RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10447
(166 letters)
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 188 bits (478), Expect = 5e-56
Identities = 71/157 (45%), Positives = 97/157 (61%)
Query: 9 LSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQ 68
IE FD VL PLW+G HRGK L +FLKA+G++IPLM EYA + T+E M I+ REF+
Sbjct: 392 YGIEQFDEVLCPLWEGASQHRGKELVSFLKAMGFIIPLMSPEYACHDTREHMEIVFREFK 451
Query: 69 SPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTV 128
SPDEEMKK +L V + C ++D++ P FF FW R A DRR+Y+Q+V TTV
Sbjct: 452 SPDEEMKKDLLVVERICDKVGTDTPWKLRDQVSPEFFSPFWRRRSAGDRRSYKQVVLTTV 511
Query: 129 EIANKVGASEIINRVVDDLKDENEQYRKMVMESIEKT 165
+A G + ++++ DE E YRKM + +
Sbjct: 512 ILAKMGGDPRVSRKILEYYSDEPEPYRKMNAGLVSRI 548
>gnl|CDD|227091 COG4748, COG4748, Uncharacterized conserved protein [Function
unknown].
Length = 365
Score = 31.7 bits (72), Expect = 0.14
Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 55 YTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKD---EILPPFFKNFWNH 111
YTKE+ L +E +P E K V G + + + +I+ F F N
Sbjct: 173 YTKEIKAYLAKETNNPSVEFVKFFAAKV-----YTGFKTTSVDEKFTDIVKNAFSQFIND 227
Query: 112 RMALDRRNYRQLVDTTV 128
R+ ++ ++ DT
Sbjct: 228 RVNDRLKSAKKSEDTVD 244
>gnl|CDD|222308 pfam13672, PP2C_2, Protein phosphatase 2C. Protein phosphatase 2C
is a Mn++ or Mg++ dependent protein serine/threonine
phosphatase.
Length = 211
Score = 31.5 bits (72), Expect = 0.15
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 5/50 (10%)
Query: 67 FQSPDEEMKKIVLKVVKQ-----CCATDGVEAQYIKDEILPPFFKNFWNH 111
SPD + + ++ + TDG+ + +E PFF
Sbjct: 147 LTSPDALEEFRIRRLTLEPGDALALMTDGLSDSLVTEEPFRPFFAPLLET 196
>gnl|CDD|235715 PRK06147, PRK06147, 3-oxoacyl-(acyl carrier protein) synthase;
Validated.
Length = 348
Score = 29.2 bits (66), Expect = 0.84
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 13/56 (23%)
Query: 29 RGKGL-----AAF------LKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEE 73
RG GL AA L+ + Y I ++ E Y KE L +R F+ E
Sbjct: 232 RGDGLTQAIRAALAEAGCGLEDMDYRIADLNGE--QYRFKEAALAEMRLFRVRKEF 285
>gnl|CDD|178163 PLN02548, PLN02548, adenosine kinase.
Length = 332
Score = 29.3 bits (66), Expect = 0.88
Identities = 12/31 (38%), Positives = 13/31 (41%), Gaps = 8/31 (25%)
Query: 72 EEMKKIVLKVVKQCCATDGVEAQYIKDEILP 102
EEMKK C GV Y +DE P
Sbjct: 85 EEMKK--------CATAAGVNVHYYEDESTP 107
>gnl|CDD|133069 cd03857, M14-like_1, Peptidase M14-like domain; uncharacterized
subfamily. 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 = 226
Score = 28.6 bits (64), Expect = 1.4
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 19 KPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAE-YANYYT-KEVMLILIREFQSPDEEMKK 76
+PLW T L G +DA+ + N + +L L+R+ S +E K
Sbjct: 8 RPLWMVTLTTAEGMKKRALAKEGKPRVWIDAQIHGNESAGSDALLELLRQLASASDEEAK 67
Query: 77 IVLKVV 82
++ +V
Sbjct: 68 MLENIV 73
>gnl|CDD|237596 PRK14053, PRK14053, methyltransferase; Provisional.
Length = 194
Score = 27.9 bits (62), Expect = 1.9
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 10/54 (18%)
Query: 103 PFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGA--SEIINRVVDDLKDENEQY 154
PF +N R A+ R ++Q VE+ +++G E I ++VDD KD+ E Y
Sbjct: 106 PFIENI--SREAVQR--FQQ----QVELLDRIGLTDLEEIRKIVDDYKDKGEAY 151
>gnl|CDD|182809 PRK10884, PRK10884, SH3 domain-containing protein; Provisional.
