RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15634
(113 letters)
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 55.0 bits (133), Expect = 1e-11
Identities = 17/32 (53%), Positives = 22/32 (68%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
HIKRPMNAFM++S+ RRK+ + P N I
Sbjct: 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAI 32
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 46.8 bits (112), Expect = 2e-08
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
KRP++AF ++S+ QR K+ +NP + N+ I
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEI 31
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 42.7 bits (101), Expect = 8e-07
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
KRPM+AFM++S+ R KI +NP + N+
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNA 30
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding
preferences. Two phylogenically distinct groups of
Class I proteins bind DNA in a sequence specific
fashion and contain a single HMG box. One group
(SOX-TCF) includes transcription factors, TCF-1, -3,
-4; and also SRY and LEF-1, which bind four-way DNA
junctions and duplex DNA targets. The second group
(MATA) includes fungal mating type gene products MC,
MATA1 and Ste11. Class II and III proteins (HMGB-UBF)
bind DNA in a non-sequence specific fashion and contain
two or more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 38.4 bits (90), Expect = 4e-05
Identities = 8/29 (27%), Positives = 18/29 (62%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
KRP++A+ ++S+ R ++ +NP +
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVG 29
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA
in a non-sequence specific fashion and contain two or
more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 31.8 bits (73), Expect = 0.013
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKM 55
KRP++A+ ++S+ QR K+ +NP
Sbjct: 2 KRPLSAYFLFSQEQRPKLKKENPDA 26
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include the fungal mating type gene products
MC, MATA1 and Ste11.
Length = 77
Score = 31.5 bits (72), Expect = 0.021
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
I RP NAF+++ + + ++ +NP + N+ I
Sbjct: 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEI 32
>gnl|CDD|107318 cd06323, PBP1_ribose_binding, Periplasmic sugar-binding domain of
the thermophilic Thermoanaerobacter tengcongensis ribose
binding protein (ttRBP) and its mesophilic homologs.
Periplasmic sugar-binding domain of the thermophilic
Thermoanaerobacter tengcongensis ribose binding protein
(ttRBP) and its mesophilic homologs. Members of this
group are belonging to the type I periplasmic binding
protein superfamily, whose members are involved in
chemotaxis, ATP-binding cassette transport, and
intercellular communication in central nervous system.
The thermophilic and mesophilic ribose-binding proteins
are structurally very similar, but differ substantially
in thermal stability.
Length = 268
Score = 30.7 bits (70), Expect = 0.11
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 75 ELKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
+ + V A + ++ FDR KGL++ NI
Sbjct: 146 VVDKYPGLKVVASQPAD-FDRAKGLNVMENI 175
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 27.9 bits (62), Expect = 1.1
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPK 54
KRP++A+ ++S R +I +NPK
Sbjct: 72 KRPLSAYFLYSAENRDEIRKENPK 95
>gnl|CDD|131577 TIGR02525, plasmid_TraJ, plasmid transfer ATPase TraJ. Members of
this protein family are predicted ATPases associated
with plasmid transfer loci in bacteria. This family is
most similar to the DotB ATPase of a type-IV
secretion-like system of obligate intracellular
pathogens Legionella pneumophila and Coxiella burnetii
(TIGR02524) [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 372
Score = 27.8 bits (62), Expect = 1.3
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 20 TSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNC-HIMHFLCPQKIELKS 78
+ H LG H+K P A R + + P+M + F+ I+ ++ Q++ L++
Sbjct: 249 SGHFCLGTLHVKSPGEAI-------SRCLQMYPPEMREAAAFDLLSILQYIIVQRL-LRT 300
Query: 79 KRDIHVEACRKSNLFDRD 96
D +A R+ +FD
Sbjct: 301 T-DGKRQAVREYIVFDDS 317
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 27.5 bits (61), Expect = 1.6
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 14 MPPGLDTSHLN--LGEQHIKRPMNA 36
MPPG SHL+ LGE+ I +NA
Sbjct: 183 MPPGHIVSHLDAILGEEGIAHEVNA 207
>gnl|CDD|237305 PRK13207, ureC, urease subunit alpha; Reviewed.
Length = 568
Score = 27.4 bits (62), Expect = 1.8
Identities = 9/15 (60%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 61 FNCHIMHFLCPQKIE 75
+ HI HF+CPQ+IE
Sbjct: 132 IDTHI-HFICPQQIE 145
>gnl|CDD|223875 COG0804, UreC, Urea amidohydrolase (urease) alpha subunit [Amino
acid transport and metabolism].
Length = 568
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/15 (60%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 61 FNCHIMHFLCPQKIE 75
+ HI HF+CPQ+IE
Sbjct: 132 IDTHI-HFICPQQIE 145
>gnl|CDD|238221 cd00375, Urease_alpha, Urease alpha-subunit; Urease is a
nickel-dependent metalloenzyme that catalyzes the
hydrolysis of urea to form ammonia and carbon dioxide.
