RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16544
(63 letters)
>gnl|CDD|216524 pfam01485, IBR, IBR domain. The IBR (In Between Ring fingers)
domain is often found to occur between pairs of ring
fingers (pfam00097). This domain has also been called
the C6HC domain and DRIL (for double RING finger
linked) domain. Proteins that contain two Ring fingers
and an IBR domain (these proteins are also termed RBR
family proteins) are thought to exist in all eukaryotic
organisms. RBR family members play roles in protein
quality control and can indirectly regulate
transcription. Evidence suggests that RBR proteins are
often parts of cullin-containing ubiquitin ligase
complexes. The ubiquitin ligase Parkin is an RBR family
protein whose mutations are involved in forms of
familial Parkinson's disease.
Length = 63
Score = 41.4 bits (97), Expect = 6e-07
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 17 EKYEDFMVRRVLSIEPDARWCPTPDCGKVF 46
EKY +++ + + +WCPTPDCG +
Sbjct: 1 EKYLKLSLKKYVESPKNLKWCPTPDCGNII 30
>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers. the domains occurs
between pairs og RING fingers.
Length = 64
Score = 40.9 bits (96), Expect = 8e-07
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 17 EKYEDFMVRRVLSIEPDARWCPTPDCGKVF 46
EKYE ++ + PD +WCP PDC
Sbjct: 1 EKYERLLLESYVESNPDLKWCPAPDCSAAI 30
>gnl|CDD|211326 cd02552, PseudoU_synth_TruD_like, Pseudouridine synthase, TruD
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruD and Saccharomyces cerevisiae
Pus7. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule
to pseudouridines (5-ribosyluracil, psi). E. coli TruD
and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs.
In addition S. cerevisiae Pus7 makes psi35 in U2 small
nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35
in U2 snRNA and psi13 in tRNAs are highly
phylogenetically conserved. Psi34 is the mammalian U2
snRNA counterpart of yeast U2 snRNA psi35.
Length = 232
Score = 26.0 bits (58), Expect = 1.1
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 17 EKYEDFMVRRVLSIEPDARWCPTPD 41
++ EDF+V +L P P +
Sbjct: 5 QRPEDFVVNEILLDGPVVHLWPKGE 29
>gnl|CDD|233267 TIGR01090, apt, adenine phosphoribosyltransferase. A
phylogenetic analysis suggested omitting the
bi-directional best hit homologs from the spirochetes
from the seed for This model and making only tentative
predictions of adenine phosphoribosyltransferase
function for this lineage. The trusted cutoff score is
made high for this reason. Most proteins scoring
between the trusted and noise cutoffs are likely to act
as adenine phosphotransferase [Purines, pyrimidines,
nucleosides, and nucleotides, Salvage of nucleosides
and nucleotides].
Length = 169
Score = 25.7 bits (57), Expect = 1.3
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 6 IHSILSDQALFEKYEDFMVRRVLSIEPDARWCP 38
I +L++ LF D +V R D P
Sbjct: 21 ITPLLNNPELFRFLIDLLVERYKDANIDYIVGP 53
>gnl|CDD|180452 PRK06186, PRK06186, hypothetical protein; Validated.
Length = 229
Score = 24.9 bits (55), Expect = 2.4
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 5/36 (13%)
Query: 23 MVRRVLSIEPDARWCPTPDCGKV-----FDGQFLVP 53
+ VL + D W PTP+ FDG + VP
Sbjct: 26 LAAAVLGLPVDYEWLPTPEITDPEDLAGFDGIWCVP 61
>gnl|CDD|227407 COG5075, COG5075, Uncharacterized conserved protein [Function
unknown].
Length = 305
Score = 25.2 bits (55), Expect = 2.7
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 2 KIQYIHSILSDQALFEK--YEDFMVRRVLSIEPDARWCP 38
+ +++++IL + A E+ YED V I PD +W
Sbjct: 140 RWKWVNNILYEGAENERIVYEDESVINGFIIIPDMKWDG 178
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 24.1 bits (53), Expect = 5.8
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 32 PDARWCPTPD 41
PDARW TP+
Sbjct: 345 PDARWRQTPE 354
>gnl|CDD|227484 COG5155, ESP1, Separase, a protease involved in sister chromatid
separation [Cell division and chromosome partitioning /
Posttranslational modification, protein turnover,
chaperones].
Length = 1622
Score = 24.2 bits (52), Expect = 6.6
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 2 KIQYIHSILSDQALFEKYEDFMVRRVLSIE 31
KI LS L++ + M+ +LS E
Sbjct: 270 KIYLNSFYLSYSMLYDGLDKIMLLDILSYE 299
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 23.8 bits (51), Expect = 8.4
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 3/52 (5%)
Query: 5 YIHSILSDQALFEKYEDFMVRRV-LSIEPDA--RWCPTPDCGKVFDGQFLVP 53
I + + E+ E +S D + P+ D + +G+ VP
Sbjct: 812 LIRELFTKPKTLEQAELGCKINAFISFVFDGWYMYNPSTDLVGLSNGEMAVP 863
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
0.326 0.142 0.454
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,287,356
Number of extensions: 234230
Number of successful extensions: 296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 296
Number of HSP's successfully gapped: 9
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)