RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1719
(73 letters)
>gnl|CDD|193454 pfam12981, DUF3865, Domain of Unknown Function with PDB structure
(DUF3865). Family based of PDB:3B5P encoded by
ZP_00108531 from nitrogen-fixing cyanobacterium Nostoc
punctiforme pcc 73102 is a CADD-like protein of unknown
function. Superposition between protein structures
encoded by CT610 from Chlamydia trachomatis (PDB code
1rwc), pyrroloquinolinquinone synthase C (PqqC, PDB code
1otv) and ZP_00108531 revealed that putative active
sites in CT610 and ZP_00108531 are identical. ( REF:
http://www.topsan.org/Proteins/JCSG/3B5P).
Length = 231
Score = 28.0 bits (62), Expect = 0.28
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 9 EAALDHIEAEMAARGVTQALIDETRAAPETRMLEDLAAEAARGQDLEY 56
+ D + + G T A+ E A PE ++ +L E A +DL+Y
Sbjct: 125 LSLFDR-QVDYVL-GATYAI--EATAIPELTLIVELVHEGAIPKDLQY 168
>gnl|CDD|100087 cd03085, PGM1, Phosphoglucomutase 1 (PGM1) catalyzes the
bidirectional interconversion of glucose-1-phosphate
(G-1-P) and glucose-6-phosphate (G-6-P) via a glucose
1,6-diphosphate intermediate, an important metabolic
step in prokaryotes and eukaryotes. In one direction,
G-1-P produced from sucrose catabolism is converted to
G-6-P, the first intermediate in glycolysis. In the
other direction, conversion of G-6-P to G-1-P generates
a substrate for synthesis of UDP-glucose which is
required for synthesis of a variety of cellular
constituents including cell wall polymers and
glycoproteins. The PGM1 family also includes a
non-enzymatic PGM-related protein (PGM-RP) thought to
play a structural role in eukaryotes, as well as
pp63/parafusin, a phosphoglycoprotein that plays an
important role in calcium-regulated exocytosis in
ciliated protozoans. PGM1 belongs to the
alpha-D-phosphohexomutase superfamily which includes
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Other members of this superfamily include
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 548
Score = 27.2 bits (61), Expect = 0.64
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 16/74 (21%)
Query: 3 YDICEAEAA---LDHIEAEMAARGVTQALIDETRAAPETRMLEDLAAEAARGQDLEYKDP 59
Y+ ++EAA +DH+ A ++ D+ + A+ D Y DP
Sbjct: 419 YEEVDSEAANKMMDHLRALVSDLPGVGKSGDKGY-------------KVAKADDFSYTDP 465
Query: 60 ASGATPSVNGLRYK 73
G+ GLR
Sbjct: 466 VDGSVSKKQGLRII 479
>gnl|CDD|177942 PLN02307, PLN02307, phosphoglucomutase.
Length = 579
Score = 27.3 bits (61), Expect = 0.65
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 18/73 (24%)
Query: 3 YDICEAEAA---LDHIEAEMAARGVTQALIDETRAAPETRMLEDLAAEAARGQDLEYKDP 59
Y+ ++EAA +DH+ + + + A D EY DP
Sbjct: 452 YENVDSEAANKMMDHLRDLVNK------------SKKGIKYGV---YTLAFADDFEYTDP 496
Query: 60 ASGATPSVNGLRY 72
G+ S G+R+
Sbjct: 497 VDGSVSSKQGIRF 509
>gnl|CDD|237250 PRK12893, PRK12893, allantoate amidohydrolase; Reviewed.
