RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5049
(153 letters)
>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 = 45.6 bits (109), Expect = 2e-06
Identities = 16/50 (32%), Positives = 20/50 (40%)
Query: 45 SGIRRISVLAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLVFFFSKVGQTS 94
G R L N RY RR L LG V G + P++ +K S
Sbjct: 251 GGPERRERLQENVRYLRRGLKELGFPVGGSPSHIIPPLIGDDPAKAVAFS 300
Score = 28.7 bits (65), Expect = 1.1
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 7 LAQNTRYFRRKLNRLGLILY 26
L +N RY RR L LG +
Sbjct: 259 LQENVRYLRRGLKELGFPVG 278
>gnl|CDD|178101 PLN02483, PLN02483, serine palmitoyltransferase.
Length = 489
Score = 41.7 bits (98), Expect = 4e-05
Identities = 15/49 (30%), Positives = 32/49 (65%)
Query: 46 GIRRISVLAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLVFFFSKVGQTS 94
G ++++ + N+ +FR +L ++G V G DSPV+P++++ +K+ S
Sbjct: 367 GAQKLAQIRENSNFFRSELQKMGFEVLGDNDSPVMPIMLYNPAKIPAFS 415
>gnl|CDD|235893 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
Provisional.
Length = 397
Score = 35.2 bits (82), Expect = 0.008
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 53 LAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLV 84
L N RYFR + G + G + P++PV++
Sbjct: 302 LWENARYFREGMTAAGFTL-GPGEHPIIPVML 332
Score = 27.5 bits (62), Expect = 2.9
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 3 LISVLAQNTRYFRRKLNRLGLIL 25
L L +N RYFR + G L
Sbjct: 298 LRDRLWENARYFREGMTAAGFTL 320
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 33.0 bits (76), Expect = 0.050
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 49 RISVLAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLV 84
R L +FR L LGL V +SP++PV++
Sbjct: 295 RRERLQELAAFFRSLLKALGL-VLLPSESPIIPVIL 329
>gnl|CDD|238744 cd01467, vWA_BatA_type, VWA BatA type: Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses. In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Members of this subgroup are bacterial in
origin. They are typified by the presence of a MIDAS
motif.
Length = 180
Score = 31.1 bits (71), Expect = 0.12
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 61 RRKLNRLGLIVYGHRDSPVVPV---LVFFFSKVGQTSIGLGVEQTALNDGLSL 110
RR+ +R+GL+V+ P+ + IGL + TA+ D + L
Sbjct: 39 RRENDRIGLVVFAGAAFTQAPLTLDRESLKELLEDIKIGLAGQGTAIGDAIGL 91
>gnl|CDD|130881 TIGR01822, 2am3keto_CoA, 2-amino-3-ketobutyrate coenzyme A ligase.
This model represents a narrowly defined clade of animal
and bacterial (almost exclusively Proteobacterial)
2-amino-3-ketobutyrate--CoA ligase. This enzyme can act
in threonine catabolism. The closest homolog from
Bacillus subtilis, and sequences like it, may be
functionally equivalent but were not included in the
model because of difficulty in finding reports of
function [Energy metabolism, Amino acids and amines].
Length = 393
Score = 30.2 bits (68), Expect = 0.38
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 53 LAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLVF 85
L NTRYFR ++ G + D P++PV+++
Sbjct: 298 LWANTRYFRERMEAAGFDIKP-ADHPIIPVMLY 329
Score = 27.1 bits (60), Expect = 4.1
Identities = 25/79 (31%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 3 LISVLAQNTRYFRRKLNRLGLILYVLFQAQTKPPRSHCICFISGIRRISVLAHNTRYFRR 62
L L NTRYFR ++ G P H I + + +VLA F R
Sbjct: 294 LRDRLWANTRYFRERMEAAGF---------DIKPADHPIIPV--MLYDAVLAQR---FAR 339
Query: 63 KLNRLGLIVYGHRDSPVVP 81
+L G+ V G PVVP
Sbjct: 340 RLLEEGIYVTGFF-YPVVP 357
>gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Alanine Racemase. This family
includes predominantly bacterial alanine racemases
(AR), some serine racemases (SerRac), and putative
bifunctional enzymes containing N-terminal
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase (murF) and C-terminal AR domains. These proteins
are fold type III PLP-dependent enzymes that play
essential roles in peptidoglycan biosynthesis. AR
catalyzes the interconversion between L- and D-alanine,
which is an essential component of the peptidoglycan
layer of bacterial cell walls. SerRac converts L-serine
into its D-enantiomer (D-serine) for peptidoglycan
synthesis. murF catalyzes the addition of D-Ala-D-Ala
to UDPMurNAc-tripeptide, the final step in the
synthesis of the cytoplasmic precursor of bacterial
cell wall peptidoglycan. Members of this family contain
an N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain. They exist 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. AR and other
members of this family require dimer formation and the
presence of the PLP cofactor for catalytic activity.
