RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9009
(258 letters)
>gnl|CDD|200460 cd11321, AmyAc_bac_euk_BE, Alpha amylase catalytic domain found in
bacterial and eukaryotic branching enzymes. Branching
enzymes (BEs) catalyze the formation of alpha-1,6 branch
points in either glycogen or starch by cleavage of the
alpha-1,4 glucosidic linkage yielding a non-reducing end
oligosaccharide chain, and subsequent attachment to the
alpha-1,6 position. By increasing the number of
non-reducing ends, glycogen is more reactive to
synthesis and digestion as well as being more soluble.
This group includes bacterial and eukaryotic proteins.
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 = 104 bits (262), Expect = 5e-26
Identities = 35/42 (83%), Positives = 38/42 (90%)
Query: 90 GNEFGHPEWLDFPRAGNNSSYWHARRQWNLTDDELLKYKFLN 131
GNEFGHPEWLDFPR GNN SY +ARRQWNL DD+LL+YKFLN
Sbjct: 361 GNEFGHPEWLDFPREGNNWSYHYARRQWNLVDDDLLRYKFLN 402
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 88.6 bits (220), Expect = 5e-20
Identities = 28/42 (66%), Positives = 33/42 (78%)
Query: 90 GNEFGHPEWLDFPRAGNNSSYWHARRQWNLTDDELLKYKFLN 131
GNEFGHPEW+DFPR GN SY RR+W+L D + L+YKFLN
Sbjct: 573 GNEFGHPEWIDFPREGNGWSYDKCRRRWDLADADHLRYKFLN 614
>gnl|CDD|215519 PLN02960, PLN02960, alpha-amylase.
Length = 897
Score = 61.0 bits (148), Expect = 1e-10
Identities = 20/33 (60%), Positives = 26/33 (78%)
Query: 90 GNEFGHPEWLDFPRAGNNSSYWHARRQWNLTDD 122
GNEFGHPE ++FPRA NN S+ A R+W+L +D
Sbjct: 735 GNEFGHPERVEFPRASNNFSFSLANRRWDLLED 767
>gnl|CDD|178782 PLN03244, PLN03244, alpha-amylase; Provisional.
Length = 872
Score = 43.5 bits (102), Expect = 6e-05
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 90 GNEFGHPEWLDFPRAGNNSSYWHARRQWNLTDDELLKYKF 129
GNEFGHPE ++FP NN S+ A R W+L ++E+ + F
Sbjct: 710 GNEFGHPERIEFPMPSNNFSFSLANRCWDLLENEVHHHLF 749
>gnl|CDD|199862 cd06238, M14-like_1_1, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavage.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 270
Score = 30.7 bits (70), Expect = 0.56
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 12/49 (24%)
Query: 131 NSNETPATLDNTVV----CLSPDGREETQDFPFGCWVN---MRTPESNP 172
+E A LDNTVV +PDGR+ F W N P ++P
Sbjct: 79 QGDEIEALLDNTVVLIDPMQNPDGRDR-----FVNWFNSTRGMVPNADP 122
Score = 27.6 bits (62), Expect = 5.6
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 12/47 (25%)
Query: 199 PTLPATLDNTVV----CLSPDGREETQDFPFGCWVNT---RTPESNP 238
+ A LDNTVV +PDGR+ F W N+ P ++P
Sbjct: 81 DEIEALLDNTVVLIDPMQNPDGRDR-----FVNWFNSTRGMVPNADP 122
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 28.8 bits (65), Expect = 2.1
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 173 LKYLLSKNECEILSMEGFK---LVPHIECP 199
L +LS + + L +EGFK +P I C
Sbjct: 77 LNEILSLLDADFLLIEGFKELLNIPKILCL 106
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.1 bits (66), Expect = 2.7
Identities = 12/19 (63%), Positives = 13/19 (68%), Gaps = 4/19 (21%)
Query: 2 GGWH---NTDFKSSLTNRS 17
GGWH NT FKSS NR+
Sbjct: 120 GGWHGLGNTRFKSS-VNRA 137
>gnl|CDD|218467 pfam05147, LANC_like, Lanthionine synthetase C-like protein.
Lanthionines are thioether bridges that are putatively
generated by dehydration of Ser and Thr residues
followed by addition of cysteine residues within the
peptide. This family contains the lanthionine synthetase
C-like proteins 1 and 2 which are related to the
bacterial lanthionine synthetase components C (LanC).
LANCL1 (P40 seven-transmembrane-domain protein) and
LANCL2 (testes-specific adriamycin sensitivity protein)
are thought to be peptide-modifying enzyme components in
eukaryotic cells. Both proteins are produced in large
quantities in the brain and testes and may have role in
the immune surveillance of these organs. Lanthionines
are found in lantibiotics, which are peptide-derived,
post-translationally modified antimicrobials produced by
several bacterial strains. This region contains seven
internal repeats.
Length = 352
Score = 28.1 bits (63), Expect = 4.1
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 37 GIFLFLLRLLDPEINRFKNTDL 58
GI FLL LL+PE +RF + L
Sbjct: 331 GILYFLLDLLNPEESRFPSALL 352
>gnl|CDD|235081 PRK02870, PRK02870, heat shock protein HtpX; Provisional.
Length = 336
Score = 28.1 bits (63), Expect = 4.4
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 10/59 (16%)
Query: 29 RAGKMRTN-------GIFLFLLRLLDPEINRFKNTDLDFSQLFTEESTFYINNIFPIAT 80
R +++T IFLF+ L+D + + TF IFP AT
Sbjct: 18 RRNRLKTRAVIATYLAIFLFIGLLVDAIRIASEYPAASLGKALLALLTFQ---IFPTAT 73
>gnl|CDD|204155 pfam09160, FimH_man-bind, FimH, mannose binding. Members of this
family adopt a secondary structure consisting of a beta
sandwich, with nine strands arranged in two sheets in a
Greek key topology. They are predominantly found in
bacterial mannose-specific adhesins, since they are
capable of binding to D-mannose.
Length = 147
Score = 27.4 bits (61), Expect = 5.1
Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 17/73 (23%)
Query: 46 LDPEINRFKNTDLDFSQLFT---EESTFYINNIFPIATAPFPLVCIKGNEFGHPEWLDFP 102
L P + +N +D SQL + + I + + +G+ FG
Sbjct: 21 LSPVVQVGQNIVVDLSQLISCKNDYPGGSITDYLNL---------TQGSAFGGSL----- 66
Query: 103 RAGNNSSYWHARR 115
A S YW+
Sbjct: 67 DAFTGSLYWYGST 79
>gnl|CDD|200414 TIGR04163, rSAM_cobopep, peptide-modifying radical SAM enzyme CbpB.
Members of this family are radical SAM enzymes that
modify a short peptide encoded by an upstream gene. A
role in metal chelation is suggested.
Length = 428
Score = 27.8 bits (62), Expect = 5.4
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 129 FLNSNETPATLDNTVVCLSPDGRE 152
FL++ E P + N V C P GR+
Sbjct: 234 FLHAGEVPTCMLNPVRCTQPGGRD 257
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
0.320 0.136 0.439
Gapped
Lambda K H
0.267 0.0641 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,025,908
Number of extensions: 1186654
Number of successful extensions: 809
Number of sequences better than 10.0: 1
Number of HSP's gapped: 809
Number of HSP's successfully gapped: 14
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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 (21.8 bits)
S2: 58 (26.3 bits)