RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17595
(153 letters)
>gnl|CDD|238465 cd00925, Cyt_c_Oxidase_VIa, Cytochrome c oxidase subunit VIa.
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 VIa is expressed in two
tissue-specific isoforms in mammals but not fish. VIa-H
is the heart and skeletal muscle isoform; VIa-L is the
liver or non-muscle isoform. Mammalian VIa-H induces a
slip in CcO (decrease in proton/electron stoichiometry)
at high intramitochondrial ATP/ADP ratios, while VIa-L
induces a permanent slip in CcO, depending on the
presence of cardiolipin and palmitate.
Length = 86
Score = 111 bits (279), Expect = 6e-33
Identities = 43/74 (58%), Positives = 54/74 (72%), Gaps = 1/74 (1%)
Query: 78 RLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFPWGDGNHTL 137
LW+ ++++ ALP AL + YL+H+ E E H RPEFV+ E+L IR + FPWGDGN TL
Sbjct: 14 ELWKKISFYVALPAVALCMLNAYLKHK-EHEEHERPEFVEYEHLNIRTKPFPWGDGNKTL 72
Query: 138 FHNKHVNALPEGYE 151
FHN HVNALP GYE
Sbjct: 73 FHNPHVNALPTGYE 86
>gnl|CDD|145298 pfam02046, COX6A, Cytochrome c oxidase subunit VIa.
Length = 116
Score = 102 bits (256), Expect = 5e-29
Identities = 35/74 (47%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 78 RLWRNLTYFGALPCCALVGVYVYLEHQAEEEH--HV--RPEFVKREYLYIRNRRFPWGDG 133
+LW+ L+Y+ A+P AL + Y EH H+ R EFV+ EY IR + FPWGDG
Sbjct: 43 KLWKKLSYYVAIPAIALCAINAYFLEAEHAEHREHLPDREEFVEYEYQNIRTKPFPWGDG 102
Query: 134 NHTLFHNKHVNALP 147
+ TLF N HVNA P
Sbjct: 103 DKTLFWNPHVNAHP 116
>gnl|CDD|178205 PLN02595, PLN02595, cytochrome c oxidase subunit VI protein.
Length = 102
Score = 37.9 bits (87), Expect = 3e-04
Identities = 25/63 (39%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 80 WRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFPWG-DGNHTLF 138
W +TY G C AL VYV + HH + Y++IRN+ FPWG DG +
Sbjct: 44 WEKITYLGIASCTAL-AVYVL-----SKGHHHGEDPPAYPYMHIRNKEFPWGPDGLFEVK 97
Query: 139 HNK 141
HNK
Sbjct: 98 HNK 100
Score = 28.6 bits (63), Expect = 0.61
Identities = 27/80 (33%), Positives = 36/80 (45%), Gaps = 10/80 (12%)
Query: 3 SRLGQMMMRKFSTSPA--MKSSAGNPDAVKL--WRNLTYFGALPCCALVGVYVYLEHQAE 58
SR K S +P SSAG+ DA + W +TY G C AL VYV
Sbjct: 11 SRAVTRAAPKTSVAPKRNFSSSAGHDDAYEAAKWEKITYLGIASCTAL-AVYVL-----S 64
Query: 59 EAHHVRPEFVKREYLYIRNR 78
+ HH + Y++IRN+
Sbjct: 65 KGHHHGEDPPAYPYMHIRNK 84
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 33.6 bits (77), Expect = 0.028
Identities = 19/62 (30%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 72 YLYIRNRLWRNLTYFGALPCCAL----VGVYVYLEHQAEEEHHVRPEFVKREYLYIRNRR 127
+ +R L Y AL A + V L AE H+ RP F L IR R
Sbjct: 513 FEELRELL---KKYLEALQEAARALAELDVLANLAEVAETLHYTRPRFGDDPQLRIREGR 569
Query: 128 FP 129
P
Sbjct: 570 HP 571
Score = 29.4 bits (66), Expect = 0.76
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 45 ALVGVYVYLEHQAEEAHHVRPEFVKREYLYIRN 77
A + V L AE H+ RP F L IR
Sbjct: 535 AELDVLANLAEVAETLHYTRPRFGDDPQLRIRE 567
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 29.2 bits (66), Expect = 1.1
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 97 VYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFP 129
V L A E+++VRPEFV L I+ R P
Sbjct: 554 VLSSLAEIAAEQNYVRPEFVDSNDLEIKEGRHP 586
>gnl|CDD|185438 PTZ00087, PTZ00087, thrombosponding-related protein; Provisional.
Length = 340
Score = 26.8 bits (59), Expect = 4.7
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 90 PCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRNRRF 128
P C VG + L +E R EF+ Y+ I+N +F
Sbjct: 48 PECT-VGKGLQLGQAKQESDVNRKEFLLHNYVVIKNSQF 85
>gnl|CDD|224231 COG1312, UxuA, D-mannonate dehydratase [Carbohydrate transport and
metabolism].
Length = 362
Score = 26.6 bits (59), Expect = 5.6
Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 22 SAGNPDAVKLWRNLTYF--GALPCCALVGV 49
G D KLW NL YF +P VGV
Sbjct: 177 LYGGIDEEKLWENLAYFLKEVIPVAEEVGV 206
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 0.139 0.454
Gapped
Lambda K H
0.267 0.0614 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,186,878
Number of extensions: 744688
Number of successful extensions: 747
Number of sequences better than 10.0: 1
Number of HSP's gapped: 741
Number of HSP's successfully gapped: 23
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
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: 40 (21.6 bits)
S2: 55 (25.2 bits)