RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2137
(382 letters)
>gnl|CDD|212559 cd11661, SANT_MTA3_like, Myb-Like Dna-Binding Domain of MTA3 and
related proteins. Members in this SANT/myb family
include domains found in mouse metastasis-associated
protein 3 (MTA3) proteins and arginine-glutamic
dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2,
N-CoR and TFIIIB) DNA-binding domains are a diverse set
of proteins that share a common 3 alpha-helix bundle.
MTA3 has been shown to interact with nucleosome
remodeling and deacetylase (NuRD) proteins CHD4 and
HDAC1, and the core cohesin complex protein RAD21 in the
ovary, and regulate G2/M progression in proliferating
granulosa cells. RERE belongs to the atrophin family and
has been identified as a nuclear receptor corepressor;
altered expression levels of RERE are associated with
cancer in humans while mutations of Rere in mice cause
failure in closing the anterior neural tube and fusion
of the telencephalic and optic vesicles during
embryogenesis.
Length = 46
Score = 94.6 bits (236), Expect = 1e-24
Identities = 32/46 (69%), Positives = 38/46 (82%)
Query: 160 EWSASEANLFEEALEKYGKDFNDIRNDFLPWKTLKNIIEYYYMWKT 205
EWS SEA LFEE L KYGKDF+DIR DFLPWK++ ++E+YYMWK
Sbjct: 1 EWSESEAKLFEEGLRKYGKDFHDIRQDFLPWKSVGELVEFYYMWKK 46
>gnl|CDD|240060 cd04709, BAH_MTA, BAH, or Bromo Adjacent Homology domain, as
present in MTA1 and similar proteins. The
Metastasis-associated protein MTA1 is part of the NURD
(nucleosome remodeling and deacetylating) complex and
plays a role in cellular transformation and metastasis.
BAH domains are found in a variety of proteins playing
roles in transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 164
Score = 90.9 bits (226), Expect = 8e-22
Identities = 45/61 (73%), Positives = 51/61 (83%), Gaps = 1/61 (1%)
Query: 32 SKELTNKQKHQLKQRELFLSRQVETLPATHIRGKCSVTLLNETESLLSYLNKEPRSFVVS 91
S +LT KQ+HQL+ RELFLSRQVETLPATHIRGKCSVTLLN+TES SYL +E +F S
Sbjct: 68 SDDLTPKQRHQLRHRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLARED-TFFYS 126
Query: 92 L 92
L
Sbjct: 127 L 127
Score = 79.0 bits (195), Expect = 2e-17
Identities = 29/59 (49%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 270 FGHAFSTRLAMPRDELDTFFYCLVFDPAQKTLLADKGEIRVGSKYQSDITPYLGEASKD 328
S R + R+ DTFFY LV+DP QKTLLAD+GEIRVG YQ+ + S D
Sbjct: 107 LNDTESARSYLARE--DTFFYSLVYDPEQKTLLADQGEIRVGPSYQAKLPDLQPFPSPD 163
>gnl|CDD|216509 pfam01448, ELM2, ELM2 domain. The ELM2 (Egl-27 and MTA1 homology
2) domain is a small domain of unknown function. It is
found in the MTA1 protein that is part of the NuRD
complex. The domain is usually found to the N terminus
of a myb-like DNA binding domain pfam00249. ELM2 is also
found associated with an ARID DNA binding domain
pfam01388 in a member from Arabidopsis thaliana. This
suggests that ELM2 may also be involved in DNA binding,
or perhaps is a protein-protein interaction domain.
Length = 55
Score = 63.4 bits (155), Expect = 3e-13
Identities = 20/57 (35%), Positives = 39/57 (68%), Gaps = 2/57 (3%)
Query: 308 IRVGSKYQSDITPYLGEASKDPNCRESKDFETLVWTPHHSLTDKQIDQFLVISRSVG 364
IRVG YQ++I L E+ KD + E +D LVW+P + L++++++++L++++S
Sbjct: 1 IRVGPDYQAEIPELLPESEKDQDKEEDED--QLVWSPDNELSEQKLEEYLLVAKSRY 55
>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding
domains.
