RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16990
(250 letters)
>gnl|CDD|153058 cd03588, CLECT_CSPGs, C-type lectin-like domain (CTLD) of the type
found in chondroitin sulfate proteoglycan core proteins.
CLECT_CSPGs: C-type lectin-like domain (CTLD) of the
type found in chondroitin sulfate proteoglycan core
proteins (CSPGs) in human and chicken aggrecan, frog
brevican, and zebra fish dermacan. CTLD refers to a
domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. In cartilage,
aggrecan forms cartilage link protein stabilized
aggregates with hyaluronan (HA). These aggregates
contribute to the tissue's load bearing properties.
Aggregates having other CSPGs substituting for aggrecan
may contribute to the structural integrity of many
different tissues. Xenopus brevican is expressed in the
notochord and the brain during early embryogenesis.
Zebra fish dermacan is expressed in dermal bones and may
play a role in dermal bone development. CSPGs do
contain LINK domain(s) which bind HA. These LINK
domains are considered by one classification system to
be a variety of CTLD, but are omitted from this
hierarchical classification based on insignificant
sequence similarity.
Length = 124
Score = 28.7 bits (64), Expect = 1.3
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 113 RPEQPARLFPIGENNHELIGHNK----DVP--YH 140
RP QP F GE+ +I H + DVP YH
Sbjct: 83 RPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYH 116
>gnl|CDD|131979 TIGR02933, nifM_nitrog, nitrogen fixation protein NifM. Members of
this protein family, found in a subset of
nitrogen-fixing bacteria, are the nitrogen fixation
protein NifM. NifM, homologous to peptidyl-prolyl
cis-trans isomerases, appears to be an accessory protein
for NifH, the Fe protein, also called component II or
dinitrogenase reductase, of nitrogenase [Central
intermediary metabolism, Nitrogen fixation].
Length = 256
Score = 29.4 bits (66), Expect = 1.5
Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 3/55 (5%)
Query: 106 NHELIVCRPEQPAR---LFPIGENNHELIGHNKDVPYHSISSPRSKFAVLNNRHA 157
H RPEQ L + E++ E + + + FA RH+
Sbjct: 113 RHAEQFKRPEQRLTRHLLLTVNEDDREAVRTRILAILRRLRGKPAAFAEQAMRHS 167
>gnl|CDD|176171 cd08482, PBP2_TrpI, The C-terminal substrate binding domain of
LysR-type transcriptional regulator TrpI, which is
involved in control of tryptophan synthesis, contains
type 2 periplasmic binding fold. TrpI and
indoleglycerol phosphate (InGP), are required to
activate transcription of the trpBA, the genes for
tryptophan synthase. The trpBA is induced by the InGp
substrate, rather than by tryptophan, but the exact
mechanism of the activation event is not known. This
substrate-binding domain of TrpI shows significant
homology to the type 2 periplasmic binding proteins
(PBP2), which are responsible for the uptake of a
variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 195
Score = 28.1 bits (63), Expect = 3.6
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 88 RSGRVVSIGIAPWGIVENNHELIVCRPEQ 116
SGR+V APWG +E ++ RP +
Sbjct: 158 ASGRLV----APWGFIETGSHYVLLRPAR 182
>gnl|CDD|129732 TIGR00646, MG010, DNA primase-related protein. The DNA primase
DnaG of E. coli and its apparent orthologs in other
eubacterial species are approximately 600 residues in
length. Within this set, a conspicuous outlier in
percent identity, as seen in a UPGMA difference tree, is
the branch containing the Mycoplasmas. This lineage is
also unique in containing the small, DNA primase-related
protein modelled by This model, which is homologous to
the central third of DNA primase. Several small regions
of sequence similarity specifically to Mycoplasma
sequences rather than to all DnaG homologs suggests that
the divergence of this protein from DnaG post-dated the
separation of bacterial lineages. The function of this
DNA primase-related protein is unknown [Unknown
function, General].
Length = 218
Score = 26.8 bits (59), Expect = 9.0
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 141 SISSPRSKFAVLNNRHAYFLLVDNGTAGKYGAEIILRRKLEKYISNQKLHPGKSKIVGAK 200
+IS + KF F+ DN AGK A LE+ + +K++ K
Sbjct: 140 TISDKQMKFFKQKKIEKIFICFDNDFAGKNAA-----ANLEEILKKAGF---ITKVIEIK 191
Query: 201 GGENGEPLVFASTNEIWTASL 221
+F N+ W A+L
Sbjct: 192 AAAKDWNDLFLLNNKNWAAAL 212
>gnl|CDD|180775 PRK06954, PRK06954, acetyl-CoA acetyltransferase; Provisional.
Length = 397
Score = 27.2 bits (60), Expect = 9.6
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 72 GVTRQVGDALLMERSQRSGRVVSIG-----IAPWGIVENNHELIVCRPEQPARLFP 122
G TR+ DA +E R+ R G IAP + + ++ R EQP + P
Sbjct: 175 GFTREAQDAFAIESLARAKRANEDGSFAWEIAPVTVAGKKGDTVIDRDEQPFKANP 230
>gnl|CDD|223578 COG0504, PyrG, CTP synthase (UTP-ammonia lyase) [Nucleotide
transport and metabolism].
Length = 533
Score = 27.1 bits (61), Expect = 9.9
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 8/25 (32%)
Query: 94 SIGIAPWGIVENNHELIVCRPEQPA 118
SIGI P ++++CR E+P
Sbjct: 199 SIGIQP--------DILICRSERPL 215
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 27.3 bits (61), Expect = 10.0
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 196 IVGAKGG----ENGEPLVFASTNEIWTASLHTSPSN 227
IVG G + GE +F ++ E+ T L P
Sbjct: 166 IVGVTGTPGKTKKGELSIFPTSFEVLTKCLLMLPDK 201
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
0.316 0.135 0.404
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,765,741
Number of extensions: 1211697
Number of successful extensions: 911
Number of sequences better than 10.0: 1
Number of HSP's gapped: 911
Number of HSP's successfully gapped: 10
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.1 bits)