RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2997
(415 letters)
>gnl|CDD|238462 cd00922, Cyt_c_Oxidase_IV, Cytochrome c oxidase subunit IV.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Subunits I, II,
and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Found only in
eukaryotes, subunit IV is the largest of the
nuclear-encoded subunits. It binds ATP at the matrix
side, leading to an allosteric inhibition of enzyme
activity at high intramitochondrial ATP/ADP ratios. In
mammals, subunit IV has a lung-specific isoform and a
ubiquitously expressed isoform.
Length = 136
Score = 127 bits (320), Expect = 2e-35
Identities = 55/140 (39%), Positives = 75/140 (53%), Gaps = 4/140 (2%)
Query: 46 EVVGHGRNGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHWNALSKEEKKMLYRASF 105
EVVG+G N + Y D P P IR++ +++ LREKEKG W L+ EEKK LYR SF
Sbjct: 1 EVVGYGANSLPTYADIPDRPLPMIRFRELSAEIKALREKEKGDWKQLTLEEKKALYRISF 60
Query: 106 RQTFAEFTRHGAYPDTEYLGSVGLSMVVIAVSLFYYAFLKAFFLPPLPATMTPEGWENTV 165
+T E E+ G + I ++ + +AF P P T T E E +
Sbjct: 61 GETGPEMNAPTG----EWKTVFGGVLAFIGITGVIFGLQRAFVYGPKPHTFTEEWQEAQL 116
Query: 166 TKMIQLQWNPITGMASKWDY 185
+M+ ++ NPITG ASKWDY
Sbjct: 117 ERMLDMKVNPITGYASKWDY 136
Score = 116 bits (294), Expect = 1e-31
Identities = 55/155 (35%), Positives = 75/155 (48%), Gaps = 19/155 (12%)
Query: 229 EVVGHGRNGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHWNALSKEEKKMLYRASF 288
EVVG+G N + Y D P P IR++ +++ LREKEKG W L+ EEKK LYR SF
Sbjct: 1 EVVGYGANSLPTYADIPDRPLPMIRFRELSAEIKALREKEKGDWKQLTLEEKKALYRISF 60
Query: 289 RQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSLFYYAFLKAFFLP 348
+T E E+ G + I ++ + +AF
Sbjct: 61 GETGPEMNAPTG----EWKTVFGGVLAFIG---------------ITGVIFGLQRAFVYG 101
Query: 349 PLPTTMTPEGWENTVTKMIQLQWNPITGMASKWDY 383
P P T T E E + +M+ ++ NPITG ASKWDY
Sbjct: 102 PKPHTFTEEWQEAQLERMLDMKVNPITGYASKWDY 136
>gnl|CDD|202477 pfam02936, COX4, Cytochrome c oxidase subunit IV. Cytochrome c
oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the
terminal oxidase in the mitochondrial electron transport
chain. This family is composed of cytochrome c oxidase
subunit IV. The Dictyostelium member of this family is
called COX VI. The yeast protein MTC3 appears to be the
yeast COX IV subunit.
Length = 142
Score = 125 bits (316), Expect = 7e-35
Identities = 59/145 (40%), Positives = 78/145 (53%), Gaps = 4/145 (2%)
Query: 46 EVVGHGRNGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHWNALSKEEKKMLYRASF 105
VVG+G NG Y D P R++ ++ LREKEKG W +LS EEKK LYR SF
Sbjct: 1 RVVGYGANGNPTYADLPDRWEPMPRFREQSELIMALREKEKGDWKSLSLEEKKALYRISF 60
Query: 106 RQTFAEFTRHGAYPDTEYLGSVGLSMVVIAVSLFYYAFLKAFFLPPLPATMTPEGWENTV 165
+T EF P E+ +G + + +S + ++ F PPLP TM E E
Sbjct: 61 GETGPEFVA----PKGEWKTVLGGVLAGLGISFGLFILMRTFAYPPLPKTMNKEWQEAQN 116
Query: 166 TKMIQLQWNPITGMASKWDYENDRW 190
+M L+ NPITG+AS +DYEN W
Sbjct: 117 ERMKDLKINPITGLASGYDYENKVW 141
Score = 115 bits (291), Expect = 4e-31
Identities = 59/160 (36%), Positives = 76/160 (47%), Gaps = 19/160 (11%)
Query: 229 EVVGHGRNGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHWNALSKEEKKMLYRASF 288
VVG+G NG Y D P R++ ++ LREKEKG W +LS EEKK LYR SF
Sbjct: 1 RVVGYGANGNPTYADLPDRWEPMPRFREQSELIMALREKEKGDWKSLSLEEKKALYRISF 60
Query: 289 RQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSLFYYAFLKAFFLP 348
+T EF G V+ + L +S + ++ F P
Sbjct: 61 GETGPEFVA-----------PKGEWKTVLGGVLAGL--------GISFGLFILMRTFAYP 101
Query: 349 PLPTTMTPEGWENTVTKMIQLQWNPITGMASKWDYENDRW 388
PLP TM E E +M L+ NPITG+AS +DYEN W
Sbjct: 102 PLPKTMNKEWQEAQNERMKDLKINPITGLASGYDYENKVW 141
>gnl|CDD|237151 PRK12612, PRK12612, putative monovalent cation/H+ antiporter
subunit F; Reviewed.
