RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13230
(132 letters)
>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8. This PCI_Csn8
domain is conserved from plants to humans. It is a
signature protein motif found in components of CSN (COP9
signalosome). It functions as a structural scaffold for
subunit-subunit interactions within the complex and is a
key regulator of photomorphogenic development.
Length = 144
Score = 78.1 bits (193), Expect = 2e-19
Identities = 38/123 (30%), Positives = 58/123 (47%), Gaps = 24/123 (19%)
Query: 23 PYKNEMLGLNLLYLLSQNRVAEFHMELERI------------------------QYEDMI 58
K E+ GL LL LL+QN +A+F + L+RI Y
Sbjct: 1 ELKTELYGLILLKLLTQNDIADFRLLLKRIPQAIKESNPEIQQLLTLGQLLWENDYAKFW 60
Query: 59 FLAKDGVPSPRYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGK 118
+ S Y F+ L DT R+EIA+ + KAY+ IS+ D A+ L + S++++ +F K
Sbjct: 61 QTLRSNDWSEDYTPFIAGLEDTIRDEIAALVGKAYSSISIDDLAELLGLSSDEELEKFAK 120
Query: 119 KVK 121
K
Sbjct: 121 KRG 123
>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family. This
large family includes diverse proteins involved in large
complexes. The alignment contains one highly conserved
negatively charged residue and one highly conserved
positively charged residue that are probably important
for the function of these proteins. The family includes
the yeast nuclear export factor Sac3, and mammalian
GANP/MCM3-associated proteins, which facilitate the
nuclear localisation of MCM3, a protein that associates
with chromatin in the G1 phase of the cell-cycle. The
26S protease (or 26S proteasome) is responsible for
degrading ubiquitin conjugates. It consists of 19S
regulatory complexes associated with the ends of 20S
proteasomes. The 19S regulatory complex is composed of
about 20 different polypeptides and confers
ATP-dependence and substrate specificity to the 26S
enzyme. The conserved region occurs at the C-terminal of
the Nin1-like regulatory subunit. This family includes
several eukaryotic translation initiation factor 3
subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation
factor 3 (eIF3) is a multisubunit complex that is
required for binding of mRNA to 40 S ribosomal subunits,
stabilisation of ternary complex binding to 40 S
subunits, and dissociation of 40 and 60 S subunits.
Length = 155
Score = 58.4 bits (142), Expect = 7e-12
Identities = 29/112 (25%), Positives = 44/112 (39%), Gaps = 21/112 (18%)
Query: 16 FSRVPESPYKNEMLGLNLLYLLSQNRVAEFHMELERIQYEDM--------IFLAK----- 62
+ +SP + E + LLYLLS N +++FH ELE + E + L +
Sbjct: 44 DDLLGKSPNEAEFIAYYLLYLLSNNPISDFHTELELLPDEIRNDPYIQFALELEQALMEG 103
Query: 63 ------DGVPSPRY--NAFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLH 106
+ Y +E +D R E I KAY I + A+ L
Sbjct: 104 NYHRFFRLLKKAPYLYACLLERFLDRIRKEALKAISKAYRSIPLSYLAELLG 155
>gnl|CDD|140327 PTZ00306, PTZ00306, NADH-dependent fumarate reductase; Provisional.
Length = 1167
Score = 30.5 bits (69), Expect = 0.23
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 4/81 (4%)
Query: 54 YEDMIFLAKDGVPSPRYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQ----KLHIGS 109
YE+++ V S ++ +L++ T +E+A K Y+ + A K
Sbjct: 299 YENVLEGPASKVYSSTFDWKRRSLLEPTESELAQVSVKCYSCMYADALATASLVKRDPVK 358
Query: 110 EKQMVEFGKKVKNIVYFYIFY 130
+ M+E + V+N V Y Y
Sbjct: 359 VRYMLENWRYVRNRVTDYTTY 379
>gnl|CDD|235533 PRK05617, PRK05617, 3-hydroxyisobutyryl-CoA hydrolase; Provisional.
