RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9185
(248 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 74.4 bits (184), Expect = 6e-18
Identities = 29/54 (53%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 143 YKKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
+K +RER R +N AF+ LR LP PP KKLSK E LR+AI YI+HLQ
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPT--PPNKKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 72.2 bits (178), Expect = 5e-17
Identities = 29/61 (47%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 140 ERDYKKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLL 199
+ ++ RER R +N AFD LR+ LP PP KKLSK E LR A+ YI+ LQ LL
Sbjct: 1 RKSRREAHNLRERRRRERINDAFDELRSLLPTL-PPSKKLSKAEILRKAVDYIKSLQELL 59
Query: 200 E 200
+
Sbjct: 60 Q 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 70.7 bits (174), Expect = 2e-16
Identities = 29/51 (56%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 150 RERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLLE 200
RER R R +N AFD LR+ LP P KKLSK E LR+AI YI+ LQ L+
Sbjct: 3 RERRRRRKINEAFDELRSLLPTL-PKNKKLSKAEILRLAIEYIKSLQEELQ 52
>gnl|CDD|222512 pfam14048, MBD_C, C-terminal domain of methyl-CpG binding protein 2
and 3. CpG-methylation is a frequently occurring
epigenetic modification of vertebrate genomes resulting
in transcriptional repression. This domain was found at
the C-terminus of the methyl-CpG-binding domain (MBD)
containing proteins MBD2 and MBD3, the latter was shown
to not bind directly to methyl-CpG DNA but rather
interact with components of the NuRD/Mi2 complex, an
abundant deacetylase complex. The domain is subject to
structure determination by the Joint Center of
Structural Genomics.
Length = 96
Score = 33.8 bits (78), Expect = 0.013
Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 5/69 (7%)
Query: 40 EILHNADL-NFVKDESSSPSSSTLISSQC----LPSSMTSGQISSSTLTVLHPMEYCYPP 94
E+L DL ++ + TL+ S S+ +GQ SSS +P
Sbjct: 5 ELLSTLDLPKGLQSLGPGITDETLLQSLASALHTSSAPITGQTSSSDALEKNPGVGLNTD 64
Query: 95 PPLSLPVLV 103
PL LV
Sbjct: 65 QPLCKAFLV 73
>gnl|CDD|216666 pfam01728, FtsJ, FtsJ-like methyltransferase. This family consists
of FtsJ from various bacterial and archaeal sources FtsJ
is a methyltransferase, but actually has no effect on
cell division. FtsJ's substrate is the 23S rRNA. The 1.5
A crystal structure of FtsJ in complex with its cofactor
S-adenosylmethionine revealed that FtsJ has a
methyltransferase fold. This family also includes the N
terminus of flaviviral NS5 protein. It has been
hypothesised that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 177
Score = 30.3 bits (69), Expect = 0.53
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 229 DDSCVDCGSAIGQWTQYA 246
+ +D G+A G ++Q
Sbjct: 23 GKTVLDLGAAPGGFSQVL 40
>gnl|CDD|234789 PRK00549, PRK00549, competence damage-inducible protein A;
Provisional.
Length = 414
Score = 28.6 bits (65), Expect = 3.3
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 149 DRERTRMRDMNRAFDLLRNRL 169
R R R + A DLLR L
Sbjct: 391 SRSDIRERAVTYALDLLRRAL 411
>gnl|CDD|213391 cd12148, fungal_TF_MHR, fungal transcription factor regulatory
middle homology region. This domain is present in the
large family of fungal zinc cluster transcription
factors that contain an N-terminal GAL4-like C6 zinc
binuclear cluster DNA-binding domain. Examples of
members of this large fungal group are the following
Saccharomyces cerevisiae transcription factors, GAL4,
STB5, DAL81, CAT8, RDR1, HAL9, PUT3, PPR1, ASG1, RSF2,
PIP2, as well as the C-terminal domain of the Cep3, a
subunit of the yeast centromere-binding factor 3. It has
been suggested that this region plays a regulatory role.
