RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10393
(113 letters)
>gnl|CDD|217283 pfam02913, FAD-oxidase_C, FAD linked oxidases, C-terminal domain.
This domain has a ferredoxin-like fold.
Length = 247
Score = 29.3 bits (66), Expect = 0.30
Identities = 12/68 (17%), Positives = 22/68 (32%), Gaps = 2/68 (2%)
Query: 21 SIAKRYGGIPAGESNGRRGYMLTYIIAYIRDFACDYYFIGDSFETSVPWDKTVLLCINVK 80
E R Y + +RD + + + SVPW + L ++K
Sbjct: 90 GAGDVVVAEDEAERE-RLWRARKYAMP-LRDALGGAGPLVFTEDVSVPWSRLPDLVADIK 147
Query: 81 KRLTRECT 88
+ L +
Sbjct: 148 ELLAKYGL 155
>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 = 28.6 bits (64), Expect = 0.41
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 = 27.4 bits (61), Expect = 1.6
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 57 YFIGDSFETSVPWDKTVLLCINVKKRLTREC 87
+++G SF+ +PW++ C VK EC
Sbjct: 107 FYLGHSFQFPLPWEQ----CPLVKNSSDPEC 133
>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|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 = 25.8 bits (57), Expect = 4.6
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 42 LTYIIAYIRDFACDYYFI-GDSFETSVPWDKTVLLCINVKKRLTRECTGRWLPVLL 96
I+ + D+ I GD F+++ P + + L I +RL +PV +
Sbjct: 30 FEEIVELAIEEKVDFVLIAGDLFDSNNPSPEALELLIEALRRLKEAG----IPVFI 81
>gnl|CDD|176990 CHL00049, ndhB, NADH dehydrogenase subunit 2.
Length = 494
Score = 26.1 bits (58), Expect = 4.8
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|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 = 7.2
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
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 0.141 0.455
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: 6,020,138
Number of extensions: 512445
Number of successful extensions: 429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 428
Number of HSP's successfully gapped: 13
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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)