Length = 206
Score = 27.7 bits (62), Expect = 2.5
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 19/48 (39%)
Query: 109 WNHRMALDRRNYRQLVDTTVEIANKVGASE-IINRVVDDLKDENEQYR 155
WN R T E+ KV S+ +IN LK+EN++ +
Sbjct: 116 WNQR--------------TAEMQQKVAQSDSVIN----GLKEENQKLK 145
>gnl|CDD|235097 PRK02999, PRK02999, malate synthase G; Provisional.
Length = 726
Score = 28.2 bits (64), Expect = 2.6
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 5/25 (20%)
Query: 26 RTHRGKGL-----AAFLKAIGYLIP 45
R H G AFL IGYL+P
Sbjct: 69 RAHPGPPHDLAAYKAFLTEIGYLVP 93
>gnl|CDD|225747 COG3206, GumC, Uncharacterized protein involved in
exopolysaccharide biosynthesis [Cell envelope
biogenesis, outer membrane].
Length = 458
Score = 27.4 bits (61), Expect = 3.6
Identities = 7/53 (13%), Positives = 20/53 (37%)
Query: 87 ATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEI 139
+ D A + + + + + ++ RR L + E+ ++ +E
Sbjct: 164 SNDPKLAAKLANALAQAYLADQLEAQLEAFRRASDSLDERLEELRARLQEAEA 216
>gnl|CDD|216319 pfam01134, GIDA, Glucose inhibited division protein A.
Length = 391
Score = 27.1 bits (61), Expect = 4.8
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 109 WNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVME 160
R +DR Y + + T+E + +I V DL EN + + +V E
Sbjct: 86 RALRAQVDRDLYSKEMTETLENHPNL---TLIQGEVTDLIPENGKVKGVVTE 134
>gnl|CDD|221732 pfam12719, Cnd3, Nuclear condensing complex subunits, C-term
domain. The Cnd1-3 proteins are the three non-SMC
(structural maintenance of chromosomes) proteins that
go to make up the mitotic condensation complex along
with the two SMC protein families, XCAP-C and XCAP-E,
(or in the case of fission yeast, Cut3 and Cut14). The
five-member complex seems to be conserved from yeasts
to vertebrates. This domain is the C-terminal,
cysteine-rich domain of Cnd3. The complex shuttles
between the nucleus, during mitosis, and the cytoplasm
during the rest of the cycle. Thus this family is made
up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members.
Length = 302
Score = 26.9 bits (60), Expect = 5.2
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 37 LKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVV 82
LK +G L L+D + A +E + +L++ F DEE+K L+ +
Sbjct: 49 LKCLG-LCCLLDKDLA----EENLPLLLQCFSKGDEELKITALRAL 89
>gnl|CDD|236993 PRK11820, PRK11820, hypothetical protein; Provisional.
Length = 288
Score = 26.6 bits (60), Expect = 7.3
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 130 IANKVGASEIINRVVDDLKDENEQYR 155
+ +K +EI N VV+ LK EQ R
Sbjct: 257 LGSKSNDAEITNLVVE-LKVLIEQMR 281
>gnl|CDD|173876 cd08511, PBP2_NikA_DppA_OppA_like_5, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This
family represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of 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. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 467
Score = 26.5 bits (59), Expect = 7.6
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 105 FKNFWNH-RMALDRRNYRQLVDTTVEIAN-KVGASEIINRV 143
++WN + LDR YR + D TV +AN + G +II R+
Sbjct: 176 NPHYWNAGKPHLDRLVYRPIPDATVRLANLRSGDLDIIERL 216
>gnl|CDD|149411 pfam08340, DUF1732, Domain of unknown function (DUF1732). This
domain of unknown function is often found at the
C-terminus of bacterial proteins, many of which are
hypothetical, including proteins of the YicC family
which have pfam03755 at the N-terminus. These include a
protein important in the stationary phase of growth, and
required for growth at high temperature. Structural
modelling suggests this domain may bind nucleic acids.
Length = 86
Score = 25.1 bits (56), Expect = 8.9
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 130 IANKVGASEIINRVVDDLKDENEQYRKMVM 159
I +K EI VV +LK E E+ R+ V
Sbjct: 55 IGSKSNDLEITQLVV-ELKVEIEKIREQVQ 83
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
0.321 0.137 0.401
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,686,445
Number of extensions: 822135
Number of successful extensions: 955
Number of sequences better than 10.0: 1
Number of HSP's gapped: 953
Number of HSP's successfully gapped: 40
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
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: 55 (25.0 bits)