RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1305
(68 letters)
>gnl|CDD|173847 cd01158, SCAD_SBCAD, Short chain acyl-CoA dehydrogenases and
eukaryotic short/branched chain acyl-CoA
dehydrogenases. Short chain acyl-CoA dehydrogenase
(SCAD). SCAD is a mitochondrial beta-oxidation enzyme.
It catalyzes the alpha,beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of SCAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. This subgroup also
contains the eukaryotic short/branched chain acyl-CoA
dehydrogenase(SBCAD), the bacterial butyryl-CoA
dehydorgenase(BCAD) and 2-methylbutyryl-CoA
dehydrogenase, which is involved in isoleucine
catabolism. These enzymes are homotetramers.
Length = 373
Score = 97.0 bits (242), Expect = 4e-26
Identities = 36/67 (53%), Positives = 54/67 (80%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALH 60
M++KT RDFA++E+ P+AA++D++ FP + IK++ LGLMG+ + EEYGGAGLD LA
Sbjct: 5 MIRKTVRDFAEKEIAPLAAEMDEKGEFPREVIKEMAELGLMGIPIPEEYGGAGLDFLAYA 64
Query: 61 VAMEEIA 67
+A+EE+A
Sbjct: 65 IAIEELA 71
>gnl|CDD|217220 pfam02771, Acyl-CoA_dh_N, Acyl-CoA dehydrogenase, N-terminal
domain. The N-terminal domain of Acyl-CoA
dehydrogenase is an all-alpha domain.
Length = 113
Score = 89.8 bits (224), Expect = 2e-25
Identities = 33/67 (49%), Positives = 47/67 (70%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALH 60
L+ T R+FA++E+ P AA+ D+E FP + +KLG LGL+G+ + EEYGGAGLD L
Sbjct: 6 ALRDTVREFAEEEVAPHAAEWDEEGEFPRELWRKLGELGLLGLTIPEEYGGAGLDYLEYA 65
Query: 61 VAMEEIA 67
+ EE+A
Sbjct: 66 LVAEELA 72
>gnl|CDD|173845 cd01156, IVD, Isovaleryl-CoA dehydrogenase. Isovaleryl-CoA
dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase,
which catalyzes the third step in leucine catabolism,
the conversion of isovaleryl-CoA (3-methylbutyryl-CoA)
into 3-methylcrotonyl-CoA. IVD is a homotetramer and
has the greatest affinity for small branched chain
substrates.
Length = 376
Score = 82.1 bits (203), Expect = 1e-20
Identities = 33/67 (49%), Positives = 52/67 (77%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALH 60
ML+++ R+FAQ+E+ P+AAK+D+++ FP D +K+G LGL+G+ EEYGG+G+ LA
Sbjct: 8 MLRQSVREFAQKEIAPLAAKIDRDNEFPRDLWRKMGKLGLLGITAPEEYGGSGMGYLAHV 67
Query: 61 VAMEEIA 67
+ MEEI+
Sbjct: 68 IIMEEIS 74
>gnl|CDD|224871 COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism].
Length = 393
Score = 59.8 bits (145), Expect = 2e-12
Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 3/71 (4%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHL---FPADQIKKLGALGLMGVLVDEEYGGAGLDTL 57
L+ R+FA++EL P AA++D+ FP + ++ L GL+G+ + EEYGG GL L
Sbjct: 11 ALRAEVREFAEEELAPEAAEIDRRIEDERFPRELLRALAEAGLLGLTIPEEYGGLGLSPL 70
Query: 58 ALHVAMEEIAQ 68
+EE+A+
Sbjct: 71 EQAAVLEELAR 81
>gnl|CDD|173851 cd01162, IBD, Isobutyryl-CoA dehydrogenase. Isobutyryl-CoA
dehydrogenase (IBD) catalyzes the alpha, beta-
dehydrogenation of short branched chain acyl-CoA
intermediates in valine catabolism. It is predicted to
be a homotetramer.
Length = 375
Score = 55.5 bits (134), Expect = 5e-11
Identities = 22/66 (33%), Positives = 38/66 (57%)
Query: 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHV 61
+Q+ R FA +E+ P AA D++ FP D ++K LG G+ + ++ GG+GL L +
Sbjct: 8 IQEVARAFAAKEMAPHAADWDQKKHFPVDVLRKAAELGFGGIYIRDDVGGSGLSRLDASI 67
Query: 62 AMEEIA 67
E ++
Sbjct: 68 IFEALS 73
>gnl|CDD|215284 PLN02519, PLN02519, isovaleryl-CoA dehydrogenase.
