RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3321
(110 letters)
>gnl|CDD|217283 pfam02913, FAD-oxidase_C, FAD linked oxidases, C-terminal domain.
This domain has a ferredoxin-like fold.
Length = 247
Score = 30.0 bits (68), Expect = 0.15
Identities = 13/69 (18%), Positives = 23/69 (33%), Gaps = 2/69 (2%)
Query: 21 SIAKRYGGIPAGESNGRRGYMLTYIIAYIRDFACDYYFIGDSFETSVPWDKTVLLCINVK 80
E R Y + +RD + + + SVPW + L ++K
Sbjct: 90 GAGDVVVAEDEAERE-RLWRARKYAMP-LRDALGGAGPLVFTEDVSVPWSRLPDLVADIK 147
Query: 81 KRLTRECTV 89
+ L + V
Sbjct: 148 ELLAKYGLV 156
>gnl|CDD|241412 cd13258, PH_PLEKHJ1, Pleckstrin homology domain containing, family
J member 1 Pleckstrin homology (PH) domain. PLEKHJ1
(also called GNRPX2/Guanine nucleotide-releasing protein
x ). It contains a single PH domain. Very little
information is known about PLEKHJ1. PLEKHJ1 has been
shown to interact with IKBKG (inhibitor of kappa light
polypeptide gene enhancer in B-cells, kinase gamma) and
KRT33B (keratin 33B). 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 = 144
Score = 29.0 bits (65), Expect = 0.27
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 46 IAYIRDFACDYYFIGDSFETSVPW 69
I++I + YYF S E V W
Sbjct: 86 ISFIDEPERKYYFECRSEEQCVEW 109
>gnl|CDD|212071 cd11502, SLC6sbd_NTT5, Neurotransmitter transporter 5;
solute-binding domain. Human NTT5 is encoded by the
SLC6A16 gene. NTT5 is expressed in testis, pancreas, and
prostate; its expression is predominantly intracellular,
indicative of a vesicular location. Its substrates are
unknown. This subgroup belongs to the solute carrier 6
(SLC6) transporter family.
Length = 543
Score = 28.5 bits (64), Expect = 0.72
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 57 YFIGDSFETSVPWDKTVLLCINVKKRLTRECTVS 90
+++G SF+ +PW++ C VK EC +
Sbjct: 107 FYLGHSFQFPLPWEQ----CPLVKNSSDPECART 136
>gnl|CDD|225566 COG3022, COG3022, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 253
Score = 26.1 bits (58), Expect = 4.2
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 12/38 (31%)
Query: 10 EDVKNNEDKIYS-IAKRYGGIPAGESNGRRGYMLTYII 46
+D KN + K+ S AK+ RG ML YII
Sbjct: 190 KDEKNGKYKVISFYAKKA-----------RGLMLRYII 216
>gnl|CDD|107326 cd06331, PBP1_AmiC_like, Type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF). This group
includes the type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF), found in
bacteria and Archaea. AmiC controls expression of the
amidase operon by a ligand-triggered conformational
switch. In the absence of ligand or presence of
butyramide (repressor), AmiC (the ligand sensor and
negative regulator) adopts an open conformation and
inhibits the transcription antitermination function of
AmiR by direct protein-protein interaction. In the
presence of inducing ligands such as acetamide, AmiC
adopts a closed conformation which disrupts a silencing
AmiC-AmiR complex and the expression of amidase and
other genes of the operon is induced. FmdDEF is
predicted to be an ATP-dependent transporter and closely
resembles the periplasmic binding protein and the two
transmembrane proteins present in various hydrophobic
amino acid-binding transport systems.
Length = 333
Score = 26.0 bits (58), Expect = 4.7
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 90 SLVGRIKSARADFILPT 106
S++ +IK+A D +L T
Sbjct: 178 SVIEKIKAAGPDVVLST 194
>gnl|CDD|119356 cd02877, GH18_hevamine_XipI_class_III, This conserved domain family
includes xylanase inhibitor Xip-I, and the class III
plant chitinases such as hevamine, concanavalin B, and
PPL2, all of which have a glycosyl hydrolase family 18
(GH18) domain. Hevamine is a class III endochitinase
that hydrolyzes the linear polysaccharide chains of
chitin and peptidoglycan and is important for defense
against pathogenic bacteria and fungi. PPL2 (Parkia
platycephala lectin 2) is a class III chitinase from
Parkia platycephala seeds that hydrolyzes beta(1-4)
glycosidic bonds linking
2-acetoamido-2-deoxy-beta-D-glucopyranose units in
chitin.
