RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17596
(105 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 (280), Expect = 8e-34
Identities = 42/86 (48%), Positives = 55/86 (63%), Gaps = 1/86 (1%)
Query: 18 AMKSAAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
+LW+ ++++ ALP AL + YL+H+ E E H RPEFV+ E+L IR
Sbjct: 2 TAAKGEHAAGTSELWKKISFYVALPAVALCMLNAYLKHK-EHEEHERPEFVEYEHLNIRT 60
Query: 78 RRFPWGDGNHSLFHNKHVNALPEGYE 103
+ FPWGDGN +LFHN HVNALP GYE
Sbjct: 61 KPFPWGDGNKTLFHNPHVNALPTGYE 86
>gnl|CDD|145298 pfam02046, COX6A, Cytochrome c oxidase subunit VIa.
Length = 116
Score = 107 bits (270), Expect = 5e-32
Identities = 41/114 (35%), Positives = 53/114 (46%), Gaps = 19/114 (16%)
Query: 2 ASRLGQMMMRKFSTSPAMK------------SAAGNPDAVKLWRNLTYFGALPCCALVGV 49
Q R S++ A A G KLW+ L+Y+ A+P AL +
Sbjct: 6 LRAPAQTQRRFASSAAAGGNAFVREREAVKEHAEG---TTKLWKKLSYYVAIPAIALCAI 62
Query: 50 YVYLEHQAEEEH--HV--RPEFVKREYLYIRNRRFPWGDGNHSLFHNKHVNALP 99
Y EH H+ R EFV+ EY IR + FPWGDG+ +LF N HVNA P
Sbjct: 63 NAYFLEAEHAEHREHLPDREEFVEYEYQNIRTKPFPWGDGDKTLFWNPHVNAHP 116
>gnl|CDD|178205 PLN02595, PLN02595, cytochrome c oxidase subunit VI protein.
Length = 102
Score = 41.0 bits (95), Expect = 8e-06
Identities = 35/96 (36%), Positives = 46/96 (47%), Gaps = 11/96 (11%)
Query: 3 SRLGQMMMRKFSTSPA--MKSAAGNPDAVKL--WRNLTYFGALPCCALVGVYVYLEHQAE 58
SR K S +P S+AG+ DA + W +TY G C AL VYV
Sbjct: 11 SRAVTRAAPKTSVAPKRNFSSSAGHDDAYEAAKWEKITYLGIASCTAL-AVYVL-----S 64
Query: 59 EEHHVRPEFVKREYLYIRNRRFPWG-DGNHSLFHNK 93
+ HH + Y++IRN+ FPWG DG + HNK
Sbjct: 65 KGHHHGEDPPAYPYMHIRNKEFPWGPDGLFEVKHNK 100
>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 = 0.011
Identities = 14/37 (37%), Positives = 16/37 (43%)
Query: 45 ALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFP 81
A + V L AE H+ RP F L IR R P
Sbjct: 535 AELDVLANLAEVAETLHYTRPRFGDDPQLRIREGRHP 571
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 29.2 bits (66), Expect = 0.37
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 49 VYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFP 81
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 = 27.2 bits (60), Expect = 1.7
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 42 PCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRNRRF 80
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 = 26.9 bits (60), Expect = 1.8
Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 22 AAGNPDAVKLWRNLTYF--GALPCCALVGV 49
G D KLW NL YF +P VGV
Sbjct: 177 LYGGIDEEKLWENLAYFLKEVIPVAEEVGV 206
>gnl|CDD|129413 TIGR00313, cobQ, cobyric acid synthase CobQ. [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 475
Score = 26.7 bits (59), Expect = 2.7
Identities = 22/97 (22%), Positives = 32/97 (32%), Gaps = 11/97 (11%)
Query: 7 QMMMRKFSTSPAMKSAAGNPDAVKLWRNLTYFG----ALPCCALV-------GVYVYLEH 55
QM+ ++ +S G+ + + L TYFG V V Y H
Sbjct: 330 QMLGKELIDKEKKESDVGDIEGLGLLDAKTYFGEDKITKQSQGRVEGNNRGETVKGYEIH 389
Query: 56 QAEEEHHVRPEFVKREYLYIRNRRFPWGDGNHSLFHN 92
+ +P F + N WG H LF N
Sbjct: 390 EGFTRSKEKPLFKIERFGNCGNDGNAWGTYLHGLFEN 426
>gnl|CDD|217727 pfam03786, UxuA, D-mannonate dehydratase (UxuA). UxuA (this
family) and UxuB are required for hexuronate
degradation.
Length = 350
Score = 25.8 bits (57), Expect = 4.8
Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 22 AAGNPDAVKLWRNLTYF--GALPCCALVGV 49
A D KLW NL YF +P VGV
Sbjct: 171 AYKKIDEEKLWDNLAYFLDEIIPVAEEVGV 200
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 25.4 bits (56), Expect = 6.8
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 5/21 (23%)
Query: 75 IRNRRFPWG-----DGNHSLF 90
+R R++PWG D HS F
Sbjct: 240 VRGRKYPWGVVEIDDEEHSDF 260
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 25.2 bits (56), Expect = 8.4
Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 5/22 (22%)
Query: 75 IRNRRFPWG-----DGNHSLFH 91
+R R++PWG + H F
Sbjct: 219 VRGRKYPWGVVEVENEEHCDFV 240
>gnl|CDD|234440 TIGR04013, B12_SAM_MJ_1487, B12-binding domain/radical SAM domain
protein, MJ_1487 family. Members of this family have
both a B12 binding homology domain (pfam02310) and a
radical SAM domain (pfam04055), and occur only once per
genome. Some species with members of this family have a
related protein with similar domain architecture. This
protein is occurs largely in archaeal methanogens but
also in a few bacteria, including Thermotoga maritima
and Myxococcus xanthus [Unknown function, Enzymes of
unknown specificity].
Length = 382
Score = 24.9 bits (55), Expect = 9.8
Identities = 12/22 (54%), Positives = 12/22 (54%), Gaps = 5/22 (22%)
Query: 63 VRPEFVKREYL-----YIRNRR 79
VRPEFV E L Y NRR
Sbjct: 247 VRPEFVTEEALELIKKYCDNRR 268
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
0.322 0.136 0.438
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,553,835
Number of extensions: 468214
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 20
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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: 53 (24.3 bits)