RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13305
(171 letters)
>gnl|CDD|219038 pfam06459, RR_TM4-6, Ryanodine Receptor TM 4-6. This region covers
TM regions 4-6 of the ryanodine receptor 1 family.
Length = 217
Score = 79.4 bits (196), Expect = 1e-18
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 5 EEDPIELVHVDQDFFYMEHVMRLMAALHSLVSLAMLIAYYNLKVPLAI 52
EE+ I + + YME V+R +A LH+++S LI YY LKVPL I
Sbjct: 170 EEEGIVYFVLQESTGYMEPVLRFLAVLHTIISFLCLIGYYCLKVPLVI 217
>gnl|CDD|222413 pfam13843, DDE_Tnp_1_7, Transposase IS4.
Length = 352
Score = 29.9 bits (68), Expect = 0.58
Identities = 22/108 (20%), Positives = 38/108 (35%), Gaps = 8/108 (7%)
Query: 27 LMAALHSLVSLAMLI---AYYNLKVPLAIFKRE--KEIARRLEFDGLYIAEQPEDD--DI 79
++ + L SL + + A+ R + I R L FD + D I
Sbjct: 54 ILMGVVRLPSLEDYWSTDPFLGNPIFRAVMSRNRFEFILRCLHFDDNATRDPGTDKLAKI 113
Query: 80 KSHWDRLVISANRPSDDPRRSITIDEENLCCRGSVDVSVDINRCPVDY 127
+ DRL + P +++ +DE + +G I P Y
Sbjct: 114 RPLIDRLNENFQE-VYTPSQNLVVDESLVLFKGRCSFRQYIPNKPRKY 160
>gnl|CDD|233181 TIGR00913, 2A0310, amino acid permease (yeast). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 478
Score = 28.8 bits (65), Expect = 1.5
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 34 LVSLAMLIAYYNLKVPLAIF 53
LV+ +M I Y+ KV A++
Sbjct: 102 LVTASMTIQYWTDKVNPAVW 121
>gnl|CDD|177099 MTH00001, ND4L, NADH dehydrogenase subunit 4L; Provisional.
Length = 99
Score = 27.7 bits (62), Expect = 1.6
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 14/58 (24%)
Query: 9 IELVHVDQDFFYM----------EHVMRLM----AALHSLVSLAMLIAYYNLKVPLAI 52
IELV + F ++ E + +M AA S + LA+++AYY ++ +++
Sbjct: 34 IELVLLSTFFLFLINSIEIDLLIEQIFTIMGLTIAAAESAIGLAIMVAYYRIRGTISL 91
>gnl|CDD|205438 pfam13258, DUF4049, Domain of unknown function (DUF4049). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is typically
between 310 and 324 amino acids in length.
Length = 318
Score = 28.0 bits (62), Expect = 2.6
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 101 ITIDEENLC-CRGSVDVSVDINRCPVDYVPLA-IF-KREKEI 139
I DEE C C G++ V + + P+D LA IF K+ K
Sbjct: 184 IIRDEERKCYCLGALQVPFNQMKNPLDPEELANIFNKKHKTH 225
>gnl|CDD|163508 TIGR03796, NHLM_micro_ABC1, NHLM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes a multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHLM, Nitrile Hydratase Leader
Microcin [Transport and binding proteins, Amino acids,
peptides and amines, Cellular processes, Biosynthesis
of natural products].
Length = 710
Score = 27.6 bits (62), Expect = 3.6
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 36 SLAMLIAYYNLKVPLAIFKRE 56
SLAM++AYY VPL + E
Sbjct: 17 SLAMILAYYGRYVPLEELREE 37
>gnl|CDD|237163 PRK12663, PRK12663, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 497
Score = 27.2 bits (61), Expect = 5.4
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 19 FYMEHVMRLMAALHSLV-SLAMLIAYYNLKVPLAIFKRE 56
FY+ H M + AL + SL L Y +L+ ++++E
Sbjct: 328 FYLVHDMVVKTALFLIAGSLVRLTGYRSLQYLGGLYRKE 366
>gnl|CDD|177240 MTH00192, ND4L, NADH dehydrogenase subunit 4L; Provisional.
Length = 99
Score = 26.0 bits (57), Expect = 5.4
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 28 MAALHSLVSLAMLIAYYNLKVPLAI 52
+AA S + LA+L+AY+ L + I
Sbjct: 67 VAAAESAIGLAILVAYFRLTGTITI 91
>gnl|CDD|177231 MTH00180, ND4L, NADH dehydrogenase subunit 4L; Provisional.