Length = 49
Score = 43.4 bits (103), Expect = 4e-06
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 159 EEWSASEANLFEEALEKYG-KDFNDIRNDFLPWKTLKNIIEYYYMWKTT 206
EW+ E L E ++KYG ++ I LP +T + E +
Sbjct: 2 GEWTEEEDELLIELVKKYGKNNWEKIA-KELPGRTAEQCRERWRNLLKP 49
>gnl|CDD|239835 cd04370, BAH, BAH, or Bromo Adjacent Homology domain (also called
ELM1 and BAM for Bromo Adjacent Motif). BAH domains have
first been described as domains found in the polybromo
protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure
of Chromatin). They also occur in mammalian DNA
methyltransferases and the MTA1 subunits of histone
deacetylase complexes. A BAH domain is also found in
Yeast Sir3p and in the origin receptor complex protein 1
(Orc1p), where it was found to interact with the
N-terminal lobe of the silence information regulator 1
protein (Sir1p), confirming the initial hypothesis that
BAH plays a role in protein-protein interactions.
Length = 123
Score = 43.9 bits (104), Expect = 1e-05
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 34 ELTNKQKHQLKQRELFLSRQVETLPATHIRGKCSVTLLNETESLLSYLNKE-PRSFVVSL 92
E +RELFLS ++ +P I GKC V ++E E L NK F L
Sbjct: 51 ETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRL 110
>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains.
Tandem copies of the domain bind telomeric DNA tandem
repeatsas part of the capping complex. Binding is
sequence dependent for repeats which contain the G/C
rich motif [C2-3 A (CA)1-6]. The domain is also found in
regulatory transcriptional repressor complexes where it
also binds DNA.
Length = 45
Score = 41.8 bits (99), Expect = 1e-05
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 160 EWSASEANLFEEALEKYG-KDFNDIRNDFLPWKTLKNIIEYYYMWK 204
W+ E L EA++KYG ++ I LP +T K E +
Sbjct: 1 PWTEEEDELLLEAVKKYGKNNWEKIA-KELPGRTPKQCRERWRNLL 45
>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain. This
family contains the DNA binding domains from Myb
proteins, as well as the SANT domain family.
Length = 47
Score = 40.6 bits (96), Expect = 3e-05
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 160 EWSASEANLFEEALEKYG-KDFNDIRNDFLPWKTLKNIIEYYYMWK 204
W+ E L EA++K+G +++ I LP +T + +
Sbjct: 3 PWTPEEDELLIEAVKKHGNGNWSKIA-KHLPGRTDNQCKNRWNNYL 47
>gnl|CDD|216495 pfam01426, BAH, BAH domain. This domain has been called BAH (Bromo
adjacent homology) domain and has also been called ELM1
and BAM (Bromo adjacent motif) domain. The function of
this domain is unknown but may be involved in
protein-protein interaction.
Length = 120
Score = 42.7 bits (101), Expect = 3e-05
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 46 RELFLSRQVETLPATHIRGKCSVTLLNETESLLSYLNK-EPRSFVVSL 92
E+FLS + + +P I GKC+V + ++ ESL EP F L
Sbjct: 60 DEVFLSDECDDVPLEDIIGKCNVIIKSDPESLQPRKINGEPDVFFCEL 107
>gnl|CDD|214664 smart00439, BAH, Bromo adjacent homology domain.
Length = 121
Score = 39.2 bits (92), Expect = 5e-04
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 46 RELFLSRQVETLPATHIRGKCSVTLLNETESLLSYL-NKEPRSFVV 90
E+FLS + +T+P + I GKC+V ++ L EP F
Sbjct: 61 NEVFLSDEYDTVPLSDIIGKCNVLYKSDYPGLRPEGSIGEPDVFFC 106
>gnl|CDD|240068 cd04717, BAH_polybromo, BAH, or Bromo Adjacent Homology domain,
as present in polybromo and yeast RSC1/2. The human
polybromo protein (BAF180) is a component of the
SWI/SNF chromatin-remodeling complex PBAF. It is
thought that polybromo participates in transcriptional
regulation. Saccharomyces cerevisiae RSC1 and RSC2 are
part of the 15-subunit nucleosome remodeling RSC
complex. BAH domains are found in a variety of proteins
playing roles in transcriptional silencing and the
remodeling of chromatin. It is assumed that in most or
all of these instances the BAH domain mediates
protein-protein interactions.
Length = 121
Score = 31.4 bits (72), Expect = 0.25
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 45 QRELFLSRQVETLPATHIRGKCSV 68
+ E+F S ET+P I GKC+V
Sbjct: 60 KNEVFKSPLYETVPVEEIVGKCAV 83
>gnl|CDD|222028 pfam13289, SIR2_2, SIR2-like domain. This family of proteins are
related to the sirtuins.
Length = 139
Score = 30.0 bits (68), Expect = 0.85
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 167 NLFEEALEKYGKDFNDIRNDFLPWKTLKNIIEYYYM 202
+L E+ALE+ GK + +D Y +
Sbjct: 10 DLLEDALEEEGKPIIVVSDDLALANLESGRPLIYKL 45
>gnl|CDD|227448 COG5118, BDP1, Transcription initiation factor TFIIIB, Bdp1 subunit
[Transcription].
