RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8727
(300 letters)
>gnl|CDD|216042 pfam00650, CRAL_TRIO, CRAL/TRIO domain.
Length = 152
Score = 84.2 bits (209), Expect = 5e-20
Identities = 29/121 (23%), Positives = 50/121 (41%), Gaps = 1/121 (0%)
Query: 118 PKRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYET-LMEDEENQVRGFVHFNDGAGV 176
RDK GR V+ RPG +P K + +++ + E L+ E Q+ G D G+
Sbjct: 7 HGRDKEGRPVLYLRPGRHDPKKSSLEELVRFLVLVLERALLLLPEGQIEGITVIIDMKGL 66
Query: 177 SFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIRKRIK 236
S ++ + +I+K + P R +I I+N + K R++I
Sbjct: 67 SLSNMDKWPISFLKKILKILQDNYPERLGKILIVNAPWIFNVIWKLIKPFLDPKTREKIH 126
Query: 237 V 237
Sbjct: 127 F 127
>gnl|CDD|238099 cd00170, SEC14, Sec14p-like lipid-binding domain. Found in
secretory proteins, such as S. cerevisiae
phosphatidylinositol transfer protein (Sec14p), and in
lipid regulated proteins such as RhoGAPs, RhoGEFs and
neurofibromin (NF1). SEC14 domain of Dbl is known to
associate with G protein beta/gamma subunits.
Length = 157
Score = 79.7 bits (197), Expect = 3e-18
Identities = 44/135 (32%), Positives = 68/135 (50%), Gaps = 6/135 (4%)
Query: 106 QELLKLGYLFATPKRDKLGRRVIIARPGVFNPHKYTNSH-MLQIHGMTYETLMEDEENQV 164
+EL +LG + RDK GR V+I R G + K +S +L+ T E L+++++ QV
Sbjct: 2 EELKELGKVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQV 61
Query: 165 RGFVHFNDGAGVSFPHLTLFTP--KEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDF 222
GFV D G+S HL K+ ++I+++ P R K ++IIN K
Sbjct: 62 EGFVVIIDLKGLSLSHLLPDPSLLKKILKILQDN---YPERLKAVYIINPPWFFKVLWKI 118
Query: 223 GLNLVSEKIRKRIKV 237
+SEK RK+I
Sbjct: 119 VKPFLSEKTRKKIVF 133
>gnl|CDD|215024 smart01100, CRAL_TRIO_N, CRAL/TRIO, N-terminal domain.
Length = 48
Score = 56.0 bits (136), Expect = 9e-11
Identities = 23/46 (50%), Positives = 32/46 (69%)
Query: 38 ALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERY 83
AL +LR+ + K+ + RLD FLLRFLR++KF V A+E LE+Y
Sbjct: 3 ALEELRELLEKHPDLLPPRLDDAFLLRFLRARKFDVEKAKEMLEKY 48
Score = 37.5 bits (88), Expect = 3e-04
Identities = 15/23 (65%), Positives = 19/23 (82%)
Query: 245 FLLRFLRSKKFSVPMAEEALERY 267
FLLRFLR++KF V A+E LE+Y
Sbjct: 26 FLLRFLRARKFDVEKAKEMLEKY 48
>gnl|CDD|217718 pfam03765, CRAL_TRIO_N, CRAL/TRIO, N-terminal domain. This
all-alpha domain is found to the N-terminus of
pfam00650.
Length = 48
Score = 44.1 bits (105), Expect = 1e-06
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 36 EDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERY 83
E+ L +LR+ + + + +LD FLLRFLR++KF V A + L++
Sbjct: 1 EEKLEELREKLQELKDLLKDKLDDAFLLRFLRARKFDVEKAIKMLKKT 48
Score = 30.6 bits (70), Expect = 0.074
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 245 FLLRFLRSKKFSVPMAEEALERY 267
FLLRFLR++KF V A + L++
Sbjct: 26 FLLRFLRARKFDVEKAIKMLKKT 48
>gnl|CDD|214706 smart00516, SEC14, Domain in homologues of a S. cerevisiae
phosphatidylinositol transfer protein (Sec14p). Domain
in homologues of a S. cerevisiae phosphatidylinositol
transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and
the RasGAP, neurofibromin (NF1). Lipid-binding domain.
The SEC14 domain of Dbl is known to associate with G
protein beta/gamma subunits.
