RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13624
(187 letters)
>gnl|CDD|152640 pfam12205, GIT1_C, G protein-coupled receptor kinase-interacting
protein 1 C term. This domain family is found in
eukaryotes, and is approximately 120 amino acids in
length. The family is found in association with
pfam01412, pfam00023, pfam08518. GIT1 plays an important
role in cell adhesion, motility, cytoskeletal remodeling
and membrane trafficking. To perform this function, it
localises p21-activated kinase (PAK) and PAK-interactive
exchange factor to focal adhesions. Its activation is
regulated by interaction between its paxillin-binding C
terminal and the LD motifs of paxillin. The C terminal
folds into a four helix bundle.
Length = 123
Score = 83.0 bits (205), Expect = 6e-21
Identities = 52/118 (44%), Positives = 76/118 (64%), Gaps = 14/118 (11%)
Query: 80 MPQSEEVVRRTDQVTKRIQEL--AAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNN 137
+P +E+V+R+T+Q+TK IQEL AA K SFVP +E I AV+E++A+FP+ N+
Sbjct: 8 LPSTEDVIRKTEQITKNIQELLRAAQ---EGKHESFVPCSENILTAVNEMAALFPERPNS 64
Query: 138 DLIRHALRSLNTSTVRLQAEC--AQLEGSA-------ERVRSCAYNMAKANKQLLTQF 186
+ +R++LR L +S RLQ EC A G A ++V CAY++AKA KQL+T
Sbjct: 65 ETVRNSLRLLTSSAERLQNECKKAVPPGIAVDMQLVTQQVIQCAYDIAKAAKQLVTIT 122
>gnl|CDD|183876 PRK13169, PRK13169, DNA replication intiation control protein
YabA; Reviewed.
Length = 110
Score = 30.6 bits (70), Expect = 0.18
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 4 EAHITHLNNEIAKLKTQVQQVIGENETLK 32
E ++ L E+ LK Q+ +++ EN L+
Sbjct: 14 EQNLGVLLKELGALKKQLAELLEENTALR 42
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 30.0 bits (68), Expect = 0.64
Identities = 29/181 (16%), Positives = 59/181 (32%), Gaps = 23/181 (12%)
Query: 10 LNNEIAKLKTQVQQVIGENETLKAALN---ARNSATHHQPPETEPVSDSSWCSPQRPASM 66
L ++ +++ + E E + LN A+ A Q EPV +
Sbjct: 195 LPDQEGDYYSEISEAQEELEAARLELNEAIAQRDALKRQLGGEEPVLLAGSSVANSELDG 254
Query: 67 YNVTVNAQ------STTTRMPQSEEVVRRTDQVTKR-IQELAAHMRSSDKCHSFVPHAER 119
+ Q T + P R Q+ ++ +E +A ++ P ++
Sbjct: 255 RIEALEKQLDALRLRYTDKHPDVIATKREIAQLEEQKEEEGSAKNGGPERGEIANPVYQQ 314
Query: 120 IRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECAQLEGSAERVRSCAYNMAKAN 179
++I ++E A + SL L A +LE + + + N
Sbjct: 315 LQIELAEAEA-------------EIASLEARVAELTARIERLESLLRTIPEVEAELTQLN 361
Query: 180 K 180
+
Sbjct: 362 R 362
>gnl|CDD|218915 pfam06156, DUF972, Protein of unknown function (DUF972). This
family consists of several hypothetical bacterial
sequences. The function of this family is unknown.
Length = 106
Score = 28.4 bits (64), Expect = 0.84
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 4 EAHITHLNNEIAKLKTQVQQVIGENETLK 32
E + L E+ +LK Q+ +++ EN L+
Sbjct: 14 EQQLNQLLAELGELKQQLAELLEENAELR 42
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the family
being composed of Afadin- and alpha -Actinin-Binding
Proteins Localised at Cell-Cell Adherens Junctions.
