RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2797
(225 letters)
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 189 bits (483), Expect = 3e-60
Identities = 79/160 (49%), Positives = 101/160 (63%), Gaps = 21/160 (13%)
Query: 51 EIWVAIIFSYIMVSVVLFLVSRFSPHEWRLLNYSDPGHPHHSPSPHHGPSPPSVIANDFS 110
E+W+ I+ +Y++V VVLFL+ RFSP+EWR P N F+
Sbjct: 1 EVWLCILAAYLLVGVVLFLLERFSPYEWR---------------------GPPEEPNQFT 39
Query: 111 LSNSFWFSLGAFMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLTVERMVNP 170
LSNS WFS GA +QQG PRS+SGRI+ VWWFF LIL+SSYTANLAAFLTVERM +P
Sbjct: 40 LSNSLWFSFGALVQQGHRELPRSLSGRILVGVWWFFALILLSSYTANLAAFLTVERMQSP 99
Query: 171 INSVEDLADQSDVLYGTVKDASTYHFFEVSAVNLVADVVR 210
I S+EDLA Q+ + YGT++ ST+ FF+ S +
Sbjct: 100 IQSLEDLAKQNKIGYGTLRGGSTFEFFKESKNPTYRRMWE 139
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 47.3 bits (113), Expect = 1e-06
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKK 33
+ IA ++IT ER++ VDFS P+ G ++++K
Sbjct: 61 IIIAGMTITPERKKQVDFSDPYYYSGQVLVVRK 93
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins
(PBPs) to transport a wide variety of substrates, such
as, amino acids, peptides, sugars, vitamins and
inorganic ions. PBPs have two cell-membrane
translocation functions: bind substrate, and interact
with the membrane bound complex. A diverse group of
periplasmic transport receptors for
lysine/arginine/ornithine (LAO), glutamine, histidine,
sulfate, phosphate, molybdate, and methanol are
included in the PBPb CD.
Length = 218
Score = 45.8 bits (109), Expect = 3e-06
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKP 39
+ A ++IT ER + VDFS P+ G I++KK S K
Sbjct: 61 LIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSPIKS 99
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding
proteins. bacterial proteins, eukaryotic ones are in
PBPe.
Length = 219
Score = 39.6 bits (93), Expect = 5e-04
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKK 33
+ A ++IT ER + VDFS P+ G I+++K
Sbjct: 62 VVAAGMTITPERAKQVDFSDPYYRSGQVILVRK 94
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 37.3 bits (87), Expect = 0.002
Identities = 16/28 (57%), Positives = 19/28 (67%)
Query: 170 PINSVEDLADQSDVLYGTVKDASTYHFF 197
PI SVEDLA Q+ + YGT +ST FF
Sbjct: 1 PITSVEDLAKQTKIEYGTQDGSSTLAFF 28
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 37.3 bits (86), Expect = 0.003
Identities = 15/36 (41%), Positives = 24/36 (66%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSK 36
+ IA ++IT ER++ VDFS P+ G +++KK S
Sbjct: 100 IIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSD 135
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 36.6 bits (85), Expect = 0.005
Identities = 12/32 (37%), Positives = 23/32 (71%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIK 32
+A+A ++IT ER++ +DFS + G+ +M+K
Sbjct: 86 LALAGITITDERKKAIDFSDGYYKSGLLVMVK 117
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 35.0 bits (81), Expect = 0.017
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 1 MAIAPLSITSERERVVDFSKPFMTLGISIMIKKPSKQKP 39
+A +SIT +R++ +DFS P+ G ++KK S
Sbjct: 86 AIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAK 124
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 32.0 bits (73), Expect = 0.21
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 3 IAPLSITSERERVVDFSKPFMTLGISIMIKK 33
I ++I+ ER++ DFS P+ GI ++KK
Sbjct: 105 INQVTISDERKKKYDFSTPYTVSGIQALVKK 135
>gnl|CDD|183381 PRK11917, PRK11917, bifunctional adhesin/ABC transporter
aspartate/glutamate-binding protein; Reviewed.
Length = 259
Score = 31.4 bits (71), Expect = 0.31
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 3 IAPLSITSERERVVDFSKPFMTLGISIMIKK 33
IA +IT ER+R+ +FS+P+ I +++ K
Sbjct: 106 IATFTITPERKRIYNFSEPYYQDAIGLLVLK 136
>gnl|CDD|147980 pfam06109, HlyE, Haemolysin E (HlyE). This family consists of
several enterobacterial haemolysin (HlyE)
proteins.Hemolysin E (HlyE) is a novel pore-forming
toxin of Escherichia coli, Salmonella typhi, and
Shigella flexneri. HlyE is unrelated to the well
characterized pore-forming E. coli hemolysins of the RTX
family, haemolysin A (HlyA), and the enterohaemolysin
encoded by the plasmid borne ehxA gene of E. coli 0157.