Length = 280
Score = 25.7 bits (57), Expect = 6.0
Identities = 9/40 (22%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 21 SIAKRYGGIPAGESNGRRGYM----LTYIIAYIRDFACDY 56
S AK + G+PA GY+ L ++ ++ + ++
Sbjct: 218 SNAKVFLGLPASPEAAGSGYVDPSELASLVLPVKQKSPNF 257
>gnl|CDD|176990 CHL00049, ndhB, NADH dehydrogenase subunit 2.
Length = 494
Score = 25.7 bits (57), Expect = 6.8
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 8/33 (24%)
Query: 28 GIPAGESNGRRGY--MLTYIIAYI----RDFAC 54
GI G+SN GY M+TY++ YI FAC
Sbjct: 322 GIIVGDSND--GYASMITYMLFYIFMNLGTFAC 352
>gnl|CDD|239818 cd04323, AsnRS_cyto_like_N, AsnRS_cyto_like_N: N-terminal,
anticodon recognition domain of the type found in human
and Saccharomyces cerevisiae cytoplasmic
asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai
AsnRs and, in various putative bacterial AsnRSs. This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. The enzymes in
this group are homodimeric class2b aminoacyl-tRNA
synthetases (aaRSs). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the transfer
of the activated AA to the terminal ribose of tRNA. In
the case of the class2b aaRSs, the activated AA is
attached to the 3'OH of the terminal ribose. Eukaryotes
contain 2 sets of aaRSs, both of which are encoded by
the nuclear genome. One set concerns with cytoplasmic
synthesis, whereas the other exclusively with
mitochondrial protein synthesis. AsnRS is
immunodominant antigen of the filarial nematode B.
malayai and of interest as a target for anti-parasitic
drug design. Human AsnRS has been shown to be a
pro-inflammatory chemokine which interacts with CCR3
chemokine receptors on T cells, immature dendritic cells
and macrophages.
Length = 84
Score = 24.5 bits (54), Expect = 7.5
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 81 KRLTRECTVSLVGRIKSARADFILPT 106
K LT+E +V + G +K P
Sbjct: 45 KSLTQESSVEVTGEVKEDPRAKQAPG 70
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1);
Provisional.
Length = 1466
Score = 25.4 bits (55), Expect = 7.9
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 79 VKKRLTRECTVSLVGRIKSARADFILPTKLM 109
V+K L ++ T L +IK+ + F LP K +
Sbjct: 24 VEKELNKKGTFELYKKIKTQKIPFFLPFKCL 54
>gnl|CDD|163616 cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal
metallophosphatase domain. Mre11 (also known as SbcD
in Escherichia coli) is a subunit of the MRX protein
complex. This complex includes: Mre11, Rad50, and
Xrs2/Nbs1, and plays a vital role in several nuclear
processes including DNA double-strand break repair,
telomere length maintenance, cell cycle checkpoint
control, and meiotic recombination, in eukaryotes.
During double-strand break repair, the MRX complex is
required to hold the two ends of a broken chromosome
together. In vitro studies show that Mre11 has 3'-5'
exonuclease activity on dsDNA templates and
endonuclease activity on dsDNA and ssDNA templates. In
addition to the N-terminal phosphatase domain, the
eukaryotic MRE11 members of this family have a
C-terminal DNA binding domain (not included in this
alignment model). MRE11-like proteins are found in
prokaryotes and archaea was well as in eukaryotes.
Mre11 belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and
acid sphingomyelinases (ASMases). The conserved domain
is a double beta-sheet sandwich with a di-metal active
site made up of residues located at the C-terminal side
of the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 25.0 bits (55), Expect = 8.3
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 42 LTYIIAYIRDFACDYYFI-GDSFETSVPWDKTVLLCINVKKRL 83
I+ + D+ I GD F+++ P + + L I +RL
Sbjct: 30 FEEIVELAIEEKVDFVLIAGDLFDSNNPSPEALELLIEALRRL 72
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
0.324 0.142 0.429
Gapped
Lambda K H
0.267 0.0691 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,730,730
Number of extensions: 488327
Number of successful extensions: 433
Number of sequences better than 10.0: 1
Number of HSP's gapped: 432
Number of HSP's successfully gapped: 18
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.3 bits)