RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10707
(130 letters)
>gnl|CDD|239576 cd03496, SQR_TypeC_CybS, SQR catalyzes the oxidation of succinate
to fumarate coupled to the reduction of quinone to
quinol. Eukaryotic SQRs reduce high potential quinones
such as ubiquinone. SQR is also called succinate
dehydrogenase or Complex II, and is part of the citric
acid cycle and the aerobic respiratory chain. SQR is
composed of a flavoprotein catalytic subunit, an
iron-sulfur protein and one or two hydrophobic
transmembrane subunits. Members of this subfamily are
classified as Type C SQRs because they contain two
transmembrane subunits and one heme group. CybS and
CybL are the two transmembrane proteins of eukaryotic
SQRs. They contain heme and quinone binding sites. CybS
is the eukaryotic homolog of the bacterial SdhD subunit.
The two-electron oxidation of succinate in the
flavoprotein active site is coupled to the two-electron
reduction of quinone in the transmembrane subunits via
electron transport through FAD and three iron-sulfur
centers. The reversible reduction of quinone is an
essential feature of respiration, allowing transfer of
electrons between respiratory complexes. Mutations in
human Complex II result in various physiological
disorders including hereditary paraganglioma and
pheochromocytoma tumors. The gene encoding for the SdhD
subunit is classified as a tumor suppressor gene.
Length = 104
Score = 95.8 bits (239), Expect = 5e-27
Identities = 37/105 (35%), Positives = 58/105 (55%), Gaps = 3/105 (2%)
Query: 24 SDHTTLWTIERFLSAGLLAVIPAAYLVPSV--ALEYALVVSIVMHSHWGIEALVVDYARP 81
+ WT ER L+ LL + PAA+ P + ++ AL ++++HSHWG E+ ++DY
Sbjct: 1 LHGSYHWTFERILAVSLLPLTPAAFFAPGLSPVMDAALAAALLLHSHWGFESCIIDYVPK 60
Query: 82 EVVGVALAKIFHLSVYILSIITLAGLMNLILNGGGVVEGTKKLWA 126
V G L K+ +Y S ++LAGL N G+ + KKLW+
Sbjct: 61 RVGG-KLHKLAMYLLYAGSALSLAGLYYFNTNDVGLTKAVKKLWS 104
>gnl|CDD|218557 pfam05328, CybS, CybS. This family consists of several eukaryotic
succinate dehydrogenase [ubiquinone] cytochrome B small
subunit, mitochondrial precursor (CybS) proteins. SDHD
encodes the small subunit (cybS) of cytochrome b in
succinate-ubiquinone oxidoreductase (mitochondrial
complex II). Mitochondrial complex II is involved in the
Krebs cycle and in the aerobic electron transport chain.
It contains four proteins. The catalytic core consists
of a flavoprotein and an iron-sulfur protein; these
proteins are anchored to the mitochondrial inner
membrane by the large subunit of cytochrome b (cybL) and
cybS, which together comprise the heme-protein
cytochrome b. Mutations in the SDHD gene can lead to
hereditary paraganglioma, characterized by the
development of benign, vascularised tumours in the head
and neck.
Length = 107
Score = 94.2 bits (235), Expect = 2e-26
Identities = 38/107 (35%), Positives = 60/107 (56%), Gaps = 3/107 (2%)
Query: 22 SKSDHTTLWTIERFLSAGLLAVIPAAYL--VPSVALEYALVVSIVMHSHWGIEALVVDYA 79
+KS + WT ER L+ GLL + PA +L PS ++ L ++++H HWG ++ ++DY
Sbjct: 2 NKSHGSYHWTFERILAVGLLPLTPAPFLAGSPSPVMDATLAAALLLHCHWGFQSCIIDYI 61
Query: 80 RPEVVGVALAKIFHLSVYILSIITLAGLMNLILNGGGVVEGTKKLWA 126
V G L K+ +Y+ + +TL GL N G+ E KKLW+
Sbjct: 62 PKRVYG-KLHKLAMYLLYLGTALTLYGLYYFETNDVGLTEAVKKLWS 107
>gnl|CDD|180839 PRK07103, PRK07103, polyketide beta-ketoacyl:acyl carrier protein
synthase; Validated.
