAQDH 59
>gnl|CDD|180994 PRK07480, PRK07480, putative aminotransferase; Validated.
Length = 456
Score = 23.7 bits (52), Expect = 8.2
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 15 PAIADICAEYDMWLHVD 31
P I IC +YD+ L D
Sbjct: 243 PEIQRICRKYDILLVAD 259
>gnl|CDD|189344 pfam00016, RuBisCO_large, Ribulose bisphosphate carboxylase large
chain, catalytic domain. The C-terminal domain of
RuBisCO large chain is the catalytic domain adopting a
TIM barrel fold.
Length = 309
Score = 23.5 bits (51), Expect = 9.0
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 7 VLGAFDPIPAIADICAEYDMWLHVDAAWGGGALVSRKHRH 46
+ G + ++A + M LH+ A G A+ R+ H
Sbjct: 117 LTGGYTANTSLATWARDNGMLLHIHRA--GHAVYDRQKNH 154
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 23.3 bits (51), Expect = 9.4
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 16 AIADICAEYDMWLHVDAA 33
I I E+ + LH+D A
Sbjct: 153 EIRAIAREHGIPLHLDGA 170
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
0.323 0.140 0.473
Gapped
Lambda K H
0.267 0.0605 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,350,943
Number of extensions: 239327
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 275
Number of HSP's successfully gapped: 54
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.5 bits)