Length = 412
Score = 27.2 bits (61), Expect = 0.67
Identities = 18/60 (30%), Positives = 20/60 (33%), Gaps = 3/60 (5%)
Query: 7 EAEAALD-HIEAEMAARGVTQALIDETRAAPET--RMLEDLAAEAARGQDLEYKDPASGA 63
EAAL AARGV + P L L AA L + SGA
Sbjct: 298 AMEAALRAACAKIAAARGVQVTVETVWDFPPVPFDPALVALVEAAAEALGLSHMRMVSGA 357
>gnl|CDD|193505 cd03884, M20_bAS, M20 Peptidase beta-alanine synthase, an
amidohydrolase. Peptidase M20 family, beta-alanine
synthase (bAS; N-carbamoyl-beta-alanine amidohydrolase
and beta-ureidopropionase; EC 3.5.1.6) subfamily. bAS is
an amidohydrolase and is the final enzyme in the
pyrimidine catabolic pathway, which is involved in the
regulation of the cellular pyrimidine pool. The bAS
catalyzes the irreversible hydrolysis of the
N-carbamylated beta-amino acids to beta-alanine or
aminoisobutyrate under the release of carbon dioxide and
ammonia. Also included in this subfamily is allantoate
amidohydrolase (allantoate deiminase), which catalyzes
the conversion of allantoate to (S)-ureidoglycolate, one
of the crucial alternate steps in purine metabolism. It
is possible that these two enzymes arose from the same
ancestral peptidase that evolved into two structurally
related enzymes with distinct catalytic properties and
biochemical roles within the cell. Yeast requires
beta-alanine as a precursor of pantothenate and coenzyme
A biosynthesis, but generates it mostly via degradation
of spermine. Disorders in pyrimidine degradation and
beta-alanine metabolism caused by beta-ureidopropionase
deficiency (UPB1 gene) in humans are normally associated
with neurological disorders.
Length = 399
Score = 27.0 bits (61), Expect = 0.70
Identities = 16/58 (27%), Positives = 19/58 (32%), Gaps = 4/58 (6%)
Query: 9 EAALDHIEAEMAARGVTQALIDETRAAPETRM---LEDLAAEAARGQDLEYKDPASGA 63
A E A RGV I+ +P L AA L Y+ SGA
Sbjct: 294 AAIRAAAEEIAARRGVE-VEIERLSDSPPVPFDPELVAALEAAAEALGLSYRRLPSGA 350
>gnl|CDD|239430 cd03314, MAL, Methylaspartate ammonia lyase (3-methylaspartase,
MAL) is a homodimeric enzyme, catalyzing the
magnesium-dependent reversible alpha,beta-elimination of
ammonia from L-threo-(2S,3S)-3-methylaspartic acid to
mesaconic acid. This reaction is part of the main
catabolic pathway for glutamate. MAL belongs to the
enolase superfamily of enzymes, characterized by the
presence of an enolate anion intermediate which is
generated by abstraction of the alpha-proton of the
carboxylate substrate by an active site residue and is
stabilized by coordination to the essential Mg2+ ion.
Length = 369
Score = 26.2 bits (58), Expect = 1.5
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 7 EAEAALDHIEAE-----MAAR-GVTQALIDETRAAPETRMLEDLAAE 47
A A LD + + A R GV+QAL+D A M E L E
Sbjct: 73 PAAAVLDKMRLDGNRLHTAIRYGVSQALLDAVALAQRRTMAEVLCDE 119
>gnl|CDD|182023 PRK09665, PRK09665, PTS system galactitol-specific transporter
subunit IIA; Provisional.
Length = 150
Score = 25.9 bits (57), Expect = 1.8
Identities = 21/55 (38%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 11 ALDHIEAEMAARGVT-----QALIDETRAAPETRMLEDLAAEAARGQDLEYKDPA 60
AL HI EM A+GV QALI P MLE A + + K PA
Sbjct: 18 ALTHIGNEMLAKGVVHDTYPQALIAREAEFPTGIMLEQHAVAIPHCEAIHAKSPA 72
>gnl|CDD|164577 CHL00203, fabH, 3-oxoacyl-acyl-carrier-protein synthase 3;
Provisional.
