RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13719
(139 letters)
>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
motor. This family represents the C-terminal region of
dynein heavy chain. The chain also contains ATPase
activity and microtubule binding ability and acts as a
motor for the movement of organelles and vesicles along
microtubules. Dynein is also involved in cilia and
flagella movement. The dynein subunit consists of at
least two heavy chains and a number of intermediate and
light chains. The 380 kDa motor unit of dynein belongs
to the AAA class of chaperone-like ATPases. The core of
the 380 kDa motor unit contains a concatenated chain of
six AAA modules, of which four correspond to the ATP
binding sites with P-loop signatures described
previously, and two are modules in which the P loop has
been lost in evolution. This C-terminal domain carries
the D6 region of the dynein motor where the P-loop has
been lost in evolution but the general structure of a
potential ATP binding site appears to be retained.
Length = 706
Score = 91.2 bits (227), Expect = 2e-22
Identities = 39/94 (41%), Positives = 51/94 (54%), Gaps = 3/94 (3%)
Query: 10 EGVYVCGLFLEGAGWNKSNRSLCEPLPLQLIYKLPVLHCKPVVNQHKPLDTLYECPVYYT 69
+G YV GLFLEGA W+ N L E P +L +PV+ K V + ++YECPVY T
Sbjct: 614 DGFYVHGLFLEGARWDGQNGLLLESRPKELFSPMPVIWVKAVPADKQEEKSVYECPVYKT 673
Query: 70 AKRGE--YIVPVGLDSGEIPPDHWVKRGTAILLT 101
RG Y+ L + E PP W+ G A+LL
Sbjct: 674 ETRGGTTYVFTFLLKTKE-PPSKWILAGVALLLQ 706
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 29.7 bits (68), Expect = 0.49
Identities = 9/17 (52%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 101 TLSSDTCQGLFERHKLL 117
TL D Q L+E HKL+
Sbjct: 301 TL--DIAQSLYETHKLI 315
>gnl|CDD|241183 cd12739, RRM2_ESRP1, RNA recognition motif 2 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. Additional research indicated that ESRP1
functions as a tumor suppressor in colon cancer cells.
It may be involved in posttranscriptional regulation of
various genes by exerting a differential effect on
protein translation via 5' untranslated regions (UTRs)
of mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 109
Score = 27.7 bits (61), Expect = 1.2
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 95 GTAILLTLSSDTCQGLFERHKLLFGVRIIEIFGKSYNAAVMRVV 138
G A +L + Q ++HK L G R IE+F +S A V +V+
Sbjct: 62 GDAFVLFACEEYAQNALKKHKDLLGKRYIELF-RSTAAEVQQVL 104
>gnl|CDD|241184 cd12740, RRM2_ESRP2, RNA recognition motif 2 in epithelial splicing
regulatory protein 2 (ESRP2) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP2, also termed
RNA-binding motif protein 35B (RBM35B), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. ESRP2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 107
Score = 27.3 bits (60), Expect = 1.8
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 95 GTAILLTLSSDTCQGLFERHKLLFGVRIIEIFGKSYNAAVMRVV 138
G A +L + Q ++HK + G R IE+F +S A V +V+
Sbjct: 62 GDAFVLFACEEYAQNALKKHKGILGKRYIELF-RSTAAEVQQVL 104
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 28.1 bits (62), Expect = 1.8
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 12/54 (22%)
Query: 27 SNRSLCEPLPL----QLIYKLPVLHCKPVVNQHKPLDTLY-ECPV----YYTAK 71
S ++L P PL +L P +HC + KPLDTLY +CP Y AK
Sbjct: 1399 SKKNLIVPEPLKEEEELGGNPPDIHCYAAL---KPLDTLYVKCPTEKAAYEAAK 1449
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 26.5 bits (59), Expect = 2.2
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 95 GTAILLTLSSDTCQGLFERHKLLFGVRIIEIF 126
G A +L + + Q +HK G R IE+F
Sbjct: 47 GDAFVLFETEEDAQRALGKHKENLGSRYIELF 78
>gnl|CDD|236184 PRK08203, PRK08203, hydroxydechloroatrazine ethylaminohydrolase;
Reviewed.
Length = 451
Score = 26.4 bits (59), Expect = 6.8
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 79 VGLDSGEIPPDHWVKRGTAILLTLSSDTCQGLFERH 114
+G G +PPD V+ AIL Q L +R+
Sbjct: 160 LGESDGGLPPDSVVEDEDAIL-----ADSQRLIDRY 190
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 26.1 bits (58), Expect = 8.4
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 60 TLYEC-----PVYYTAKRGEYIVPVGLDSGEIPP 88
T+Y C +Y ++ +Y+ P+ D G I P
Sbjct: 1041 TIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISP 1074
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
0.323 0.142 0.450
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,040,549
Number of extensions: 605871
Number of successful extensions: 384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 383
Number of HSP's successfully gapped: 10
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.6 bits)