RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15688
(70 letters)
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 60.8 bits (148), Expect = 1e-13
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60
M PG+ S I +G IV ++ E K LA+G+ +S ++ KG V+N H++
Sbjct: 96 MAPGIVSADGEIK---EGDIVVVVDEKKGRPLAVGIALMSGKEMEEKKKGKAVKNIHHVG 152
Query: 61 DGLWNMKN 68
D LW
Sbjct: 153 DKLWEASV 160
>gnl|CDD|129543 TIGR00451, unchar_dom_2, uncharacterized domain 2. This
uncharacterized domain is found a number of enzymes and
uncharacterized proteins, often at the C-terminus. It is
found in some but not all members of a family of related
tRNA-guanine transglycosylases (tgt), which exchange a
guanine base for some modified base without breaking the
phosphodiester backbone of the tRNA. It is also found in
rRNA pseudouridine synthase, another enzyme of RNA base
modification not otherwise homologous to tgt. It is
found, again at the C-terminus, in two putative
glutamate 5-kinases. It is also found in a family of
small, uncharacterized archaeal proteins consisting
mostly of this domain.
Length = 107
Score = 54.0 bits (130), Expect = 2e-11
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60
M PG+ I +G V ++ E K LA+G+ +S +++ ++KG V+N H++
Sbjct: 50 MRPGIVDADEDI---KEGDDVVVVDENKDRPLAVGIALMSGEEMKEMDKGKAVKNIHHIG 106
Query: 61 D 61
D
Sbjct: 107 D 107
>gnl|CDD|237757 PRK14560, PRK14560, putative RNA-binding protein; Provisional.
Length = 160
Score = 46.8 bits (112), Expect = 3e-08
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60
M PG+ + +G IV ++ E LA+G + D++V KG V+N H++
Sbjct: 96 MAPGIVE---ADEDIKEGDIVFVVEETHGKPLAVGRALMDGDEMVEEKKGKAVKNIHHVG 152
Query: 61 DGLWNMKN 68
D +W +
Sbjct: 153 DEIWEFEV 160
>gnl|CDD|234310 TIGR03684, arCOG00985, arCOG04150 universal archaeal PUA-domain
protein. This universal archaeal protein contains a
domain possibly associated with RNA binding (pfam01472,
TIGR00451).
Length = 150
Score = 43.4 bits (103), Expect = 5e-07
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLN 60
M PG+ I +G IV ++ E LA+G+ + +++V KG V+N H++
Sbjct: 89 MAPGIVEADPSIK---EGDIVFVVDETHGKPLAVGIALMDAEEMVEEKKGKAVKNIHHVG 145
Query: 61 DGLWN 65
D +W
Sbjct: 146 DKIWE 150
>gnl|CDD|201816 pfam01472, PUA, PUA domain. The PUA domain named after
Pseudouridine synthase and Archaeosine
transglycosylase, was detected in archaeal and
eukaryotic pseudouridine synthases, archaeal
archaeosine synthases, a family of predicted ATPases
that may be involved in RNA modification, a family of
predicted archaeal and bacterial rRNA methylases.
Additionally, the PUA domain was detected in a family
of eukaryotic proteins that also contain a domain
homologous to the translation initiation factor
eIF1/SUI1; these proteins may comprise a novel type of
translation factors. Unexpectedly, the PUA domain was
detected also in bacterial and yeast glutamate kinases;
this is compatible with the demonstrated role of these
enzymes in the regulation of the expression of other
genes. It is predicted that the PUA domain is an RNA
binding domain.
Length = 74
Score = 39.4 bits (93), Expect = 4e-06
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYL 59
+ PG+ +G V ++ E K +A+GL S++++ ++ G V+ L
Sbjct: 20 LAPGVVEVDGDF---RRGDEVVVVTE-KGELVAVGLANYSSEEMAKIKGGKAVKVRRVL 74
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 32.1 bits (74), Expect = 0.011
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 5 LTSPG--AIITPVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVE 54
L +PG + + KG +V++ K +A+G + +D+I++ KGI V+
Sbjct: 244 LYAPGIAKLEKGIKKGDLVAVFTL-KGELVALGKALMDSDEILKAEKGIVVD 294
>gnl|CDD|233857 TIGR02412, pepN_strep_liv, aminopeptidase N, Streptomyces lividans
type. This family is a subset of the members of the
zinc metallopeptidase family M1 (pfam01433), with a
single member characterized in Streptomyces lividans 66
and designated aminopeptidase N. The spectrum of
activity may differ somewhat from the aminopeptidase N
clade of E. coli and most other Proteobacteria, well
separated phylogenetically within the M1 family. The M1
family also includes leukotriene A-4
hydrolase/aminopeptidase (with a bifunctional active
site).
