RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5036
(176 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 = 58.1 bits (141), Expect = 5e-12
Identities = 15/34 (44%), Positives = 26/34 (76%)
Query: 98 QWHSLTREEQAKYYEKARQERQLHMELYPGWSAR 131
+W +L+ EE+ YYE+A++ ++LHM+LYP + R
Sbjct: 39 RWKALSNEEKQPYYEEAKKLKELHMKLYPDYKWR 72
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 41.4 bits (98), Expect = 8e-06
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 99 WHSLTREEQAKYYEKARQERQLHMELYPGWS 129
W +L+ EE+ Y EKA +E+ + + YP +
Sbjct: 39 WKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69
>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 = 38.8 bits (91), Expect = 9e-05
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 98 QWHSLTREEQAKYYEKARQERQLHMELYP 126
W SL+ EE+ KY EKA ++++ + + P
Sbjct: 38 MWKSLSEEEKKKYEEKAEKDKERYEKEMP 66
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 38.1 bits (89), Expect = 2e-04
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 92 NKNQMIQWHSLTREEQAKYYEKARQERQLHMELYPGW 128
+K +W L+ EE+A Y EKA+++++ + E P +
Sbjct: 33 SKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
>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 = 34.2 bits (79), Expect = 0.005
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 6/44 (13%)
Query: 99 WHSLTREEQAKYYEKARQERQLHMELYPGWSARDNYGYGAKKKK 142
W S + E +A Y E A +E++ H YP +Y Y +K
Sbjct: 40 WRSESPEVKAYYKELAEEEKERHAREYP------DYKYTPRKSS 77
>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 = 28.7 bits (65), Expect = 0.31
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 98 QWHSLTREEQAKYYEKARQERQ 119
+W L+ EE+ KY EKA ++++
Sbjct: 38 KWKELSEEEKKKYEEKAEKDKE 59
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 28.2 bits (63), Expect = 0.59
Identities = 11/41 (26%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 84 ARSGNEITNKNQMI-----QWHSLTREEQAKYYEKARQERQ 119
R G ++ + +W +++ EE+ KY EKAR++++
Sbjct: 23 KREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKAREDKK 63
>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
Length = 309
Score = 29.7 bits (67), Expect = 0.69
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 48 RWGGMSKPSIM---SWHVGSVNFICNFILIGPQGQTKPEARSGNEITNKNQ-MIQW 99
++G KP+ + SW SV F LI P+G + G +TN Q +++W
Sbjct: 174 QYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRW 229
>gnl|CDD|173689 cd05598, STKc_LATS, Catalytic domain of the Protein
Serine/Threonine Kinase, Large Tumor Suppressor.
Serine/Threonine Kinases (STKs), Large Tumor Suppressor
(LATS) subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
LATS subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. LATS was originally identified in Drosophila
using a screen for genes whose inactivation led to
overproliferation of cells. In tetrapods, there are two
LATS isoforms, LATS1 and LATS2. Inactivation of LATS1 in
mice results in the development of various tumors,
including sarcomas and ovarian cancer. LATS functions as
a tumor suppressor and is implicated in cell cycle
regulation.
Length = 376
Score = 29.4 bits (66), Expect = 0.93
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 108 AKYYEKARQERQLHMELYPGWSARDNYGYGAKKKKRKKE 146
+KYY+K RQ ME WS D +++RK++
Sbjct: 157 SKYYQKGDHHRQDSMEPSEEWSEIDRCRLKPLERRRKRQ 195
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 27.9 bits (62), Expect = 2.2
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 79 QTKPEARSGNEITNKNQMIQWHSLTREEQAKYYEKARQER---QLHMELY 125
+ P+ G K +W LT EE+ YY++A +R Q E Y
Sbjct: 91 KENPKLTFGEV--GKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEY 138
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 27.6 bits (62), Expect = 3.5
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 101 SLTREEQAKYYEKARQERQ 119
L+ EEQ K EK R+++
Sbjct: 302 KLSPEEQRKLEEKERKKQA 320
>gnl|CDD|172378 PRK13857, PRK13857, type IV secretion system pilin subunit VirB2;
Provisional.
Length = 120
Score = 26.0 bits (57), Expect = 7.1
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 7/30 (23%)
Query: 51 GMSKPSIMSWHVGSVNFICNFILIGPQGQT 80
G + P+ M VN IC FIL GP GQ+
Sbjct: 51 GGTDPATM------VNNICTFIL-GPFGQS 73
>gnl|CDD|236947 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 26.3 bits (59), Expect = 9.3
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 124 LYPGWSARDNYGYGAKKKKRKKE 146
LYP S R+N YG K + K
Sbjct: 87 LYPHMSVRENMAYGLKIRGMPKA 109
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
0.316 0.132 0.409
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: 9,003,472
Number of extensions: 795836
Number of successful extensions: 676
Number of sequences better than 10.0: 1
Number of HSP's gapped: 676
Number of HSP's successfully gapped: 22
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.4 bits)