Length = 87
Score = 30.3 bits (69), Expect = 0.42
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 2/43 (4%)
Query: 310 VGLSMVVIAEITIFLITNFLSHSTVSLFYYAFLKAFFLPPLPT 352
V MV A I L + S++Y L A L L T
Sbjct: 35 VISDMVFYAMALILLCLGLYNG--TSIYYDIALAAGLLGFLGT 75
>gnl|CDD|240541 cd13136, MATE_DinF_like, DinF and similar proteins, a subfamily of
the multidrug and toxic compound extrusion (MATE)-like
proteins. Escherichia coli DinF is a membrane protein
that has been found to protect cells against oxidative
stress and bile salts. The expression of DinF is
regulated as part of the SOS system. It may act by
detoxifying oxidizing molecules that have the potential
to damage DNA. Some member of this family have been
reported to enhance the virulence of plant pathogenic
bacteria by enhancing their ability to grow in the
presence of toxic compounds. Proteins from the MATE
family are involved in exporting metabolites across the
cell membrane and are often responsible for multidrug
resistance (MDR).
Length = 424
Score = 31.8 bits (73), Expect = 0.62
Identities = 12/38 (31%), Positives = 15/38 (39%), Gaps = 2/38 (5%)
Query: 299 GAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSL 336
G YLG V L + T+F + FL T L
Sbjct: 31 GHLGSAAYLGAVALGTTIFN--TLFWLFGFLRMGTTGL 66
>gnl|CDD|240390 PTZ00376, PTZ00376, aspartate aminotransferase; Provisional.
Length = 404
Score = 28.7 bits (65), Expect = 6.4
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 3 LRFSHDEPTPSYPRNPGWINRHAIVQ 28
L+ T Y NP W N I +
Sbjct: 117 LKRFLPAGTTVYVSNPTWPNHVNIFK 142
>gnl|CDD|148734 pfam07297, DPM2, Dolichol phosphate-mannose biosynthesis regulatory
protein (DPM2). This family consists of several
eukaryotic dolichol phosphate-mannose biosynthesis
regulatory (DPM2) proteins. Biosynthesis of
glycosylphosphatidylinositol and N-glycan precursor is
dependent upon a mannosyl donor, dolichol
phosphate-mannose (DPM). DPM2, an 84 amino acid membrane
protein expressed in the endoplasmic reticulum (ER),
makes a complex with DPM1 that is essential for the ER
localisation and stable expression of DPM1. Moreover,
DPM2 enhances binding of dolichol phosphate, a substrate
of DPM synthase. Biosynthesis of DPM in mammalian cells
is regulated by DPM2.
Length = 80
Score = 26.2 bits (58), Expect = 8.8
Identities = 8/41 (19%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 127 VGLSMVVIAVSLFYYAFLKAFFLP------PLPATMTPEGW 161
VGL ++ +++ +F Y + LP + + P +
Sbjct: 8 VGLGLLAVSLIIFTYYTIWVILLPFVDSDHVIHSFFLPREY 48
>gnl|CDD|233534 TIGR01693, UTase_glnD, [Protein-PII] uridylyltransferase. This
model describes GlnD, the
uridylyltransferase/uridylyl-removing enzyme for the
nitrogen regulatory protein PII. Not all homologs of PII
share the property of uridylyltransferase modification
on the characteristic Tyr residue (see Prosite pattern
PS00496 and document PDOC00439), but the modification
site is preserved in the PII homolog of all species with
a member of this family [Central intermediary
metabolism, Nitrogen metabolism, Regulatory functions,
Protein interactions].
Length = 850
Score = 28.1 bits (63), Expect = 9.4
Identities = 20/67 (29%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 35 LTRLFPFTGNREVVGHGRNGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHWNALSK 94
L RL+ F G E G + YG L P+ D DLL L + + K
Sbjct: 29 LIRLWDFIGISEHSGIALVAVGGYGRGELAPYS-------DIDLLFLHDGKPAEE-VEPK 80
Query: 95 EEKKMLY 101
E + LY
Sbjct: 81 IE-RFLY 86
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
0.321 0.139 0.448
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: 22,421,561
Number of extensions: 2201393
Number of successful extensions: 1993
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1988
Number of HSP's successfully gapped: 20
Length of query: 415
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 316
Effective length of database: 6,546,556
Effective search space: 2068711696
Effective search space used: 2068711696
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: 60 (26.9 bits)