RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3720
(190 letters)
>gnl|CDD|238832 cd01662, Ubiquinol_Oxidase_I, Ubiquinol oxidase subunit I.
Ubiquinol oxidase, the terminal oxidase in the
respiratory chains of aerobic bacteria, is a multi-chain
transmembrane protein located in the cell membrane. It
catalyzes the reduction of O2 and simultaneously pumps
protons across the membrane. The number of subunits in
ubiquinol oxidase varies from two to five. Subunit I
contains a heme-copper binuclear center (the active site
where O2 is reduced to water) formed by a high-spin heme
and a copper ion. It also contains a low-spin heme,
believed to participate in the transfer of electrons
from ubiquinol to the binuclear center. For every
reduction of an O2 molecule, eight protons are taken
from the inside aqueous compartment and four electrons
are taken from ubiquinol on the opposite side of the
membrane. The four electrons and four of the protons
are used in the reduction of O2; the four remaining
protons are pumped across the membrane. This charge
separation of four charges contributes to the
electrochemical gradient used for ATP synthesis. Two
proton channels, the D-pathway and K-pathway, leading to
the binuclear center have been identified in subunit I.
It is generally believed that the channels contain water
molecules that act as 'proton wires' to transfer the
protons. A well-defined pathway for the transfer of
pumped protons beyond the binuclear center has not been
identified. Electrons are believed to be transferred
directly from ubiquinol (the electron donor) to the
low-spin heme, and directly from the low-spin heme to
the binuclear center.
Length = 501
Score = 31.0 bits (71), Expect = 0.38
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 12 YLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKGD 52
YLP PGW N + IGA +I V L ++ VS RKG
Sbjct: 436 YLPG-PGWDPLNLISTIGAFLIAAGVLLFLINVIVSIRKGK 475
Score = 31.0 bits (71), Expect = 0.38
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 73 YLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKGD 113
YLP PGW N + IGA +I V L ++ VS RKG
Sbjct: 436 YLPG-PGWDPLNLISTIGAFLIAAGVLLFLINVIVSIRKGK 475
>gnl|CDD|225142 COG2233, UraA, Xanthine/uracil permeases [Nucleotide transport and
metabolism].
Length = 451
Score = 30.3 bits (69), Expect = 0.53
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 13/68 (19%)
Query: 8 DFSPY--LPWV-------PGW-IDWNAVVPIGATVIVVFV---GLLVVCFAVSRRKGDGQ 54
DFS PW G DW A++ + IV V G + ++ R DG+
Sbjct: 220 DFSGVAEAPWFALPTPFYFGMAFDWGAILTMLPVAIVTIVEHTGDITATGEITGRDLDGK 279
Query: 55 TRLRGTIM 62
RLR ++
Sbjct: 280 PRLRRGLL 287
>gnl|CDD|224205 COG1286, CvpA, Uncharacterized membrane protein, required for
colicin V production [General function prediction only].
Length = 182
Score = 28.8 bits (65), Expect = 1.5
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 37 VGLLVVCFAVSRRKG--DGQTRLRGTIMPPFKTSDFSPYL-PWVPGWIDWNAVVPIGATV 93
+ ++V F + R+G L I+ F S F L P + +I + IG +
Sbjct: 9 LIIIVASFLLGLRRGFIREVLSLLSWILAAFVASLFYKPLAPLLREYIP-YPNIAIGIAI 67
Query: 94 IVVFVGLLVVCFAV 107
+ FV LL+V V
Sbjct: 68 AIFFVILLIVGAFV 81
Score = 26.5 bits (59), Expect = 7.4
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 11 PYLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAV 46
P P + +I + IG + + FV LL+V V
Sbjct: 47 PLAPLLREYIP-YPNIAIGIAIAIFFVILLIVGAFV 81
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 29.0 bits (65), Expect = 1.8
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 122 IVYNQSMVGGMNTVDKRHIN----EELGYIAP 149
IV ++S V G+ + R I+ EEL YI
Sbjct: 587 IVISESNVKGLGIISYRTIDAAAAEELSYITG 618
>gnl|CDD|223913 COG0843, CyoB, Heme/copper-type cytochrome/quinol oxidases, subunit
1 [Energy production and conversion].
Length = 566
Score = 28.8 bits (65), Expect = 2.0
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 11 PYLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKG 51
P VPG+ N + +GA ++ + V L ++ VS RKG
Sbjct: 444 ATYPGVPGFTPLNVIATVGAFILGLGVLLFLLNLVVSLRKG 484
Score = 28.8 bits (65), Expect = 2.0
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 72 PYLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKG 112
P VPG+ N + +GA ++ + V L ++ VS RKG
Sbjct: 444 ATYPGVPGFTPLNVIATVGAFILGLGVLLFLLNLVVSLRKG 484
>gnl|CDD|132021 TIGR02976, phageshock_pspB, phage shock protein B. This model
describes the PspB protein of the psp (phage shock
protein) operon, as found in Escherichia coli and many
related species. Expression of a phage protein called
secretin protein IV, and a number of other stresses
including ethanol, heat shock, and defects in protein
secretion trigger sigma-54-dependent expression of the
phage shock regulon. PspB is both a regulator and an
effector protein of the phage shock response [Cellular
processes, Adaptations to atypical conditions].
