RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4528
(87 letters)
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 36.0 bits (84), Expect = 1e-04
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAAD 40
I+ F L+ L+P P + +KL K IL+ A +
Sbjct: 11 INEAFDELRSLLPTLPKN-KKLSKAEILRLAIE 42
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four
helix bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide
sequences such as N-box (5-CACGc/aG-3), those which
have a COE domain (Collier/Olf-1/EBF) which is involved
in both in dimerization and in DNA binding, and those
which bind pentanucleotides ACGTG or GCGTG and have a
PAS domain which allows the dimerization between PAS
proteins, the binding of small molecules (e.g.,
dioxin), and interactions with non-PAS proteins.
Length = 60
Score = 29.5 bits (67), Expect = 0.040
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAAD 40
I+ F L+ L+P P +KL K IL++A D
Sbjct: 19 INDAFDELRSLLPTLPPS-KKLSKAEILRKAVD 50
>gnl|CDD|203838 pfam08013, Tagatose_6_P_K, Tagatose 6 phosphate kinase. Proteins
in this family are tagatose 6 phosphate kinases.
Length = 423
Score = 28.7 bits (65), Expect = 0.32
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 24 GDPEKLPKEIILKRAADLAEA 44
GDP L E + +RAA LA
Sbjct: 133 GDPVPLSDETVAERAARLAAV 153
>gnl|CDD|223660 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
recombination, and repair].
Length = 1139
Score = 28.4 bits (64), Expect = 0.38
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 13/57 (22%)
Query: 8 IDYGF-QRLQKLIPRHPGD------------PEKLPKEIILKRAADLAEALYSMPRN 51
+ YG +L KLIP PG E L + +KR +LA L +PR+
Sbjct: 450 LPYGEVDKLAKLIPFWPGLTLAVAYEEEPELKELLDSDPEVKRLIELARKLEGLPRH 506
>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar
to the La autoantigen. This domain is found in plant
proteins related to the La autoantigen. A variety of
La-related proteins (LARPs or La ribonucleoproteins),
with differing domain architecture, appear to function
as RNA-binding proteins in eukaryotic cellular
processes.
Length = 90
Score = 27.0 bits (60), Expect = 0.65
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 11 GFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEAL 45
F R++ L+ G PE +P++ + +AEAL
Sbjct: 43 SFSRMRSLLGLGGGKPEDVPEDTL----KAVAEAL 73
>gnl|CDD|143454 cd07136, ALDH_YwdH-P39616, Bacillus subtilis aldehyde
dehydrogenase ywdH-like. Uncharacterized Bacillus
subtilis ywdH aldehyde dehydrogenase (locus P39616)
most closely related to the ALDHs and fatty ALDHs of
families 3 and 14, and similar sequences, are included
in this CD.
Length = 449
Score = 27.5 bits (62), Expect = 0.78
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 10/40 (25%)
Query: 7 TIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALY 46
T D F R+++L +KL K+ I K ++ EAL
Sbjct: 16 TKDVEF-RIEQL--------KKL-KQAIKKYENEILEALK 45
>gnl|CDD|221669 pfam12621, DUF3779, Phosphate metabolism protein. This domain
family is found in eukaryotes, and is approximately 100
amino acids in length. The family is found in
association with pfam02714. There are two completely
conserved residues (W and D) that may be functionally
important. This family is likely to be involved in
phosphate metabolism however there is little
accompanying literature to confirm this.
Length = 95
Score = 26.8 bits (60), Expect = 0.80
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 6 PTIDYGFQRLQKLIPRHPGDPEKLPKEII 34
P I ++ L+KL+P P + P+E+
Sbjct: 4 PDIYASYRALRKLLPAGYNLPIEYPEEVE 32
>gnl|CDD|153275 cd07591, BAR_Rvs161p, The Bin/Amphiphysin/Rvs (BAR) domain of
Saccharomyces cerevisiae Reduced viability upon
starvation protein 161 and similar proteins. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. This subfamily is composed of fungal
proteins with similarity to Saccharomyces cerevisiae
Reduced viability upon starvation protein 161 (Rvs161p)
and Schizosaccharomyces pombe Hob3 (homolog of Bin3). S.
cerevisiae Rvs161p plays a role in regulating cell
polarity, actin cytoskeleton polarization, vesicle
trafficking, endocytosis, bud formation, and the mating
response. It forms a heterodimer with another BAR domain
protein Rvs167p. Rvs161p and Rvs167p share common
functions but are not interchangeable. Their BAR domains
cannot be replaced with each other and the
overexpression of one cannot suppress the mutant
phenotypes of the other. S. pombe Hob3 is important in
regulating filamentous actin localization and may be
required in activating Cdc42 and recruiting it to cell
division sites. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 224
Score = 27.3 bits (61), Expect = 0.83
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 14 RLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQL 54
+++KLI + DP KLP+ ++ D A+ +Y N+QL
Sbjct: 131 KVRKLIDKPSEDPTKLPR---AEKELDEAKEVYET-LNDQL 167
>gnl|CDD|236979 PRK11779, sbcB, exonuclease I; Provisional.
Length = 476
Score = 26.3 bits (59), Expect = 2.1
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 3 LNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYS 47
L + L++L + D EK +LK D AE L
Sbjct: 433 LTPERLQQYAAELEQLAQEYEDDEEKQA---LLKALYDYAEELVP 474
>gnl|CDD|226512 COG4025, COG4025, Predicted membrane protein [Function unknown].