Length = 404
Score = 54.1 bits (130), Expect = 1e-10
Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 2/68 (2%)
Query: 3 QKTCRDFAQQELKPIAAKLDKEHLFPADQ--IKKLGALGLMGVLVDEEYGGAGLDTLALH 60
+++ + FAQ+ + P AA +D + FP D K +G L G+ EEYGG GL L
Sbjct: 34 KESVQQFAQENIAPHAAAIDATNSFPKDVNLWKLMGDFNLHGITAPEEYGGLGLGYLYHC 93
Query: 61 VAMEEIAQ 68
+AMEEI++
Sbjct: 94 IAMEEISR 101
>gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase. MCADs are
mitochondrial beta-oxidation enzymes, which catalyze
the alpha,beta dehydrogenation of the corresponding
medium chain acyl-CoA by FAD, which becomes reduced.
The reduced form of MCAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. MCAD is a homotetramer.
Length = 378
Score = 54.1 bits (130), Expect = 2e-10
Identities = 27/66 (40%), Positives = 39/66 (59%)
Query: 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHV 61
Q+T R FA++E+ P+AA+ DK +P IK+ LGLM + E+ GG GL T +
Sbjct: 8 FQETARKFAREEIIPVAAEYDKSGEYPWPLIKRAWELGLMNTHIPEDCGGLGLGTFDTCL 67
Query: 62 AMEEIA 67
EE+A
Sbjct: 68 ITEELA 73
>gnl|CDD|173849 cd01160, LCAD, Long chain acyl-CoA dehydrogenase. LCAD is an
acyl-CoA dehydrogenases (ACAD), which is found in the
mitochondria of eukaryotes and in some prokaryotes. It
catalyzes the alpha, beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of LCAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. LCAD acts as a homodimer.
Length = 372
Score = 52.5 bits (126), Expect = 5e-10
Identities = 24/68 (35%), Positives = 35/68 (51%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALH 60
+ R F +E+ P + +K P + +K G GL+GV EEYGG G D L+
Sbjct: 5 AFRDVVRRFFAKEVAPFHHEWEKAGEVPREVWRKAGEQGLLGVGFPEEYGGIGGDLLSAA 64
Query: 61 VAMEEIAQ 68
V EE+A+
Sbjct: 65 VLWEELAR 72
>gnl|CDD|185640 PTZ00461, PTZ00461, isovaleryl-CoA dehydrogenase; Provisional.
Length = 410
Score = 49.6 bits (118), Expect = 6e-09
Identities = 24/68 (35%), Positives = 39/68 (57%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALH 60
L++T F+++ + A + D F D K+LG LG+MGV V E GGAG+D +A
Sbjct: 43 ALRETVAKFSREVVDKHAREDDINMHFNRDLFKQLGDLGVMGVTVPEADGGAGMDAVAAV 102
Query: 61 VAMEEIAQ 68
+ E+++
Sbjct: 103 IIHHELSK 110
>gnl|CDD|173840 cd01151, GCD, Glutaryl-CoA dehydrogenase. Glutaryl-CoA
dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase,
which catalyzes the oxidative decarboxylation of
glutaryl-CoA to crotonyl-CoA and carbon dioxide in the
catabolism of lysine, hydroxylysine, and tryptophan. It
uses electron transfer flavoprotein (ETF) as an
electron acceptor. GCD is a homotetramer. GCD
deficiency leads to a severe neurological disorder in
humans.
Length = 386
Score = 48.5 bits (116), Expect = 1e-08
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALH 60
++ T R+F Q+EL P + +E F I+++G LGL+G + + YG AGL ++A
Sbjct: 19 AIRDTAREFCQEELAPRVLEAYREEKFDRKIIEEMGELGLLGATI-KGYGCAGLSSVAYG 77
Query: 61 VAMEEIA 67
+ E+
Sbjct: 78 LIAREVE 84
>gnl|CDD|173850 cd01161, VLCAD, Very long chain acyl-CoA dehydrogenase. VLCAD is
an acyl-CoA dehydrogenase (ACAD), which is found in the
mitochondria of eukaryotes and in some bacteria. It
catalyzes the alpha,beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of ACAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. VLCAD acts as a homodimer.