Length = 75
Score = 26.2 bits (58), Expect = 3.2
Identities = 9/53 (16%), Positives = 21/53 (39%)
Query: 86 VVPIGATVIVVFVGLLVVCFAVSRRKGDGQTRLRDDIVYNQSMVGGMNTVDKR 138
+ I + V+FV L + ++ + DD Q + + +++R
Sbjct: 5 FLAIPLIIFVIFVAPLWLILHYRSKRKTAASLSTDDQALLQELYAKADRLEER 57
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 27.7 bits (62), Expect = 3.5
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 109 RRKGDGQTRLRDDIVY---NQSMVGG--MNTVDKRHINEELGYIA 148
RR G+ Y +V +N++ I+ LGY+A
Sbjct: 162 RRVIRGRKGDSSSEPYTIGGVPLVDLRDLNSLPPEVISASLGYMA 206
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 27.5 bits (62), Expect = 4.7
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 30 ATVIVVFVGLLVVCFAVSRRKGDGQTRLR 58
TV+V ++ + ++++RK + L
Sbjct: 13 VTVVVAIAAVVALIVSLAQRKKSQKGELE 41
Score = 27.5 bits (62), Expect = 4.7
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 91 ATVIVVFVGLLVVCFAVSRRKGDGQTRLR 119
TV+V ++ + ++++RK + L
Sbjct: 13 VTVVVAIAAVVALIVSLAQRKKSQKGELE 41
>gnl|CDD|225330 COG2610, GntT, H+/gluconate symporter and related permeases
[Carbohydrate transport and metabolism / Amino acid
transport and metabolism].
Length = 442
Score = 27.6 bits (62), Expect = 5.1
Identities = 19/114 (16%), Positives = 36/114 (31%), Gaps = 27/114 (23%)
Query: 26 VPIGATVIV-VFVGLLVVCFA-------VSRRKG------DGQTRLRGTIMPPFKTSDFS 71
IG ++ + V + V A + R+ L +P F S +
Sbjct: 170 ADIGTVILYGLIVAIPTVIIAGPLFAKLLGRKIKALPAGEGSLKELDEKELPSFGVSLAT 229
Query: 72 PYLPWVP-------------GWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKG 112
+P + G + +G VI + + LLV + + +G
Sbjct: 230 ILVPILLMALKTIASLLLPKGSPALEVLEFLGNPVIALLIALLVAIYTLGMGRG 283
>gnl|CDD|107322 cd06327, PBP1_SBP_like_1, Periplasmic solute-binding domain of
active transport proteins that belong to the type I
periplasmic binding fold protein family. Periplasmic
solute-binding domain of active transport proteins that
belong to the type I periplasmic binding fold protein
family. Solute binding proteins are the primary specific
receptors that initiate uptake of a broad range of
solutes, including amino acids, peptides and inorganic
ions. The members are predicted to have a similar
function to an active transport system for short chain
amides and urea by sequence comparison and phylogenetic
analysis. Moreover, this binding domain has high
sequence identity to the family of hydrophobic amino
acid transporters (HAAT), and thus may also be involved
in transport of amino acids.
Length = 334
Score = 27.1 bits (61), Expect = 5.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 59 GTIMPPFKTSDFSPYLP 75
G++ P TSDFS YL
Sbjct: 168 GSVRHPLGTSDFSSYLL 184
>gnl|CDD|213748 TIGR02891, CtaD_CoxA, cytochrome c oxidase, subunit I. This large
family represents subunit I's (CtaD, CoxA, CaaA) of
cytochrome c oxidases of bacterial origin. Cytochrome c
oxidase is the component of the respiratory chain that
catalyzes the reduction of oxygen to water. Subunits
I-III form the functional core of the enzyme complex.
Subunit I is the catalytic subunit of the enzyme.
Electrons originating in cytochrome c are transferred
via the copper A center of subunit II and heme a of
subunit I to the bimetallic center formed by heme a3 and
copper B. This cytochrome c oxidase shows proton pump
activity across the membrane in addition to the electron
transfer. In the bacilli an apparent split (paralogism)
has created a sister clade (TIGR02882) encoding subunits
(QoxA) of the aa3-type quinone oxidase complex which
reacts directly with quinones, bypassing the interaction
with soluble cytochrome c. This model attempts to
exclude these sequences, placing them between the
trusted and noise cutoffs. These families, as well as
archaeal and eukaryotic cytochrome c subunit I's are
included within the superfamily model, pfam00115 [Energy
metabolism, Electron transport].
Length = 499
Score = 27.6 bits (62), Expect = 5.2
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 12 YLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKG 51
Y P + G+ N + IGA ++ + + S RKG
Sbjct: 435 YPPQM-GFATLNLISTIGAFILAAGFLVFLWNLIWSLRKG 473
Score = 27.6 bits (62), Expect = 5.2
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 73 YLPWVPGWIDWNAVVPIGATVIVVFVGLLVVCFAVSRRKG 112
Y P + G+ N + IGA ++ + + S RKG
Sbjct: 435 YPPQM-GFATLNLISTIGAFILAAGFLVFLWNLIWSLRKG 473
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
0.324 0.141 0.460
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,240,841
Number of extensions: 968834
Number of successful extensions: 1316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1309
Number of HSP's successfully gapped: 60
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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: 41 (22.0 bits)
S2: 56 (25.5 bits)