Length = 284
Score = 26.0 bits (57), Expect = 2.6
Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 14/88 (15%)
Query: 7 TIDYGFQRLQKLIPRH-PGDPEKLPKEIILKRAADLAEALYS-------------MPRNN 52
+ F + + P KL KE + A + L + R
Sbjct: 8 RFVWKFTAAVGYVTVNLPWIVVKLLKEGPKRSAMKTEQLLRTIGESASKVEKVMEKVREF 67
Query: 53 QLPLPAPPRSPHHFNSYTGQLNVTVQEN 80
Q+PLP P+ P F G+ N E
Sbjct: 68 QIPLPEEPQPPFKFLEIRGKRNAAAHEL 95
>gnl|CDD|226939 COG4573, GatZ, Predicted tagatose 6-phosphate kinase [Carbohydrate
transport and metabolism].
Length = 426
Score = 25.9 bits (57), Expect = 2.8
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 24 GDPEKLPKEIILKRAADLAEA 44
GDP L E + +RAA LA
Sbjct: 134 GDPIPLDDETVAERAARLAAV 154
>gnl|CDD|215328 PLN02609, PLN02609, catalase.
Length = 492
Score = 25.9 bits (57), Expect = 3.6
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 52 NQLPLPA-PPRSPHHFNSYTGQLNVT 76
N L LP P+ HH N + G +N
Sbjct: 359 NYLQLPVNAPKCAHHNNHHEGFMNFM 384
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 25.1 bits (55), Expect = 6.6
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 11 GFQRLQKLIPRHPGDPEKLPKEIILKR----AADLAEALYSMP 49
G + +L+ DP+K P+E+ K+ A L EA M
Sbjct: 270 GEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKMK 312
>gnl|CDD|237570 PRK13959, PRK13959, phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 341
Score = 25.0 bits (55), Expect = 6.7
Identities = 8/22 (36%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 25 DPEKLPKEIILKRAADLAEALY 46
DP LP E++ + +DL +A
Sbjct: 297 DPPPLPDEVV-EAVSDLYKAGT 317
>gnl|CDD|238334 cd00594, KU, Ku-core domain; includes the central DNA-binding
beta-barrels, polypeptide rings, and the C-terminal arm
of Ku proteins. The Ku protein consists of two tightly
associated homologous subunits, Ku70 and Ku80, and was
originally identified as an autoantigen recognized by
the sera of patients with an autoimmunity disease. In
eukaryotes, the Ku heterodimer contributes to genomic
integrity through its ability to bind DNA double-strand
breaks and facilitate repair by non-homologous
end-joining. The bacterial Ku homologs does not contain
the conserved N-terminal extension that is present in
the eukaryotic Ku protein.
Length = 272
Score = 24.9 bits (55), Expect = 6.9
Identities = 15/31 (48%), Positives = 16/31 (51%)
Query: 15 LQKLIPRHPGDPEKLPKEIILKRAADLAEAL 45
L + IP P D P E I KR DL EAL
Sbjct: 238 LGEEIPEPPEDLTLPPPEEIPKRVIDLLEAL 268
>gnl|CDD|181829 PRK09409, PRK09409, IS2 transposase TnpB; Reviewed.
Length = 301
Score = 24.7 bits (53), Expect = 8.2
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 12/76 (15%)
Query: 10 YGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQLPLPAPPRSPHHFNSY 69
YG++R+ L+ R + + +P A A+ +Y + R N L L P P ++
Sbjct: 66 YGYRRVWALL-RRQAELDGMP--------AINAKRVYRIMRQNALLLERKPAVPPSKRAH 116
Query: 70 TGQLNVTVQENGNGQW 85
TG+ V V+E+ N +W
Sbjct: 117 TGR--VAVKES-NQRW 129
>gnl|CDD|203734 pfam07704, PSK_trans_fac, Rv0623-like transcription factor. This
entry represents the Rv0623-like family of
transcription factors associated with the PSK operon.
Length = 81
Score = 23.8 bits (52), Expect = 8.4
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 36 KRAADLAEALYSMPRNNQLPLPAPPRSPHH 65
+R L E L ++ R PL P RSP
Sbjct: 41 RRKIPLLERLAAIRRKAAAPLLPPDRSPDD 70
>gnl|CDD|200213 TIGR02810, agaZ_gatZ, D-tagatose-bisphosphate aldolase, class II,
non-catalytic subunit. Aldolases specific for
D-tagatose-bisphosphate occur in distinct pathways in
Escherichia coli and other bacteria, one for the
degradation of galactitol (formerly dulcitol) and one
for degradation of N-acetyl-galactosamine and
D-galactosamine. This family represents a protein of
both systems that behaves as a non-catalytic subunit of
D-tagatose-bisphosphate aldolase, required both for full
activity and for good stability of the aldolase. Note
that members of this protein family appear in public
databases annotated as putative tagatose 6-phosphate
kinases, possibly in error [Energy metabolism, Sugars].
Length = 420
Score = 24.6 bits (54), Expect = 8.8
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 24 GDPEKLPKEIILKRAADLAEA 44
GDP LP I +RAA L
Sbjct: 130 GDPAPLPDATIAERAARLCAV 150
>gnl|CDD|183329 PRK11829, PRK11829, biofilm formation regulator HmsP; Provisional.
Length = 660
Score = 24.5 bits (53), Expect = 9.6
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 13 QRLQKLIPRHPGDPEKLPKEII-------LKRAADLAEAL 45
L+ LI + DP++L EI L A L L
Sbjct: 509 PHLKTLISHYHIDPQQLLLEITETAQIQDLDEALRLLREL 548
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
0.314 0.135 0.417
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,752,029
Number of extensions: 394019
Number of successful extensions: 352
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 26
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)