RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17890
(118 letters)
>gnl|CDD|220160 pfam09271, LAG1-DNAbind, LAG1, DNA binding. Members of this family
are found in various eukaryotic hypothetical proteins
and in the DNA-binding protein LAG-1. They adopt a beta
sandwich structure, with nine strands in two
beta-sheets, in a Greek-key topology, and allow for DNA
binding. This domain is also known as RHR-N
(Rel-homology region) as it related to Rel domain
proteins.
Length = 138
Score = 115 bits (289), Expect = 2e-34
Identities = 43/76 (56%), Positives = 56/76 (73%), Gaps = 3/76 (3%)
Query: 46 VIVILHAKVAQKSYGNEKRFFCPPPCIYLYGEGWRLRQEQLLREGESEQAAQLCAFIGIG 105
+ ILHAKVAQKSYGNEKRF CPPPC+YL G GWRL+ + L G S+QA ++ +IGIG
Sbjct: 1 TVSILHAKVAQKSYGNEKRFLCPPPCVYLIGPGWRLKPQPLQPNGISDQATEISPYIGIG 60
Query: 106 NSDQ---DMQQLDLNN 118
S+Q +MQ+L+ +
Sbjct: 61 GSEQQQAEMQKLNFDG 76
>gnl|CDD|183111 PRK11382, frlB, fructoselysine-6-P-deglycase; Provisional.
Length = 340
Score = 33.8 bits (77), Expect = 0.012
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 14 EGWVPHSLHYRNDDQRLTREAMERYLRDRSDMVIVILHAKVAQ 56
E VP ND+ R T E +++ R+D VIVI +A+++Q
Sbjct: 256 EPGVPFLFLLGNDESRHTTERAINFVKQRTDNVIVIDYAEISQ 298
>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type.
Members of this protein family include secreted (or
membrane-anchored) pullulanases of Gram-negative
bacteria and pullulanase-type starch debranching enzymes
of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
linkages. Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. This
family is closely homologous to, but architecturally
different from, the Gram-positive pullulanases of
Gram-positive bacteria (TIGR02102) [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 898
Score = 30.9 bits (70), Expect = 0.11
Identities = 16/37 (43%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 70 PCIYLYGEGWRLRQEQLLREGESEQAAQL-CAFIGIG 105
P IY YGEGW + R A QL A GIG
Sbjct: 518 PEIYFYGEGWDFGEVANNRRF--INATQLNLAGTGIG 552
>gnl|CDD|152159 pfam11723, Aromatic_hydrox, Homotrimeric ring hydroxylase. This
domain is found on aromatic hydroxylating enzymes such
as 2-oxo-1,2-dihydroquinoline 8-monooxygenase from
Pseudomonas putida and carbazole 1,9a-dioxygenase from
Janthinobacterium. These enzymes are homotrimers and are
distantly related to the typical oxygenase. This domain
is found C terminal to the Rieske domain which binds an
iron-sulphur cluster.
Length = 240
Score = 29.0 bits (65), Expect = 0.43
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 14 EGWVPHSLHYRNDDQRLTREAMERYLRD----------RSDMVIVILHAKVAQKSYG 60
E W +L+ NDD RE+M+ + D D IV ++ + G
Sbjct: 182 EKWREAALNGFNDDDIWARESMQPFYADDRGWSEEQLFEPDAAIVAWRKLASEHARG 238
>gnl|CDD|130264 TIGR01196, edd, 6-phosphogluconate dehydratase. A close homolog,
designated MocB (mannityl opine catabolism), is found in
a mannopine catabolism region of a plasmid of
Agrobacterium tumefaciens. However, it is not essential
for mannopine catabolism, branches within the cluster of
6-phosphogluconate dehydratases (with a short branch
length) in a tree rooted by the presence of other
dehydyatases. It may represent an authentic
6-phosphogluconate dehydratase, redundant with the
chromosomal copy shown to exist in plasmid-cured
strains. This model includes mocB above the trusted
cutoff, although the designation is somewhat tenuous
[Energy metabolism, Entner-Doudoroff].
Length = 601
Score = 29.0 bits (65), Expect = 0.53
Identities = 16/41 (39%), Positives = 20/41 (48%)
Query: 74 LYGEGWRLRQEQLLREGESEQAAQLCAFIGIGNSDQDMQQL 114
L+ EG R+E L E S A C F G NS+Q M +
Sbjct: 195 LFAEGKVGREELLKSEMASYHAPGTCTFYGTANSNQMMMEF 235
>gnl|CDD|221053 pfam11271, DUF3068, Protein of unknown function (DUF3068). Some
members in this family of proteins with unknown function
are annotated as membrane proteins however this cannot
be confirmed.
Length = 300
Score = 28.5 bits (64), Expect = 0.72
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 32 REAMERYLRDRSDMVIVILHAKVA 55
E RYLRD +V+L A
Sbjct: 232 EEQQRRYLRDGVGKEVVVLDATFT 255
>gnl|CDD|99871 cd06118, citrate_synt_like_1, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism.