Length = 149
Score = 28.0 bits (63), Expect = 2.0
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 3 SEAHITHLNNEIAKLKTQVQQVIGENETLKAA---LNARNSATHHQ 45
EA I L N I +LKTQ++ + E L+A L + +
Sbjct: 62 LEAEIERLQNTIERLKTQLEDLERELALLQAKERQLEKKLKTLEQK 107
>gnl|CDD|206557 pfam14389, Lzipper-MIP1, Leucine-zipper of ternary complex factor
MIP1. This leucine-zipper is towards the N-terminus of
MIP1 proteins. These proteins, here largely from
plants, are subunits of the TORC2 (rictor-mTOR) protein
complex controlling cell growth and proliferation. The
leucine-zipper is likely to be the region that
interacts with plant MADS-box factors,.
Length = 88
Score = 27.1 bits (61), Expect = 2.0
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 6 HITHLNNEIAKLKTQVQQVIGENETLKAALNARNSATHHQPPETEP 51
+ L E+AKL+ Q+QQ E L+ AL R+S + P + P
Sbjct: 9 RRSALEQEVAKLQKQLQQEEDLREALEKALG-RSSGSLLPLPSSLP 53
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 28.2 bits (63), Expect = 2.8
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 7 ITHLNNEIAKLKTQVQQVIGENETLKAALNA 37
ITHL ++I L+ + + ENE L+ L A
Sbjct: 237 ITHLLSQIVDLQKKCKSYALENEELQQHLAA 267
>gnl|CDD|193486 cd04081, CBM35_galactosidase-like, Carbohydrate Binding Module
family 35 (CBM35); appended mainly to enzymes that bind
alpha-D-galactose (CBM35-Gal), including glycoside
hydrolase (GH) families GH31 and GH43. This family
includes carbohydrate binding module family 35 (CBM35);
these are non-catalytic carbohydrate binding domains
that are appended mainly to enzymes that bind
alpha-D-galactose (CBM35-Gal), including glycoside
hydrolase (GH) families GH31 and GH43. Examples of
proteins which contain CBM35s belonging to this family
includes the CBM35 of an exo-beta-1,3-galactanase from
Phanerochaete chrysosporium 9(Pc1,3Gal43A) which is
appended to a GH43 domain, and the CBM6 of domain of
two bifunctional proteins with
beta-L-arabinopyranosidase/alpha-D-galactopyranosidase
activities from Fusarium oxysporum 12S, Foap1 and Foap2
(Fo/AP1 and Fo/AP2), that are appended to GH31 domains.
CBM35s are unique in that they display conserved
specificity through extensive sequence similarity but
divergent function through their appended catalytic
modules. They are known to bind alpha-D-galactose (Gal),
mannan (Man), xylan, glucuronic acid (GlcA), a
beta-polymer of mannose, and possibly glucans, forming
four subfamilies based on general ligand specificities
(galacto, urono, manno, and gluco configurations). Some
CBM35s bind their ligands in a calcium-dependent manner.
In contrast to most CBMs that are generally rigid
proteins, CBM35 undergoes significant conformational
change upon ligand binding. GH43 includes
beta-xylosidases and beta-xylanases, using
aryl-glycosides as substrates, while family GH31
includes alpha-glucosidases and alpha-xylosidases that
cleave a terminal carbohydrate moiety from substrates
that vary considerably in size, mostly accommodating
alpha-D-glucose and alpha-D-xylose.
Length = 123
Score = 27.2 bits (61), Expect = 2.8
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 152 VRLQAECAQLEGSAERVRSCAY 173
R +AE A L G A RV SC+
Sbjct: 1 TRYEAEAATLGGGA-RVVSCSG 21
>gnl|CDD|114903 pfam06211, BAMBI, BMP and activin membrane-bound inhibitor (BAMBI)
N-terminal domain. This family consists of several
eukaryotic BMP and activin membrane-bound inhibitor
(BAMBI) proteins. Members of the transforming growth
factor-beta (TGF-beta) superfamily, including TGF-beta,
bone morphogenetic proteins (BMPs), activins and nodals,
are vital for regulating growth and differentiation.