Length = 409
Score = 43.6 bits (103), Expect = 8e-07
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLD 55
ML F ++ P AK D+ P + +L LGL G+ V EEYGG GL+
Sbjct: 33 MLVGPVEKFFEEVNDP--AKNDQLEKIPRKTLTQLKELGLFGLQVPEEYGGLGLN 85
>gnl|CDD|178141 PLN02526, PLN02526, acyl-coenzyme A oxidase.
Length = 412
Score = 41.8 bits (98), Expect = 3e-06
Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHV 61
L+K R+ ++E+ PI + ++ FP I KLG+LG+ G + + YG GL A +
Sbjct: 36 LRKRVRECMEKEVAPIMTEYWEKAEFPFHIIPKLGSLGIAGGTI-KGYGCPGLSITASAI 94
Query: 62 AMEEIAQ 68
A E+A+
Sbjct: 95 ATAEVAR 101
>gnl|CDD|132251 TIGR03207, cyc_hxne_CoA_dh, cyclohexanecarboxyl-CoA
dehydrogenase. Cyclohex-1-ene-1carboxyl-CoA is an
intermediate in the anaerobic degradation of
benzoyl-CoA derived from varioius aromatic compounds,
in Rhodopseudomonas palustris but not Thauera
aromatica. The aliphatic compound
cyclohexanecarboxylate, can be converted to the same
intermediate in two steps. The first step is its
ligation to coenzyme A. The second is the action of
this enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
Length = 372
Score = 40.7 bits (95), Expect = 8e-06
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHV 61
L T R FA++ + P + DK + + ++ +G +G +G + EE+GG G+ LA V
Sbjct: 8 LADTARRFARERIAPGFKERDKTRVLDRELMRDMGEMGFIGPELPEEHGGLGMGCLAAGV 67
Query: 62 AMEEIA 67
E+IA
Sbjct: 68 IHEQIA 73
>gnl|CDD|188537 TIGR04022, sulfur_SfnB, sulfur acquisition oxidoreductase, SfnB
family. Members of this protein family belong to the
greater family of acyl-CoA dehydrogenases. This family
includes the sulfate starvation induced protein SfnB of
Pseudomonas putida strain DS1, which is both encoded
nearby to and phylogenetically closely correlated with
the dimethyl sulphone monooxygenase SfnG. This family
shows considerable sequence similarity to the
Rhodococcus dibenzothiophene desulfurization enzyme
DszC, although that enzyme falls outside of the scope
of this family [Central intermediary metabolism, Sulfur
metabolism].
Length = 391
Score = 38.4 bits (90), Expect = 6e-05
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 4 KTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLD--TLA 58
+ R A E P AA+ D+E P ++ GL G+ V YGGAG+ TLA
Sbjct: 12 EIARRLAA-EFAPGAAERDRERRLPWAELDAFSQSGLWGITVPRAYGGAGVSYATLA 67
>gnl|CDD|173852 cd01163, DszC, Dibenzothiophene (DBT) desulfurization enzyme C.
DszC is a flavin reductase dependent enzyme, which
catalyzes the first two steps of DBT desulfurization in
mesophilic bacteria. DszC converts DBT to
DBT-sulfoxide, which is then converted to DBT-sulfone.
Bacteria with this enzyme are candidates for the
removal of organic sulfur compounds from fossil fuels,
which pollute the environment. An equivalent enzyme
tdsC, is found in thermophilic bacteria. This alignment
also contains a closely related uncharacterized
subgroup.
Length = 377
Score = 33.1 bits (76), Expect = 0.004
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 18 AAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68
AA+ D++ P +++ L GL + V +EYGG G L+ + E+A
Sbjct: 14 AAERDRQRGLPYEEVALLRQSGLGTLRVPKEYGGLGASLPDLYEVVRELAA 64
>gnl|CDD|183454 PRK12341, PRK12341, putative acyl-CoA dehydrogenase; Provisional.
