RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13658
(228 letters)
>gnl|CDD|128922 smart00678, WWE, Domain in Deltex and TRIP12 homologues. Possibly
involved in regulation of ubiquitin-mediated
proteolysis.
Length = 73
Score = 76.6 bits (189), Expect = 1e-18
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 88 RWEWEGDVHGEWHAYDMQAQCLIEYSWAKGDQTIDISKTHLGFPYILNFCNLTQVRNTTG 147
WE+EG +G+W YD + IE ++A G + ++S GFPY ++F +TQ TG
Sbjct: 2 VWEYEGR-NGKWWPYDPRVSEDIEEAYAAGKKLCELSI--CGFPYTIDFNAMTQYNQATG 58
Query: 148 NVRNIRRTQQAPYPL 162
R +RR +PY
Sbjct: 59 TTRKVRRVTYSPYSK 73
Score = 53.5 bits (129), Expect = 6e-10
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 9/76 (11%)
Query: 7 VVWEWLNRNRRWRPFTPEVTQLIERAHSKN---LTSVILSDADPNLQNYFINLHTLQQCS 63
VWE+ RN +W P+ P V++ IE A++ I Y I+ + + Q +
Sbjct: 1 YVWEYEGRNGKWWPYDPRVSEDIEEAYAAGKKLCELSICG------FPYTIDFNAMTQYN 54
Query: 64 EIDGAITNVRRSFYPP 79
+ G VRR Y P
Sbjct: 55 QATGTTRKVRRVTYSP 70
>gnl|CDD|202417 pfam02825, WWE, WWE domain. The WWE domain is named after three of
its conserved residues and is predicted to mediate
specific protein- protein interactions in ubiquitin and
ADP ribose conjugation systems.
Length = 72
Score = 73.9 bits (182), Expect = 1e-17
Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 81 SPAGKGARWEWEGDVHGEWHAYDMQAQCLIEYSWAKGDQTIDISKTHLGFPYILNFCNLT 140
S AG WEWE +G+W Y IE ++A + T+++S G PY ++F ++T
Sbjct: 2 SKAGVVVVWEWEDS-NGKWTPYSPHVSKHIENAYAAKEPTLELS--ICGRPYTIDFNSMT 58
Query: 141 QVRNTTGNVRNIRR 154
Q+R TG R +RR
Sbjct: 59 QLREETGTTRPVRR 72
Score = 56.9 bits (138), Expect = 3e-11
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 4 HAVVVWEWLNRNRRWRPFTPEVTQLIERAHSKNLTSVILSDADPNLQNYFINLHTLQQCS 63
VVVWEW + N +W P++P V++ IE A++ ++ + + Y I+ +++ Q
Sbjct: 5 GVVVVWEWEDSNGKWTPYSPHVSKHIENAYAAKEPTL---ELSICGRPYTIDFNSMTQLR 61
Query: 64 EIDGAITNVRR 74
E G VRR
Sbjct: 62 EETGTTRPVRR 72
>gnl|CDD|226906 COG4529, COG4529, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 474
Score = 31.6 bits (72), Expect = 0.33
Identities = 12/50 (24%), Positives = 18/50 (36%)
Query: 30 ERAHSKNLTSVILSDADPNLQNYFINLHTLQQCSEIDGAITNVRRSFYPP 79
E H N+ + +S P++ F+ Q D N YPP
Sbjct: 49 EPEHLLNVPAARMSAFAPDIPQDFVRWLQKQLQRYRDPEDINHDGQAYPP 98
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 30.7 bits (70), Expect = 0.46
Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 18/75 (24%)
Query: 121 IDISKTHLGFPYIL-----NFCNLTQVRNTTGNVRNIRRTQQAPYP----------LIKL 165
D++ G P L NF Q+ +R IR+ Q PY L++
Sbjct: 164 KDLTFIDEGNPDFLENGLVNFEKRRQIAEI---LREIRQLQSQPYNLRPNRSDIQSLLQQ 220
Query: 166 STNQMAEIQGQMSAS 180
+ + E + S
Sbjct: 221 LLDHLDEEEELYQLS 235
>gnl|CDD|149163 pfam07932, DAP_C, D-aminopeptidase, domain C. D-aminopeptidase is
a dimeric enzyme with each monomer being composed of
three domains. Domain C is organised to form a beta
barrel made up of eight antiparallel beta strands. It is
connected to domain B by a short linker sequence, and
interacts extensively with the domain A, the catalytic
domain. The gamma loop of domain C forms part of the
wall of the catalytic pocket; domain C is in fact
thought to confer substrate and inhibitor specificity to
the enzyme.
Length = 97
Score = 28.6 bits (64), Expect = 1.0
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 210 HGPVHPMSPVYEDIWR 225
GP+ M + D+W
Sbjct: 37 KGPMELMRYLGPDVWL 52
>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases. Small GTP-binding proteins of the Ras
superfamily function as molecular switches in
fundamental events such as signal transduction,
cytoskeleton dynamics and intracellular trafficking.
Guanine-nucleotide-exchange factors (GEFs) positively
regulate these GTP-binding proteins in response to a
variety of signals. GEFs catalyze the dissociation of
GDP from the inactive GTP-binding proteins. GTP can then
bind and induce structural changes that allow
interaction with effectors.