BAMBI is related to TGF-beta-family type I receptors but
lacks an intracellular kinase domain. BAMBI is
co-expressed with the ventralising morphogen BMP4 during
Xenopus embryogenesis and requires BMP signalling for
its expression. The protein stably associates with
TGF-beta-family receptors and inhibits BMP and activin
as well as TGF-beta signalling.
Length = 107
Score = 26.4 bits (58), Expect = 4.6
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 125 SELSAIF-----PQNTNNDLIRHALRSLNTSTVRLQAECAQLE-GSAERVRSCAYNM 175
SEL+A F PQNTN+ L L SL ST ++ G + + C +M
Sbjct: 43 SELNACFTRLLDPQNTNSPLTHGCLDSLLNSTDTCHSKSTFNHSGGSAPLECCHEDM 99
>gnl|CDD|215553 PLN03052, PLN03052, acetate--CoA ligase; Provisional.
Length = 728
Score = 27.4 bits (61), Expect = 5.0
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 112 SFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSL 147
SF P R+ +S+ AIF Q D+I +S+
Sbjct: 266 SFAPSEIATRLKISKAKAIFTQ----DVIVRGGKSI 297
>gnl|CDD|134031 PRK00014, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 230
Score = 26.9 bits (59), Expect = 5.5
Identities = 18/58 (31%), Positives = 26/58 (44%)
Query: 49 TEPVSDSSWCSPQRPASMYNVTVNAQSTTTRMPQSEEVVRRTDQVTKRIQELAAHMRS 106
TE D + + RPA + +NA T R E + V I ELAAH+++
Sbjct: 159 TEGSVDLAALAGLRPAGVLCELMNADGTMMRGASLERYAAKEGLVALAIDELAAHLQA 216
>gnl|CDD|218161 pfam04589, RFX1_trans_act, RFX1 transcription activation region.
The RFX family is a family of winged-helix DNA binding
proteins. RFX1 is a regulatory factor essential for
expression of MHC class II genes. This region is to
found N terminal to the RFX DNA binding region
(pfam02257) in some mammalian RFX proteins, and is
thought to activate transcription when associated with
DNA. Deletion analysis has identified the region 233-351
in human RFX1 as being required for maximal activation.
Length = 150
Score = 26.5 bits (58), Expect = 5.7
Identities = 16/62 (25%), Positives = 24/62 (38%)
Query: 39 NSATHHQPPETEPVSDSSWCSPQRPASMYNVTVNAQSTTTRMPQSEEVVRRTDQVTKRIQ 98
S P + + S PAS V A S T P + V R QV +++Q
Sbjct: 3 TSEGGSDSPASVALQTSVPAQAPVPASQQRSVVQATSQTKGGPVQQLPVHRVQQVPQQVQ 62
Query: 99 EL 100
++
Sbjct: 63 QV 64
>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 211
Score = 26.5 bits (59), Expect = 7.3
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 131 FPQNTNNDLIRHALRSLNTST 151
F + +LI+HALR+L +
Sbjct: 174 FEDCSLEELIKHALRALRETL 194
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family is
long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 27.0 bits (60), Expect = 7.3
Identities = 33/149 (22%), Positives = 48/149 (32%), Gaps = 24/149 (16%)
Query: 30 TLKAALNARNSA--THHQPPETEPVSDSSWCSPQRPASMYNVTVNA-------QSTTTRM 80
+ A NAR A H P + Q + NVTV + M
Sbjct: 1430 SAAAGANARAQAGGAHTNPTAAPTSAPGKTPGTQPAFNSPNVTVTVAIDNRTTKRIKFEM 1489
Query: 81 PQSEEVVRRTDQVTKRIQELAAHMRSS------------DKCHSFVPHAERIRIAVSELS 128
+E + T+ + K + L + S E+I+ + L+
Sbjct: 1490 KVAEPMT--TNDIDKLSKTLGKAFKDSASTKLLAELAKQTNAEYAKTPDEKIQAQLDGLN 1547
Query: 129 AIFPQNT-NNDLIRHALRSLNTSTVRLQA 156
F T ND ALRSL VR +A
Sbjct: 1548 EHFADKTVQNDDQYEALRSLKRLVVRQEA 1576
>gnl|CDD|153138 cd06350, PBP1_GPCR_family_C_like, Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). The metabotropic glutamate
receptors (mGluR) are key receptors in the modulation of
excitatory synaptic transmission in the central nervous
system. The mGluRs are coupled to G proteins and are
thus distinct from the iGluRs which internally contain
ligand-gated ion channels. The mGluR structure is
divided into three regions: the extracellular region,
the seven-spanning transmembrane region and the
cytoplasmic region. The extracellular region is further
devided into the ligand-binding domain (LBD) and the
cysteine-rich domain. The LBD has sequence similarity to
the LIVBP, which is a bacterial periplasmic protein
(PBP), as well as to the extracellular region of both
iGluR and the gamma-aminobutyric acid (GABA)b receptor.
