RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7185
(311 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 41.6 bits (98), Expect = 8e-06
Identities = 17/25 (68%), Positives = 20/25 (80%)
Query: 159 LKRHTRTHTGEKPHVCDVCSKGFST 183
L+RH RTHTGEKP+ C VC K FS+
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 37.8 bits (88), Expect = 2e-04
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 186 SLNTHRRIHSGERPHVCPICFKTFT 210
+L H R H+GE+P+ CP+C K+F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 33.9 bits (78), Expect = 0.004
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 214 NLYYHRITHVKDKPHKCGACGKSF 237
NL H TH +KP+KC CGKSF
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSF 24
Score = 32.4 bits (74), Expect = 0.013
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 275 NLRTHSYSHSGSWPYKCTVCIKGFA 299
NLR H +H+G PYKC VC K F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 45.5 bits (107), Expect = 2e-05
Identities = 47/188 (25%), Positives = 64/188 (34%), Gaps = 13/188 (6%)
Query: 137 KSPSKTMLPCTVCGKSFDRPSLLKRHTRTHTG-EKPHVCDVCSKGFSTSSSLNTHRR--I 193
S + ++ S S + + + G P C+ FS SS L H R
Sbjct: 254 SSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVN 313
Query: 194 HSGE--RPHVCPI--CFKTFTASSNLYYHRITHVKDKPHKC--GACGKSFPTPGNLRTHS 247
HSGE +P CP C K F+ + L H + H P K F N
Sbjct: 314 HSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQ 373
Query: 248 YS--HSGSWPYKIHAPSVGACGKSFPTPGNLRTHSYSHSGSWP--YKCTVCIKGFAKSSN 303
+ K +C ++F NL H +H P K C K F + N
Sbjct: 374 SLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYN 433
Query: 304 LKNHMTIH 311
L H IH
Sbjct: 434 LIPHKKIH 441
Score = 37.8 bits (87), Expect = 0.006
Identities = 27/90 (30%), Positives = 32/90 (35%), Gaps = 2/90 (2%)
Query: 121 SATVGAENEFSRKAKKKSPSKTMLPCTVCGKSFDRPSLLKRHTRTHTGEKPHVCDV--CS 178
S + K S + C C SF R L RH R+HTGEKP C C
Sbjct: 11 SNNSVLSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCD 70
Query: 179 KGFSTSSSLNTHRRIHSGERPHVCPICFKT 208
K FS L+ H R H +
Sbjct: 71 KSFSRPLELSRHLRTHHNNPSDLNSKSLPL 100
Score = 35.1 bits (80), Expect = 0.045
Identities = 35/119 (29%), Positives = 47/119 (39%), Gaps = 11/119 (9%)
Query: 144 LPCTVCGKSFDRPSLLKRHTRTHTGEKPHVCDVCSKGFSTSSSLNT-------HRRIHSG 196
P ++CGK F R LKRH HT P + + S LN +
Sbjct: 324 CPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKN 383
Query: 197 ERPHVC--PICFKTFTASSNLYYHRITHVKDKPH--KCGACGKSFPTPGNLRTHSYSHS 251
++ C + F SNL H ITH+ +P+ K C KSF NL H H+
Sbjct: 384 DKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT 442
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 37.5 bits (87), Expect = 0.002
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 171 PHVCDVCSKGFSTSSSLNTHRRIHSGERPHVCPICFKTFTASSNLYYH 218
P+VC +C FS+S SL H I E VCP+C K F + + H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDH 118
Score = 27.1 bits (60), Expect = 6.1
Identities = 19/53 (35%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 140 SKTMLP--CTVCGKSFDRPSLLKRHTRTHTGEKPHVCDVCSKGFSTSSSLNTH 190
SK + P C +C F LK+H R K VC VC K F + S H
Sbjct: 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDH 118
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 34.2 bits (79), Expect = 0.003
Identities = 15/21 (71%), Positives = 15/21 (71%)
Query: 146 CTVCGKSFDRPSLLKRHTRTH 166
C CGKSF R S LKRH RTH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 30.4 bits (69), Expect = 0.060
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 173 VCDVCSKGFSTSSSLNTHRRIH 194
C C K FS S+L H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.5 bits (64), Expect = 0.28
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 201 VCPICFKTFTASSNLYYHRITH 222
CP C K+F+ SNL H TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 27.3 bits (61), Expect = 0.80
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 229 KCGACGKSFPTPGNLRTHSYSH 250
KC CGKSF NL+ H +H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 3.5
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 290 KCTVCIKGFAKSSNLKNHMTIH 311
