RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9433
(105 letters)
>gnl|CDD|239579 cd03499, SQR_TypeC_SdhC, Succinate:quinone oxidoreductase (SQR)
Type C subfamily, Succinate dehydrogenase C (SdhC)
subunit; composed of bacterial SdhC and eukaryotic large
cytochrome b binding (CybL) proteins. SQR catalyzes the
oxidation of succinate to fumarate coupled to the
reduction of quinone to quinol. Members of this family
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. Proteins in this
subfamily are classified as Type C SQRs because they
contain two transmembrane subunits and one heme group.
The heme and quinone binding sites reside in the
transmembrane subunits. The SdhC or CybL protein is one
of the two transmembrane subunits of bacterial and
eukaryotic SQRs. The two-electron oxidation of succinate
in the flavoprotein active site is coupled to the
two-electron reduction of quinone in the membrane anchor
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.
Length = 117
Score = 80.7 bits (200), Expect = 3e-21
Identities = 38/106 (35%), Positives = 57/106 (53%), Gaps = 4/106 (3%)
Query: 1 ITSVLSITHRGTGVAL--TAYALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAF 58
+T++LSI HR TGVAL L + + S S L + + F L +
Sbjct: 14 LTAILSILHRITGVALFLGLPLLLWWLLASLSSPESFESVSALL--GSWLGKLVLFGLTW 71
Query: 59 PVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVLTL 104
+ YH NGIRHLIWD G+ L +K VY +GYA+L +++ ++L +
Sbjct: 72 ALFYHLLNGIRHLIWDLGKGLELKTVYKSGYAVLVLSVVLTVLLGI 117
>gnl|CDD|177738 PLN00127, PLN00127, succinate dehydrogenase (ubiquinone) cytochrome
b subunit; Provisional.
Length = 178
Score = 62.6 bits (152), Expect = 1e-13
Identities = 32/107 (29%), Positives = 54/107 (50%), Gaps = 2/107 (1%)
Query: 1 ITSVLSITHRGTGVALTAYALGLAGVGLTTDINSVVSFVDALNLSAPILLAG-KFILAFP 59
+ ++ SIT+R TG L+ A G + L +V + ++ P+++ KF ++FP
Sbjct: 72 VVALSSITNRVTGCVLSGGAAGGGVLALVGGSEAVPATMEGFKSGGPLIVFPAKFAVSFP 131
Query: 60 VSYHTANGIRHLIWD-TGRALTIKKVYTTGYAMLGAAILTNLVLTLL 105
YHT G+RHL+WD T L V + Y + GA+ + +L
Sbjct: 132 FVYHTLGGLRHLVWDKTTEGLDNPSVEASSYGLFGASAALSAAAAVL 178
>gnl|CDD|216313 pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase
transmembrane subunit. This family includes a
transmembrane protein from both the Succinate
dehydrogenase and Fumarate reductase complexes.
Length = 123
Score = 60.9 bits (148), Expect = 2e-13
Identities = 38/106 (35%), Positives = 54/106 (50%), Gaps = 4/106 (3%)
Query: 1 ITSVLSITHRGTGVALTAYALGLAGVGLTTDIN----SVVSFVDALNLSAPILLAGKFIL 56
+ ++LSI HR TGVAL + L L + S V LS+P L +L
Sbjct: 18 LGTILSILHRITGVALAVLLIHLLLWLLLLALLLGPESYARVVGVAWLSSPFKLILLLLL 77
Query: 57 AFPVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVL 102
+ YH ANG+RHLIWD G+ L +K TG +L +++ L+L
Sbjct: 78 LLALFYHAANGLRHLIWDVGKGLELKTARKTGLLVLALSVVLTLLL 123
>gnl|CDD|234076 TIGR02970, succ_dehyd_cytB, succinate dehydrogenase, cytochrome
b556 subunit. In E. coli and many other bacteria, two
small, hydrophobic, mutually homologous subunits of
succinate dehydrogenase, a TCA cycle enzyme, are SdhC
and SdhD. This family is the SdhC, the cytochrome b
subunit, called b556 in bacteria and b560 in
mitochondria. SdhD (see TIGR02968) is called the
hydrophobic membrane anchor subunit, although both SdhC
and SdhD participate in anchoring the complex. In some
bacteria, this cytochrome b subunit is replaced my a
member of the cytochrome b558 family (see TIGR02046)
[Energy metabolism, TCA cycle].