iGluRs are divided into three main subtypes based on
pharmacological profile: NMDA, AMPA, and kainate
receptors. All family C GPCRs have a large extracellular
N terminus that contain a domain with homology to
bacterial periplasmic amino acid-binding proteins.
Length = 348
Score = 26.6 bits (59), Expect = 7.8
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 112 SFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVR 153
E+ I ++ P ++ + I+ L+ L +ST R
Sbjct: 179 DLEEELEKNGICIAF-VEAIPPSSTEEDIKRILKKLKSSTAR 219
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 26.9 bits (60), Expect = 8.2
Identities = 27/137 (19%), Positives = 60/137 (43%), Gaps = 17/137 (12%)
Query: 4 EAHITHLNNEIAKLKTQVQQVIGENETLKAALNARNSATHHQPPETEPVSDSSWCSPQRP 63
A + LN AK+K++++Q + + P T+ +S+ P R
Sbjct: 254 SAALNKLNTAAAKIKSKIEQFQKVIKMYEKG--------GVCPTCTQQISE----GPDRI 301
Query: 64 ASMYNVTVNAQST----TTRMPQSEEVVRRTDQVTKRIQELAAHMRSSDK-CHSFVPHAE 118
+ + Q + T + + EE++ ++ +K++ EL + ++ + + V A+
Sbjct: 302 TKIKDKLKELQHSLEKLDTAIDELEEIMDEFNEQSKKLLELKNKISTNKQSLITLVDKAK 361
Query: 119 RIRIAVSELSAIFPQNT 135
+++ A+ EL A F N
Sbjct: 362 KVKAAIEELQAEFVDNA 378
>gnl|CDD|222239 pfam13581, HATPase_c_2, Histidine kinase-like ATPase domain.
Length = 125
Score = 26.1 bits (58), Expect = 8.5
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 117 AERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECA 159
E + +AV E A+ TN + HA R VR++ E
Sbjct: 29 LEEVELAVEE--AL----TN--AVEHAYREDPEGPVRVRLEID 63
>gnl|CDD|215624 PLN03191, PLN03191, Type I inositol-1,4,5-trisphosphate
5-phosphatase 2; Provisional.
Length = 621
Score = 26.8 bits (59), Expect = 8.6
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 18/71 (25%)
Query: 56 SWCSPQRPASMY------NVTVNA-----QSTTTRMPQSEEVVRRTDQVTKRIQELAAHM 104
W S + PA +Y V +NA + +P+ E ++RRT + K + + H
Sbjct: 130 DWLSTEEPADIYIIGFQEVVPLNAGNVLGAEDSRPIPKWEAIIRRT--LNKSNKPESKH- 186
Query: 105 RSSDKCHSFVP 115
K +S P
Sbjct: 187 ----KSYSAPP 193
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 25.2 bits (56), Expect = 9.7
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 10 LNNEIAKLKTQVQQVIGENETLKA 33
LN EIA L+ ++ ++ ENE L+A
Sbjct: 22 LNQEIAALQAELAKLKAENEELEA 45
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
0.313 0.121 0.338
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,549,531
Number of extensions: 723754
Number of successful extensions: 1009
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1002
Number of HSP's successfully gapped: 45
Length of query: 187
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 96
Effective length of database: 6,901,388
Effective search space: 662533248
Effective search space used: 662533248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)