Length = 237
Score = 28.8 bits (65), Expect = 2.1
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 8/53 (15%)
Query: 122 DISKTHLGFPYIL-----NFCNLTQVRNTTGNVRNIRRTQQAPYPLIKLSTNQ 169
D++ H G P L NF ++ +R IR+ Q Y L +
Sbjct: 166 DLTFLHEGNPDFLEGNLVNFEKRRKIAEI---LREIRQLQSNSYELNRDEDIL 215
>gnl|CDD|107262 cd06267, PBP1_LacI_sugar_binding_like, Ligand binding domain of
the LacI tanscriptional regulator family belonging to
the type I periplasmic-binding fold protein
superfamily. Ligand binding domain of the LacI
tanscriptional regulator family belonging to the type I
periplasmic-binding fold protein superfamily. In most
cases, ligands are monosaccharide including lactose,
ribose, fructose, xylose, arabinose, galactose/glucose,
and other sugars. The LacI family of proteins consists
of transcriptional regulators related to the lac
repressor. In this case, the domain sugar binding
changes the DNA binding activity of the repressor
domain.
Length = 264
Score = 28.0 bits (63), Expect = 3.7
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 20 PFTPEVTQLIERAHSKNLTSVILSDADPNLQNYFINLHTLQQCSEIDGAI 69
PF E+ + IE A + SV+L ++D + + L L +DG I
Sbjct: 12 PFFAELLRGIEEAAREAGYSVLLCNSDEDPEKEREALELLLS-RRVDGII 60
>gnl|CDD|222115 pfam13419, HAD_2, Haloacid dehalogenase-like hydrolase.
Length = 176
Score = 27.3 bits (61), Expect = 4.7
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 9 WEWLNRNRRWRPFTPEVTQLIERAHSKNLTSVILSDADPNLQ 50
N R PF P+V +L+ R +K + VILS+
Sbjct: 67 LLEYNLESRLEPF-PDVVELLRRLKAKGVKLVILSNGSREAV 107
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of seven General Transcription
Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and
TFIID) that are involved in accurate initiation of
transcription by RNA polymerase II in eukaryotes. TFIID
plays an important role in the recognition of promoter
DNA and assembly of the pre-initiation complex. TFIID
complex is composed of the TBP and at least 13 TAFs.
TAFs are named after their electrophoretic mobility in
polyacrylamide gels in different species. A new, unified
nomenclature has been suggested for the pol II TAFs to
show the relationship between TAF orthologs and
paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. These TAFs, with the help of
specific activators, are required only for expression of
a subset of genes and are not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; the HFD is the interaction motif involved
in heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 27.7 bits (62), Expect = 5.2
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 195 HTTSSNITRTLRNIFHGPVHPMSPVY 220
+T ITRTL P P++ Y
Sbjct: 304 NTLQPRITRTLLKALLDPKKPLTTHY 329
>gnl|CDD|173383 PTZ00089, PTZ00089, transketolase; Provisional.
Length = 661
Score = 27.7 bits (62), Expect = 5.7
Identities = 8/28 (28%), Positives = 11/28 (39%)
Query: 10 EWLNRNRRWRPFTPEVTQLIERAHSKNL 37
W R ++ P+ Q IER L
Sbjct: 310 AWKKRFAKYTAAFPKEAQAIERRFKGEL 337
>gnl|CDD|237974 PRK15489, nfrB, bacteriophage N4 adsorption protein B;
Provisional.
Length = 703
Score = 27.8 bits (62), Expect = 5.9
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 8 VWEWLNRNRRWRPFTPEVTQLIER 31
++ WL R RR+RP T E QL ER
Sbjct: 47 LYRWLTRERRYRPLTAE--QLRER 68
>gnl|CDD|240392 PTZ00381, PTZ00381, aldehyde dehydrogenase family protein;
Provisional.
Length = 493
Score = 26.9 bits (60), Expect = 9.3
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 21 FT--PEVTQLIERAHSKNLTSVIL 42
FT P V +L+ +A ++NLT L
Sbjct: 191 FTGSPRVGKLVMQAAAENLTPCTL 214
>gnl|CDD|143406 cd07087, ALDH_F3-13-14_CALDH-like, ALDH subfamily: Coniferyl
aldehyde dehydrogenase, ALDH families 3, 13, and 14, and
other related proteins. ALDH subfamily which includes
NAD(P)+-dependent, aldehyde dehydrogenase, family 3
member A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and
fatty aldehyde dehydrogenase, family 3 member A2
(ALDH3A2, EC=1.2.1.3), and also plant ALDH family
members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14
(YMR110C) and the protozoan family 13 member (ALDH13),
as well as coniferyl aldehyde dehydrogenases (CALDH,
EC=1.2.1.68), and other similar sequences, such as the
Pseudomonas putida benzaldehyde dehydrogenase I that is
involved in the metabolism of mandelate.
Length = 426
Score = 27.1 bits (61), Expect = 9.4
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 21 FT--PEVTQLIERAHSKNLTSVIL 42
FT P V +++ A +K+LT V L
Sbjct: 182 FTGSPAVGKIVMEAAAKHLTPVTL 205
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 0.132 0.425
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,431,574
Number of extensions: 995716
Number of successful extensions: 837
Number of sequences better than 10.0: 1
Number of HSP's gapped: 832
Number of HSP's successfully gapped: 26
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
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 (21.8 bits)
S2: 57 (25.8 bits)