Length = 120
Score = 55.7 bits (135), Expect = 2e-11
Identities = 33/106 (31%), Positives = 54/106 (50%), Gaps = 2/106 (1%)
Query: 1 ITSVLSITHRGTGVALTAYALGLA-GVGLTTDINSVVSFVDALNLSAPILLAGKFILAFP 59
IT++LSI HR TGV L L + L+ + V AL LS+P+ + L +
Sbjct: 16 ITAILSILHRITGVLLFFGLPFLLWWLSLSLSSPESFATVHAL-LSSPLGKLILWGLLWA 74
Query: 60 VSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVLTLL 105
+ YH GIRHL+WD G L +K + + +L +++ ++ +
Sbjct: 75 LLYHLLAGIRHLLWDLGYGLELKSARISAWVVLVLSLVLTILAGIW 120
>gnl|CDD|224920 COG2009, SdhC, Succinate dehydrogenase/fumarate reductase,
cytochrome b subunit [Energy production and conversion].
Length = 132
Score = 50.8 bits (122), Expect = 2e-09
Identities = 34/109 (31%), Positives = 50/109 (45%), Gaps = 4/109 (3%)
Query: 1 ITSVLSITHRGTGVALTAY---ALGLAGVGLTTDINSVVSFVDALNLSAPILLA-GKFIL 56
IT SI HR +GV L + + LA L + +F L ++ L
Sbjct: 16 ITMYASILHRISGVILAFFLFVHILLASSWLAGSASFNAAFEFYHALLGSFIVKLVLLGL 75
Query: 57 AFPVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVLTLL 105
+ YH NGIRHL+WD G L +K V TG A++ + +T +L +
Sbjct: 76 VLALLYHGLNGIRHLLWDFGYGLELKGVGYTGAALVFFSAVTLTLLLWV 124
>gnl|CDD|239573 cd03493, SQR_QFR_TM, Succinate:quinone oxidoreductase (SQR) and
Quinol:fumarate reductase (QFR) family, transmembrane
subunits; SQR catalyzes the oxidation of succinate to
fumarate coupled to the reduction of quinone to quinol,
while QFR catalyzes the reverse reaction. SQR, also
called succinate dehydrogenase or Complex II, is part
of the citric acid cycle and the aerobic respiratory
chain, while QFR is involved in anaerobic respiration
with fumarate as the terminal electron acceptor. SQRs
may reduce either high or low potential quinones while
QFRs oxidize only low potential quinols. SQR and QFR
share a common subunit arrangement, composed of a
flavoprotein catalytic subunit, an iron-sulfur protein
and one or two hydrophobic transmembrane subunits. The
structural arrangement allows efficient electron
transfer between the catalytic subunit, through
iron-sulfur centers, and the transmembrane subunit(s)
containing the electron donor/acceptor (quinol or
quinone). The reversible reduction of quinone is an
essential feature of respiration, allowing the transfer
of electrons between respiratory complexes. SQRs and
QFRs can be classified into five types (A-E) according
to the number of their hydrophobic subunits and heme
groups. This classification is consistent with the
characteristics and phylogeny of the catalytic and
iron-sulfur subunits. Type E proteins, e.g.
non-classical archael SQRs, contain atypical
transmembrane subunits and are not included in this
hierarchy. The heme and quinone binding sites reside in
the transmembrane subunits. Although succinate
oxidation and fumarate reduction are carried out by
separate enzymes in most organisms, some bifunctional
enzymes that exhibit both SQR and QFR activities exist.
