RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14437
(160 letters)
>gnl|CDD|241475 cd13321, PH_PLEKHM1, Pleckstrin homology domain-containing family M
member 1 Pleckstrin homology (PH) domain. PLEKHM1 is
thought to function in vesicular transport in
osteoclasts. Mutations in the PLEKHM1 gene are
associated with osteopetrosis OPTB6. PLEKHM1 contains an
N-terminal RUN domain (RPIP8/RaP2 interacting protein 8,
UNC-14 and NESCA/new molecule containing SH3 at the
carboxyl-terminus), followed by a PH domain, and either
a C1 domain or a DUF4206 domain at its C-terminus. The
RUN domain is thought to be involved in Rab-mediated
membrane trafficking, possibly as a Rab-binding site. 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 = 132
Score = 32.1 bits (73), Expect = 0.057
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 6 VLNFNVTPIRCRIKVHKDHLNGKEEAIAPCKLHCDPNSAKEMLLLAPSTDDQKLWVQRLS 65
V N + +RC V H +G+ E + P K++ L APS D+ + W+ R+
Sbjct: 75 VCVENCSLLRCE-SVGPAHSDGRFELVFP---------GKKLALRAPSRDEAEDWLDRIR 124
Query: 66 KKIQKC 71
+ +QK
Sbjct: 125 EALQKV 130
Score = 29.0 bits (65), Expect = 0.53
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 110 SAKEMLLLAPSTDDQKLWVQRLSKKIQKC 138
K++ L APS D+ + W+ R+ + +QK
Sbjct: 102 PGKKLALRAPSRDEAEDWLDRIREALQKV 130
>gnl|CDD|198375 cd07809, FGGY_D-XK_1, D-xylulose kinases, subgroup 1; members of
the FGGY family of carbohydrate kinases. This subgroup
is composed of D-xylulose kinases (XK, also known as
xylulokinase; EC 2.7.1.17) from bacteria and eukaryota.
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. Some uncharacterized sequences are also
included in this subfamily. EcXK exists as a dimer. Each
monomer consists of two large domains separated by an
open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. The presence of Mg2+ or Mn2+ might be
required for catalytic activity. Members of this
subgroup belong to the FGGY family of carbohydrate
kinases.
Length = 487
Score = 31.5 bits (72), Expect = 0.16
Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 6/88 (6%)
Query: 60 WVQRLSKKIQKCGYKANTLSDGVK-ISPRPKDH----LNGKEEAIAPCKLHCDPNSAKEM 114
W+ L + ++ A V+ I + H L+ + E + P KL CD +A E
Sbjct: 49 WIDALVEAFRQALADAGIDPKEVRAIGVSGQQHGLVPLDAQGEVLRPAKLWCDTETAPEN 108
Query: 115 LLLAPSTDDQKLWVQRLSKKIQKCGYKA 142
L K W++RL GY A
Sbjct: 109 AELIEKLGGAKAWIERLGNAPLT-GYTA 135
Score = 27.3 bits (61), Expect = 4.7
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 25 LNGKEEAIAPCKLHCDPNSAKEMLLLAPSTDDQKLWVQRLSKKIQKCGYKA 75
L+ + E + P KL CD +A E L K W++RL GY A
Sbjct: 86 LDAQGEVLRPAKLWCDTETAPENAELIEKLGGAKAWIERLGNAPLT-GYTA 135
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 31.2 bits (71), Expect = 0.18
Identities = 17/76 (22%), Positives = 29/76 (38%)
Query: 29 EEAIAPCKLHCDPNSAKEMLLLAPSTDDQKLWVQRLSKKIQKCGYKANTLSDGVKISPRP 88
E + C +CDP+ +EM + D+ W+ R +K+ D + S
Sbjct: 65 IEVVIGCPFNCDPDDPEEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDI 124
Query: 89 KDHLNGKEEAIAPCKL 104
+ L +A P L
Sbjct: 125 EKALEEGPKAFQPGLL 140
Score = 28.9 bits (65), Expect = 1.2
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 96 EEAIAPCKLHCDPNSAKEMLLLAPSTDDQKLWVQRLSKKIQK 137
E + C +CDP+ +EM + D+ W+ R +K+
Sbjct: 65 IEVVIGCPFNCDPDDPEEMCDECRAKGDELEWLPREKRKVPF 106
>gnl|CDD|217552 pfam03429, MSP1b, Major surface protein 1B. The major surface
protein (MSP1) of the cattle pathogen Anaplasma is a
heterodimer comprised of MSP1a and MSP1b. This family is
the MSP1b chain. There MSP1 proteins are putative
adhesins for bovine erythrocytes.
Length = 726
Score = 27.0 bits (59), Expect = 6.0
Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 6/90 (6%)
Query: 61 VQRLSKKIQKCGYKANTLSDGVKISPRPKDHLNGKEEAIAPCKLHCDPNSAKEMLLLAP- 119
+ ++ I++ G A + V+++ + + EA+ L+ ++ LLA
Sbjct: 551 ISHITNVIRQAGKDAQKIDPQVEVAEISPETIYAMSEALYA--LNMQESAIINNALLAAV 608
Query: 120 ---STDDQKLWVQRLSKKIQKCGYKANTLS 146
S DDQ + ++ I+ C + NTL+
Sbjct: 609 NDSSKDDQAIVTDLINATIEVCTEQTNTLA 638
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 925
Score = 26.9 bits (60), Expect = 6.1
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 45 KEMLLLAPSTDDQKLWVQRLSKKIQKCGYKANTLSDG--VKISPRPKDHLNGK 95
++LLAP +K ++L +K++K G+ A DG + PK N K
Sbjct: 144 TRVILLAPIVRGRKGEFRKLLEKLRKQGF-ARVRVDGEVYPLEDPPKLEKNKK 195
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
0.315 0.131 0.400
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,736,894
Number of extensions: 654141
Number of successful extensions: 486
Number of sequences better than 10.0: 1
Number of HSP's gapped: 486
Number of HSP's successfully gapped: 16
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.9 bits)