Length = 410
Score = 28.6 bits (63), Expect = 3.9
Identities = 16/117 (13%), Positives = 34/117 (29%), Gaps = 4/117 (3%)
Query: 87 PMEYCYPPPPLSLPVLVEQSLVKYETPNTVTSTAPTPYSGANTTRCHRKISDSERDYKKT 146
E P P + + S P+ ++ + R +I + +
Sbjct: 178 SDEDIDVPLPSNEDDELSPSSSPPPPPSEEPTSLSFFIALIRLARILGRILRLLYSPRAS 237
Query: 147 ACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIR----HLQCLL 199
+ + + +++ + R LPP + SL + L LL
Sbjct: 238 SPEDSLETILELDAELEEWRASLPPELRLDSSSLESPSLLPQRLLLHLLYHLLLILL 294
>gnl|CDD|144451 pfam00859, CTF_NFI, CTF/NF-I family transcription modulation
region.
Length = 295
Score = 28.1 bits (62), Expect = 4.3
Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 9/90 (10%)
Query: 62 LISSQCLPSSMTSGQISSSTLTVLH------PMEYCYPPPPLSLPVLVEQSLVKYETPNT 115
+ C PSS +GQ + S + PM PPPP++ PV + K T +T
Sbjct: 193 FVQLVCDPSSQQAGQPNGSGQGKVPNHFLPTPMLAPPPPPPMARPVPLPMPDTKPPTTST 252
Query: 116 ---VTSTAPTPYSGANTTRCHRKISDSERD 142
TS YS +T+ +R + RD
Sbjct: 253 EGGATSPTSPTYSTPSTSPANRFVGLGPRD 282
>gnl|CDD|218503 pfam05214, Baculo_p33, Baculovirus P33. This family consists of a
series of Baculovirus P33 protein homologues of unknown
function.
Length = 250
Score = 27.6 bits (62), Expect = 6.5
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 14/54 (25%)
Query: 154 RMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLLEYGPEYET 207
RM DM R P K+L+KI L + Y+ H+ CL+ Y ET
Sbjct: 20 RMLDMIRM------------APSKELAKI--LAKEVTYLYHIACLITYKDVQET 59
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 27.3 bits (61), Expect = 8.1
Identities = 14/49 (28%), Positives = 22/49 (44%)
Query: 102 LVEQSLVKYETPNTVTSTAPTPYSGANTTRCHRKISDSERDYKKTACDR 150
L+++ L E + A + Y G N R HR +D++ A DR
Sbjct: 278 LIDEGLSGGEVLEELLRVARSRYRGDNLARLHRLAADADARLTDGANDR 326
>gnl|CDD|221745 pfam12737, Mating_C, C-terminal domain of homeodomain 1. Mating in
fungi is controlled by the loci that determine the
mating type of an individual, and only individuals with
differing mating types can mate. Basidiomycete fungi
have evolved a unique mating system, termed tetrapolar
or bifactorial incompatibility, in which mating type is
determined by two unlinked loci; compatibility at both
loci is required for mating to occur. The multi-allelic
tetrapolar mating system is considered to be a novel
innovation that could have only evolved once, and is
thus unique to the mushroom fungi. This domain is
C-terminal to the homeodomain transcription factor
region.
Length = 418
Score = 27.1 bits (60), Expect = 9.0
Identities = 25/88 (28%), Positives = 31/88 (35%), Gaps = 3/88 (3%)
Query: 54 SSSPSSSTLISSQCLPSSMTSGQISSSTLTVLHPMEYCYPPPPLSL-PVLVEQSLVKYET 112
S S S PS SS+ + P E C P P S L E S T
Sbjct: 108 RRSSSPSDDEDEAERPSKRPRSDSISSSSSPAKPPEACLPSPAASTQDELSEASAAPLPT 167
Query: 113 PNTVTSTAPTPYSGANTTRCHRKISDSE 140
P S TP A + + R++SD
Sbjct: 168 P--SLSPPHTPTDTAPSGKRKRRLSDGF 193
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
0.313 0.127 0.371
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,785,177
Number of extensions: 1028416
Number of successful extensions: 711
Number of sequences better than 10.0: 1
Number of HSP's gapped: 705
Number of HSP's successfully gapped: 25
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
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 (21.9 bits)
S2: 58 (26.0 bits)