Length = 98
Score = 45.3 bits (108), Expect = 1e-07
Identities = 32/92 (34%), Positives = 42/92 (45%)
Query: 7 ITHRGTGVALTAYALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAFPVSYHTAN 66
I HR TGVAL + L LS+P+ +L + YH N
Sbjct: 1 ILHRITGVALLLFLPLHLLGLLALLGGPYAFAEVVAFLSSPLGKLLYLLLLLALLYHALN 60
Query: 67 GIRHLIWDTGRALTIKKVYTTGYAMLGAAILT 98
GIRHLIWD G+ L +K GYA+L ++L
Sbjct: 61 GIRHLIWDYGKGLELKLRKALGYAVLALSVLL 92
>gnl|CDD|181900 PRK09487, sdhC, succinate dehydrogenase cytochrome b556 large
membrane subunit; Provisional.
Length = 129
Score = 35.1 bits (81), Expect = 0.001
Identities = 33/108 (30%), Positives = 54/108 (50%), Gaps = 9/108 (8%)
Query: 1 ITSVLSITHRGTGVALTAYALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFIL---A 57
IT++ SI HR +GV +T A+G+ L T ++S F A + + KFI+
Sbjct: 22 ITAIASILHRVSGV-ITFVAVGILLWLLGTSLSSPEGFEQAAAIMDSFFV--KFIMWGIL 78
Query: 58 FPVSYHTANGIRHLIWDTGRALTIKKVYTTGYAMLGAAILTNLVLTLL 105
++YH GIRHL+ D G +++ G + + +VL+LL
Sbjct: 79 TALAYHVVVGIRHLLMDFGY---LEETLEAGKRSAKISFVITVVLSLL 123
>gnl|CDD|225053 COG2142, SdhD, Succinate dehydrogenase, hydrophobic anchor
subunit [Energy production and conversion].
Length = 117
Score = 31.5 bits (72), Expect = 0.025
Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 2/78 (2%)
Query: 7 ITHRGTGVALTAYALGLAGVGLTTDINSVVSFVDALNLSAPILLAGKFILAFPVSYHTAN 66
+ R T V L + LT + ++V L + P +L H N
Sbjct: 18 LLQRVTAVILVLLVIWHLYFLLTWLNATYAAWVAFL--ANPFWKVFLLLLLVAALIHAWN 75
Query: 67 GIRHLIWDTGRALTIKKV 84
G+R +I D + ++
Sbjct: 76 GLRVIIEDYIKPEKLRLA 93
>gnl|CDD|224222 COG1303, COG1303, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 179
Score = 29.2 bits (66), Expect = 0.27
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 4 VLSITHRG-------TGVALTAYALGLAGVGLTTD 31
VL + HR T VALTA A G G+ L +
Sbjct: 6 VLRLGHRPERDKRITTHVALTARAFGADGILLDGE 40
>gnl|CDD|235181 PRK03958, PRK03958, tRNA 2'-O-methylase; Reviewed.
Length = 176
Score = 27.6 bits (62), Expect = 0.93
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 4 VLSITHRG-------TGVALTAYALGLAGVGLTTD----INSVVSFVD 40
VL + HR T V LTA ALG + L ++ SV V+
Sbjct: 5 VLRLGHRPERDKRITTHVGLTARALGADKIILASNDEHVKESVEDIVE 52
>gnl|CDD|188076 TIGR00720, sda_mono, L-serine dehydratase, iron-sulfur-dependent,
single chain form. This enzyme is also called serine
deaminase and L-serine dehydratase 1. L-serine
ammonia-lyase converts serine into pyruvate in the
gluconeogenesis pathway from serine. This enzyme is
comprised of a single chain in Escherichia coli,
Mycobacterium tuberculosis, and several other species,
but has separate alpha and beta chains in Bacillus
subtilis and related species. The beta and alpha chains
are homologous to the N-terminal and C-terminal regions,
respectively, but are rather deeply branched in a UPGMA
tree. This enzyme requires iron and dithiothreitol for
activation in vitro, and is a predicted 4Fe-4S protein.