Length = 831
Score = 27.8 bits (62), Expect = 0.38
Identities = 20/84 (23%), Positives = 27/84 (32%), Gaps = 24/84 (28%)
Query: 5 LTSPGA-IITP---VDKGTIVSIMAEGK----QHALAIGLTTLSTDDIVRVNK------- 49
L + G +TP D G + ++ E H +AIGL L DD+ R
Sbjct: 439 LETAGVNTLTPEITTDGGVVSALYPESSGPPRPHRIAIGLYDLDRDDLRRTTLVPLTISG 498
Query: 50 ---------GIGVENFHYLNDGLW 64
G LND
Sbjct: 499 ERTAVPQLVGKRAPALVLLNDDDL 522
>gnl|CDD|219589 pfam07808, RED_N, RED-like protein N-terminal region. This family
contains sequences that are similar to the N-terminal
region of Red protein. This and related proteins contain
a RED repeat which consists of a number of RE and RD
sequence elements. The region in question has several
conserved NLS sequences and a putative trimeric
coiled-coil region, suggesting that these proteins are
expressed in the nucleus. The function of Red protein is
unknown, but efficient sequestration to nuclear bodies
suggests that its expression may be tightly regulated of
that the protein self-aggregates extremely efficiently.
Length = 238
Score = 27.5 bits (61), Expect = 0.44
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 37 TTLSTDDIVRVNKGIGVENFHYLNDGLWNMKNIK 70
TL+T++ V +NK + YL G N +N K
Sbjct: 205 VTLTTNNSV-LNKLTQI--LSYLRAGTSNKENKK 235
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 26.7 bits (59), Expect = 1.1
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 15 VDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVE 54
++KG V ++ K A+A+G+ +ST DI +KG+ +
Sbjct: 268 IEKGDTVVVITL-KGEAVAVGIALMSTKDIANADKGVVAD 306
>gnl|CDD|188163 TIGR01735, FGAM_synt, phosphoribosylformylglycinamidine synthase,
single chain form. This model represents a
single-molecule form of
phosphoribosylformylglycinamidine synthase, also called
FGAM synthase, an enzyme of purine de novo biosynthesis.
This form is found mostly in eukaryotes and
Proteobacteria. In Bacillus subtilis PurL (FGAM synthase
II) and PurQ (FGAM synthase I), homologous to different
parts of this model, perform the equivalent function;
the unrelated small protein PurS is also required and
may be a third subunit [Purines, pyrimidines,
nucleosides, and nucleotides, Purine ribonucleotide
biosynthesis].
Length = 1310
Score = 25.9 bits (57), Expect = 1.7
Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 8 PGAIITPVDKGTIVSIMAEGKQ---HALAIGLTTLSTDDIVRVNKG 50
GA+I V K + +++ + AL +G+ T + ++R++
Sbjct: 941 LGAVIQ-VAKPDLAAVLELLRAAGLTALILGIGTPTGHPMIRISVN 985
>gnl|CDD|130940 TIGR01885, Orn_aminotrans, ornithine aminotransferase. This model
describes the final step in the biosynthesis of
ornithine from glutamate via the non-acetylated pathway.
Ornithine amino transferase takes L-glutamate
5-semialdehyde and makes it into ornithine, which is
used in the urea cycle, as well as in the biosynthesis
of arginine. This model includes low-GC bacteria and
eukaryotic species. The genes from two species are
annotated as putative acetylornithine aminotransferases
- one from Porphyromonas gingivalis (OMNI|PG1271), and
the other from Staphylococcus aureus (OMNI|SA0170).
