RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14727
(67 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 64.4 bits (158), Expect = 4e-16
Identities = 25/45 (55%), Positives = 31/45 (68%)
Query: 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
RR RTTFT +QLEELE F + YP RE+LA K+ LTE +V+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 56.1 bits (136), Expect = 9e-13
Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
RR RT FT +QLEELE F + YP RE+LA ++ LTE +V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 55.3 bits (134), Expect = 1e-12
Identities = 23/46 (50%), Positives = 32/46 (69%)
Query: 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+RR RT+FT +QLEELE F + YP RE+LA K+ L+E +V+
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 40.9 bits (96), Expect = 5e-06
Identities = 15/49 (30%), Positives = 21/49 (42%)
Query: 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ R T +QL LE F YP TR L++ +N+ VQ
Sbjct: 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96
>gnl|CDD|172388 PRK13867, PRK13867, type IV secretion system chaperone VirE1;
Provisional.
Length = 65
Score = 26.0 bits (57), Expect = 0.61
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 24 RNRTTFTLQQLEELET-AFAQTHYPDVFTREDLAM 57
+NR +++ +E+ + H P+ FT DL M
Sbjct: 10 KNRPVSPIEEPQEIHIEELSDNHQPNGFTSLDLEM 44
>gnl|CDD|152624 pfam12189, VirE1, Single-strand DNA-binding protein. This family
of proteins is found in bacteria. Proteins in this
family are approximately 60 amino acids in length.
There is a conserved IELE sequence motif. VirE1 is an
acidic chaperone protein which binds to VirE2, a ssDNA
binding protein. These proteins are virulence factors
of the plant pathogens Agrobacteria. VirE1 competes for
the ssDNA binding site of VirE2.
Length = 62
Score = 25.3 bits (55), Expect = 1.4
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 24 RNRTTFTLQQLEELETAFAQTHYPDVFTREDLAM 57
+NR + + E+ + +H FT DL M
Sbjct: 10 KNRPVSSPEAPNEIAEEQSYSHPSSGFTSLDLEM 43
>gnl|CDD|211803 TIGR03298, argP, transcriptional regulator, ArgP family. ArgP used
to be known as IciA. ArgP is a positive regulator of
argK. It is a negative autoregulator in presence of
arginine. It competes with DnaA for oriC iteron (13-mer)
binding. It activates dnaA and nrd transcription. It has
been demonstrated to be part of the pho regulon
(PMID:10589831). ArgP mutants convey canavanine (an
L-arginine structural homolog) sensitivity (PMID:
15150242) [Cellular processes, Toxin production and
resistance, DNA metabolism, DNA replication,
recombination, and repair, Regulatory functions, DNA
interactions].
Length = 278
Score = 25.3 bits (56), Expect = 2.8
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 40 AFAQTHYPDVFTREDLAM 57
AFA ++PD T LA
Sbjct: 170 AFAARYFPDGVTAAALAR 187
>gnl|CDD|235115 PRK03317, PRK03317, histidinol-phosphate aminotransferase;
Provisional.
Length = 368
Score = 24.8 bits (55), Expect = 3.1
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 5 SYSYHPAIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQ--THYPDV 49
SYS HP I + + FTL +++ A A H PDV
Sbjct: 121 SYSMHPIIARGTHTEWVEGPRAADFTL----DVDAAVAAIAEHRPDV 163
>gnl|CDD|239400 cd03126, alpha_CA_XII_XIV, Carbonic anhydrase alpha, isozymes XII
and XIV. Carbonic anhydrases (CAs) are zinc-containing
enzymes that catalyze the reversible hydration of carbon
dioxide in a two-step mechanism: a nucleophilic attack
of a zinc-bound hydroxide ion on carbon dioxide,
followed by the regeneration of the active site by
ionization of the zinc-bound water molecule and removal
of a proton from the active site. They are ubiquitous
enzymes involved in fundamental processes like
photosynthesis, respiration, pH homeostasis and ion
transport. There are three evolutionary distinct groups
- alpha, beta and gamma carbonic anhydrases - which show
no significant sequence identity or structural
similarity. Most alpha CAs are monomeric enzymes. The
zinc ion is complexed by three histidine residues. This
sub-family comprises the membrane proteins CA XII and
XIV.