Escherichia coli Pseudomonas aeruginosa have two copies
of this protein [Energy metabolism, Amino acids and
amines, Energy metabolism, Glycolysis/gluconeogenesis].
Length = 450
Score = 27.7 bits (62), Expect = 1.2
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 16/94 (17%)
Query: 5 LSITHRGTGVALTAYA--LGLAG-VGLTTDINSVVSFVDALNLSAPILLAGKFILAFPVS 61
L++T +G G T A LGL G + T DI+S+ + ++ + + +LL G+ + F
Sbjct: 52 LALTGKGHG---TDKAVLLGLMGFLPETVDIDSIEARIEEVLENKRLLLGGQHEIPFDYE 108
Query: 62 YHT----------ANGIRHLIWDTGRALTIKKVY 85
NG+R ++ + +K Y
Sbjct: 109 KDLIFHNEFLPLHPNGMRFTAYNGDGEVLYEKTY 142
>gnl|CDD|239580 cd03500, SQR_TypeA_SdhD_like, Succinate:quinone oxidoreductase
(SQR) Type A subfamily, Succinate dehydrogenase D
(SdhD)-like subunit; SQR catalyzes the oxidation of
succinate to fumarate coupled to the reduction of
quinone to quinol. Members of this subfamily reduce low
potential quinones such as menaquinone and
thermoplasmaquinone. 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
similar to the Thermoplasma acidophilum SQR and are
classified as Type A because they contain two
transmembrane subunits as well as two heme groups.
Although there are no structures available for this
subfamily, the presence of two hemes has been proven
spectroscopically for T. acidophilum. The two membrane
anchor subunits are similar to the SdhD and SdhC
subunits of bacterial SQRs, which contain heme and
quinone binding sites. The two-electron oxidation of
succinate in the flavoprotein active site is coupled to
the two-electron reduction of quinone in the membrane
anchor 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.
Length = 106
Score = 26.9 bits (60), Expect = 1.3
Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 3/97 (3%)
Query: 9 HRGTGVALTAYALGLAGVGLTTDINSVVSFVDALN-LSAPILLAGKFILAFPVSYHTANG 67
R TGV L G V + V+ F N L++P+ +L H NG
Sbjct: 8 QRITGVFLVFLLAGHFWVQHMDNGGDVIDFAFVANRLASPLWKVWDLLLLVLALLHGGNG 67
Query: 68 IRHLIWDTGRALTIKKV--YTTGYAMLGAAILTNLVL 102
+R+++ D R +++ A L +L V+
Sbjct: 68 LRNILLDYVRRPRLRRAVKGLLYVAGLLLIVLGTYVI 104
>gnl|CDD|237478 PRK13709, PRK13709, conjugal transfer nickase/helicase TraI;
Provisional.
Length = 1747
Score = 27.1 bits (60), Expect = 2.2
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 4 VLSITHRGTGVALTAYALGLAGVGLTTDINSVVSFVDAL 42
+L T R T V G AGVG TT +V+S V+ L
Sbjct: 979 ILESTDRFTVVQ------GYAGVGKTTQFRAVMSAVNTL 1011
>gnl|CDD|198363 cd07791, FGGY_GK2_bacteria, bacterial glycerol kinase 2-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
putative bacterial glycerol kinases (GK), which may be
coded by the GK-like gene, GK2. Sequence comparison
shows members in this CD are homologs of Escherichia
coli GK. They retain all functionally important
residues, and may catalyze the Mg-ATP dependent
phosphorylation of glycerol to yield glycerol
3-phosphate (G3P). GKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 484
Score = 26.6 bits (59), Expect = 2.9
Identities = 19/48 (39%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 7 ITHRGTGVALTAYALGLAGV------GLTTDINSVVSFVDAL-NLSAP 47
IT G VA A LGL T N V FV AL L AP
Sbjct: 299 ITVTGAAVAWMADLLGLPDPAALSELAATASDNGGVYFVPALTGLGAP 346
>gnl|CDD|182840 PRK10921, PRK10921, twin-arginine protein translocation system
subunit TatC; Provisional.