Length = 326
Score = 26.1 bits (57), Expect = 1.8
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 24 VTQALIDETRAAPETRMLEDLAAEAA 49
T+ I + AP + L LAAEAA
Sbjct: 34 STRTGIKKRHLAPSSTSLTKLAAEAA 59
>gnl|CDD|217114 pfam02574, S-methyl_trans, Homocysteine S-methyltransferase. This
is a family of related homocysteine S-methyltransferases
enzymes: 5-methyltetrahydrofolate--homocysteine
S-methyltransferases also known EC:2.1.1.13;
Betaine--homocysteine S-methyltransferase (vitamin B12
dependent), EC:2.1.1.5; and Homocysteine
S-methyltransferase, EC:2.1.1.10.
Length = 303
Score = 25.0 bits (55), Expect = 3.5
Identities = 10/47 (21%), Positives = 17/47 (36%)
Query: 3 YDICEAEAALDHIEAEMAARGVTQALIDETRAAPETRMLEDLAAEAA 49
D EA+AA+ +E A G + ++ + L A
Sbjct: 156 PDFLEAKAAVRAVEEVFEAPGWISFPVFDSGTLVDGTGLTLSGATIE 202
>gnl|CDD|200213 TIGR02810, agaZ_gatZ, D-tagatose-bisphosphate aldolase, class II,
non-catalytic subunit. Aldolases specific for
D-tagatose-bisphosphate occur in distinct pathways in
Escherichia coli and other bacteria, one for the
degradation of galactitol (formerly dulcitol) and one
for degradation of N-acetyl-galactosamine and
D-galactosamine. This family represents a protein of
both systems that behaves as a non-catalytic subunit of
D-tagatose-bisphosphate aldolase, required both for full
activity and for good stability of the aldolase. Note
that members of this protein family appear in public
databases annotated as putative tagatose 6-phosphate
kinases, possibly in error [Energy metabolism, Sugars].
Length = 420
Score = 24.6 bits (54), Expect = 4.7
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 3/46 (6%)
Query: 14 HIEAEMAARGVTQALIDET---RAAPETRMLEDLAAEAARGQDLEY 56
H++A M+ G L D T RAA + E A E Y
Sbjct: 121 HLDASMSCAGDPAPLPDATIAERAARLCAVAESAATEEQGETKPVY 166
>gnl|CDD|236036 PRK07512, PRK07512, L-aspartate oxidase; Provisional.
Length = 513
Score = 24.9 bits (55), Expect = 4.9
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 14 HIEAEMAARGVTQALIDETRAAPETRMLEDLAAEA 48
H+ + A + +ALI RA P +LE A
Sbjct: 128 HVGGDGAGAAIMRALIAAVRATPSITVLEGAEARR 162
>gnl|CDD|188327 TIGR03464, HpnC, squalene synthase HpnC. This family of genes are
members of a superfamily (pfam00494) of phytoene and
squalene synthases which catalyze the head-t0-head
condensation of polyisoprene pyrophosphates. The genes
of this family are often found in the same genetic locus
with squalene-hopene cyclase genes, and are never
associated with genes for the metabolism of phytoene. In
the organisms Zymomonas mobilis and Bradyrhizobium
japonicum these genes have been characterized as
squalene synthases (farnesyl-pyrophosphate ligases).
Often, these genes appear in tandem with the HpnD gene
which appears to have resulted from an ancient gene
duplication event. Presumably these proteins form a
heteromeric complex, but this has not yet been
experimentally demonstrated.
