RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14513
(209 letters)
>gnl|CDD|214507 smart00082, LRRCT, Leucine rich repeat C-terminal domain.
Length = 51
Score = 39.0 bits (91), Expect = 6e-05
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 105 NPWTCDCSIQWLIDYVAKRQRTDPELNYNLHCSQPVKFSNVHLLSNPLLS 154
NP+ CDC ++WL+ ++ + +L C+ P L
Sbjct: 1 NPFICDCELRWLLRWLQANEHLQD--PVDLRCASPSSLRGPLLELLHSEF 48
>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat.
Length = 60
Score = 39.1 bits (92), Expect = 8e-05
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 32 NSELYAIRKNTFKNLLNLQTLYCNFNPKLTFIHPYSFNNDWSLKEFYINNNAI 84
N+ L I FK L NL+ L + N LT I P +F+ SL+ ++ N +
Sbjct: 9 NNRLTVIPDGAFKGLPNLKVLDLSGN-NLTSISPEAFSGLPSLRSLDLSGNNL 60
Score = 34.1 bits (79), Expect = 0.004
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 48 NLQTLYCNFNPKLTFIHPYSFNNDWSLKEFYINNNAITSL-PHELGDWDSLEVLDIQSNP 106
NL++L + N +LT I +F +LK ++ N +TS+ P SL LD+ N
Sbjct: 1 NLKSLDLSNN-RLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNN 59
>gnl|CDD|188093 TIGR00864, PCC, polycystin cation channel protein. The Polycystin
Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a
huge protein of 4303aas. Its repeated leucine-rich (LRR)
segment is found in many proteins. It contains 16
polycystic kidney disease (PKD) domains, one
LDL-receptor class A domain, one C-type lectin family
domain, and 16-18 putative TMSs in positions between
residues 2200 and 4100. Polycystin-L has been shown to
be a cation (Na+, K+ and Ca2+) channel that is activated
by Ca2+. Two members of the PCC family (polycystin 1 and
2) are mutated in autosomal dominant polycystic kidney
disease, and polycystin-L is deleted in mice with renal
and retinal defects. Note: this model is restricted to
the amino half for technical reasons.
Length = 2740
Score = 37.4 bits (86), Expect = 0.004
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 10/86 (11%)
Query: 79 INNNAITSLPHELGDWD---SLEVLDIQSNPWTCDCSIQWLIDYVAKRQ--RTDPELNYN 133
I+NN I+++ E G +L +D+ NP+ CDC + L + ++ PE
Sbjct: 2 ISNNKISTI--EEGICANLCNLSEIDLSGNPFECDCGLARLPRWAEEKGVKVRQPEAAL- 58
Query: 134 LHCSQPVKFSNVHLLSNPLLSHISGE 159
C+ P + LL PLL E
Sbjct: 59 --CAGPGALAGQPLLGIPLLDSGCDE 82
>gnl|CDD|205079 pfam12799, LRR_4, Leucine Rich repeats (2 copies). Leucine rich
repeats are short sequence motifs present in a number of
proteins with diverse functions and cellular locations.
These repeats are usually involved in protein-protein
interactions. Each Leucine Rich Repeat is composed of a
beta-alpha unit. These units form elongated non-globular
structures. Leucine Rich Repeats are often flanked by
cysteine rich domains.
Length = 43
Score = 30.9 bits (71), Expect = 0.045
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 73 SLKEFYINNNAITSLPHELGDWDSLEVLDIQSNP 106
+L+ ++NN IT LP L + +LE LD+ N
Sbjct: 2 NLETLDLSNNQITDLP-PLSNLPNLETLDLSGNK 34
Score = 26.7 bits (60), Expect = 1.6
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 48 NLQTLYCNFNPKLTFIHPYSFNNDWSLKEFYINNNAITSLPH 89
NL+TL + N ++T + P S +L+ ++ N IT L
Sbjct: 2 NLETLDLSNN-QITDLPPLSNLP--NLETLDLSGNKITDLSP 40
>gnl|CDD|205486 pfam13306, LRR_5, Leucine rich repeats (6 copies). This family
includes a number of leucine rich repeats. This family
contains a large number of BSPA-like surface antigens
from Trichomonas vaginalis.