KC C K F++ SNLK H+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 6.1
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 266 CGKSFPTPGNLRTHSYSH 283
CGKSF NL+ H +H
Sbjct: 5 CGKSFSRKSNLKRHLRTH 22
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 37.0 bits (85), Expect = 0.010
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 21/72 (29%)
Query: 196 GERPHVCPI--CFKTFTASSNLYYHR-------ITH------------VKDKPHKCGACG 234
+P+ CP+ C K + + L YH H KDKP++C C
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 235 KSFPTPGNLRTH 246
K + L+ H
Sbjct: 406 KRYKNLNGLKYH 417
Score = 30.5 bits (68), Expect = 1.1
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 21/73 (28%)
Query: 168 GEKPHVCDV--CSKGFSTSSSLNTHRR-------------------IHSGERPHVCPICF 206
KP+ C V C+K + + L H + ++P+ C +C
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 207 KTFTASSNLYYHR 219
K + + L YHR
Sbjct: 406 KRYKNLNGLKYHR 418
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 34.2 bits (79), Expect = 0.034
Identities = 21/63 (33%), Positives = 23/63 (36%), Gaps = 26/63 (41%)
Query: 160 KRHTRTHTG-------EKPHVCDVCSKGFSTSSSLNTHRRIHSGERPHVCPIC------F 206
KRH G K VC VC G+ H GE P VCPIC F
Sbjct: 116 KRHAEMFRGLLERLEEGKVWVCPVC--GY-----------THEGEAPEVCPICGAPKEKF 162
Query: 207 KTF 209
+ F
Sbjct: 163 EKF 165
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 30.5 bits (69), Expect = 0.073
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 172 HVCDVCSKGFSTSSSLNTHRRIH 194
+ C C K F + S+L H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 29.0 bits (65), Expect = 0.19
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 289 YKCTVCIKGFAKSSNLKNHMTIH 311
Y+C C K F S L+ HM H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 29.0 bits (65), Expect = 0.21
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 146 CTVCGKSFDRPSLLKRHTRTH 166
C CGK F S L+ H RTH
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
Score = 27.8 bits (62), Expect = 0.53
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 228 HKCGACGKSFPTPGNLRTHSYSH 250
++C CGK F + LR H +H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.4 bits (61), Expect = 0.69
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 200 HVCPICFKTFTASSNLYYHRITH 222
+ CP C K F + S L H TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|227619 COG5302, COG5302, Post-segregation antitoxin (ccd killing mechanism
protein) encoded by the F plasmid [General function
prediction only].
Length = 80
Score = 30.3 bits (68), Expect = 0.28
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 96 VQEANVVISLDSLQRYWARPLDLTKSATVGAENEFSRKA 134
V ANV + + L+R A L+++ A E + A
Sbjct: 10 VTAANVTVDDELLERARALGLNISALAETAIAAELRKSA 48
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 28.0 bits (63), Expect = 0.51
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 228 HKCGACGKSFPTPGNLRTHSYSH 250
H CG CGK+F + L H SH
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
Score = 27.2 bits (61), Expect = 0.85
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 172 HVCDVCSKGFSTSSSLNTHRRIH 194
H C VC K FS+ +L H++ H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
Score = 25.3 bits (56), Expect = 5.6
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 200 HVCPICFKTFTASSNLYYHRITH 222
H C +C KTF++ L H+ +H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR transcriptional
regulator proteins. The ros chromosomal gene is present
in octopine and nopaline strains of Agrobacterium
tumefaciens as well as in Rhizobium meliloti. This gene
encodes a 15.5-kDa protein that specifically represses
the virC and virD operons in the virulence region of the
Ti plasmid and is necessary for succinoglycan
production. Sinorhizobium meliloti can produce two types
of acidic exopolysaccharides, succinoglycan and
galactoglucan, that are interchangeable for infection of
alfalfa nodules. MucR from Sinorhizobium meliloti acts
as a transcriptional repressor that blocks the
expression of the exp genes responsible for
galactoglucan production therefore allowing the
exclusive production of succinoglycan.