Length = 381
Score = 32.8 bits (75), Expect = 0.005
Identities = 14/64 (21%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 7 RDFAQQELKPIAAKLDKEHLFPADQIKKL--GALGLMGVLVDEEYGGAGLDTLALHVAME 64
R+F ++ + D+ +P + ++ L + ++GV EE+GG D + + +E
Sbjct: 22 RNFPEEYFR----TCDENGTYPREFMRALADNGISMLGV--PEEFGGTPADYVTQMLVLE 75
Query: 65 EIAQ 68
E+++
Sbjct: 76 EVSK 79
>gnl|CDD|179566 PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated.
Length = 380
Score = 31.7 bits (72), Expect = 0.014
Identities = 13/50 (26%), Positives = 27/50 (54%)
Query: 19 AKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68
A+ D++ ++P +K L +G+ +L+ EE+GG + L E+ +
Sbjct: 30 AECDRDSVYPERFVKALADMGIDSLLIPEEHGGLDAGFVTLAAVWMELGR 79
>gnl|CDD|173842 cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to
fadE5. Putative acyl-CoA dehydrogenase (ACAD).
Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze
the alpha,beta dehydrogenation of the corresponding
trans-enoyl-CoA by FAD, which becomes reduced. The
reduced form of ACAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. The ACD family includes the eukaryotic
beta-oxidation, as well as amino acid catabolism
enzymes. These enzymes share high sequence similarity,
but differ in their substrate specificities. The
mitochondrial ACD's are generally homotetramers and
have an active site glutamate at a conserved position.
Length = 407
Score = 30.4 bits (69), Expect = 0.039
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 12/73 (16%)
Query: 5 TCRDFAQQELKPIAAKLDKE--------HLFPADQIKKLGAL---GLMGVLVDEEYGGAG 53
A+ L P+ A D+E + P + L A G M + V EEYGG G
Sbjct: 4 EVARLAENVLAPLNADGDREGPVFDDGRVVVPPPFKEALDAFAEAGWMALGVPEEYGGQG 63
Query: 54 LDTLALHVAMEEI 66
L ++ A+ EI
Sbjct: 64 LPI-TVYSALAEI 75
>gnl|CDD|219653 pfam07942, N2227, N2227-like protein. This family features
sequences that are similar to a region of hypothetical
yeast gene product N2227. This is thought to be
expressed during meiosis and may be involved in the
defence response to stressful conditions.
Length = 268
Score = 30.0 bits (68), Expect = 0.050
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 17/69 (24%)
Query: 6 CRDFA---QQE----LKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLA 58
RD++ Q E KPI +L+ LFP+ + + +LV GAGL LA
Sbjct: 23 VRDWSAEGQVERDPLYKPIIEELN--RLFPSRSHDR----SKIRILVP----GAGLGRLA 72
Query: 59 LHVAMEEIA 67
+A
Sbjct: 73 YELATLGYQ 81
>gnl|CDD|173838 cd00567, ACAD, Acyl-CoA dehydrogenase. Both mitochondrial
acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA
oxidases (AXO) catalyze the alpha,beta dehydrogenation
of the corresponding trans-enoyl-CoA by FAD, which
becomes reduced. The reduced form of ACAD is reoxidized
in the oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. In contrast, AXO catalyzes
a different oxidative half-reaction, in which the
reduced FAD is reoxidized by molecular oxygen. The ACAD
family includes the eukaryotic beta-oxidation enzymes,
short (SCAD), medium (MCAD), long (LCAD) and very-long
(VLCAD) chain acyl-CoA dehydrogenases. These enzymes
all share high sequence similarity, but differ in their
substrate specificities. The ACAD family also includes
amino acid catabolism enzymes such as Isovaleryl-CoA
dehydrogenase (IVD), short/branched chain acyl-CoA
dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase
(IBDH), glutaryl-CoA deydrogenase (GCD) and
Crotonobetainyl-CoA dehydrogenase. The mitochondrial
ACAD's are generally homotetramers, except for VLCAD,
which is a homodimer. Related enzymes include the SOS
adaptive reponse proten aidB, Naphthocyclinone
hydroxylase (NcnH), and and Dibenzothiophene (DBT)
desulfurization enzyme C (DszC).
