RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1108
(79 letters)
>gnl|CDD|145298 pfam02046, COX6A, Cytochrome c oxidase subunit VIa.
Length = 116
Score = 65.1 bits (159), Expect = 2e-15
Identities = 26/94 (27%), Positives = 37/94 (39%), Gaps = 19/94 (20%)
Query: 2 ASRLGQMMMRKFSTSPAMK------------SSAGNPDAVKLWRNLTYFGALPCCALVGV 49
Q R S++ A + G KLW+ L+Y+ A+P AL +
Sbjct: 6 LRAPAQTQRRFASSAAAGGNAFVREREAVKEHAEG---TTKLWKKLSYYVAIPAIALCAI 62
Query: 50 YVYLEHQAEEEH--HV--RPEFVKREYLYIRNRN 79
Y EH H+ R EFV+ EY IR +
Sbjct: 63 NAYFLEAEHAEHREHLPDREEFVEYEYQNIRTKP 96
>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 = 61.2 bits (149), Expect = 3e-14
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 18 AMKSSAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
+LW+ ++++ ALP AL + YL+H+ E E H RPEFV+ E+L IR
Sbjct: 2 TAAKGEHAAGTSELWKKISFYVALPAVALCMLNAYLKHK-EHEEHERPEFVEYEHLNIRT 60
Query: 78 RN 79
+
Sbjct: 61 KP 62
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 29.7 bits (67), Expect = 0.10
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 45 ALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
A + V L AE H+ RP F L IR
Sbjct: 535 AELDVLANLAEVAETLHYTRPRFGDDPQLRIRE 567
>gnl|CDD|178205 PLN02595, PLN02595, cytochrome c oxidase subunit VI protein.
Length = 102
Score = 28.3 bits (62), Expect = 0.22
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 EEHHVRPEFVKREYLYIRNR 78
+ HH + Y++IRN+
Sbjct: 65 KGHHHGEDPPAYPYMHIRNK 84
>gnl|CDD|224231 COG1312, UxuA, D-mannonate dehydratase [Carbohydrate transport and
metabolism].
Length = 362
Score = 27.3 bits (61), Expect = 0.82
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
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 26.9 bits (60), Expect = 1.1
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 49 VYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
V L A E+++VRPEFV L I+
Sbjct: 554 VLSSLAEIAAEQNYVRPEFVDSNDLEIKE 582
>gnl|CDD|217727 pfam03786, UxuA, D-mannonate dehydratase (UxuA). UxuA (this
family) and UxuB are required for hexuronate
degradation.
Length = 350
Score = 26.2 bits (58), Expect = 1.8
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 24 GNPDAVKLWRNLTYF--GALPCCALVGV 49
D KLW NL YF +P VGV
Sbjct: 173 KKIDEEKLWDNLAYFLDEIIPVAEEVGV 200
>gnl|CDD|180519 PRK06298, PRK06298, type III secretion system protein; Validated.
Length = 356
Score = 25.2 bits (55), Expect = 4.4
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 7 QMMMRKFSTSPAMKSSAGNPD 27
++ M KF K + GNP+
Sbjct: 213 ELKMEKFEVKQEFKDTEGNPE 233
>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 = 24.5 bits (54), Expect = 6.2
Identities = 11/22 (50%), Positives = 11/22 (50%), Gaps = 5/22 (22%)
Query: 63 VRPEFVKREYL-----YIRNRN 79
VRPEFV E L Y NR
Sbjct: 247 VRPEFVTEEALELIKKYCDNRR 268
>gnl|CDD|183561 PRK12504, PRK12504, putative monovalent cation/H+ antiporter
subunit B; Reviewed.
Length = 178
Score = 24.5 bits (54), Expect = 6.6
Identities = 12/64 (18%), Positives = 20/64 (31%), Gaps = 8/64 (12%)
Query: 24 GNPDAVKLWRNLTYFGALPCCALVGVYVYL--------EHQAEEEHHVRPEFVKREYLYI 75
G PD K++ + L L +Y + A HV +++ Y
Sbjct: 77 GRPDVDKVFERINVPAVLIALVLFVALLYAVPDLPAFGDPNAPAHSHVTQYYIENTYRET 136
Query: 76 RNRN 79
N
Sbjct: 137 GIPN 140
>gnl|CDD|235172 PRK03906, PRK03906, mannonate dehydratase; Provisional.
Length = 385
Score = 24.4 bits (54), Expect = 7.1
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 27 DAVKLWRNLTYF--GALPCCALVGV 49
D KL NL YF +P VGV
Sbjct: 204 DEEKLRENLAYFLKAIIPVAEEVGV 228
>gnl|CDD|185438 PTZ00087, PTZ00087, thrombosponding-related protein; Provisional.
Length = 340
Score = 24.5 bits (53), Expect = 7.8
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 42 PCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
P C VG + L +E R EF+ Y+ I+N
Sbjct: 48 PECT-VGKGLQLGQAKQESDVNRKEFLLHNYVVIKN 82
>gnl|CDD|202369 pfam02742, Fe_dep_repr_C, Iron dependent repressor, metal binding
and dimerisation domain. This family includes the
Diphtheria toxin repressor.
Length = 70
Score = 23.3 bits (51), Expect = 8.6
Identities = 6/18 (33%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 54 EHQAEE-EHHVRPEFVKR 70
+AE EH + E + R
Sbjct: 34 HEEAERLEHVLSDELIDR 51
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
0.323 0.134 0.416
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: 4,071,408
Number of extensions: 307675
Number of successful extensions: 303
Number of sequences better than 10.0: 1
Number of HSP's gapped: 300
Number of HSP's successfully gapped: 16
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)