RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11221
(202 letters)
>gnl|CDD|238974 cd02016, TPP_E1_OGDC_like, Thiamine pyrophosphate (TPP) family,
E1 of OGDC-like subfamily, TPP-binding module; composed
of proteins similar to the E1 component of the
2-oxoglutarate dehydrogenase multienzyme complex
(OGDC). OGDC catalyzes the oxidative decarboxylation of
2-oxoglutarate to succinyl-CoA and carbon dioxide, a
key reaction of the tricarboxylic acid cycle.
Length = 265
Score = 96.8 bits (242), Expect = 1e-24
Identities = 33/52 (63%), Positives = 41/52 (78%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
FE FLA K+ +KRFGLEG E LIPA+ ++ID++ ELGVE VV+GM HRG L
Sbjct: 1 FEQFLATKFPGQKRFGLEGAESLIPALDELIDRAAELGVEEVVIGMAHRGRL 52
>gnl|CDD|236499 PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component;
Reviewed.
Length = 924
Score = 86.7 bits (216), Expect = 5e-20
Identities = 26/52 (50%), Positives = 37/52 (71%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
FE FL K+ +KRF LEG E LIP + ++I ++ +LGV+ +V+GM HRG L
Sbjct: 204 FERFLHTKFVGQKRFSLEGGESLIPMLDEIIRRAGKLGVKEIVIGMAHRGRL 255
>gnl|CDD|223641 COG0567, SucA, 2-oxoglutarate dehydrogenase complex, dehydrogenase
(E1) component, and related enzymes [Energy production
and conversion].
Length = 906
Score = 84.2 bits (209), Expect = 4e-19
Identities = 27/52 (51%), Positives = 36/52 (69%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
FE FL K+ KRF LEG E LIP + ++ID++ + GV+ VV+GM HRG L
Sbjct: 190 FERFLHTKFPGAKRFSLEGGESLIPMLDELIDRAGKQGVKEVVIGMAHRGRL 241
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 77.6 bits (191), Expect = 9e-17
Identities = 45/135 (33%), Positives = 62/135 (45%), Gaps = 21/135 (15%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRG--NLISETTG 86
FE FL K+ KRF LEG + L+P +K++I S G VV+GM HRG N++ G
Sbjct: 204 FERFLGAKFPGAKRFSLEGLDALVPMLKEIIRHSVNSGTRDVVLGMAHRGRLNVLVNVLG 263
Query: 87 QGLQKVPRLF-----SQNPQNNGDIR-HFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTL 140
+ + + F S P GD++ H FSS T T G HL L
Sbjct: 264 KPPEDIFSEFAGKHKSHLPDGTGDVKYHMGRFSSDFT------------TDGKL-VHLAL 310
Query: 141 NCWPRAMFLSTPVCI 155
P + + +PV I
Sbjct: 311 AFNPSHLEIVSPVVI 325
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 71.8 bits (177), Expect = 9e-15
Identities = 27/52 (51%), Positives = 36/52 (69%)
Query: 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNL 80
FE FL K+ +KRF LEG E LIP + V+D++ E G++ VV+GM HRG L
Sbjct: 508 FETFLQTKYVGQKRFSLEGGESLIPLLDAVLDQAAEHGLDEVVIGMAHRGRL 559
>gnl|CDD|237962 PRK15418, PRK15418, transcriptional regulator LsrR; Provisional.
Length = 318
Score = 28.5 bits (64), Expect = 2.4
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 8/80 (10%)
Query: 26 NSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVES--VVMGMPHRGNLIS- 82
NS FE L + + + F L+ +L PA+ D LG+ + ++M + L++
Sbjct: 64 NSRFEGCLELENALRQHFSLQHIRVL-PALAD-ADIGGRLGIGAAHMLMSLLQPQQLLAV 121
Query: 83 ---ETTGQGLQKVPRLFSQN 99
E T LQ + S
Sbjct: 122 GFGEATMNTLQHLSGFISSQ 141
>gnl|CDD|132840 cd07201, cPLA2_Grp-IVB-IVD-IVE-IVF, Group IVB, IVD, IVE, and IVF
cytosolic phospholipase A2; catalytic domain;
Ca-dependent. Group IVB, IVD, IVE, and IVF cPLA2
consists of two domains: the regulatory C2 domain and
alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE,
and IVF cPLA2 are also referred to as cPLA2-beta,
-delta, -epsilon, and -zeta respectively. cPLA2-beta is
approximately 30% identical to cPLA2-alpha and it shows
low enzymatic activity compared to cPLA2alpha.
cPLA2-beta hydrolyzes palmitic acid from
1-[14C]palmitoyl-2-arachidonoyl-PC and arachidonic acid
from 1-palmitoyl-2[14C]arachidonoyl-PC, but not from
1-O-alkyl-2[3H]arachidonoyl-PC. cPLA2-delta, -epsilon,
and -zeta are approximately 45-50% identical to
cPLA2-beta and 31-37% identical to cPLA2-alpha. It's
possible that cPLA2-beta, -delta, -epsilon, and -zeta
may have arisen by gene duplication from an ancestral
gene. The catalytic domain of cytosolic phospholipase A2
(PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond
of phospholipids to release arachidonic acid. At the
active site, cPLA2 contains a serine nucleophile through
which the catalytic mechanism is initiated. The active
site is partially covered by a solvent-accessible
flexible lid. cPLA2 displays interfacial activation as
it exists in both "closed lid" and "open lid" forms.
