RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9768
(406 letters)
>gnl|CDD|227887 COG5600, COG5600, Transcription-associated recombination protein
[DNA replication, recombination, and repair].
Length = 413
Score = 174 bits (444), Expect = 2e-50
Identities = 86/371 (23%), Positives = 156/371 (42%), Gaps = 16/371 (4%)
Query: 41 KNVEDYVIRRYLEHPIFELVSAHLKCVQSIQANNFNEAYLSQSTIVQGFIKMFQQCK--- 97
I+R V+ L+ ++ + + S ++Q K
Sbjct: 44 DAKLKETIQR-PFGRNDTAVTLVLQKFLNL-GRDKDPWSKRSSELLQELYKNLTAELSYS 101
Query: 98 EDNWLLPVVQTVSLNLRLVSNKVDNKALASSIQDGNSGAKPRDALETTTEMLMTCFRICT 157
L +V+ L + +D L + +L F
Sbjct: 102 SAPHLEVLVKNAVRMLGREIWNLTVVKKQLYGLLELKSELNQDNLSKISRLLTRMFNSIL 161
Query: 158 SDNRTSENDSKKWGMLPFVNQLFKVYFRISKLHLMKPLIRAIESSQYKDKS--SLSQQIT 215
+D + N SKK G+ N LF++Y R+ + L + ++A + D S SQ +
Sbjct: 162 NDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKEVSMPDISEYQKSQVVV 221
Query: 216 YKYYVGRKAMFDSDYKTANEYLTFAFQRCHKSSKKNKRLILIYLVPVKMLLG-FMPTREL 274
+ YY+G + + ++ A +L AF +C +N++ IL Y +P +L+ F PT++L
Sbjct: 222 FHYYLGIYYLLNENFHEAFLHLNEAFLQCPWLITRNRKRILPYYIPTSLLVNKFPPTKDL 281
Query: 275 LDKYDLLQLWDVTV-AVKGGQINQLSDAMTKHQTFFIKCGIYL-ILEKLKMITYRNF--- 329
L+++ ++ V AV+ G I A+++++ F K G+YL +L ++ +RN
Sbjct: 282 LERFKRCSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRK 341
Query: 330 -YNIHKDINKNSVVELQQFLQALHYVEGKHIDLEDTHCLLCNLIHDGQLKGYISLAHQKV 388
+ +H ++ + L LQ ++ C+L LI G L+GYIS + + V
Sbjct: 342 IWRLHGKQSRLPLSILLIVLQ--LSAIDNFHSFKEVECILVTLIGLGLLRGYISHSRRTV 399
Query: 389 VLSKTDPFPKL 399
V SK DPFP
Sbjct: 400 VFSKKDPFPVS 410
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 48.4 bits (116), Expect = 2e-07
Identities = 19/101 (18%), Positives = 42/101 (41%), Gaps = 8/101 (7%)
Query: 289 AVKGGQINQLSDAMTKHQTFFIKCGIYLILEKLKMITYRNFYNIHKDINKNSVVELQQFL 348
A G ++ + + ++ + G+ +LE L+ N+ + S + L
Sbjct: 7 AFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIREL--NLRRLAKPYSSISLSDLA 64
Query: 349 QALHYVEGKHIDLEDTHCLLCNLIHDGQLKGYISLAHQKVV 389
+ L + +++ +L LI DG+++G I + VV
Sbjct: 65 KLLG------LSVDEVEKILSKLIRDGRIRGKIDQVNGIVV 99
>gnl|CDD|219785 pfam08303, tRNA_lig_kinase, tRNA ligase kinase domain. This domain
is found in fungal tRNA ligases and has kinase activity.
tRNA ligases are enzymes required for the splicing of
precursor tRNA molecules containing introns. This family
contains a P-loop motif.
Length = 169
Score = 28.9 bits (65), Expect = 3.2
Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 11/67 (16%)
Query: 34 FKHEDFQKNVEDYVIRRYLEHPIFELVSAHLKCVQSIQANNFNEAYLSQSTIVQGFIKMF 93
F ED + V + R + + H QSI+ + E + I+ GFIK F
Sbjct: 99 FVDEDDLEEVREITRDR-----VLKRGDNH----QSIKVESMGEKKVMG--IMNGFIKRF 147
Query: 94 QQCKEDN 100
Q
Sbjct: 148 QPVNPAK 154
>gnl|CDD|219018 pfam06419, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 615
Score = 29.6 bits (67), Expect = 3.6
Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 294 QINQLSDAMTKHQT--FFIKCGIYLILEKLKMITYRNFYNIHKDINKNSVVELQQFLQAL 351
QI++L D +T+ Q + G+ + L MI + Y+ ++ +++ ++E A
Sbjct: 489 QIDELVDELTELQASYLLEESGLGDLYNALNMIFFD--YDDYEPLSELPLLEPDALKNAS 546
>gnl|CDD|233115 TIGR00755, ksgA, dimethyladenosine transferase. In both E. coli
and Saccharomyces cerevisiae, this protein is
responsible for the dimethylation of two adjacent
adenosine residues in a conserved hairpin of 16S rRNA in
bacteria, 18S rRNA in eukaryotes. This adjacent
dimethylation is the only rRNA modification shared by
bacteria and eukaryotes. A single member of this family
is present in each of the first 20 completed microbial
genomes. This protein is essential in yeast, but not in
E. coli, where its deletion leads to resistance to the
antibiotic kasugamycin. Alternate name:
S-adenosylmethionine--6-N',N'-adenosyl (rRNA)
dimethyltransferase [Protein synthesis, tRNA and rRNA
base modification].
Length = 253
Score = 29.2 bits (66), Expect = 3.9
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 222 RKAMFDSDYKTANEYLTFAFQRCHKSSKKNKRLIL--IYLVPVKMLLGFMPTR--ELLDK 277
R+ D + L AFQ+ K+ + N + +L L V LG PT E L
Sbjct: 184 RETFPVKDEALFEKLLKAAFQQRRKTLRNNLKNLLPKEKLEEVLTQLGIDPTARAEQLSP 243
Query: 278 YDLLQL 283
D L+L
Sbjct: 244 EDFLRL 249
>gnl|CDD|221106 pfam11398, DUF2813, Protein of unknown function (DUF2813). This
entry contains YjbD from Escherichia coli, which is
annotated as a nucleotide triphosphate hydrolase.
Length = 373
Score = 29.1 bits (66), Expect = 4.8
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 326 YRNFYNIHKDIN-KNSVVELQQFLQALHYVEGKHIDLEDTHCLLCNLIH 373
R +Y + ++N V + FL +G+ IDL+D L+ LI
Sbjct: 108 QRIYYRVSGELNEDGDVTTTRSFLDN----DGEPIDLDDIEKLVRELIS 152
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 26.4 bits (59), Expect = 8.8
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 18 RDSNGLSVCFSFKNPTF-KHEDFQKNVED 45
+D G S F F N F HE QK VE+
Sbjct: 35 KDDEGKSKGFGFVN--FENHEAAQKAVEE 61
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
0.322 0.135 0.397
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,752,235
Number of extensions: 1837655
Number of successful extensions: 1470
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1465
Number of HSP's successfully gapped: 13
Length of query: 406
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 307
Effective length of database: 6,546,556
Effective search space: 2009792692
Effective search space used: 2009792692
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 (21.9 bits)
S2: 60 (26.8 bits)