Length = 342
Score = 29.0 bits (66), Expect = 0.72
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 7/77 (9%)
Query: 35 YLLSQ--NRVAEFHMEL--ERIQYEDMIF--LAKDGVPSPRYNAFMETLIDTTRNEIASC 88
Y LS+ + ++ L RI D ++ LA VPS A ++ LI + A
Sbjct: 150 YFLSRAPGALGT-YLALTGARISAADALYAGLADHFVPSADLPALLDALISLRWDSGADV 208
Query: 89 IEKAYTVISVGDTAQKL 105
++ A + A +L
Sbjct: 209 VDAALAAFATPAPASEL 225
>gnl|CDD|190374 pfam02643, DUF192, Uncharacterized ACR, COG1430. Two structures
have been solved for members of this large (>500
members) family of bacterial proteins present mostly in
environmental bacteria and metagenomes (distant
homologues are also present in several Plasmodium
species). TOPSAN analysis for pdb:3pjy shows that there
is much similarity with the other solved structure,
pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a
homologue of Thermotoga maritima TM1668,
UniProt:Q9X1Z6., The homologue in Caulobacter
crescentus (CC1388), UniProt:Q9A8G6, is associated with
CspD, a cold shock protein (CC1387), UniProt:Q9A8G7.
However, the genomic context of UniProt:Q2GA55 is most
conserved with a putative xylose isomerase, suggesting
a possible role in extracellular sugar processing.
Saro_0821, UniProt:Q2GA57, is annotated as an
AMP-dependent synthetase and ligase. PDB:3m7a structure
corresponds to the C-terminal (27-165) fragment of the
YP_496102 (Saro_0823) protein and it is structurally
unique, as the best hits from Dali have a Z-score of
3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely
candidate for a new fold. Interestingly, many of the
top Dali hits are involved in sugar metabolism. There
are no obvious active site-like cavities on the protein
surface of 3m7a (http://www.topsan.org/Proteins/JCSG/).
Length = 104
Score = 26.4 bits (59), Expect = 2.4
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 33 LLYLLSQNRVAEFHMELERIQYEDMIFLAKDGV 65
+L++ + F M+ I D+IF+ DG
Sbjct: 28 MLFVFPEPSPHTFWMKNTLIPL-DIIFIDADGR 59
>gnl|CDD|227411 COG5079, SAC3, Nuclear protein export factor [Intracellular
trafficking and secretion / Cell division and chromosome
partitioning].
Length = 646
Score = 27.2 bits (60), Expect = 2.7
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 65 VPSPRYNAFMETLIDTTRNEI--------ASCIEKAYTVISVGDTAQKLHIGSEKQMVEF 116
+ SP M L++ I IE A+ I D + L + + EF
Sbjct: 309 IQSPSVQYLMGCLLEKHNISIRGGALKAMEKEIESAHKNIPFVDLSGILDFEEKGEGEEF 368
Query: 117 GK 118
K
Sbjct: 369 CK 370
>gnl|CDD|233163 TIGR00872, gnd_rel, 6-phosphogluconate dehydrogenase
(decarboxylating). This family resembles a larger
family (gnd) of bacterial and eukaryotic
6-phosphogluconate dehydrogenases but differs from it by
a deep split in a UPGMA similarity clustering tree and
the lack of a central region of about 140 residues.
Among complete genomes, it is found is found in Bacillus
subtilis and Mycobacterium tuberculosis, both of which
also contain gnd, and in Aquifex aeolicus. The protein
from Methylobacillus flagellatus KT has been
characterized as a decarboxylating 6-phosphogluconate
dehydrogenase as part of an unusual formaldehyde
oxidation cycle. In some sequenced organisms members of
this family are the sole 6-phosphogluconate
dehydrogenase present and are probably active in the
pentose phosphate cycle [Energy metabolism, Pentose
phosphate pathway].
Length = 298
Score = 26.3 bits (58), Expect = 5.8
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 66 PSPRYNAFM--ETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFG 117
+PR M ++D E+A +EK VI G++ K + K + E G
Sbjct: 58 SAPRVVWVMVPHGIVDAVLEELAPTLEKGDIVIDGGNSYYKDSLRRYKLLKEKG 111
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 26.5 bits (59), Expect = 6.0
Identities = 9/48 (18%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 63 DGVPSPRYNAFMETLIDTTRNEI-ASCIEKAYTVISVGDTAQKLHIGS 109
+G+ SP+ F++ ++D + I A C E ++ + +
Sbjct: 156 EGIKSPKMQQFIDGMMDASDTPIFAECRETLNKLLDDFAFLAREGLER 203
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 0.137 0.383
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,636,201
Number of extensions: 581682
Number of successful extensions: 456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 455
Number of HSP's successfully gapped: 22
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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: 53 (24.2 bits)