Length = 130
Score = 30.2 bits (69), Expect = 0.55
Identities = 16/36 (44%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 136 KKSPSKTMLPCTVCGKSFDRPSLLKRHTRTHTGEKP 171
KKS + + C GK F LKRH RTH G P
Sbjct: 63 KKSVTPDYIICLEDGKKF---KTLKRHLRTHHGLTP 95
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 27.6 bits (61), Expect = 0.70
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 145 PCTVCGKSFDRPSLLKRHTRTH 166
C +CGKSF LKRH R H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKH 23
Score = 26.1 bits (57), Expect = 2.2
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 172 HVCDVCSKGFSTSSSLNTHRRIH 194
C +C K FS+ +L H R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 3.1
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 228 HKCGACGKSFPTPGNLRTHSYSH 250
KC CGKSF + L+ H H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.9 bits (54), Expect = 6.8
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 289 YKCTVCIKGFAKSSNLKNHMTIH 311
+KC +C K F+ LK H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.5 bits (53), Expect = 7.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 200 HVCPICFKTFTASSNLYYHRITH 222
CP+C K+F++ L H H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|238464 cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase subunit Vb.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Subunits I, II,
and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Found only in
eukaryotes, subunit Vb is one of three mammalian
subunits that lacks a transmembrane region. Subunit Vb
is located on the matrix side of the membrane and binds
the regulatory subunit of protein kinase A. The
abnormally extended conformation is stable only in the
CcO assembly.
Length = 97
Score = 28.0 bits (63), Expect = 2.2
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 194 HSGERPHVCPICFKTFTASSNLYYHRITHVKDKPHKCGACGKSF 237
+R V IC S ++ + + K KP +C CG F
Sbjct: 52 AFDKR-IVGCICE---PDSHDVIWMWLE--KGKPKRCPECGHVF 89
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 29.3 bits (66), Expect = 2.8
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 22/79 (27%)
Query: 77 TNTDIIH---------WIEVLSYLRVFLVQE------------ANVVISL-DSLQRYWAR 114
TN D++H W+ +L L+ +V E A ++ L L+RY +
Sbjct: 173 TNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSP 232
Query: 115 PLDLTKSATVGAENEFSRK 133
+ SAT+ EF+ +
Sbjct: 233 LQIICTSATLANPGEFAEE 251
>gnl|CDD|227293 COG4957, COG4957, Predicted transcriptional regulator
[Transcription].
Length = 148
Score = 28.1 bits (63), Expect = 3.3
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 136 KKSPSKTMLPCTVCGKSFDRPSLLKRHTRTHTGEKP 171
KKS + + C GK F LKRH TH G P
Sbjct: 69 KKSVTPDYIICLEDGKKFKS---LKRHLTTHYGLTP 101
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 25.6 bits (57), Expect = 3.7
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 171 PHVCDVCSKGFSTSSSLNTHRR 192
C C K F + ++L H +
Sbjct: 1 QFYCVACDKYFKSENALENHLK 22
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 28.6 bits (64), Expect = 5.1
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 119 TKSATVGAENEFSRKAKKKSPSKTMLPCTVCGKSFDRPSLLKRHTRT 165
TK A V + S+KA +PS + C VC F L H RT
Sbjct: 52 TKPAAVIS-PPQSKKATPINPSSYV--CNVCMAEFSSMDQLAEHQRT 95
>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or lesions
in the genetic loci have been linked to the aetiology of
asthma, bronchiectasis, chronic obstructive pulmonary
disease etc. Disease-causing mutations have been studied
by 36Cl efflux assays in vitro cell cultures and
electrophysiology, all of which point to the impairment
of chloride channel stability and not the biosynthetic
processing per se [Transport and binding proteins,
Anions].
Length = 1490
Score = 28.7 bits (64), Expect = 5.2
Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 12/85 (14%)
Query: 65 LSYLRKGLPSSSTNTDII---HWIEVLSYLRVFLVQEANVVISLDSLQRYWAR------- 114
L +RK L S +N +I H +E L + FLV E + V DS+Q+
Sbjct: 1389 LQIIRKTLKQSFSNCTVILSEHRVEALLECQQFLVIEGSSVKQYDSIQKLLNETSLFKQA 1448
Query: 115 --PLDLTKSATVGAENEFSRKAKKK 137
D K + N RK + K
Sbjct: 1449 MSAADRLKLFPLHRRNSSKRKPQPK 1473
>gnl|CDD|236166 PRK08149, PRK08149, ATP synthase SpaL; Validated.