Movement of the cPLA2 lid possibly exposes a greater
hydrophobic surface and the active site. cPLA2 belongs
to the alpha-beta hydrolase family which is identified
by a characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Calcium is required for
cPLA2 to bind with membranes or phospholipids. The
calcium-dependent phospholipid binding domain resides in
the N-terminal region of cPLA2; it is homologous to the
C2 domain superfamily which is not included in this
hierarchy. It includes PLA2G4B, PLA2G4D, PLA2G4E, and
PLA2G4F from humans.
Length = 541
Score = 27.3 bits (61), Expect = 5.8
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 7/71 (9%)
Query: 95 LFSQNPQNNGDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVC 154
+FS N + ++ +T + W + + P L R L TP
Sbjct: 261 IFSLNLLD-------AWYLATGSEDFWHRWTRDKVNDIEDEPPLPPRPPERLTTLLTPGG 313
Query: 155 ILHETFRPIFT 165
L + FR T
Sbjct: 314 PLSQAFRDFLT 324
>gnl|CDD|237881 PRK14985, PRK14985, maltodextrin phosphorylase; Provisional.
Length = 798
Score = 27.3 bits (61), Expect = 7.5
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 20 SSATFSNSEFEAFLAKKWSSEKRFGL 45
S F+ +F+A L ++W +RFGL
Sbjct: 1 SQPIFNKKQFQAALTRQW---QRFGL 23
>gnl|CDD|114869 pfam06176, WaaY, Lipopolysaccharide core biosynthesis protein
(WaaY). This family consists of several bacterial
lipopolysaccharide core biosynthesis proteins (WaaY or
RfaY). The waaY, waaQ, and waaP genes are located in the
central operon of the waa (formerly rfa) locus on the
chromosome of Escherichia coli. This locus contains
genes whose products are involved in the assembly of the
core region of the lipopolysaccharide molecule. WaaY is
the enzyme that phosphorylates HepII in this system.
Length = 229
Score = 26.7 bits (59), Expect = 8.0
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 44 GLEGCEILI------PAMKQVIDKSTELGVESVVMGMPHRGNLISETTG 86
G+E ++ +KQ I+ + G+ V G PHRGN I G
Sbjct: 127 GVELNDMPEISEDVKAKIKQSIESLHQHGM---VSGDPHRGNFIVSKDG 172
>gnl|CDD|187873 cd09742, Csm6_III-A, CRISPR/Cas system-associated protein Csm6.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain;
loosely associated with CRISPR/Cas systems; also known
as APE2256 family.
Length = 183
Score = 26.5 bits (59), Expect = 8.3
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 1/24 (4%)
Query: 146 AMFLSTPVCILHETFR-PIFTPII 168
L PV +HE+F + P +
Sbjct: 149 GSLLGAPVYYIHESFSELVELPPL 172
>gnl|CDD|216274 pfam01062, Bestrophin, Bestrophin, RFP-TM, chloride channel.
Bestrophin is a 68-kDa basolateral plasma membrane
protein expressed in retinal pigment epithelial cells
(RPE). It is encoded by the VMD2 gene, which is mutated
in Best macular dystrophy, a disease characterized by a
depressed light peak in the electrooculogram. VMD2
encodes a 585-amino acid protein with an approximate
mass of 68 kDa which has been designated bestrophin.
Bestrophin shares homology with the Caenorhabditis
elegans RFP gene family, named for the presence of a
conserved arginine (R), phenylalanine (F), proline (P),
amino acid sequence motif. Bestrophin is a plasma
membrane protein, localised to the basolateral surface
of RPE cells consistent with a role for bestrophin in
the generation or regulation of the EOG light peak.
Bestrophin and other RFP family members represent a new
class of chloride channels, indicating a direct role for
bestrophin in generating the light peak. The VMD2 gene
underlying Best disease was shown to represent the first
human member of the RFP-TM protein family. More than 97%
of the disease-causing mutations are located in the
N-terminal RFP-TM domain implying important functional
properties. The bestrophins are four-pass transmembrane
chloride-channel proteins, and the RFP-TM or bestrophin
domain extends from the N-terminus through approximately
350 amino acids and contains all of the TM domains as
well as nearly all reported disease causing mutations.
Interestingly, the RFP motif is not conserved
evolutionarily back beyond Metazoa, neither is it in
plant members.
Length = 284
Score = 26.7 bits (60), Expect = 8.5
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 136 PHLTLNCWPRAMFLSTPVCILHET--FRPIFTPIIFFFF 172
H + + L P + F P+FT +IF+FF
Sbjct: 214 VHRAVYLY----CLLLPFGLQDTLGWFTPLFTVLIFYFF 248
>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 26.5 bits (59), Expect = 8.9
Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 8/56 (14%)
Query: 4 FVISNSSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVI 59
V++ + +V L F+ E L ++GC L ++ +
Sbjct: 182 VVMTGNGGLVEIQGLAEDGPFTEDELLELLDL--------AIKGCNELRELQREAL 229
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
0.326 0.139 0.425
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,264,202
Number of extensions: 932092
Number of successful extensions: 1001
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1001
Number of HSP's successfully gapped: 19
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.3 bits)