Fungal ARs and eukaryotic serine racemases, which are
fold types I and II PLP-dependent enzymes respectively,
are excluded from this family.
Length = 367
Score = 28.2 bits (64), Expect = 1.5
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 53 LAHNTRYFRRKLN---RLGLIV----YGHRDSPVVPVLV 84
L HN R RR L ++ +V YGH V L
Sbjct: 11 LRHNLRVIRRLLGPGTKIMAVVKADAYGHGAVEVAKALE 49
>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 = 28.2 bits (63), Expect = 1.6
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 53 LAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLV 84
L NTR+F+ L +LG G ++P+ PV++
Sbjct: 290 LWDNTRFFKAGLGKLGYDT-GGSETPITPVVI 320
>gnl|CDD|200301 TIGR03621, F420_MSMEG_2516, probable F420-dependent oxidoreductase,
MSMEG_2516 family. Coenzyme F420 is produced by
methanogenic archaea, a number of the Actinomycetes
(including Mycobacterium tuberculosis), and rare members
of other lineages. The resulting information-rich
phylogenetic profile identifies candidate F420-dependent
oxidoreductases within the family of luciferase-like
enzymes (pfam00296), where the species range for the
subfamily encompasses many F420-positive genomes without
straying beyond. This family is uncharacterized, and
named for member MSMEG_2516 from Mycobacterium smegmatis
[Unknown function, Enzymes of unknown specificity].
Length = 295
Score = 27.7 bits (62), Expect = 2.5
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 41 ICFISGIRRISVLAHNTRYFRRKLNRLGLIVYGHRDSPV------VPVLV 84
I F S R+ L Y RR L + GH +P P+L+
Sbjct: 106 IPFDSPGVRVDRLEETLTYLRRLLADEPVTFPGHHGTPRPRQGPRPPLLI 155
>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 = 27.6 bits (62), Expect = 2.8
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 49 RISVLAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLVF 85
R L R L LG + +P+VPV++
Sbjct: 270 RREKLLALIARLRAGLEALGFTLMPS-CTPIVPVIIG 305
>gnl|CDD|238365 cd00713, GltS, Glutamine amidotransferases class-II (Gn-AT),
glutamate synthase (GltS)-type. GltS is a homodimer that
synthesizes L-glutamate from 2-oxoglutarate and
L-glutamine, an important step in ammonia assimilation
in bacteria, cyanobacteria and plants. The N-terminal
glutaminase domain catalyzes the hydrolysis of glutamine
to glutamic acid and ammonia, and has a fold similar to
that of other glutamine amidotransferases such as
glucosamine-fructose 6-phosphate synthase (GLMS or
GFAT), glutamine phosphoribosylpyrophosphate (Prpp)
amidotransferase (GPATase), asparagine synthetase B
(AsnB), and beta lactam synthetase (beta-LS), as well as
the Ntn hydrolase folds of the proteasomal alpha and
beta subunits.
Length = 413
Score = 27.5 bits (62), Expect = 3.5
Identities = 9/22 (40%), Positives = 10/22 (45%)
Query: 60 FRRKLNRLGLIVYGHRDSPVVP 81
+L GL V G RD PV
Sbjct: 93 IEEELEAEGLRVLGWRDVPVDN 114
>gnl|CDD|111823 pfam02976, MutH, DNA mismatch repair enzyme MutH.
Length = 100
Score = 26.0 bits (58), Expect = 4.4
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 57 TRYFRRKLNRLGLI-VYGHRDSPV 79
T + R KL R+ I G RD P+
Sbjct: 53 TSHVRNKLKRVLWIPYEGERDIPL 76
>gnl|CDD|204090 pfam08903, DUF1846, Domain of unknown function (DUF1846). This
family of proteins are functionally uncharacterized.
Some members of the family are annotated as
ATP-dependent peptidases. However, we can find no
support for this annotation.