Length = 128
Score = 32.5 bits (75), Expect = 0.051
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 30 TANSELYAIRKNTFKNLLNLQTLYCNFNPKLTFIHPYSFNNDWSLKEFYINNN 82
T S L +I F N +L ++ LT I Y+F+N SL I +N
Sbjct: 40 TLPSSLTSIGSYAFYNCSSLTSI--TIPSSLTSIGEYAFSNCSSLTSITIPSN 90
>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function
unknown].
Length = 394
Score = 33.4 bits (76), Expect = 0.060
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 44 KNLLNLQTLYCNFNPKLTFIHPYSFNNDWSLKEFYINNNAITSLPHELGDWDSLEVLDIQ 103
L NL +L + N +T I P +LKE +++N I SLP L + +L+ LD+
Sbjct: 113 LELTNLTSLDLDNNN-ITDIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLS 171
Query: 104 SNPWT 108
N +
Sbjct: 172 FNDLS 176
Score = 28.0 bits (62), Expect = 3.7
Identities = 26/126 (20%), Positives = 46/126 (36%), Gaps = 3/126 (2%)
Query: 40 KNTFKNLLNLQTLYCNFNPKLTFIHPYSFNNDWSLKEFYINNNAITSLPHELGDWDSLEV 99
++ NL NL L + N N +L+ ++NN I+S+ LG +L
Sbjct: 225 LSSLSNLKNLSGLELSNNKLEDLPESIG--NLSNLETLDLSNNQISSIS-SLGSLTNLRE 281
Query: 100 LDIQSNPWTCDCSIQWLIDYVAKRQRTDPELNYNLHCSQPVKFSNVHLLSNPLLSHISGE 159
LD+ N + + L+ + + L N ++LSN S
Sbjct: 282 LDLSGNSLSNALPLIALLLLLLELLLNLLLTLKALELKLNSILLNNNILSNGETSSPEAL 341
Query: 160 CVKGAL 165
+ +L
Sbjct: 342 SILESL 347
>gnl|CDD|188972 cd09573, SAM_STIM1, SAM domain of STIM1 subfamily proteins. SAM
(sterile alpha motif) domain of STIM1 (Stromal
interaction molecule) subfamily proteins is a putative
protein-protein interaction domain. STIM1 and STIM2
human proteins are type I transmembrane proteins. The
N-terminal part of them includes "hidden" EF-hand and
SAM domains. This region is responsible for sensing
changes in store-operated and basal cytoplasmic Ca2+
levels and initiates oligomerization. "Hidden" EF hand
and SAM domains have a stable intramolecular
association, and the SAM domain is a component that
regulates stability within STIM proteins.
Destabilization of the EF-SAM association during Ca2+
depletion leads to partial unfolding and aggregation
(homooligomerization), thus activating the
store-operated Ca2+ entry. Immunoprecipitation analysis
indicates that STIM1 and STIM2 can form co-precipitable
oligomeric associations in vivo. It was suggested that
STIM1 protein is an activator of store operated channels
in plasma membrane.
Length = 74
Score = 26.5 bits (58), Expect = 3.0
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 107 WTCDCSIQWLIDYVAKRQ 124
WT D +QWLI YV Q
Sbjct: 5 WTVDEVVQWLITYVELPQ 22
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 28.5 bits (63), Expect = 3.0
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 66 YSFNNDWSLKEFYINNN-AITSLPHELGDWDSLEVLDIQSN 105
Y+ NND L + +NN A TS + GD +++V D S+
Sbjct: 176 YTINNDVYLSDVIFDNNQAYTSTSYSDGDGGAIDVTDNNSD 216
>gnl|CDD|185577 PTZ00363, PTZ00363, rab-GDP dissociation inhibitor; Provisional.