However, it is evident that expression of HlyE in the
absence of the RTX toxins is sufficient to give a
hemolytic phenotype in E. coli. HlyE is a protein of 34
kDa that is expressed during anaerobic growth of E.
coli. Anaerobic expression is controlled by the
transcription factor, FNR, such that, upon ingestion and
entry into the anaerobic mammalian intestine, HlyE is
produced and may then contribute to the colonisation of
the host.
Length = 299
Score = 30.4 bits (68), Expect = 0.59
Identities = 33/127 (25%), Positives = 53/127 (41%), Gaps = 8/127 (6%)
Query: 91 HSPSPHHGPSPPSVIANDFSLSNSFWFSLGAFMQQGSDISPRSISGRIVGAVWWFFTLIL 150
H+ S + +IA D L+N F F Q I + +G G V F LI+
Sbjct: 132 HASSQSFNNASGKLIALDSQLANDFDEKSDYFQGQVDKIRKEAYAGAAAGVVAGPFGLII 191
Query: 151 ISSYTANLAAFLTVERMVNPINSVEDLADQSDVLYGTVKDASTYHFFEVSAVNL-VADVV 209
S A + + + + SV+D + L TVK A+ ++ A L + D +
Sbjct: 192 SYSIAAGVVEGKLIPALKEKLKSVKDFFES---LAATVKQANK----DIDAAKLKLKDEI 244
Query: 210 RALGEQK 216
A+G+ K
Sbjct: 245 AAIGDIK 251
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 301
Score = 30.1 bits (69), Expect = 0.91
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 8/44 (18%)
Query: 173 SVEDLADQSDVLYGTVK-DASTYHFFEVSAVNLVADVVRALGEQ 215
S+ +LA +SDVL +T H VN A+V+ ALG
Sbjct: 185 SLLELAAESDVLVVACPGGPATRH-----LVN--AEVLEALGPD 221
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 27.9 bits (63), Expect = 1.2
Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 107 NDFSLSNSFWFSLGAFMQQG-SDISPRSISGRIVGAVWWFFTLILISSYTANLA 159
+ ++ +FS G DI P + +GR+ ++ + L + A L
Sbjct: 21 WGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74
>gnl|CDD|178021 PLN02399, PLN02399, phospholipid hydroperoxide glutathione
peroxidase.
Length = 236
Score = 28.7 bits (64), Expect = 1.9
Identities = 14/56 (25%), Positives = 21/56 (37%)
Query: 81 LNYSDPGHPHHSPSPHHGPSPPSVIANDFSLSNSFWFSLGAFMQQGSDISPRSISG 136
L S + + P PPS+ SL +S S AF+ G + + G
Sbjct: 4 LTTSSSSYASFKTVFNSSPPPPSMAFLVPSLKSSTGISKSAFLSNGFSLKSPNSPG 59
>gnl|CDD|211985 TIGR04262, orph_peri_GRRM, extracellular substrate-binding orphan
protein, GRRM family. This subfamily belongs to
bacterial extracellular solute-binding protein family 3
(pfam00497). In that family, most members are ABC
transporter periplasmic substrate-binding proteins.
However, members of the present subfamily are orphans in
the sense of being adjacent to neither ABC transporter
ATP-binding proteins or permease subunits. Instead, most
members are encoded next to the two signature proteins
of the proposed Glycine-Rich Repeat Modification (GRRM)
system, a radical SAM/SPASM protein GrrM (TIGR04261) and
the Gly-rich repeat protein itself GrrA (TIGR04260).
Length = 257
Score = 28.9 bits (65), Expect = 2.1
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 9 TSERERVVDFSKPFMTLGISIMIKKPSKQKPRVL 42
T ER+ VD+S PF GI ++ K + P L
Sbjct: 76 TWERQMFVDYSLPFAVSGIRLLAPKGNDGTPESL 109
>gnl|CDD|183107 PRK11376, hlyE, hemolysin E; Provisional.
Length = 303
Score = 27.7 bits (61), Expect = 4.7
Identities = 30/114 (26%), Positives = 48/114 (42%), Gaps = 8/114 (7%)
Query: 104 VIANDFSLSNSFWFSLGAFMQQGSDISPRSISGRIVGAVWWFFTLILISSYTANLAAFLT 163
++A D L+N F F Q I + +G G V F LI+ S A +
Sbjct: 148 LLALDSQLTNDFSEKSSYFQSQVDKIRKEAYAGAAAGVVAGPFGLIISYSIAAGVVEGKL 207
Query: 164 VERMVNPINSVEDLADQSDVLYGTVKDASTYHFFEVSAVNL-VADVVRALGEQK 216
+ + N + SV++ L TVK A+ ++ A L + + A+GE K
Sbjct: 208 IPELKNKLKSVQNFFTT---LSNTVKQANK----DIDAAKLKLTTEIAAIGEIK 254
>gnl|CDD|213918 TIGR04305, fol_rel_CADD, putative folate metabolism protein, CADD
family. This protein family, related to but outside the
family of PqqC proteins involved in PQQ biosynthesis,
includes the well-studied Chlamydia protein CADD
(Chlamydia protein Associating with Death Domains),
which can induce apoptosis in a host cell. Other members
of this family occur in Rickettsia and Wolbachia,
unrelated in terms of phylogeny (both are
alphaproteobacteria) but similar in living
intracellularly. Local gene context in these species,
although not in Trichodesmium or Nitrosomonas eutropha,
suggests a role in folate metabolism, and some species
with this protein lack FolE but have other folate
synthesis proteins.