Length = 507
Score = 31.2 bits (70), Expect = 1.1
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 13/79 (16%)
Query: 159 EEWSASEANLFEEALEKYGKDFNDIRNDFLPWKTLKNIIEYYYMWKTTDRYVQQKRVKAV 218
WS E F +AL +G DF+ I + F P + K I +++++++V
Sbjct: 366 LRWSKKEIEKFYKALSIWGTDFSLISSLF-PNRERKQI---------KAKFIKEEKVNPE 415
Query: 219 EAESKLKQVYIPN---YNK 234
L + + YNK
Sbjct: 416 RINEALNEKKPFDQVEYNK 434
>gnl|CDD|214804 smart00754, CHRD, A domain in the BMP inhibitor chordin and in
microbial proteins.
Length = 118
Score = 28.9 bits (65), Expect = 1.6
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 22 TTDNGHPG-GTSKELTNKQKHQLKQRELFLSRQVETLPATHIRGK 65
T P G+ K LT+++ QL L+++ + P IRG+
Sbjct: 71 PTSREGPFAGSVKTLTDEELRQLLAGNLYVNVHTKANPGGEIRGQ 115
>gnl|CDD|212558 cd11660, SANT_TRF, Telomere repeat binding factor-like DNA-binding
domains of the SANT/myb-like family. Human telomere
repeat binding factors, TRF1 and TRF2, function as part
of the 6 component shelterin complex. TRF2 binds DNA and
recruits RAP1 (via binding to the RAP1 protein
c-terminal (RCT)) and TIN2 in the protection of
telomeres from DNA repair machinery. Metazoan shelterin
consists of 3 DNA binding proteins (TRF2, TRF1, and
POT1) and 3 recruited proteins that bind to one or more
of these DNA-binding proteins (RAP1, TIN2, TPP1).
Schizosaccharomyces pombe TAZ1 is an orthlog and binds
RAP1. Human TRF1 and TRF2 bind double-stranded DNA.
hTRF2 consists of a basic N-terminus, a TRF homology
domain, the RAP1 binding motif (RBM), the TIN2 binding
motif (TBM) and a myb-like DNA binding domain, SANT,
named after 'SWI3, ADA2, N-CoR and TFIIIB', several
factors that share this domain. Tandem copies of the
domain bind telomeric DNA tandem repeats as part of the
capping complex. The single myb-like domain of TRF-type
proteins is similar to the tandem myb_like domains found
in yeast RAP1.
Length = 50
Score = 27.5 bits (62), Expect = 1.6
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 13/48 (27%)
Query: 161 WSASEANLFEEALEKYGK-DFNDIRNDFLP------------WKTLKN 195
W+ E E +EKYG ++ I D+ W+ LK
Sbjct: 3 WTDEEDEALVEGVEKYGVGNWAKILKDYFFVNNRTSVDLKDKWRNLKK 50
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 30.3 bits (68), Expect = 1.7
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 1/70 (1%)
Query: 132 DKHKYSLAEAISSLVPSTGPVLCRDEMEEWS-ASEANLFEEALEKYGKDFNDIRNDFLPW 190
+K E S P PV DE+ E +S ANL EE +KY + N
Sbjct: 81 EKETEGKTEEKKSTAPKNAPVEPADELPEIDESSVANLSEEERKKYAAKLKEKGNKAYRN 140
Query: 191 KTLKNIIEYY 200
K I+ Y
Sbjct: 141 KDFNKAIKLY 150
>gnl|CDD|216942 pfam02234, CDI, Cyclin-dependent kinase inhibitor. Cell cycle
progression is negatively controlled by cyclin-dependent
kinases inhibitors (CDIs). CDIs are involved in cell
cycle arrest at the G1 phase.
Length = 51
Score = 26.8 bits (60), Expect = 2.6
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 150 GPVLCRDEMEEW-SASEANLFEEALEKYGKDF 180
GPV +E+EE+ +A+ EE EK+ DF
Sbjct: 5 GPVD-HEELEEFFAAALKEQQEEFSEKWNFDF 35
>gnl|CDD|234845 PRK00823, phhB, pterin-4-alpha-carbinolamine dehydratase;
Validated.
Length = 97
Score = 27.9 bits (63), Expect = 2.8
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 260 EIERS--FDDYKFGHAFSTRLAMPRDELD 286
IER+ F ++ AF R+A +E D
Sbjct: 29 AIERTFKFKNFNEAFAFMNRVAEIAEEED 57
>gnl|CDD|233289 TIGR01140, L_thr_O3P_dcar, L-threonine-O-3-phosphate decarboxylase.