Length = 410
Score = 30.0 bits (68), Expect = 0.33
Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 37 SA-GLLAVIPAAYLVPSVALEYALVVSIVMH-SHWGIEAL 74
SA G LAVI AA LV S +++ + V +M S+W +AL
Sbjct: 167 SASGQLAVIQAARLVQSGSVDACIAVGALMDLSYWECQAL 206
>gnl|CDD|192905 pfam11982, DUF3483, Domain of unknown function (DUF3483). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is about 230
amino acids in length. This domain is found associated
with pfam02754.
Length = 224
Score = 28.9 bits (65), Expect = 0.57
Identities = 14/60 (23%), Positives = 21/60 (35%)
Query: 35 FLSAGLLAVIPAAYLVPSVALEYALVVSIVMHSHWGIEALVVDYARPEVVGVALAKIFHL 94
F L +PAA ++P+ + L + WG L + A A HL
Sbjct: 138 FALGFFLTTLPAAGILPADLGGWVLAALLAAAVAWGGSELFFGMTWGGPMKHAFAGALHL 197
>gnl|CDD|180343 PRK05993, PRK05993, short chain dehydrogenase; Provisional.
Length = 277
Score = 27.3 bits (61), Expect = 2.2
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 70 GIEALVVDYARPEVVGVALAKIFHLS 95
G+EA +DYA PE + +A++ LS
Sbjct: 48 GLEAFQLDYAEPESIAALVAQVLELS 73
>gnl|CDD|236104 PRK07811, PRK07811, cystathionine gamma-synthase; Provisional.
Length = 388
Score = 26.1 bits (58), Expect = 7.0
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 66 HSHWGIEALVVDYARPEVVGVALA 89
+ WG+E VD + + V A+
Sbjct: 121 FTRWGVEYTPVDLSDLDAVRAAIT 144
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 25.9 bits (57), Expect = 7.3
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 33 ERFLSAGLLAVIPAAYLVPSVALEYALVVSIVMHSHWGIEALVVDYARPEVVGVALAKIF 92
ER L+A ++ + + +P L+ + +G + Y V + A++
Sbjct: 382 ERLLTALVIPFMSCSARLPV----IVLLFAAAFPGKYGGIVIFSLYLLGFVAALITARLL 437
Query: 93 HLSVY 97
V+
Sbjct: 438 PGEVF 442
>gnl|CDD|182937 PRK11061, PRK11061, fused phosphoenolpyruvate-protein
phosphotransferase PtsP/GAF domain; Provisional.
Length = 748
Score = 25.7 bits (57), Expect = 8.5
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 36 LSAGLLAVIPAAYLVPSVALEYALVVSIVMHSHWGIEALVVDYARPEVVGV 86
L+A LLA +P L V + A +SH I LV P V+G
Sbjct: 330 LTATLLAELPQDRLAGVVVRDGA------ANSHAAI--LVRALGIPTVMGA 372
>gnl|CDD|233669 TIGR01984, UbiH, 2-polyprenyl-6-methoxyphenol 4-hydroxylase. This
model represents the FAD-dependent monoxygenase
responsible for the second hydroxylation step in the
aerobic ubiquinone bioynthetic pathway. The scope of
this model is limited to the proteobacteria. This family
is closely related to the UbiF hydroxylase which
catalyzes the final hydroxylation step. The enzyme has
also been named VisB due to a mutant VISible light
sensitive phenotype [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 382
Score = 25.7 bits (57), Expect = 8.8
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 7 KHFSTTQVQHD-------AAVHSKSDHTTLWTIERFLSAGLLAVIP 45
+ S +HD A + + H ERF G LA++P
Sbjct: 166 ELLSIPTEEHDYNQTALIANIRHEQPHQG-CAFERFTPHGPLALLP 210
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 0.135 0.395
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,653,954
Number of extensions: 613377
Number of successful extensions: 626
Number of sequences better than 10.0: 1
Number of HSP's gapped: 621
Number of HSP's successfully gapped: 48
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
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)