After homology searching using BLAST it was determined
that these two sequences were most closely related to
ornithine aminotransferases. This model's seed includes
one characterized hit, from Bacillus subtilis
(SP|P38021).
Length = 401
Score = 25.7 bits (57), Expect = 1.7
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 14 PVDKGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFH 57
P ++ IVS A+G H +G ++STD R N G V F
Sbjct: 125 PENQAIIVS--AKGNFHGRTLGAISMSTDPDSRTNFGPYVPGFK 166
>gnl|CDD|215256 PLN02462, PLN02462, sedoheptulose-1,7-bisphosphatase.
Length = 304
Score = 25.5 bits (56), Expect = 2.3
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 29 QHALAIGLTTLSTDDIVRVNKGIGVENFHYLNDGLW 64
Q A A+G+ T +V + G G F L+DG W
Sbjct: 133 QVAAAMGIYGPRTTYVVALKDGPGTHEFLLLDDGKW 168
>gnl|CDD|224940 COG2029, COG2029, Uncharacterized conserved protein [Function
unknown].
Length = 189
Score = 24.7 bits (54), Expect = 4.7
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 21 VSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVENFHYLND 61
+++ EG AIGL L DI+ + + V +
Sbjct: 137 INVKTEGVPDVDAIGLEDLGYGDILEFMERVAVAYVREIEK 177
>gnl|CDD|234906 PRK01123, PRK01123, shikimate kinase; Provisional.
Length = 282
Score = 24.5 bits (54), Expect = 4.7
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 12/61 (19%)
Query: 1 MCPGLTSPGAIITPVDKGTIVSIMAEGKQHALAIGLTT-----LSTDDIVRVNKGIGVEN 55
M T+ GA GTI++ +A GK A I L T LS D + G +
Sbjct: 1 MRGRATALGA-------GTIINAIATGKGSAFGIDLKTTATVELSDDGGGIEGEISGNPD 53
Query: 56 F 56
Sbjct: 54 A 54
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 24.6 bits (54), Expect = 5.0
Identities = 14/55 (25%), Positives = 17/55 (30%), Gaps = 5/55 (9%)
Query: 19 TIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGVE-----NFHYLNDGLWNMKN 68
TI SI E K A TL ++ R G + D N K
Sbjct: 47 TINSIFGERKVSVSAFQSETLRPREVSRTVDGFKLNIIDTPGLLESQDQRVNRKI 101
>gnl|CDD|219178 pfam06792, UPF0261, Uncharacterized protein family (UPF0261).
Length = 403
Score = 24.4 bits (54), Expect = 5.8
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 4 GLTSPGAIITPVDKGTIVSIMAEG 27
+S A+I D+G ++ MA G
Sbjct: 57 AGSSIEAVIAGGDRGEAMAAMARG 80
>gnl|CDD|235967 PRK07208, PRK07208, hypothetical protein; Provisional.
Length = 479
Score = 24.1 bits (53), Expect = 6.4
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 51 IGVENFHYLNDGLWNM 66
+G+E F + D LWNM
Sbjct: 354 LGLEYFCFEGDDLWNM 369
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 347
Score = 24.2 bits (53), Expect = 7.6
Identities = 11/58 (18%), Positives = 17/58 (29%), Gaps = 11/58 (18%)
Query: 17 KGTIVSIMAEGKQHALAIGLTTLSTDDIVRVNKGIGV-----ENFHYLNDGLWNMKNI 69
+G I A G + + +VR I + G W KN+
Sbjct: 235 RGVDCVIEAVGFEETFEQAV------KVVRPGGTIANVGVYGKPDPLPLLGEWFGKNL 286
>gnl|CDD|168683 PRK06813, PRK06813, homoserine dehydrogenase; Validated.
Length = 346
Score = 24.1 bits (52), Expect = 9.0
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 43 DIVRVNKGIGVENFHYLNDGLWNMKNIK 70
DIV ++KG V N+ +N+ + N++
Sbjct: 117 DIVAISKGALVTNWREINE-AAKIANVR 143
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
0.318 0.138 0.412
Gapped
Lambda K H
0.267 0.0621 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,525,278
Number of extensions: 264475
Number of successful extensions: 237
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 22
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.4 bits)