Length = 258
Score = 26.3 bits (58), Expect = 3.7
Identities = 26/83 (31%), Positives = 36/83 (43%), Gaps = 20/83 (24%)
Query: 24 AGVGLTTDINSVVSFVDALNLSAPILLAGKFILAFPVSYHTANGIRHLIWD---TGRALT 80
GV ++TDI S +SFV AL +AF VS+ I L W T L
Sbjct: 143 EGVQVSTDIASYLSFVMAL------------FMAFGVSFEVPVAIVLLCWMGVTTPEDLR 190
Query: 81 IKKVYTTGYAMLGAAILTNLVLT 103
K+ Y +L A + ++LT
Sbjct: 191 KKRPY-----VLVGAFVVGMLLT 208
>gnl|CDD|239581 cd03501, SQR_TypeA_SdhC_like, Succinate:quinone oxidoreductase
(SQR) Type A subfamily, Succinate dehydrogenase C
(SdhC)-like subunit; SQR catalyzes the oxidation of
succinate to fumarate coupled to the reduction of
quinone to quinol. Members of this subfamily reduce low
potential quinones such as menaquinone and
thermoplasmaquinone. 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
similar to the Thermoplasma acidophilum SQR and are
classified as Type A because they contain two
transmembrane subunits as well as two heme groups.
Although there are no structures available for this
subfamily, the presence of two hemes has been proven
spectroscopically for T. acidophilum. The two membrane
anchor subunits are similar to the SdhD and SdhC
subunits of bacterial SQRs, which contain heme and
quinone binding sites. The two-electron oxidation of
succinate in the flavoprotein active site is coupled to
the two-electron reduction of quinone in the membrane
anchor 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.
Length = 101
Score = 25.3 bits (56), Expect = 4.0
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 9 HRGTGVALTAYALGLAGVGLTTDINSVVSFVDAL-NLSAPILLAGKFILAFPVSYHTANG 67
HR TGV + Y L L + L++ ++ + +PI G+F L V +H NG
Sbjct: 7 HRITGVVILFY-LFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVFHALNG 65
Query: 68 IRHLIWDTG 76
IR ++ D G
Sbjct: 66 IRLILVDFG 74
>gnl|CDD|213989 cd07434, PHP_PolIIIA_DnaE2, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III at
DnaE2 gene. PolIIIA DnaE2 plays a role in SOS
mutagenesis/translesion synthesis and has dominant
effects in determining GC variability in the bacterial
genome. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five
eubacterial DNA polymerases that are responsible for
the replication of the DNA duplex. PolIIIA core enzyme
catalyzes the reaction for polymerizing both DNA
strands. PolC PHP is located in a different location
compared to dnaE1, 2, and 3. dnaE1 is the longest
compared to dnaE2 and dnaE3. A unique motif was also
identified in dnaE1 and dnaE3 genes. The PHP domain has
four conserved sequence motifs and contains an
invariant histidine that is involved in metal ion
coordination. PHP domains found in DnaEs of
thermophilic origin exhibit 3'-5' exonuclease activity.
Length = 260
Score = 25.1 bits (56), Expect = 7.4
Identities = 6/19 (31%), Positives = 9/19 (47%), Gaps = 1/19 (5%)
Query: 17 TAYALGLAGVGLTTDINSV 35
A LG + + TD S+
Sbjct: 25 RAAELGYRALAI-TDECSL 42
>gnl|CDD|193569 cd08656, M28_like_6, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions.
Length = 281
Score = 24.9 bits (55), Expect = 9.4
Identities = 5/19 (26%), Positives = 8/19 (42%)
Query: 61 SYHTANGIRHLIWDTGRAL 79
S A + +W T + L
Sbjct: 188 SLRYAPSLVKKVWSTAKKL 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 0.138 0.395
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,283,875
Number of extensions: 463002
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 741
Number of HSP's successfully gapped: 64
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)