RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16572
(65 letters)
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 47.6 bits (114), Expect = 4e-09
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 18 TFPIDTAKTRLQVQGQQLDQQYAKLKYRGMTDVLLQISRKDGFWALY 64
T+P+D KTRLQ KY+G+ D +I +++G LY
Sbjct: 23 TYPLDVVKTRLQSSAAG-----GSRKYKGILDCFKKIYKEEGIRGLY 64
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 32.4 bits (74), Expect = 0.006
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 6/48 (12%)
Query: 19 FPIDTAKTRLQVQ-GQQLDQQYAKLKYRGMTDVLLQISRKDGFWALYS 65
+P+D A+TRL G+ D+++ G+ D L++IS++ GF +LY
Sbjct: 132 YPLDFARTRLASDIGKGGDREF-----TGLFDCLMKISKQTGFLSLYQ 174
>gnl|CDD|241311 cd13157, PTB_tensin-related, Tensin-related
Phosphotyrosine-binding (PTB) domain. Tensin plays
critical roles in renal function, muscle regeneration,
and cell migration. It binds to actin filaments and
interacts with the cytoplasmic tails of beta-integrin
via its PTB domain, allowing tensin to link actin
filaments to integrin receptors. Tensin functions as a
platform for assembly and disassembly of signaling
complexes at focal adhesions by recruiting
tyrosine-phosphorylated signaling molecules, and also
by providing interaction sites for other proteins. In
addition to its PTB domain, it contains a C-terminal
SH2 domain. PTB domains have a common PH-like fold and
are found in various eukaryotic signaling molecules.
This domain was initially shown to binds peptides with
a NPXY motif with differing requirements for
phosphorylation of the tyrosine, although more recent
studies have found that some types of PTB domains can
bind to peptides lack tyrosine residues altogether. In
contrast to SH2 domains, which recognize
phosphotyrosine and adjacent carboxy-terminal residues,
PTB-domain binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 129
Score = 28.1 bits (63), Expect = 0.21
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 16 IGTFPIDTAKTRLQVQGQQLDQQYAKLKY--RGMTDVLLQIS 55
IG+FP+ LQ + + +Q LK V+L IS
Sbjct: 9 IGSFPVSG--LDLQERADSVGKQLDSLKPSTSRGRPVILSIS 48
>gnl|CDD|221037 pfam11231, DUF3034, Protein of unknown function (DUF3034). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 257
Score = 26.1 bits (58), Expect = 1.3
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 18 TFPIDTAKTRLQVQGQQLDQQYAKLKYRGMTDVLL----QIS 55
TF + T L + G +L Q K R D++ Q+S
Sbjct: 68 TFDLGTLGAALGLPGYELKQDIFGAKVRLAGDLVYDQLPQVS 109
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 25.8 bits (57), Expect = 1.7
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 11 CLLLSIGTFPIDTAKTRLQVQGQQLDQQY---AKLKYRGMTDVL 51
CLL+ ++AK RL+V LD L+ RG D+L
Sbjct: 559 CLLVY-KNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLL 601
>gnl|CDD|179681 PRK03946, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 307
Score = 25.0 bits (55), Expect = 3.2
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 38 QYAKLKYRGMTDVLLQISRKDG---------FWALYS 65
Q A + Y+G TD L +K+ F AL++
Sbjct: 111 QKAGIPYKGHTDALRDRFKKEAIMMLGCEELFVALFT 147
>gnl|CDD|100092 cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and
PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2
is thought to be a phosphopentomutase that catalyzes the
conversion of the nucleoside breakdown products,
ribose-1-phosphate and deoxyribose-1-phosphate to the
corresponding 5-phosphopentoses. PGM2L1 is thought to
catalyze the 1,3-bisphosphoglycerate-dependent synthesis
of glucose 1,6-bisphosphate and other
aldose-bisphosphates that serve as cofactors for several
sugar phosphomutases and possibly also as regulators of
glycolytic enzymes. PGM2 and PGM2L1 belong to the
alpha-D-phosphohexomutase superfamily which includes
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Other members of this superfamily include
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 487
Score = 24.8 bits (55), Expect = 3.2
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 39 YAKLKYRGMT--DVLLQISRKDGFWA 62
A LK +G T D L ++ K G++
Sbjct: 386 AAYLKAQGKTLLDRLDELYEKYGYYK 411
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 24.7 bits (54), Expect = 3.7
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 21 IDTAKTRLQVQGQQLDQQYAKLK 43
I +AK LQ +QL A+LK
Sbjct: 235 IKSAKNDLQNDKKQLKADLAELK 257
>gnl|CDD|107310 cd06315, PBP1_ABC_sugar_binding_like_6, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 280
Score = 24.6 bits (54), Expect = 3.8
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 10 GCLLLSIGTFPIDTAKTRLQVQGQQLDQQYAK 41
GC +LSI PI TR+ +L Q+Y
Sbjct: 157 GCTVLSIEDVPISRTATRMPALTARLLQRYGD 188
>gnl|CDD|131618 TIGR02567, YscW, type III secretion system chaperone YscW. This
family of proteins is found within type III secretion
operons. The protein has been characterized as a
chaperone for the outer membrane pore component YscC
(TIGR02516). YscW is a lipoprotein which is itself
localized to the outer membrane and, it is believed,
facilitates the oligomerization and localization of
YscC.
Length = 124
Score = 24.4 bits (53), Expect = 4.5
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 25 KTRLQVQGQQLDQQYAKLKYRGMTDVLLQISRKDGF 60
+ +L QGQ+ Q A+ +R V+L++ + +
Sbjct: 86 RGKLSWQGQRAVQAEAQQIFRAGQKVVLRLFPIECY 121
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
0.325 0.141 0.421
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,147,713
Number of extensions: 214496
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 10
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
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: 40 (21.6 bits)
S2: 53 (24.1 bits)