Length = 99
Score = 26.1 bits (58), Expect = 5.5
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 27 LMAALHSLVSLAMLIAYYNLKVPLAI 52
+AA S + LA+L+AYY ++ +A+
Sbjct: 66 TVAAAESAIGLAILVAYYRIRGTIAV 91
>gnl|CDD|241278 cd01247, PH_FAPP1_FAPP2, Four phosphate adaptor protein 1 and 2
Pleckstrin homology (PH) domain. Human FAPP1 (also
called PLEKHA3/Pleckstrin homology domain-containing,
family A member 3) regulates secretory transport from
the trans-Golgi network to the plasma membrane. It is
recruited through binding of PH domain to
phosphatidylinositol 4-phosphate (PtdIns(4)P) and a
small GTPase ADP-ribosylation factor 1 (ARF1). These two
binding sites have little overlap the FAPP1 PH domain to
associate with both ligands simultaneously and
independently. FAPP1 has a N-terminal PH domain followed
by a short proline-rich region. FAPP1 is a member of the
oxysterol binding protein (OSBP) family which includes
OSBP, OSBP-related proteins (ORP), and Goodpasture
antigen binding protein (GPBP). They have a wide range
of purported functions including sterol transport, cell
cycle control, pollen development and vessicle transport
from Golgi recognize both PI lipids and ARF proteins.
FAPP2 (also called PLEKHA8/Pleckstrin homology
domain-containing, family A member 8), a member of the
Glycolipid lipid transfer protein(GLTP) family has an
N-terminal PH domain that targets the TGN and C-terminal
GLTP domain. FAPP2 functions to traffic glucosylceramide
(GlcCer) which is made in the Golgi. It's interaction
with vesicle-associated membrane protein-associated
protein (VAP) could be a means of regulation. Some
FAPP2s share the FFAT-like motifs found in GLTP. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 100
Score = 25.8 bits (57), Expect = 6.9
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 104 DEENLCCRGSVDVSV-DINRCPVD 126
+E + C+GS+ +SV +I P D
Sbjct: 34 EEVDQGCKGSIKMSVCEIIVHPTD 57
>gnl|CDD|239101 cd02420, Peptidase_C39D, A sub-family of peptidase family C39.
Peptidase family C39 mostly contains
bacteriocin-processing endopeptidases from bacteria.
The cysteine peptidases in family C39 cleave the
"double-glycine" leader peptides from the precursors of
various bacteriocins (mostly non-lantibiotic). The
cleavage is mediated by the transporter as part of the
secretion process. Bacteriocins are antibiotic proteins
secreted by some species of bacteria that inhibit the
growth of other bacterial species. The bacteriocin is
synthesized as a precursor with an N-terminal leader
peptide, and processing involves removal of the leader
peptide by cleavage at a Gly-Gly bond, followed by
translocation of the mature bacteriocin across the
cytoplasmic membrane. Most endopeptidases of family C39
are N-terminal domains in larger proteins (ABC
transporters) that serve both functions. The proposed
protease active site is conserved in this sub-family.
Length = 125
Score = 25.9 bits (57), Expect = 7.2
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 35 VSLAMLIAYYNLKVPLA 51
SLA+++AYY VPL+
Sbjct: 15 ASLAIILAYYGRYVPLS 31
>gnl|CDD|221660 pfam12600, DUF3769, Protein of unknown function (DUF3769). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 560 and
931 amino acids in length.
Length = 403
Score = 26.5 bits (59), Expect = 9.0
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 70 IAEQPEDDDIKSHWDRLVISANRPSDDPRRSITIDEE 106
A + ++KS +RL++ RR + ID E
Sbjct: 48 TAREISPGELKSRRNRLILDQRLSIPIGRRRLVIDRE 84
>gnl|CDD|224201 COG1282, PntB, NAD/NADP transhydrogenase beta subunit [Energy
production and conversion].
Length = 463
Score = 26.6 bits (59), Expect = 9.4
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 27 LMAALHSLVSLA-MLIAYYNLKVPLA 51
L+A +HS++ LA + IA + P A
Sbjct: 92 LVAFMHSMIGLAAVFIAMAAVGEPYA 117
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 0.140 0.415
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,365,536
Number of extensions: 899576
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 782
Number of HSP's successfully gapped: 27
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
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 (24.9 bits)