RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9354
(308 letters)
>gnl|CDD|192151 pfam08781, DP, Transcription factor DP. DP forms a heterodimer
with E2F and regulates genes involved in cell cycle
progression. The transcriptional activity of E2F is
inhibited by the retinoblastoma protein which binds to
the E2F-DP heterodimer and negatively regulates the G1-S
transition.
Length = 141
Score = 159 bits (405), Expect = 4e-49
Identities = 72/138 (52%), Positives = 98/138 (71%), Gaps = 2/138 (1%)
Query: 112 QESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKKLIQKNIDSEKIHGEPAPSSAIQLP 171
QE L +ER++ I+RI QK L +L+LQQ++LK L+Q+N + E PSS IQLP
Sbjct: 1 QEIEKLEEERQKRIERIEQKQAQLQELILQQVALKNLVQRNQELE--SSGNVPSSGIQLP 58
Query: 172 FLIVSTDKKTVIDCSMSNDKTEYLFVFDNKFEIHDDIEILKRMGLGMGLDKGEWTEEDLQ 231
F++V+T KK VIDC +S DK+EY F F++ FEIHDDIE+LKRMGL +GL+ G + E+L+
Sbjct: 59 FILVNTSKKAVIDCEISEDKSEYHFDFNSTFEIHDDIEVLKRMGLALGLESGPCSAENLK 118
Query: 232 EAKRLVAPCMEKYVNQIA 249
AK LV +E YV +IA
Sbjct: 119 TAKSLVPKALEPYVTEIA 136
>gnl|CDD|202203 pfam02319, E2F_TDP, E2F/DP family winged-helix DNA-binding
domain. This family contains the transcription factor
E2F and its dimerisation partners TDP1 and TDP2, which
stimulate E2F-dependent transcription. E2F binds to DNA
as a homodimer or as a heterodimer in association with
TDP1/2, the heterodimer having increased binding
efficiency. The crystal structure of an E2F4-DP2-DNA
complex shows that the DNA-binding domains of the E2F
and DP proteins both have a fold related to the
winged-helix DNA-binding motif. Recognition of the
central c/gGCGCg/c sequence of the consensus
DNA-binding site is symmetric, and amino acids that
contact these bases are conserved among all known E2F
and DP proteins.
Length = 67
Score = 38.7 bits (91), Expect = 2e-04
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 50 KASKGLRHFSMK---VCEKVRRKGVTTYNEVADEL 81
+ K L + K +CEK G+T NE A EL
Sbjct: 1 RKEKSLGLLTQKFLKLCEKSPD-GITDLNEAAKEL 34
>gnl|CDD|225747 COG3206, GumC, Uncharacterized protein involved in
exopolysaccharide biosynthesis [Cell envelope
biogenesis, outer membrane].
Length = 458
Score = 32.0 bits (73), Expect = 0.42
Identities = 11/56 (19%), Positives = 19/56 (33%), Gaps = 1/56 (1%)
Query: 76 EVADELVQEFSEDHNTASSEQEKKEIKWLGLPTNSLQESLNLNKERKQLIQRINQK 131
++A+ L Q + D A E ++ L L+ L E + R
Sbjct: 172 KLANALAQAYLADQLEAQLEAFRRASDSLDERLEELRARLQEA-EAQVEDFRAQHG 226
>gnl|CDD|99960 cd03784, GT1_Gtf_like, This family includes the Gtfs, a group of
homologous glycosyltransferases involved in the final
stages of the biosynthesis of antibiotics vancomycin and
related chloroeremomycin. Gtfs transfer sugar moieties
from an activated NDP-sugar donor to the oxidatively
cross-linked heptapeptide core of vancomycin group
antibiotics. The core structure is important for the
bioactivity of the antibiotics.
Length = 401
Score = 31.6 bits (72), Expect = 0.51
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 211 LKRMGLGMGLDKGEWTEEDLQEA-KRLVAP 239
+ +G G LD E T E L A +RL+ P
Sbjct: 343 VAELGAGPALDPRELTAERLAAALRRLLDP 372
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 30.2 bits (68), Expect = 1.5
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 87 EDHNTASSEQEKKEIKWLGL------PTNSLQESLN-LNKERKQLIQRINQKTRHLH 136
E H +A +E EK + + G+ SL SL L E KQL+ Q+ + L+
Sbjct: 191 EQHKSARTELEKLQAQASGVALLTPEQVQSLTASLQVLTDEEKQLLTAQQQQQQSLN 247
>gnl|CDD|173888 cd06900, lectin_VcfQ, VcfQ bacterial pilus biogenesis protein,
lectin domain. This family includes bacterial proteins
homologous to the VcfQ (also known as MshQ) bacterial
pilus biogenesis protein. VcfQ is encoded by the vcfQ
gene of the type IV pilus gene cluster of Vibrio
cholerae and is essential for type IV pilus assembly.
VcfQ has a Laminin G-like domain as well as an L-type
lectin domain.