Length = 358
Score = 27.6 bits (62), Expect = 1.7
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 15 GWVPHSLHYRNDDQRLTR 32
GW+ H + YR ++QRL R
Sbjct: 336 GWLAHIIEYRENNQRLIR 353
>gnl|CDD|233730 TIGR02104, pulA_typeI, pullulanase, type I. Pullulan is an
unusual, industrially important polysaccharide in which
short alpha-1,4 chains (maltotriose) are connected in
alpha-1,6 linkages. Enzymes that cleave alpha-1,6
linkages in pullulan and release maltotriose are called
pullulanases although pullulan itself may not be the
natural substrate. This family consists of pullulanases
related to the subfamilies described in TIGR02102 and
TIGR02103 but having a different domain architecture
with shorter sequences. Members are called type I
pullulanases.
Length = 605
Score = 27.3 bits (61), Expect = 2.0
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 70 PCIYLYGEGWRL 81
P I LYGEGW L
Sbjct: 341 PNILLYGEGWDL 352
>gnl|CDD|200480 cd11341, AmyAc_Pullulanase_LD-like, Alpha amylase catalytic domain
found in Pullulanase (also called dextrinase;
alpha-dextrin endo-1,6-alpha glucosidase), limit
dextrinase, and related proteins. Pullulanase is an
enzyme with action similar to that of isoamylase; it
cleaves 1,6-alpha-glucosidic linkages in pullulan,
amylopectin, and glycogen, and in alpha-and beta-amylase
limit-dextrins of amylopectin and glycogen. Pullulanases
are very similar to limit dextrinases, although they
differ in their action on glycogen and the rate of
hydrolysis of limit dextrins. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 406
Score = 26.7 bits (60), Expect = 2.7
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 70 PCIYLYGEGWRL 81
P I LYGEGW
Sbjct: 219 PNILLYGEGWDF 230
>gnl|CDD|215474 PLN02877, PLN02877, alpha-amylase/limit dextrinase.
Length = 970
Score = 26.3 bits (58), Expect = 4.9
Identities = 8/8 (100%), Positives = 8/8 (100%)
Query: 72 IYLYGEGW 79
IYLYGEGW
Sbjct: 591 IYLYGEGW 598
>gnl|CDD|235605 PRK05782, PRK05782, bifunctional sirohydrochlorin cobalt
chelatase/precorrin-8X methylmutase; Validated.
Length = 335
Score = 25.9 bits (57), Expect = 5.2
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 79 WRLRQEQLLREGESEQAAQLCAFIGIGN 106
WR ++++EG L AF+G GN
Sbjct: 52 WRSLLNEIIKEGYRRVIIAL-AFLGRGN 78
>gnl|CDD|236623 PRK09775, PRK09775, putative DNA-binding transcriptional regulator;
Provisional.
Length = 442
Score = 26.1 bits (58), Expect = 6.0
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 80 RLRQEQLLREGESEQAAQLCAFIG--IGNSD 108
RL + L+ E ++++A L AF G I N+D
Sbjct: 315 RLAAQGLITEEDAQRAELLWAF-GRLIANTD 344
>gnl|CDD|225107 COG2197, CitB, Response regulator containing a CheY-like receiver
domain and an HTH DNA-binding domain [Signal
transduction mechanisms / Transcription].
Length = 211
Score = 25.3 bits (56), Expect = 7.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 26 DDQRLTREAMERYLRDRSDMVIV 48
DD L RE + + L D+ +V
Sbjct: 7 DDHPLVREGLRQLLELEPDLEVV 29
>gnl|CDD|172358 PRK13831, PRK13831, conjugal transfer protein TrbI; Provisional.
Length = 432
Score = 25.5 bits (56), Expect = 8.2
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 77 EGWRLR-----QEQLLREGESEQAAQLCA 100
E WR R +EQ LRE + ++ A+L A
Sbjct: 126 EEWRARLKREQEEQYLRERQRQRMARLQA 154
>gnl|CDD|99855 cd06101, citrate_synt, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and form
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 265
Score = 25.4 bits (56), Expect = 8.6
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 15 GWVPHSLHYRNDDQRLTR 32
GW+ H + R D QR+ R
Sbjct: 243 GWLAHLIEQREDGQRIIR 260
>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX. The family
of proteins found in this equivalog include the
characterized LysX from Thermus thermophilus which is
part of a well-organized lysine biosynthesis gene
cluster. LysX is believed to carry out an ATP-dependent
acylation of the amino group of alpha-aminoadipate in
the prokaryotic version of the fungal AAA lysine
biosynthesis pathway. No species having a sequence in
this equivalog contains the elements of the more common
diaminopimelate lysine biosythesis pathway, and none has
been shown to be a lysine auxotroph. These sequences
have mainly recieved the name of the related enzyme,
"ribosomal protein S6 modification protein RimK". RimK
has been characterized in E. coli, and acts by
ATP-dependent condensation of S6 with glutamate
residues.
Length = 280
Score = 25.4 bits (56), Expect = 9.3
Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 17/59 (28%)
Query: 39 LRDRSDMVIVILHAKVAQKSY-------------GNEKRFFC----PPPCIYLYGEGWR 80
+RD+ ++ ++ H +V S G + R F IY Y WR
Sbjct: 141 IRDKDELESLLEHKEVLGGSQHKLFYIQEYINKPGRDIRVFVIGDEAIAAIYRYSNHWR 199
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
0.322 0.138 0.432
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,062,941
Number of extensions: 515693
Number of successful extensions: 550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 549
Number of HSP's successfully gapped: 28
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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: 53 (24.3 bits)