This family contains pyridoxal phosphate-binding class
II aminotransferases (see pfam00222) closely related to,
yet distinct from, histidinol-phosphate aminotransferase
(HisC). It is found in cobalamin biosynthesis operons in
Salmonella typhimurium and Bacillus halodurans (each of
which also has HisC) and has been shown to have
L-threonine-O-3-phosphate decarboxylase activity in
Salmonella. Although the gene symbol cobD was assigned
in Salmonella, cobD in other contexts refers to a
different cobalamin biosynthesis enzyme, modeled by
pfam03186 and called cbiB in Salmonella [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 330
Score = 28.7 bits (65), Expect = 5.4
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 343 TPHHSLTDKQIDQF--LVISRSVGKF 366
TP SL Q +F LV+ RS+ KF
Sbjct: 171 TPDASLAP-QAARFPGLVVLRSLTKF 195
>gnl|CDD|218422 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyze the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 29.0 bits (66), Expect = 5.7
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 276 TRLAMPRDELDTFFYCLVFDP 296
RL + RD F CLV+ P
Sbjct: 329 VRLFLRRDPFGRFVSCLVYVP 349
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 28.5 bits (64), Expect = 7.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 169 FEEALEKYGKDFNDIRNDFL 188
+ EA+E+YG D D+R
Sbjct: 273 YAEAMERYGSDKPDLRFPLE 292
>gnl|CDD|219163 pfam06757, Ins_allergen_rp, Insect allergen related repeat,
nitrile-specifier detoxification. This family
exemplifies a case of novel gene evolution. The case in
point is the arms-race between plants and their
infective insective herbivores in the area of the
glucosinolate-myrosinase system. Brassicas have
developed the glucosinolate-myrosinase system as
chemical defence mechanism against the insects, and
consequently the insects have adapted to produce a
detoxifying molecule, nitrile-specifier protein (NSP).
NSP is present in the small white butterfly Pieris
rapae. NSP is structurally different from and has no
amino acid homology to any known detoxifying enzymes,
and it appears to have arisen by a process of domain and
gene duplication of a sequence of unknown function that
is widespread in insect species and referred to as
insect-allergen-repeat protein. Thus this family is
found either as a single domain or as a multiple
repeat-domain.
Length = 181
Score = 27.6 bits (62), Expect = 7.4
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 179 DFNDIRNDFLPWKTLKNIIEYYYMWKTTDRYVQQ 212
DF+D D +P ++ + YY TD +
Sbjct: 7 DFDDFV-DLIPLDEIRALAARYY---ITDAEFRA 36
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 28.3 bits (64), Expect = 7.6
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 169 FEEALEKYGKDFNDIRNDFLPWKTLKNIIEY 199
+ EA+ +YG D D+R L ++ +
Sbjct: 276 YAEAMRRYGSDKPDLRFPLE----LIDVTDL 302
>gnl|CDD|179431 PRK02491, PRK02491, putative deoxyribonucleotide triphosphate
pyrophosphatase/unknown domain fusion protein; Reviewed.
Length = 328
Score = 28.2 bits (63), Expect = 7.9
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 26 GHPGGTSKELTNKQKHQLKQRELFLSRQVETLPA 59
G G + ELT ++K+QL R + + +E PA
Sbjct: 289 GETGRHAAELTAEEKNQLSHRGQAVKKLMEVFPA 322
>gnl|CDD|180188 PRK05664, PRK05664, threonine-phosphate decarboxylase; Reviewed.
Length = 330
Score = 28.1 bits (63), Expect = 8.9
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 343 TPHHSLTDKQIDQFLVISRSVGKF 366
TP HSL L++ RS GKF
Sbjct: 170 TPQHSLAACAHRPGLIVLRSFGKF 193
>gnl|CDD|240316 PTZ00216, PTZ00216, acyl-CoA synthetase; Provisional.
Length = 700
Score = 28.0 bits (63), Expect = 8.9
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 270 FGHAFSTRLAMPRDELDT-FFYCLVFDPAQKTL 301
F HA+ +RL ++ DT ++ VF + L
Sbjct: 394 FDHAYQSRLRALKEGKDTPYWNEKVFSAPRAVL 426
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 0.129 0.369
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,807,295
Number of extensions: 1764609
Number of successful extensions: 1150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1145
Number of HSP's successfully gapped: 33
Length of query: 382
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 283
Effective length of database: 6,546,556
Effective search space: 1852675348
Effective search space used: 1852675348
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 (22.0 bits)
S2: 60 (26.9 bits)