RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17052
(68 letters)
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane
glycoprotein with multiple putative transmembrane
helices it has a hydrophilic amino terminal and a
hydrophobic carboxy terminal. It has roles in proton
transport and assembly of the V-type ATPase complex.
This subunit is encoded by two homologous gene in yeast
VPH1 and STV1.
Length = 707
Score = 88.6 bits (220), Expect = 1e-22
Identities = 40/62 (64%), Positives = 48/62 (77%)
Query: 5 LNPDVNAFQRKFVNEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESPEAPQPREMIDLEA 64
LN DV+AFQRKFVNEVRRCDE+ERKLR LE +IKK GIP+ D G P+ P +E +DLE
Sbjct: 15 LNEDVSAFQRKFVNEVRRCDEVERKLRKLESKIKKLGIPLKDTGGKPDVPPSKEFLDLEE 74
Query: 65 SL 66
+
Sbjct: 75 EI 76
>gnl|CDD|235766 PRK06276, PRK06276, acetolactate synthase catalytic subunit;
Reviewed.
Length = 586
Score = 30.5 bits (69), Expect = 0.038
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 8 DVNAFQRKFVNEVRRCDEMERKLRYLE--KEIKKDGIPMMDVGESPEAPQ 55
D R + E+ + E++ K +LE K++KK+ IP MD + P PQ
Sbjct: 320 DAKNVLRDLLAELMK-KEIKNKSEWLERVKKLKKESIPRMDFDDKPIKPQ 368
>gnl|CDD|238409 cd00794, NOS_oxygenase_prok, Nitric oxide synthase (NOS)
prokaryotic oxygenase domain. NOS produces nitric oxide
(NO) by catalyzing a five-electron heme-based oxidation
of a guanidine nitrogen of L-arginine to L-citrulline
via two successive monooxygenation reactions producing
N(omega)-hydroxy-L-arginine (NHA) as an intermediate.
Nitric oxide synthases are homodimers. Most prokaryotes
produce NO as a byproduct of denitrification, using a
completely different set of enzymes than NOS. However,
a few prokaryotes also have a NOS, consisting solely of
the NOS oxygenase domain. Prokaryotic NOS binds to the
substrate L-Arg, zinc, and to the cofactors heme and
tetrahydrofolate.
Length = 353
Score = 29.7 bits (67), Expect = 0.077
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 5 LNPDVNAFQRKFVNEVRRCDEMERKLRYLEKEIKKDG 41
L + AF E+ E+ ++L +E EI + G
Sbjct: 2 LFKEARAFLTNMYEELGETGELNKRLAAVESEIDETG 38
>gnl|CDD|234858 PRK00892, lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine
N-acyltransferase; Provisional.
Length = 343
Score = 29.3 bits (67), Expect = 0.094
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 14 RKFVNEVRRCDEMERKLRYLEKEIKKD 40
+ +RR DE+ ++L+ LEK++++
Sbjct: 317 LRTAARLRRLDELRKRLKALEKKVEQL 343
>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
Length = 470
Score = 26.6 bits (59), Expect = 1.0
Identities = 13/44 (29%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 17 VNEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESPEAPQPREMI 60
++RR E+ R++R + + K G+ ++D+ E E+ + RE+I
Sbjct: 158 YQDLRRAAEVHRQVRRYAQSVIKPGVKLIDICERIES-KSRELI 200
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 25.9 bits (58), Expect = 1.5
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 8 DVNAFQRKFVNEVRRCDEMERKLRYLEKEIKK 39
+ A + + + ++E KLR LE E +K
Sbjct: 2 RLEALEERNSELEEQIRQLELKLRDLEAENEK 33
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 25.7 bits (57), Expect = 1.7
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 28 RKLRYLEKEIKKDGIPMMDVGESPEAPQ 55
KL + +++ + +P + G PE PQ
Sbjct: 163 HKLCHAARQLLEQTLPAIKHGNIPEIPQ 190
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 25.8 bits (57), Expect = 1.8
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 28 RKLRYLEKEIKKDGIPMMDVGESPEAPQP 56
+ R + E KK +P++D +PE P P
Sbjct: 13 QFQRTQDLEEKKLHVPVVD--RTPEEPPP 39
>gnl|CDD|147068 pfam04721, DUF750, Domain of unknown function (DUF750). This
family of proteins with unknown function shows
similarity to PNG-1, a enzyme responsible for
de-N-glycosylation of misfolded glycoproteins in the
cytosol. However, unlike PNG-1, this protein does not
contain a catalytic triad in its transglutaminase
domain.
Length = 62
Score = 23.8 bits (52), Expect = 3.9
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 3 SNLNPDVNAFQRKFVNEVRRCDEMERKLRYLEKEIKKD 40
S+ N D + Q V + R + E YL K +
Sbjct: 16 SHTNEDGSPVQPFIVKNIERVVDRELNEVYLHKIDPNE 53
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 24.8 bits (54), Expect = 4.1
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 48 GESPEAPQPREMIDLEASL 66
G+ P REMI LEA +
Sbjct: 305 GKEPARFSTREMIRLEAQM 323
>gnl|CDD|222257 pfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This
is a family of the conserved region of Leucine-tRNA
ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.
