RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7862
(101 letters)
>gnl|CDD|217919 pfam04135, Nop10p, Nucleolar RNA-binding protein, Nop10p family.
Nop10p is a nucleolar protein that is specifically
associated with H/ACA snoRNAs. It is essential for
normal 18S rRNA production and rRNA pseudouridylation
by the ribonucleoprotein particles containing H/ACA
snoRNAs (H/ACA snoRNPs). Nop10p is probably necessary
for the stability of these RNPs.
Length = 52
Score = 76.1 bits (188), Expect = 3e-20
Identities = 27/52 (51%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 40 LMYYLG-EDGKRVYTLK-KVDPAGNPTVSAHPARFSPDDKYSRERITILRRF 89
+ L G RVYTLK K G PT SAHPARFSP+DKY + R + +RF
Sbjct: 1 MKSLLRKCPGCRVYTLKDKCPECGGPTKSAHPARFSPEDKYGKYRRALKKRF 52
>gnl|CDD|225169 COG2260, COG2260, Predicted Zn-ribbon RNA-binding protein
[Translation, ribosomal structure and biogenesis].
Length = 59
Score = 63.2 bits (154), Expect = 5e-15
Identities = 23/59 (38%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 38 MYLMYYLGEDGKRVYTLK-KVDPAGNPTVSAHPARFSPDDKYSRERITILRRFGLLRTQ 95
M + YTLK K G T HP RFSP+DKY + R + +R GLL Q
Sbjct: 1 MKSLIRKCPK-CGRYTLKEKCPVCGGDTKVPHPPRFSPEDKYGKYRRELKKRLGLLPNQ 58
>gnl|CDD|237287 PRK13130, PRK13130, H/ACA RNA-protein complex component Nop10p;
Reviewed.
Length = 56
Score = 46.9 bits (112), Expect = 1e-08
Identities = 19/39 (48%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 51 VYTLKKVDP-AGNPTVSAHPARFSPDDKYSRERITILRR 88
VYTLK++ P G T + HP RFSP+DKY + R + +R
Sbjct: 13 VYTLKEICPVCGGKTKNPHPPRFSPEDKYGKYRRALKKR 51
>gnl|CDD|221691 pfam12654, DUF3786, Domain of unknown function (DUF3786). This
presumed domain is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 201 and 257 amino
acids in length. Some proteins also contains an
iron-sulfur cluster.
Length = 179
Score = 27.9 bits (63), Expect = 0.71
Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 17 LTGGSDQVYLIEYFPYFPLITMYLMYYLGEDG 48
+ G D Y+ + P P+ L+++ G++
Sbjct: 118 VDMGGDISYVFQPLPRVPV---LLIFWDGDEE 146
>gnl|CDD|222363 pfam13754, Big_3_4, Bacterial Ig-like domain (group 3). This
family consists of bacterial domains with an Ig-like
fold. Members of this family are found in a variety of
bacterial surface proteins.
Length = 54
Score = 25.7 bits (57), Expect = 1.4
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 46 EDGKRVYTLKKVDPAGNPTVSAH 68
DG T+ D AGN + S
Sbjct: 22 ADGTYTVTVTATDAAGNTSTSTS 44
>gnl|CDD|232801 TIGR00054, TIGR00054, RIP metalloprotease RseP. Members of this
nearly universal bacterial protein family are regulated
intramembrane proteolysis (RIP) proteases. Older and
synonymous gene symbols include yaeL in E. coli, mmpA in
Caulobacter crescentus, etc. This family includes a
region that hits the PDZ domain, found in a number of
proteins targeted to the membrane by binding to a
peptide ligand. The N-terminal region of this family
contains a perfectly conserved motif HEXGH as found in a
number of metalloproteinases, where the Glu is the
active site and the His residues coordinate the metal
cation [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 419
Score = 26.7 bits (59), Expect = 2.0
Identities = 10/57 (17%), Positives = 16/57 (28%), Gaps = 1/57 (1%)
Query: 22 DQVYLIEYFPYFPLITMYLMYYLGEDGK-RVYTLKKVDPAGNPTVSAHPARFSPDDK 77
+ +I P I +Y Y + V + A A P D+
Sbjct: 94 QKAIIIFAGPLANFIFAIFVYIFISLIGVPGYEVGPVIELLDKNSIALEAGIEPGDE 150
>gnl|CDD|213062 cd11746, GH94N_like, N-terminal domain of glycoside hydrolase
family 94 and related domains. The glycoside hydrolase
family 94 (previously known as glycosyltransferase
family 36) includes cellobiose phosphorylase
(EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49),
chitobiose phosphorylase (EC:2.4.1.-), amongst other
members. Their N-terminal domain is involved in
oligomerization and may play a role in catalysis, but it
is separate from the catalytic domain [an
(alpha/alpha)(6) barrel]. This GH64N domain also occurs
in tandem repeat arrangements (not at the N-terminus) in
cyclic beta 1-2 glucan synthetase and related proteins,
and as a standalone domain in distantly related proteins
of unknown function.