Length = 428
Score = 28.4 bits (64), Expect = 5.2
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 20/77 (25%)
Query: 94 FLVQEANVVISLDSLQRYWARPL-DLTKSATVGAENEFSRKAKKKSPSKTMLPCTVCGKS 152
F Q VV+ +DS+ RY AR L D+ +A + P++ P +V
Sbjct: 236 FRDQGKRVVLFIDSMTRY-ARALRDVALAA-------------GELPARRGYPASV---- 277
Query: 153 FDR-PSLLKRHTRTHTG 168
FD P LL+R T G
Sbjct: 278 FDSLPRLLERPGATLAG 294
>gnl|CDD|150725 pfam10083, DUF2321, Uncharacterized protein conserved in bacteria
(DUF2321). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 158
Score = 27.6 bits (61), Expect = 5.3
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 16/75 (21%)
Query: 176 VCSKGFSTSSSLNTHRRI------HSGERPHV-CPICFKTFTASSNLYYH-----RITHV 223
+C G ++S + + G CP C + +Y+ +
Sbjct: 9 ICLNGHQITTSASPSPELMENFCSKCGAATITSCPHC----STPIRGFYYVDGVLGLGSD 64
Query: 224 KDKPHKCGACGKSFP 238
D P C CGK FP
Sbjct: 65 YDAPSYCHNCGKPFP 79
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and recognises
the first three GAG bases of the consensus in a manner
similar to that seen in other classical zinc finger-DNA
complexes. The second basic region forms a helix that
interacts in the major groove recognising the last G of
the consensus, while the first basic region wraps around
the DNA in the minor groove and recognises the A in the
fourth position of the consensus sequence.
Length = 54
Score = 25.7 bits (56), Expect = 7.3
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 197 ERPHVCPICFKTFTASSNLYYH 218
E+P CPIC S NL H
Sbjct: 22 EQPATCPICQAVIRQSRNLRRH 43
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type zinc
fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 24.9 bits (55), Expect = 7.6
Identities = 5/21 (23%), Positives = 9/21 (42%)
Query: 170 KPHVCDVCSKGFSTSSSLNTH 190
C +C+ F+ S+ H
Sbjct: 2 GGFYCKLCNVTFTDEISVEAH 22
>gnl|CDD|224348 COG1431, COG1431, Argonaute homolog, implicated in RNA metabolism
[Translation, ribosomal structure and biogenesis].
Length = 685
Score = 27.9 bits (62), Expect = 8.2
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 63 EVLSYLRKGLPSSSTNTDIIHWIEVLSYLRVFLVQ 97
+ SYL +PS + DI+ ++L Y+ LVQ
Sbjct: 256 PLKSYLILEIPSRNEVYDILSNRKLLFYIDNLLVQ 290
>gnl|CDD|221338 pfam11955, PORR, Plant organelle RNA recognition domain. This
family, which was previously known as DUF860, has been
shown to be a component of group II intron
ribonucleoprotein particles in maize chloroplasts. The
domain is required for the splicing of the introns with
which it associates, and promotes splicing in the
context of a heterodimer with the RNase III-domain
protein RNC1. All of the members are predicted to
localise to mitochondria or chloroplasts. It seems
likely that most PORR proteins function in organellar
RNA metabolism.
Length = 332
Score = 27.6 bits (62), Expect = 9.5
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 83 HWIEVLSYLRVFLVQEANVVISLDSLQRYWARPLDLTK 120
VL L+ L+ + + + L L + R L L +
Sbjct: 16 RLRLVLR-LKDLLLSQPDHSLPLRDLSK-LRRQLGLPR 51
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
0.318 0.132 0.417
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,739,896
Number of extensions: 1301657
Number of successful extensions: 1220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1201
Number of HSP's successfully gapped: 67
Length of query: 311
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 214
Effective length of database: 6,635,264
Effective search space: 1419946496
Effective search space used: 1419946496
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: 59 (26.4 bits)