Length = 255
Score = 29.7 bits (67), Expect = 1.8
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 268 SGSFDSSQITIETVMPEEV-MSVSGSEGESDLSSDIDHVEV 307
+FD+ + +PE +S +GS G S + +ID+ +V
Sbjct: 213 ILTFDALAEQNQDAIPENFYLSFTGSTGGSTNTHEIDNFQV 253
>gnl|CDD|177934 PLN02297, PLN02297, ribose-phosphate pyrophosphokinase.
Length = 326
Score = 28.9 bits (65), Expect = 3.2
Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 5/29 (17%)
Query: 39 DEGGAYKRSREKASKGLRHFSMKVCEKVR 67
D+G A+KR K HF M VC KVR
Sbjct: 191 DDG-AWKR----FHKQFEHFPMVVCTKVR 214
>gnl|CDD|131393 TIGR02340, chap_CCT_alpha, T-complex protein 1, alpha subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
alpha chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 536
Score = 28.9 bits (65), Expect = 4.0
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 78 ADELVQEFSEDHNTASSEQEKKEIKWLGL 106
+ ELV + H A + EKK +KW GL
Sbjct: 456 STELVAKLRAYHAAAQLKPEKKHLKWYGL 484
>gnl|CDD|118696 pfam10168, Nup88, Nuclear pore component. Nup88 can be divided
into two structural domains; the N-terminal two-thirds
of the protein has no obvious structural motifs but is
the region for binding to Nup98, one of the components
of the nuclear pore. the C-terminal end is a predicted
coiled-coil domain. Nup88 is overexpressed in tumour
cells.
Length = 717
Score = 28.7 bits (64), Expect = 4.3
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 76 EVADELVQEFSEDHNTASSEQE---KKEIKWLGLPTNSLQESLNLNKERKQLIQRINQKT 132
E A++L ++F E A QE + + L + L + ++ + +QRIN++
Sbjct: 593 ERAEKLAEKFEE----AKYNQELLVNRCKRLLQSANSQLPVLSDSERDMSKELQRINKQL 648
Query: 133 RHLHDLLLQQISLKKLIQK 151
+HL ++Q+ KK Q+
Sbjct: 649 QHL-ANGIKQVKKKKNYQR 666
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 28.7 bits (65), Expect = 4.7
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 108 TNSLQESLNLNKERKQLIQRINQKTRHLHDLLLQQISL-KKLIQKNIDSE 156
NSL E L +E + ++K D L+++I L K I+ NI+ E
Sbjct: 213 DNSLVEWKELGEEGSTGNEWEDRKIGRRKDFLVRRIKLAKHFIRTNIEPE 262
>gnl|CDD|224000 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 28.6 bits (64), Expect = 5.1
Identities = 28/149 (18%), Positives = 47/149 (31%), Gaps = 36/149 (24%)
Query: 108 TNSLQESLNLNKERKQLIQRINQKTRHLHDLLLQQISLKK----LIQKNIDSEK------ 157
TN L L +L+ R L L + I+L + + ++S++
Sbjct: 692 TNGLHAQELLQ----ELLTRALSYEHGLLRWLERFIALIENNDEEQARRLESDRDLVRIM 747
Query: 158 -IHGEPAPSSAIQLPFLIV--STDKKTVIDCSMSN---DKTEYLFVFDNKFEIHDDIEIL 211
IH S ++ P + + K+ D + D K + +
Sbjct: 748 TIHK----SKGLEFPIVFLPFILSKRFNDSDVPLLVYYDGLRFELFDDLKSYPTPESQ-- 801
Query: 212 KRMGLGMGLDKGEWTEEDLQEAKRL--VA 238
+K EE L E RL VA
Sbjct: 802 --------ANKELAEEEALAEELRLLYVA 822
>gnl|CDD|218871 pfam06046, Sec6, Exocyst complex component Sec6. Sec6 is a
component of the multiprotein exocyst complex. Sec6
interacts with Sec8, Sec10 and Exo70.These exocyst
proteins localise to regions of active exocytosis-at the
growing ends of interphase cells and in the medial
region of cells undergoing cytokinesis-in an
F-actin-dependent and exocytosis- independent manner.
Length = 557
Score = 28.1 bits (63), Expect = 7.7
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 5/46 (10%)
Query: 198 FDNKFEIHDDIEILKRMGLGMGLDKGEWTEEDLQEAKRLVAPCMEK 243
F+ E L ++ L+ W EDL K L+AP
Sbjct: 91 FEECRERFLGDPDLVQV-----LENLRWVFEDLIVVKDLLAPLFPP 131
>gnl|CDD|221260 pfam11843, DUF3363, Protein of unknown function (DUF3363). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 323 to 658 amino acids in
length.
Length = 312
Score = 27.6 bits (62), Expect = 9.4
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 211 LKRMGLGMGLDKGEWT-EEDLQEAKR 235
L+R+GL + G W +E +E R
Sbjct: 9 LERLGLAEEVGPGRWRLKEGAEETLR 34
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
0.311 0.129 0.355
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,355,527
Number of extensions: 1471447
Number of successful extensions: 1313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1309
Number of HSP's successfully gapped: 57
Length of query: 308
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 211
Effective length of database: 6,635,264
Effective search space: 1400040704
Effective search space used: 1400040704
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 (21.8 bits)
S2: 59 (26.5 bits)