Length = 179
Score = 25.5 bits (56), Expect = 5.1
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 9/70 (12%)
Query: 15 VDLTGGSDQVYLIEYFPYFPLITMYLMY----YLGEDGKRVYTLKKVDPAGNPTVSAHPA 70
V LT D+ + FPYF ++ Y E G T + + A PA
Sbjct: 61 VKLTNTGDRPRELTLFPYFEWCLPDALFQGTSYDPEGGAVNCTT-----YYSYNIGARPA 115
Query: 71 RFSPDDKYSR 80
++ K
Sbjct: 116 FYATSFKPDD 125
>gnl|CDD|132432 TIGR03391, FeS_syn_CsdE, cysteine desulfurase, sulfur acceptor
subunit CsdE. Members of this protein family are CsdE,
formerly called YgdK. This protein, found as a paralog
to SufE in Escherichia coli, Yersinia pestis,
Photorhabdus luminescens, and related species, works
together and physically interacts with CsdA (a paralog
of SufS). CsdA has cysteine desulfurase activity that
is enhanced by this protein (CsdE), in which Cys-61
(numbered as in E. coli) is a sulfur acceptor site.
This gene pair, although involved in FeS cluster
biosynthesis, is not found next to other such genes as
are its paralogs from the Suf or Isc systems
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 138
Score = 25.2 bits (55), Expect = 5.3
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 3 LSGLPDSVRAHQVDLTGGSDQVYLIEYFPYFPLITMYLMYYLGEDGKRVYTLKKV 57
L LP++++ +LTG ++V+L + L L +Y +G+ V L V
Sbjct: 39 LPALPEALKTQATELTGCENRVWL----GHQVLPDGTLHFYGDSEGRIVRGLLAV 89
>gnl|CDD|213993 cd07438, PHP_HisPPase_AMP, Polymerase and Histidinol Phosphatase
domain of Histidinol phosphate phosphatase (HisPPase)
AMP bound. The PHP domain of this HisPPase family has
an unknown function. It has a second domain inserted in
the middle that binds adenosine 5-monophosphate (AMP).
The PHP (also called histidinol phosphatase-2/HIS2)
domain is associated with several types of DNA
polymerases, such as PolIIIA and family X DNA
polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. HisPPase catalyzes the
eighth step of histidine biosynthesis, in which
L-histidinol phosphate undergoes dephosphorylation to
give histidinol. The PHP domain has four conserved
sequence motifs and contains an invariant histidine that
is involved in metal ion coordination. The PHP domain of
HisPPase is structurally homologous to the other members
of the PHP family that have a distorted (beta/alpha)7
barrel fold with a trinuclear metal site on the
C-terminal side of the barrel.
Length = 155
Score = 24.7 bits (55), Expect = 8.2
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 67 AHPARFSPDDKYSRERITILRRFGL 91
AHP + K E I L+ GL
Sbjct: 94 AHPGLYKLSRKKLEELIEELKEAGL 118
>gnl|CDD|183210 PRK11574, PRK11574, oxidative-stress-resistance chaperone;
Provisional.
Length = 196
Score = 24.7 bits (54), Expect = 9.3
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 59 PAGNPTVSAHPARFS--PDDKYSRERITILRRFGLLRTQQPASAM 101
P GN T P P +++ +R+ R LL +Q P +A+
Sbjct: 120 PIGNMT--GFPTLKDKIPAEQWQDKRVVWDARVNLLTSQGPGTAI 162
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 0.140 0.421
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,483,427
Number of extensions: 470610
Number of successful extensions: 423
Number of sequences better than 10.0: 1
Number of HSP's gapped: 421
Number of HSP's successfully gapped: 21
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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 (24.1 bits)