Length = 212
Score = 27.3 bits (61), Expect = 5.6
Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 145 FFTLILISSYTANLAAFLTVERMVNPINSV--EDLADQSDVLYGTVKDASTYHFFEV 199
FF L SS+ A L A ER + + V L YG + D FF V
Sbjct: 115 FFRLCR-SSFAAGLGALYAYERQIPEVAEVKIAGLKK----FYG-ISDERGLQFFTV 165
>gnl|CDD|241246 cd01210, PTB_EPS8, Epidermal growth factor receptor kinase
substrate (EPS8)-like Phosphotyrosine-binding (PTB)
domain. EPS8 is a regulator of Rac signaling. It
consists of a PTB and an SH3 domain. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred by
residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 131
Score = 26.7 bits (60), Expect = 5.8
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 195 HFF---EVSAVNLVADVVRALGEQKNG 218
H F EV A LV D+ +AL +K+G
Sbjct: 104 HLFQCDEVGAELLVEDLQKALSGKKSG 130
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 27.5 bits (62), Expect = 6.9
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 54 VAIIFSYIMVSVVLFLVSRFSPH 76
VA + S ++ + FLV RF+P
Sbjct: 46 VAFLISAVLAMIGYFLVRRFAPE 68
>gnl|CDD|215379 PLN02708, PLN02708, Probable pectinesterase/pectinesterase
inhibitor.
Length = 553
Score = 27.5 bits (61), Expect = 6.9
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 9/50 (18%)
Query: 54 VAIIFSYIMVSVVLFLVSRFSPHEWRLLNYSDPGHPHHSPSPHHGPSPPS 103
+A + +++S++LF S S+ H HH+PSP P
Sbjct: 1 MASLLLLLLLSLLLFHSPSSS---------SNRHHHHHTPSPSPPPPSSP 41
>gnl|CDD|238504 cd01031, EriC, ClC chloride channel EriC. This domain is found
in the EriC chloride transporters that mediate the
extreme acid resistance response in eubacteria and
archaea. This response allows bacteria to survive in
the acidic environments by decarboxylation-linked
proton utilization. As shown for Escherichia coli EriC,
these channels can counterbalance the electric current
produced by the outwardly directed virtual proton pump
linked to amino acid decarboxylation. The EriC
proteins belong to the ClC superfamily of chloride ion
channels, which share a unique double-barreled
architecture and voltage-dependent gating mechanism.
The voltage-dependent gating is conferred by the
permeating anion itself, acting as the gating charge.
In Escherichia coli EriC, a glutamate residue that
protrudes into the pore is thought to participate in
gating by binding to a Cl- ion site within the
selectivity filter.
Length = 402
Score = 26.7 bits (60), Expect = 9.8
Identities = 7/37 (18%), Positives = 16/37 (43%)
Query: 40 RVLSFLDPLSEEIWVAIIFSYIMVSVVLFLVSRFSPH 76
+ F + V + S ++ + +LV +F+P
Sbjct: 25 SLYDFAANNPPLLLVLPLISAVLGLLAGWLVKKFAPE 61
>gnl|CDD|203773 pfam07819, PGAP1, PGAP1-like protein. The sequences found in this
family are similar to PGAP1. This is an endoplasmic
reticulum membrane protein with a catalytic serine
containing motif that is conserved in a number of
lipases. PGAP1 functions as a GPI inositol-deacylase;
this deacylation is important for the efficient
transport of GPI-anchored proteins from the endoplasmic
reticulum to the Golgi body.
Length = 225
Score = 26.6 bits (59), Expect = 9.9
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 94 SPHHGP--SPPSVIANDFSLSNSFWFSLGAFMQQGSDISPRSISGRI 138
SPH GP + + ++L N +W A S++ SI+G I
Sbjct: 121 SPHAGPPLTFDGDLLRFYALLNEYWRRNQADGDSLSNVGLVSITGGI 167
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 0.135 0.409
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,802,739
Number of extensions: 1130290
Number of successful extensions: 1428
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1426
Number of HSP's successfully gapped: 52
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
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: 57 (25.7 bits)