Nickel-dependent ureases are found in bacteria, fungi
and plants. Their primary role is to allow the use of
external and internally generated urea as a nitrogen
source. The enzyme consists of 3 subunits, alpha, beta
and gamma, which can be fused and present on a single
protein chain and which in turn forms multimers, mainly
trimers. The large alpha subunit is the catalytic domain
containing an active site with a bi-nickel center
complexed by a carbamylated lysine. The beta and gamma
subunits play a role in subunit association to form the
higher order trimers.
Length = 567
Score = 26.5 bits (59), Expect = 4.0
Identities = 8/14 (57%), Positives = 12/14 (85%), Gaps = 1/14 (7%)
Query: 62 NCHIMHFLCPQKIE 75
+ H+ HF+CPQ+IE
Sbjct: 133 DTHV-HFICPQQIE 145
>gnl|CDD|236798 PRK10929, PRK10929, putative mechanosensitive channel protein;
Provisional.
Length = 1109
Score = 26.2 bits (58), Expect = 4.9
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 40 WSRIQRRKIALDNPK 54
W IQRR+IA D K
Sbjct: 723 WMLIQRRRIAFDRAK 737
>gnl|CDD|190542 pfam03145, Sina, Seven in absentia protein family. The seven in
absentia (sina) gene was first identified in
Drosophila. The Drosophila Sina protein is essential
for the determination of the R7 pathway in
photoreceptor cell development: the loss of functional
Sina results in the transformation of the R7 precursor
cell to a non- neuronal cell type. The Sina protein
contains an N-terminal RING finger domain pfam00097.
Through this domain, Sina binds E2
ubiquitin-conjugating enzymes (UbcD1) Sina also
interacts with Tramtrack (TTK88) via PHYL. Tramtrack is
a transcriptional repressor that blocks photoreceptor
determination, while PHYL down-regulates the activity
of TTK88. In turn, the activity of PHYL requires the
activation of the Sevenless receptor tyrosine kinase, a
process essential for R7 determination. It is thought
that thus Sina targets TTK88 for degradation, therefore
promoting the R7 pathway. Murine and human homologues
of Sina have also been identified. The human homologue
Siah-1 also binds E2 enzymes (UbcH5) and through a
series of physical interactions, targets beta-catenin
for ubiquitin degradation. Siah-1 expression is
enhanced by p53, itself promoted by DNA damage. Thus
this pathway links DNA damage to beta-catenin
degradation. Sina proteins, therefore, physically
interact with a variety of proteins. The N-terminal
RING finger domain that binds ubiquitin conjugating
enzymes is described in pfam00097, and does not form
part of the alignment for this family. The remainder
C-terminal part is involved in interactions with other
proteins, and is included in this alignment. In
addition to the Drosophila protein and mammalian
homologues, whose similarity was noted previously, this
family also includes putative homologues from
Caenorhabditis elegans, Arabidopsis thaliana.
Length = 198
Score = 25.8 bits (57), Expect = 5.2
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 54 KMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRK 89
K+ + ++F C CP ++ L+ K H E C
Sbjct: 8 KVASKVLFPCKHAALGCPVRLPLQLKDW-HEERCEY 42
>gnl|CDD|143248 cd05771, IgC_Tapasin_R, Tapasin-R immunoglobulin-like domain.
IgC_Tapasin_R: Immunoglobulin-like domain on Tapasin-R.
Tapasin is a V-C1 (variable-constant) immunoglobulin
superfamily molecule present in the endoplasmic
reticulum (ER), where it links MHC class I molecules to
the transporter associated with antigen processing
(TAP). Tapasin-R is a tapasin-related protein that
contains similar structural motifs to Tapasin, with some
marked differences, especially in the V domain,
transmembrane and cytoplasmic regions. The majority of
Tapasin-R is located within the ER; however, there may
be some expression of Tapasin-R at the cell surface.
Tapasin-R lacks an obvious ER retention signal.
Length = 139
Score = 24.8 bits (54), Expect = 8.6
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 2 SLSSHHQH--------SYFSMPPGLDTS 21
S SSH QH S+ ++ PG + +
Sbjct: 92 SFSSHRQHQDGTYSLSSHLTLEPGTEDA 119
>gnl|CDD|221350 pfam11971, CAMSAP_CH, CAMSAP CH domain. This domain is the
N-terminal CH domain from the CAMSAP proteins.
Length = 85
Score = 24.2 bits (53), Expect = 9.6
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 63 CHIMHFLCPQKIELKS 78
++HF CPQ + L
Sbjct: 27 AALIHFYCPQLVPLHD 42
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 0.135 0.426
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,481,698
Number of extensions: 444142
Number of successful extensions: 395
Number of sequences better than 10.0: 1
Number of HSP's gapped: 395
Number of HSP's successfully gapped: 25
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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 (21.7 bits)
S2: 53 (24.2 bits)