Length = 266
Score = 24.6 bits (54), Expect = 5.1
Identities = 9/36 (25%), Positives = 14/36 (38%)
Query: 16 EAEMAARGVTQALIDETRAAPETRMLEDLAAEAARG 51
++A GV++ + RA P R L R
Sbjct: 169 RDDLARFGVSEEDLAAGRATPAVRALMAFEVSRTRA 204
>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 = 24.5 bits (54), Expect = 5.2
Identities = 14/36 (38%), Positives = 16/36 (44%)
Query: 2 PYDICEAEAALDHIEAEMAARGVTQALIDETRAAPE 37
P A AAL+ I+ E R ALI RA E
Sbjct: 251 PAVAAAALAALELIQEEPWRREKLLALIARLRAGLE 286
>gnl|CDD|223127 COG0049, RpsG, Ribosomal protein S7 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 24.5 bits (54), Expect = 5.3
Identities = 11/29 (37%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 22 RGVTQAL---IDETRAAPETRMLEDLAAE 47
R V AL ++ R E M E LA E
Sbjct: 94 RRVALALRWIVEGARKRNEKTMAERLANE 122
>gnl|CDD|236456 PRK09290, PRK09290, allantoate amidohydrolase; Reviewed.
Length = 413
Score = 24.7 bits (55), Expect = 5.4
Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 8/62 (12%)
Query: 9 EAALDHIEAEM----AARGVTQALIDETRAAPETRM---LEDLAAEAARGQDLEYKDPAS 61
+A + + A A RGV + +R P L EAA L Y+ S
Sbjct: 298 DALVAELRAAAEAIAARRGVEVEIELISRRPP-VPFDPGLVAALEEAAERLGLSYRRLPS 356
Query: 62 GA 63
GA
Sbjct: 357 GA 358
>gnl|CDD|173952 cd08193, HVD, 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the
oxidation of 5-hydroxyvalerate to 5-oxovalerate with
NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase
(HVD) is an iron-containing (type III) NAD-dependent
alcohol dehydrogenase. It plays a role in the
cyclopentanol metabolism biochemical pathway. It
catalyzes the oxidation of 5-hydroxyvalerate to
5-oxovalerate with NAD+ as cofactor. This cyclopentanol
(cpn) degradation pathway is present in some bacteria
which can use cyclopentanol as sole carbon source. In
Comamonas sp. strain NCIMB 9872, this enzyme is encoded
by the CpnD gene.
Length = 376
Score = 24.4 bits (54), Expect = 5.9
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 12 LDHIEAEMAARGVTQALIDETRAAPETRMLEDLAAEAAR 50
+D + A + A G+ + D+ A P ++E A EAAR
Sbjct: 43 IDPLLASLEAAGIEVTVFDDVEADPPEAVVEA-AVEAAR 80
>gnl|CDD|203838 pfam08013, Tagatose_6_P_K, Tagatose 6 phosphate kinase. Proteins
in this family are tagatose 6 phosphate kinases.
Length = 423
Score = 24.5 bits (54), Expect = 6.9
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 4/35 (11%)
Query: 7 EAEAALDHIEAEM----AARGVTQALIDETRAAPE 37
EA ALD IEAE+ + L P+
Sbjct: 293 EALFALDAIEAELVPPEGCSPLRAVLEAVMLDEPK 327
>gnl|CDD|173945 cd08186, Fe-ADH8, Iron-containing alcohol dehydrogenase. Type
III Iron-containing alcohol dehydrogenases (ADH).
Alcohol dehydrogenase catalyzes the reduction of
acetaldehyde to alcohol with NADP as cofactor. The ADH
of hyperthermophilic archaeon Thermococcus
hydrothermalis oxidizes a series of primary aliphatic
and aromatic alcohols preferentially from C2 to C8 but
is also active towards methanol and glycerol and
stereospecific for monoterpenes. It was suggested that
the type III ADHs in microorganisms are involved in
acetaldehyde detoxication rather than in alcohol
turnover.
Length = 383
Score = 23.9 bits (52), Expect = 8.5
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 11 ALDHIEAEMAARGVTQALIDETRAAPETRMLEDLAAEAAR 50
A D +E + G+ L ++ P +++ AA+ R
Sbjct: 43 AWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDE-AAKLGR 81
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
0.312 0.127 0.351
Gapped
Lambda K H
0.267 0.0893 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,847,915
Number of extensions: 308158
Number of successful extensions: 361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 360
Number of HSP's successfully gapped: 57
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (23.9 bits)