Length = 327
Score = 29.6 bits (67), Expect = 0.083
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLV 45
L+ + R+FA +EL+P A + + P + + +LG L +L+
Sbjct: 5 ELRDSAREFAAEELEPYARERRETPEEPWELLAELGLLLGAALLL 49
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 29.0 bits (66), Expect = 0.14
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 4 KTCRDFAQQELKPIAAKLDKEHLFPADQIK 33
+ + +LKPI LD E L P + ++
Sbjct: 50 EEGSEVPADKLKPILEVLDLEPLLPPELLR 79
>gnl|CDD|173848 cd01159, NcnH, Naphthocyclinone hydroxylase. Naphthocyclinone is
an aromatic polyketide and an antibiotic, which is
active against Gram-positive bacteria. Polyketides are
secondary metabolites, which have important biological
functions such as antitumor, immunosupressive or
antibiotic activities. NcnH is a hydroxylase involved
in the biosynthesis of naphthocyclinone and possibly
other polyketides.
Length = 370
Score = 28.9 bits (65), Expect = 0.15
Identities = 11/50 (22%), Positives = 22/50 (44%)
Query: 18 AAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIA 67
A + ++ P + ++ L +G + V + YGG D A+ +A
Sbjct: 14 APEAERARRLPDEVVRALREIGFFRMFVPKRYGGLEGDFAEFAEAIATLA 63
>gnl|CDD|226003 COG3472, COG3472, Uncharacterized conserved protein [Function
unknown].
Length = 342
Score = 25.2 bits (55), Expect = 2.7
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 14 LKPIAAKLDKEHLFPADQIKKLG 36
+ A L+K H+FP ++KLG
Sbjct: 209 TENEEADLNKHHIFPNAYLRKLG 231
>gnl|CDD|220125 pfam09140, MipZ, ATPase MipZ. MipZ is an ATPase that forms a
complex with the chromosome partitioning protein ParB
near the chromosomal origin of replication. It is
responsible for the temporal and spatial regulation of
FtsZ ring formation.
Length = 262
Score = 25.0 bits (55), Expect = 2.7
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 43 VLVDEEYGGAGLDTLALHVA 62
++V E GG+G T A+HVA
Sbjct: 3 IVVGNEKGGSGKSTTAVHVA 22
>gnl|CDD|238746 cd01469, vWA_integrins_alpha_subunit, Integrins are a class of
adhesion receptors that link the extracellular matrix to
the cytoskeleton and cooperate with growth factor
receptors to promote celll survival, cell cycle
progression and cell migration. Integrins consist of an
alpha and a beta sub-unit. Each sub-unit has a large
extracellular portion, a single transmembrane segment
and a short cytoplasmic domain. The N-terminal domains
of the alpha and beta subunits associate to form the
integrin headpiece, which contains the ligand binding
site, whereas the C-terminal segments traverse the
plasma membrane and mediate interaction with the
cytoskeleton and with signalling proteins.The VWA
domains present in the alpha subunits of integrins seem
to be a chordate specific radiation of the gene family
being found only in vertebrates. They mediate
protein-protein interactions.
Length = 177
Score = 24.6 bits (54), Expect = 3.6
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 10 AQQELKPIAAKLDKEHLFPADQIKKLGAL 38
+++ELK IA+K +EH F L +
Sbjct: 149 SREELKTIASKPPEEHFFNVTDFAALKDI 177
>gnl|CDD|176103 cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of the
LysR-type transcriptional regulator OxyR, a member of
the type 2 periplasmic binding fold protein superfamily.
OxyR senses hydrogen peroxide and is activated through
the formation of an intramolecular disulfide bond. The
OxyR activation induces the transcription of genes
necessary for the bacterial defense against oxidative
stress. The OxyR of LysR-type transcriptional regulator
family is composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The C-terminal domain also
contains the redox-active cysteines that mediate the
redox-dependent conformational switch. Thus, the
interaction between the OxyR-tetramer and DNA is notably
different between the oxidized and reduced forms. The
structural topology of this substrate-binding domain is
most similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 200
Score = 24.0 bits (53), Expect = 7.2
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 21 LDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAM 63
L++ H DQ L L G ++ L+TL VA
Sbjct: 104 LEEGHCL-RDQA--LELCRLAGAREQTDFEATSLETLRQMVAA 143
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
0.319 0.137 0.385
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,633,875
Number of extensions: 287452
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 29
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
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 (21.8 bits)
S2: 53 (24.2 bits)