RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1294
(105 letters)
>gnl|CDD|238060 cd00112, LDLa, Low Density Lipoprotein Receptor Class A domain, a
cysteine-rich repeat that plays a central role in
mammalian cholesterol metabolism; the receptor protein
binds LDL and transports it into cells by endocytosis; 7
successive cysteine-rich repeats of about 40 amino acids
are present in the N-terminal of this multidomain
membrane protein; other homologous domains occur in
related receptors, including the very low-density
lipoprotein receptor and the LDL receptor-related
protein/alpha 2-macroglobulin receptor, and in proteins
which are functionally unrelated, such as the C9
component of complement; the binding of calcium is
required for in vitro formation of the native disulfide
isomer and is necessary in establishing and maintaining
the modular structure.
Length = 35
Score = 35.6 bits (83), Expect = 2e-04
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 77 QCGSGETYTKEQHCNGVLDCKDGSDEMHC 105
+C +G C+G DC DGSDE +C
Sbjct: 7 RCANGRCIPSSWVCDGEDDCGDGSDEENC 35
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 33.0 bits (76), Expect = 0.002
Identities = 16/29 (55%), Positives = 19/29 (65%)
Query: 77 QCGSGETYTKEQHCNGVLDCKDGSDEMHC 105
QCGSGE C+G DC+DGSDE +C
Sbjct: 9 QCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
>gnl|CDD|197566 smart00192, LDLa, Low-density lipoprotein receptor domain class A.
Cysteine-rich repeat in the low-density lipoprotein
(LDL) receptor that plays a central role in mammalian
cholesterol metabolism. The N-terminal type A repeats in
LDL receptor bind the lipoproteins. Other homologous
domains occur in related receptors, including the very
low-density lipoprotein receptor and the LDL
receptor-related protein/alpha 2-macroglobulin receptor,
and in proteins which are functionally unrelated, such
as the C9 component of complement. Mutations in the LDL
receptor gene cause familial hypercholesterolemia.
Length = 33
Score = 30.3 bits (69), Expect = 0.021
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 77 QCGSGETYTKEQHCNGVLDCKDGSDE 102
QC +G C+GV DC DGSDE
Sbjct: 8 QCDNGRCIPSSWVCDGVDDCGDGSDE 33
>gnl|CDD|233103 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, alpha region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase alpha chain and the N-terminal
region of the class I fumarase (where the C-terminal
region is homologous to the tartrate dehydratase beta
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 273
Score = 29.7 bits (67), Expect = 0.19
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 64 HCHTGTLPVVLSLQC 78
HCHT +LPV +++QC
Sbjct: 249 HCHTASLPVAVNIQC 263
>gnl|CDD|180486 PRK06246, PRK06246, fumarate hydratase; Provisional.
Length = 280
Score = 27.4 bits (62), Expect = 1.1
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 64 HCHTGTLPVVLSLQC 78
CH +LPV +++QC
Sbjct: 256 PCHIASLPVAVNIQC 270
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase). This family
consists of several bacterial fumarate hydratase
proteins FumA and FumB. Fumarase, or fumarate hydratase
(EC 4.2.1.2), is a component of the citric acid cycle.
In facultative anaerobes such as Escherichia coli,
fumarase also engages in the reductive pathway from
oxaloacetate to succinate during anaerobic growth. Three
fumarases, FumA, FumB, and FumC, have been reported in
E. coli. fumA and fumB genes are homologous and encode
products of identical sizes which form thermolabile
dimers of Mr 120,000. FumA and FumB are class I enzymes
and are members of the iron-dependent hydrolases, which
include aconitase and malate hydratase. The active FumA
contains a 4Fe-4S centre, and it can be inactivated upon
oxidation to give a 3Fe-4S centre.
Length = 271
Score = 27.0 bits (61), Expect = 1.7
Identities = 5/15 (33%), Positives = 9/15 (60%)
Query: 64 HCHTGTLPVVLSLQC 78
H +LPV +++ C
Sbjct: 247 PRHIASLPVAVNVNC 261
>gnl|CDD|132295 TIGR03251, LAT_fam, L-lysine 6-transaminase. Characterized members
of this protein family are L-lysine 6-transaminase, also
called lysine epsilon-aminotransferase (LAT). The
immediate product of the reaction of this enzyme on
lysine, 2-aminoadipate 6-semialdehyde, becomes
1-piperideine 6-carboxylate, or P6C. This product may be
converted subsequently to pipecolate or
alpha-aminoadipate, lysine catabolites that may be
precursors of certain seconary metabolites.
Length = 431
Score = 27.0 bits (60), Expect = 1.7
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 12/43 (27%)
Query: 21 TGVEWCQSQGKVMCGIYPDVQCYDNRTQAC--------DSVAD 55
TG W Q G+ PD+ + +TQ C D VAD
Sbjct: 267 TGTAWAYQQ----LGVQPDIVAFGKKTQVCGIMAGRRVDEVAD 305
>gnl|CDD|224862 COG1951, TtdA, Tartrate dehydratase alpha subunit/Fumarate
hydratase class I, N-terminal domain [Energy production
and conversion].
Length = 297
Score = 26.8 bits (60), Expect = 2.3
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 64 HCHTGTLPVVLSLQC 78
H +LPV +++QC
Sbjct: 257 PRHPASLPVAVNVQC 271
>gnl|CDD|180789 PRK06997, PRK06997, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 260
Score = 26.3 bits (58), Expect = 3.5
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 3 VMKCDLFNDSKSASTFATTGVEW 25
V CD+ +D + + FA+ G W
Sbjct: 60 VFPCDVASDEQIDALFASLGQHW 82
>gnl|CDD|222726 pfam14387, DUF4418, Domain of unknown function (DUF4418). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 132 and
150 amino acids in length.
Length = 123
Score = 25.7 bits (57), Expect = 3.8
Identities = 9/18 (50%), Positives = 9/18 (50%)
Query: 59 MKDEKHCHTGTLPVVLSL 76
MK CH TLP V L
Sbjct: 89 MKPTMACHAVTLPAVRIL 106
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 25.7 bits (57), Expect = 4.5
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 71 PVVLSLQCGSGETYTKEQHCNGVLDCKDGSDE 102
PV L+ GSG + QH + + DE
Sbjct: 87 PVTFRLKSGSGPVHISGQHLVASEEDESDDDE 118
>gnl|CDD|224165 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 358
Score = 25.4 bits (56), Expect = 7.0
Identities = 10/36 (27%), Positives = 11/36 (30%), Gaps = 3/36 (8%)
Query: 7 DLFNDSKSAST---FATTGVEWCQSQGKVMCGIYPD 39
D S T G W + G MCG D
Sbjct: 38 DRLRGYPGKSLTVILRTRGCRWYREGGCYMCGYPAD 73
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
0.319 0.132 0.436
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,585,733
Number of extensions: 330043
Number of successful extensions: 199
Number of sequences better than 10.0: 1
Number of HSP's gapped: 199
Number of HSP's successfully gapped: 17
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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: 53 (24.1 bits)