Length = 158
Score = 42.7 bits (101), Expect = 4e-05
Identities = 35/134 (26%), Positives = 58/134 (43%), Gaps = 8/134 (5%)
Query: 107 ELLKLGYLFATPKRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLM--EDEENQV 164
ELLK DK GR V+I R G F+ T +L+ E ++ E + +
Sbjct: 3 ELLKAYIPGGR-GYDKDGRPVLIERAGRFDLKSVTLEELLRYLVYVLEKILQEEKKTGGI 61
Query: 165 RGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYAL-DFG 223
GF D G+S + L ++ ++I+ + P R +++IIN P L
Sbjct: 62 EGFTVIFDLKGLSMSNPDLSVLRKILKIL---QDHYPERLGKVYIINP-PWFFRVLWKII 117
Query: 224 LNLVSEKIRKRIKV 237
+ EK R++I+
Sbjct: 118 KPFLDEKTREKIRF 131
>gnl|CDD|148570 pfam07029, CryBP1, CryBP1 protein. This family consists of several
CryBP1 like proteins from Bacillus thuringiensis and
Paenibacillus popilliae. Members of this family are
thought to be involved in the overall toxicity of the
bacteria to their hosts.
Length = 161
Score = 30.9 bits (70), Expect = 0.48
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 211 NCHPSVKYALDFGLNLVSEKIRKRIKV 237
C P + Y+L GL++V E RK + V
Sbjct: 31 PCDPKLVYSLS-GLSIVKETCRKTVTV 56
>gnl|CDD|220973 pfam11084, DUF2621, Protein of unknown function (DUF2621). This
family is conserved in the Bacillaceae family. Several
members are named as YneK. The function is not known.
Length = 141
Score = 28.5 bits (64), Expect = 2.7
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 91 GDLAFSKLDPKNPTM-QELLKLGYLFATPKRD 121
G+LA L K + +L+ GY+ ATPKRD
Sbjct: 91 GELA---LKEKASRITLDLIIRGYILATPKRD 119
>gnl|CDD|173868 cd08503, PBP2_NikA_DppA_OppA_like_17, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
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 = 460
Score = 28.7 bits (65), Expect = 4.2
Identities = 8/36 (22%), Positives = 13/36 (36%), Gaps = 1/36 (2%)
Query: 132 PGVFNPHKYTNSHMLQIHGMTYETLME-DEENQVRG 166
+PH +S YE L+E D + +
Sbjct: 17 ADTLDPHTADSSADYVRGFALYEYLVEIDPDGTLVP 52
>gnl|CDD|173863 cd08498, PBP2_NikA_DppA_OppA_like_2, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
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 = 481
Score = 28.3 bits (64), Expect = 6.4
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 135 FNPHKYTNSHMLQIHGMTYETLME-DEENQV 164
+PH + L + Y+TL+ D + ++
Sbjct: 13 LDPHFHNEGPTLAVLHNIYDTLVRRDADLKL 43
>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional.
Length = 258
Score = 27.4 bits (62), Expect = 7.4
Identities = 22/65 (33%), Positives = 26/65 (40%), Gaps = 10/65 (15%)
Query: 174 AGVSFPHLTLF-TPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIR 232
AGV F H T PK I GER IHII+ +V LD N V +
Sbjct: 12 AGVHFGHQTRRWNPKMKPYIF--GER------NGIHIIDLQKTVPM-LDEAYNFVRDVAA 62
Query: 233 KRIKV 237
K+
Sbjct: 63 NGGKI 67
>gnl|CDD|220417 pfam09812, MRP-L28, Mitochondrial ribosomal protein L28. Members
of this family are components of the mitochondrial
large ribosomal subunit. Mature mitochondrial ribosomes
consist of a small (37S) and a large (54S) subunit. The
37S subunit contains at least 33 different proteins and
1 molecule of RNA (15S). The 54S subunit contains at
least 45 different proteins and 1 molecule of RNA
(21S).
Length = 146
Score = 27.0 bits (60), Expect = 9.4
Identities = 8/40 (20%), Positives = 18/40 (45%)
Query: 3 KDRKPEELSVETSVSKQGLQIAKAELREDESTREDALIQL 42
+ RK +LS E + ++ A ++ E E+ ++
Sbjct: 57 RQRKLLKLSPEDLERRALIEKCWALYQQQEREAENQQLRQ 96
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
0.322 0.138 0.393
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,830,549
Number of extensions: 1577354
Number of successful extensions: 1389
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1385
Number of HSP's successfully gapped: 28
Length of query: 300
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 204
Effective length of database: 6,679,618
Effective search space: 1362642072
Effective search space used: 1362642072
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: 59 (26.4 bits)