Length = 490
Score = 26.9 bits (60), Expect = 4.6
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 8/33 (24%)
Query: 57 TRY--------FRRKLNRLGLIVYGHRDSPVVP 81
T+Y F+ +L RLG+ VY H P P
Sbjct: 112 TQYEGQPAADLFKNRLERLGIKVYLHYPIPGYP 144
>gnl|CDD|240144 cd05013, SIS_RpiR, RpiR-like protein. RpiR contains a SIS (Sugar
ISomerase) domain, which is found in many phosphosugar
isomerases and phosphosugar binding proteins. In E.
coli, rpiR negatively regulates the expression of rpiB
gene. Both rpiB and rpiA are ribose phosphate
isomerases that catalyze the reversible reactions of
ribose 5-phosphate into ribulose 5-phosphate.
Length = 139
Score = 25.7 bits (57), Expect = 7.5
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 12/60 (20%)
Query: 43 FISGIRRISVLAHNTRYFRRKLNRLGLIVYGHRDSPVVPV---------LVFFFSKVGQT 93
+I G+ ++A Y KL RLG V D + + +V S G+T
Sbjct: 17 YIFGVGSSGLVA---EYLAYKLLRLGKPVVLLSDPHLQLMSAANLTPGDVVIAISFSGET 73
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 26.0 bits (58), Expect = 8.6
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 10/35 (28%)
Query: 46 GIRRIS----VLAHNTRYFRRKLNRLGLIVYGHRD 76
GI + L RR I++GHRD
Sbjct: 25 GIEPFTEVLPELPEPHPLMRRG------IIFGHRD 53
>gnl|CDD|233720 TIGR02091, glgC, glucose-1-phosphate adenylyltransferase. This
enzyme, glucose-1-phosphate adenylyltransferase, is
also called ADP-glucose pyrophosphorylase. The plant
form is an alpha2,beta2 heterodimer, allosterically
regulated in plants. Both subunits are homologous and
included in this model. In bacteria, both homomeric
forms of GlgC and more active heterodimers of GlgC and
GlgD have been described. This model describes the GlgC
subunit only. This enzyme appears in variants of
glycogen synthesis pathways that use ADP-glucose,
rather than UDP-glucose as in animals [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 361
Score = 26.1 bits (58), Expect = 8.9
Identities = 21/55 (38%), Positives = 25/55 (45%), Gaps = 18/55 (32%)
Query: 25 LYVLFQAQTKP-------------PRSHCICFISGIRRISVLAHNTRYFRRKLNR 66
L L + + KP P S+CI SGIRRI VL T+Y LNR
Sbjct: 12 LSPLTKRRAKPAVPFGGKYRIIDFPLSNCIN--SGIRRIGVL---TQYKSHSLNR 61
>gnl|CDD|215711 pfam00092, VWA, von Willebrand factor type A domain.
Length = 178
Score = 25.8 bits (57), Expect = 9.1
Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 18/99 (18%)
Query: 43 FISG-IRRISVLAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLVFFFSK------VGQTSI 95
FI + R+ + TR GL+ Y + L + SK V +
Sbjct: 23 FIKKLVERLDIGPDGTRV--------GLVQYSSDVTTEFS-LNDYKSKDDLLSAVSKNIY 73
Query: 96 GLGVEQTALNDGLSLYESSHLRSANLWNRPHSPSLMAVF 134
LG T L Y +L S++ +RP++P ++ +
Sbjct: 74 YLG-GGTNTGKALK-YALENLFSSSAGSRPNAPKVVILL 110
>gnl|CDD|184220 PRK13663, PRK13663, hypothetical protein; Provisional.
Length = 493
Score = 26.0 bits (58), Expect = 9.3
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 8/33 (24%)
Query: 57 TRY--------FRRKLNRLGLIVYGHRDSPVVP 81
T+Y FR +L RLG+ VY H P
Sbjct: 114 TQYDGQPAADAFRNRLERLGIKVYRHYPIKGYP 146
>gnl|CDD|235655 PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed.
Length = 385
Score = 25.9 bits (58), Expect = 9.6
Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 53 LAHNTRYFRRKLNRLGLIVYGHRDSPVVPVLV 84
LA R L LG + S + P++V
Sbjct: 296 LAALIARLRAGLRALGFQL-MDSQSAIQPLIV 326
>gnl|CDD|234806 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
Length = 1809
Score = 26.3 bits (58), Expect = 9.7
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 86 FFSKVGQTSIGLGVEQTALNDG 107
F KVG + I LG EQ L+DG
Sbjct: 1370 FIDKVGLSYITLGQEQDTLSDG 1391
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
0.327 0.142 0.433
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,893,467
Number of extensions: 709487
Number of successful extensions: 784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 783
Number of HSP's successfully gapped: 36
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.0 bits)