Length = 443
Score = 28.0 bits (63), Expect = 3.6
Identities = 11/27 (40%), Positives = 12/27 (44%)
Query: 47 LNLQTLYCNFNPKLTFIHPYSFNNDWS 73
LNL LY F P T N DW+
Sbjct: 46 LNLTQLYKKFKPGETPPESLGRNRDWN 72
>gnl|CDD|223279 COG0201, SecY, Preprotein translocase subunit SecY [Intracellular
trafficking and secretion].
Length = 436
Score = 28.0 bits (63), Expect = 4.2
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 180 LLFIMTLLLITLVVYLICMSYK----YARNHV 207
LL ++TL +I LVVY+ + YA+
Sbjct: 221 LLVLLTLAIIFLVVYVEQARRRIPIQYAKRQS 252
>gnl|CDD|217154 pfam02632, BioY, BioY family. A number of bacterial genes are
involved in bioconversion of pimelate into dethiobiotin.
BioY is a component of the BioMNY transport system
involved in biotin uptake in prokaryotes.
Length = 148
Score = 27.0 bits (61), Expect = 5.3
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 163 GALVISQLSTQFYKLYPLLFIMTLLLITLVVYLICMSYKYARNHVP 208
A VI L+ +F + LL ++ +L LV+Y++ + +
Sbjct: 69 AAFVIGLLAERFGRKRLLLLLLAMLGGLLVIYVLGALWLAVVAGLG 114
>gnl|CDD|185098 PRK15176, PRK15176, Vi polysaccharide export inner membrane protein
VexB; Provisional.
Length = 264
Score = 27.3 bits (60), Expect = 5.3
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 150 NPLLSHISGECVKGALVISQLSTQFYKLYPLLFIMTLLLITLVVYLIC 197
NPLL + E V+ + S YPL F TL L L+ +LIC
Sbjct: 214 NPLLH--ANEIVREGMFEGYHSLYLEPFYPLAFSATLFLAGLIFHLIC 259
>gnl|CDD|185268 PRK15370, PRK15370, E3 ubiquitin-protein ligase SlrP; Provisional.
Length = 754
Score = 27.4 bits (60), Expect = 6.3
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 73 SLKEFYINNNAITSLPHELGDWDSLEVLDIQSN 105
++K Y N+N +TS+P L D+++ +++ N
Sbjct: 221 NIKTLYANSNQLTSIPATLP--DTIQEMELSIN 251
>gnl|CDD|197688 smart00370, LRR, Leucine-rich repeats, outliers.
Length = 24
Score = 24.2 bits (54), Expect = 7.6
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 73 SLKEFYINNNAITSLPHEL 91
+L+E ++NN ++SLP
Sbjct: 3 NLRELDLSNNQLSSLPPGA 21
>gnl|CDD|197687 smart00369, LRR_TYP, Leucine-rich repeats, typical (most
populated) subfamily.
Length = 24
Score = 24.2 bits (54), Expect = 7.6
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 73 SLKEFYINNNAITSLPHEL 91
+L+E ++NN ++SLP
Sbjct: 3 NLRELDLSNNQLSSLPPGA 21
>gnl|CDD|224265 COG1346, LrgB, Putative effector of murein hydrolase [Cell envelope
biogenesis, outer membrane].
Length = 230
Score = 26.4 bits (59), Expect = 9.2
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 165 LVISQLSTQFYKLYPLLFIMTLLLITLVVYLICM----SYKY 202
L+ + + YK F+ LL+ T+++ + SY+
Sbjct: 15 LLAYFAAKRLYKRTKSPFLNPLLVATVLLIAFLLLFGISYED 56
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 26.8 bits (59), Expect = 9.7
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 166 VISQLSTQFYKLYPLLFIMTLLLITLVVYLICMSY 200
+I L+ ++ LFI + I L ++ C++Y
Sbjct: 112 LIPLLTHDIDQINAFLFIFPPIAIALAIFFFCIAY 146
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 0.421
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,119,137
Number of extensions: 898294
Number of successful extensions: 1079
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1060
Number of HSP's successfully gapped: 49
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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 (25.8 bits)