RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6521
(83 letters)
>gnl|CDD|223295 COG0217, COG0217, Uncharacterized conserved protein [Function
unknown].
Length = 241
Score = 54.1 bits (131), Expect = 2e-10
Identities = 19/36 (52%), Positives = 28/36 (77%)
Query: 38 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVK 73
AGHSKW NI+H KAA+D +++ +FT L K++ +A K
Sbjct: 2 AGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAK 37
>gnl|CDD|233240 TIGR01033, TIGR01033, DNA-binding regulatory protein, YebC/PmpR
family. This model describes a minimally characterized
protein family, restricted to bacteria excepting for
some eukaryotic sequences that have possible transit
peptides. YebC from E. coli is crystallized, and PA0964
from Pseudomonas aeruginosa has been shown to be a
sequence-specific DNA-binding regulatory protein
[Regulatory functions, DNA interactions].
Length = 238
Score = 53.1 bits (128), Expect = 5e-10
Identities = 19/37 (51%), Positives = 28/37 (75%)
Query: 38 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKV 74
AGHSKW NI+H KAA+D ++ +FT L K++ +A K+
Sbjct: 2 AGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKL 38
>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
Length = 245
Score = 52.8 bits (128), Expect = 7e-10
Identities = 17/36 (47%), Positives = 26/36 (72%)
Query: 38 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVK 73
AGHSKW NI+H K A+D ++ +FT L +++ +A K
Sbjct: 2 AGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAK 37
>gnl|CDD|216656 pfam01709, Transcrip_reg, Transcriptional regulator. This is a
family of transcriptional regulators. In mammals, it
activates the transcription of mitochondrially-encoded
COX1. In bacteria, it negatively regulates the
quorum-sensing response regulator by binding to its
promoter region.
Length = 234
Score = 51.7 bits (125), Expect = 2e-09
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 41 SKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVK 73
SKW NI+H KAA+D ++ +FT L K++ +A K
Sbjct: 1 SKWANIKHRKAAQDAKRGKIFTKLGKEITVAAK 33
>gnl|CDD|237084 PRK12378, PRK12378, hypothetical protein; Provisional.
Length = 235
Score = 34.8 bits (81), Expect = 0.002
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 42 KWQNIRHIKAAKDQEKATLFTNLSKKLKLAVK 73
W+NI+ KA KD K+ +F L K++ +A K
Sbjct: 4 AWENIKAKKAKKDGAKSKIFAKLGKEIYVAAK 35
>gnl|CDD|99710 cd05827, Sortase_C_3, Sortase C (SrtC) or subfamily-3 sortases
are membrane cysteine transpeptidases found in
Gram-positive bacteria that anchor surface proteins to
peptidoglycans of the bacterial cell wall envelope.
This involves a transpeptidation reaction in which the
surface protein substrate is cleaved at a conserved
cell wall sorting signal and covalently linked to
peptidoglycan for display on the bacterial surface.
Sortases are grouped into different classes and
subfamilies based on sequence, membrane topology,
genomic positioning, and cleavage site preference.
Sortase C cleaves surface proteins at the LPXTG motif
between Thr and Gly and catalyzes the formation of an
amide bond between the carboxyl group of Thr and the
amino group of cell-wall cross bridges. It is a
narrow-range enzyme required for anchoring a few
substrates. It plays a role in Streptococcus pneumoniae
pathogenesis and is required in the assembly of pili on
the surface of Corynebacterium diphtheriae. Sortase C
is characterized by the presence of a C-terminal
hydrophobic domain that could serve as a membrane
anchor.
Length = 131
Score = 26.7 bits (60), Expect = 0.99
Identities = 18/59 (30%), Positives = 21/59 (35%), Gaps = 26/59 (44%)
Query: 38 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLK-------------LAVKVTHQYVVLPN 83
GH N A LFT+L K LK LA +V VVLP+
Sbjct: 50 TGHRGLPN------------AKLFTDLDK-LKKGDKFYIHVLGETLAYQVDQIEVVLPD 95
>gnl|CDD|129778 TIGR00695, uxuA, mannonate dehydratase. This Fe2+-requiring enzyme
plays a role in D-glucuronate catabolism in Escherichia
coli. Mannonate dehydratase converts D-mannonate to
2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is
found in a glucuronate utilization operon in Bacillus
stearothermophilus T-6 [Energy metabolism, Sugars].
Length = 394
Score = 26.5 bits (58), Expect = 1.8
Identities = 15/60 (25%), Positives = 32/60 (53%)
Query: 21 NVAKINSNILSTIPVRYAGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKVTHQYVV 80
++A++ NI++ +P G++ + + A KD ++ L NL+ L+ + V +Y V
Sbjct: 169 DIAQLTRNIIAGLPGAEEGYTLDRFKELLAAYKDIDEEKLRDNLAFFLQEILPVAEEYGV 228
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 25.2 bits (56), Expect = 4.1
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 46 IRHIKAAKDQEKATLFTNLS 65
IR K +E LFTNL+
Sbjct: 389 IRLTDYLKSEEITGLFTNLT 408
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 25.0 bits (55), Expect = 5.0
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 36 RYAGHSKWQNIRHIKAA 52
Y+G + W I +K A
Sbjct: 174 GYSGEANWDIIARVKQA 190
>gnl|CDD|147901 pfam05992, SbmA_BacA, SbmA/BacA-like family. The Rhizobium
meliloti bacA gene encodes a function that is essential
for bacterial differentiation into bacteroids within
plant cells in the symbiosis between R. meliloti and
alfalfa. An Escherichia coli homolog of BacA, SbmA, is
implicated in the uptake of microcins and bleomycin.
This family is likely to be a subfamily of the ABC
transporter family.
Length = 315
Score = 24.3 bits (53), Expect = 9.8
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 40 HSKWQNIRHIKAAKD--QEKATLFTNLSKKLKLAV 72
S W +RHI+ A QE F + + L ++
Sbjct: 96 TSHWDKLRHIEGASQRVQEDTMRFARIMEDLGVSF 130
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
0.319 0.129 0.374
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,705,862
Number of extensions: 262551
Number of successful extensions: 217
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 11
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.3 bits)