Length = 249
Score = 24.8 bits (54), Expect = 4.2
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 24 RNRTTFTLQQLEELETAFAQTH 45
RN + +QL LETA T
Sbjct: 202 RNPVQISQEQLLALETALYSTE 223
>gnl|CDD|178993 PRK00378, PRK00378, nucleoid-associated protein NdpA; Validated.
Length = 334
Score = 24.4 bits (54), Expect = 4.5
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 34 LEELETAFAQTHYPDVFTREDLAMKINLTE 63
EEL+ + THY D+ + D+A +I+LTE
Sbjct: 130 NEELD--ISPTHYLDI-NQADIAARIDLTE 156
>gnl|CDD|235144 PRK03635, PRK03635, chromosome replication initiation inhibitor
protein; Validated.
Length = 294
Score = 24.3 bits (54), Expect = 4.8
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 40 AFAQTHYPDVFTREDLAM 57
AFA ++PD T E LA
Sbjct: 170 AFAARYFPDGVTAEALAK 187
>gnl|CDD|176119 cd08428, PBP2_IciA_ArgP, The C-terminal substrate binding domain
of LysR-type transcriptional regulator, ArgP (IciA),
for arginine exporter (ArgO); contains the type 2
periplasmic binding fold. The inhibitor of chromosomal
replication (iciA) protein encoded by Mycobacterium
tuberculosis, which is implicated in chromosome
replication initiation in vitro, has been identified as
arginine permease (ArgP), a LysR-type transcriptional
regulator for arginine outward transport, based on the
same amino sequence and similar DNA binding targets.
Arp has been shown to regulate various targets
including DnaA (replication), ArgO (arginine export),
dapB (lysine biosynthesis), and gdhA (glutamate
biosynthesis). With abundant nutrition, ArgP activates
the DnaA gene (to increase replication) and the ArgO
(to export redundant molecules). However, when
nutrition supply is limited, it is suggested that ArgP
might function as an inhibitor of chromosome
replication in order to slow replication. This
substrate-binding domain has significant homology to
the type 2 periplasmic binding proteins (PBP2), which
are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 195
Score = 24.1 bits (53), Expect = 5.7
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 40 AFAQTHYPDVFTREDLAM 57
FA ++P+ TRE L
Sbjct: 80 DFAARYFPNGLTREALLK 97
>gnl|CDD|235064 PRK02731, PRK02731, histidinol-phosphate aminotransferase;
Validated.
Length = 367
Score = 24.3 bits (54), Expect = 5.7
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 11 AIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQ 43
A+ DD+FV + + N + + L A+
Sbjct: 267 ALDDDAFVEKSRALNA-----EGMAWLTEFLAE 294
>gnl|CDD|226247 COG3724, AstB, Succinylarginine dihydrolase [Amino acid transport
and metabolism].
Length = 442
Score = 24.0 bits (52), Expect = 6.8
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 39 TAFAQTHYPDVFTREDLAMKINLTEARV 66
+ +Y D T DLA L E R
Sbjct: 395 NDWVDRYYRDRLTAADLADPQLLREGRE 422
>gnl|CDD|225747 COG3206, GumC, Uncharacterized protein involved in
exopolysaccharide biosynthesis [Cell envelope
biogenesis, outer membrane].
Length = 458
Score = 23.9 bits (52), Expect = 8.6
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 5/57 (8%)
Query: 15 DSFVRRKQRRNRTTFTLQQLEEL--ETAFAQTHYPDVFTREDLAM---KINLTEARV 66
+ K R ++ QL EL E A++ Y + R + ARV
Sbjct: 356 KELAQLKGRLSKLPKLQVQLRELEREAEAARSLYETLLQRYQELSIQEASPIGNARV 412
>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor;
Provisional.
Length = 231
Score = 23.7 bits (51), Expect = 9.1
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 31 LQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
L QL+E E +Y + +++A+ ++LTEAR+
Sbjct: 181 LSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARI 216
>gnl|CDD|236717 PRK10572, PRK10572, DNA-binding transcriptional regulator AraC;
Provisional.
Length = 290
Score = 23.4 bits (51), Expect = 10.0
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 2/34 (5%)
Query: 30 TLQQLEELETAFAQTHYPDVFTREDLAMKINLTE 63
+ +L Q + E LAM NL E
Sbjct: 132 LQPEFSDLFGQIEQAGQSEGRYSELLAM--NLLE 163
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
0.322 0.131 0.372
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,420,907
Number of extensions: 246385
Number of successful extensions: 309
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 19
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
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 (22.0 bits)
S2: 53 (24.1 bits)