Length = 178
Score = 24.4 bits (54), Expect = 4.9
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 6 NPDVNAFQRKFVNEVRRCDEMERKLRYLEKE 36
NP++ F+ E ++ +ER + EKE
Sbjct: 48 NPEL----AAFIEECKKTSTIERTIATAEKE 74
>gnl|CDD|238521 cd01088, MetAP2, Methionine Aminopeptidase 2. E.C. 3.4.11.18.
Also known as methionyl aminopeptidase and peptidase M.
Catalyzes release of N-terminal amino acids,
preferentially methionine, from peptides and
arylamides.
Length = 291
Score = 24.5 bits (54), Expect = 5.5
Identities = 8/35 (22%), Positives = 19/35 (54%)
Query: 18 NEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESPE 52
+ R E+ R++R + + K G+ ++++ E E
Sbjct: 2 EKYREAGEIHRQVRKYAQSLIKPGMTLLEIAEFVE 36
>gnl|CDD|224028 COG1103, COG1103, Archaea-specific pyridoxal phosphate-dependent
enzymes [General function prediction only].
Length = 382
Score = 24.3 bits (53), Expect = 6.2
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 17 VNEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESP 51
V V+R DE K R+ E++K G + +GE P
Sbjct: 275 VERVKRWDEEVEKARWFVAELEKIG-GVKQLGERP 308
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 24.3 bits (53), Expect = 6.3
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 18 NEVRRCDEMERKLRYLEKEIKKDGIPMM 45
+ +R +E ++L L +E K G+P++
Sbjct: 93 ADRKRFEEAGQELVELLEEEKLAGVPVL 120
>gnl|CDD|110514 pfam01517, HDV_ag, Hepatitis delta virus delta antigen. The
hepatitis delta virus (HDV) encodes a single protein,
the hepatitis delta antigen (HDAg). The central region
of this protein has been shown to bind RNA. Several
interactions are also mediated by a coiled-coil region
at the N terminus of the protein.
Length = 194
Score = 24.1 bits (52), Expect = 6.7
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 15 KFVNEVRRCDEMERKLRYLEKEIKK 39
++V ++ +E+E+ LR K+IKK
Sbjct: 19 QWVEARKKREELEKDLRKANKKIKK 43
>gnl|CDD|233915 TIGR02539, SepCysS, O-phospho-L-seryl-tRNA:Cys-tRNA synthase.
Aminoacylation of tRNA(Cys) with Cys, and cysteine
biosynthesis in the process, happens in
Methanocaldococcus jannaschii and several other archaea
by misacylation of tRNA(Cys) with O-phosphoserine (Sep),
followed by modification of the phosphoserine to
cysteine. In some species, direct tRNA-cys
aminoacylation also occurs but this pathway is required
for Cys biosynthesis. Members of this protein catalyze
the second step in this two step pathway, using
pyridoxal phosphate and a sulfur donor to synthesize Cys
from Sep while attached to the tRNA.
Length = 370
Score = 24.0 bits (52), Expect = 7.1
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 17 VNEVRRCDEMERKLRYLEKEIKKDGIPMMDVGESPE 52
V V+R DE +K R+ E++ G + +G+ P+
Sbjct: 264 VERVKRWDEEVKKTRWFVAELEDIGF--IQLGQKPK 297
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 23.9 bits (52), Expect = 7.9
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 9 VNAFQRKFVNEVRRCDEMERKLRYLEK----EIKKDGIP 43
+ +++ + +R +E+ERKL L K E+ G P
Sbjct: 483 IERLEKELEEKKKRVEELERKLAELRKMRKLELSGKGTP 521
>gnl|CDD|232979 TIGR00444, mazG, MazG family protein. This family of prokaryotic
proteins has no known function. It includes the
uncharacterized protein MazG in E. coli [Unknown
function, General].
Length = 248
Score = 24.0 bits (52), Expect = 8.1
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 24 DEMERKLRYLEKEIKKDGIPMMDV 47
++ ER+ R +E+ + G+ + V
Sbjct: 212 EKFERRFREVERIVAARGLELTGV 235
>gnl|CDD|233501 TIGR01637, phage_arpU, phage transcriptional regulator, ArpU
family. This model represents a family of phage
proteins, including ArpU, called a putative autolysin
regulatory protein. ArpU was described as a regulator of
cellular muramidase-2 of Enterococcus hirae but appears
to have been cloned from a prophage. This family appears
related to the RinA family of bacteriophage
transcriptional activators and to some
sporulation-specific sigma factors. We propose that this
is a phage transcriptional activator family [Mobile and
extrachromosomal element functions, Prophage functions,
Regulatory functions, DNA interactions].
Length = 132
Score = 23.9 bits (52), Expect = 8.4
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 6 NPDVNAFQRKFVNEVR-RCDEMERKL---RYLEKEIKKDGIPMMDVGES 50
N D R VN + + DE+ R++ +YLE + K D MM++G S
Sbjct: 62 NLDAEQEARAIVNAIVNQLDEISRQILYDKYLEPDQKYDYQIMMELGYS 110
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
0.317 0.134 0.381
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,542,994
Number of extensions: 266801
Number of successful extensions: 431
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 31
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
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 (21.6 bits)
S2: 53 (24.2 bits)