RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10337
(87 letters)
>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 = 92.3 bits (229), Expect = 6e-24
Identities = 35/44 (79%), Positives = 41/44 (93%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAIIER 85
+FGGNGFNS+YPVEKLMRDAKIYQIYEGT+QIQRLI+SR + +
Sbjct: 335 IFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISREHLGK 378
Score = 85.7 bits (212), Expect = 2e-21
Identities = 33/37 (89%), Positives = 37/37 (100%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+FGGNGFNS+YPVEKLMRDAKIYQIYEGT+QIQRLI+
Sbjct: 335 IFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLII 371
>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 = 73.1 bits (180), Expect = 5e-17
Identities = 23/45 (51%), Positives = 37/45 (82%)
Query: 40 IVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAIIE 84
+ +FGG G+ DYPVE+ RDAKI +IYEGT++IQRL++++ +++
Sbjct: 329 VQIFGGYGYTKDYPVERYYRDAKITEIYEGTSEIQRLVIAKHLLK 373
Score = 68.1 bits (167), Expect = 4e-15
Identities = 23/37 (62%), Positives = 31/37 (83%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+FGG G+ DYPVE+ RDAKI +IYEGT++IQRL++
Sbjct: 331 IFGGYGYTKDYPVERYYRDAKITEIYEGTSEIQRLVI 367
>gnl|CDD|201229 pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal
domain. C-terminal domain of Acyl-CoA dehydrogenase is
an all-alpha, four helical up-and-down bundle.
Length = 150
Score = 64.2 bits (157), Expect = 9e-15
Identities = 19/42 (45%), Positives = 34/42 (80%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAII 83
+ GG G++ +YP+E+L RDA++ +I EGT++IQR I++R ++
Sbjct: 109 LLGGYGYSREYPLERLYRDARVLRIGEGTSEIQRNIIARRLL 150
Score = 60.4 bits (147), Expect = 3e-13
Identities = 18/37 (48%), Positives = 30/37 (81%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GG G++ +YP+E+L RDA++ +I EGT++IQR I+
Sbjct: 109 LLGGYGYSREYPLERLYRDARVLRIGEGTSEIQRNII 145
>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 = 65.0 bits (159), Expect = 4e-14
Identities = 23/57 (40%), Positives = 37/57 (64%)
Query: 24 AKIYQIYEGTAQIQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSR 80
AK++ + + GG G++ +YPVE+ +RDA+ +I EGTA+IQRLI++R
Sbjct: 271 AKLFATEAAREVADLAMQIHGGRGYSREYPVERYLRDARAARIAEGTAEIQRLIIAR 327
Score = 59.6 bits (145), Expect = 4e-12
Identities = 20/37 (54%), Positives = 30/37 (81%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GG G++ +YPVE+ +RDA+ +I EGTA+IQRLI+
Sbjct: 289 IHGGRGYSREYPVERYLRDARAARIAEGTAEIQRLII 325
>gnl|CDD|224871 COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism].
Length = 393
Score = 64.8 bits (158), Expect = 6e-14
Identities = 23/50 (46%), Positives = 35/50 (70%)
Query: 36 IQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAIIER 85
+ V GG G+ +YPVE+ RDA+I +IYEGT++IQRLI++R ++
Sbjct: 340 ADEAVQVHGGYGYTEEYPVERYYRDARILRIYEGTSEIQRLIIARRLLGL 389
Score = 58.7 bits (142), Expect = 9e-12
Identities = 22/37 (59%), Positives = 30/37 (81%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
V GG G+ +YPVE+ RDA+I +IYEGT++IQRLI+
Sbjct: 346 VHGGYGYTEEYPVERYYRDARILRIYEGTSEIQRLII 382
>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 = 60.1 bits (146), Expect = 2e-12
Identities = 22/44 (50%), Positives = 34/44 (77%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAIIER 85
+ GG G+ DYPVE+ +RD +++QI EGT +I RLI++RA++ R
Sbjct: 332 LHGGYGYLKDYPVEQYVRDLRVHQILEGTNEIMRLIIARALLTR 375
Score = 51.3 bits (123), Expect = 4e-09
Identities = 19/37 (51%), Positives = 28/37 (75%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GG G+ DYPVE+ +RD +++QI EGT +I RLI+
Sbjct: 332 LHGGYGYLKDYPVEQYVRDLRVHQILEGTNEIMRLII 368
>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 = 57.8 bits (140), Expect = 2e-11
Identities = 20/44 (45%), Positives = 34/44 (77%)
Query: 40 IVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAII 83
I + GGNG+ +DYP +L+RDAK+Y+I GT++I+R+++ R +
Sbjct: 332 IQILGGNGYINDYPTGRLLRDAKLYEIGAGTSEIRRMVIGRELF 375
Score = 51.6 bits (124), Expect = 3e-09
Identities = 18/37 (48%), Positives = 31/37 (83%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GGNG+ +DYP +L+RDAK+Y+I GT++I+R+++
Sbjct: 334 ILGGNGYINDYPTGRLLRDAKLYEIGAGTSEIRRMVI 370
>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 = 55.9 bits (135), Expect = 7e-11
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVVFG 44
V GG+G+ +YP+E+ RDA+I IYEGT IQ L ++
Sbjct: 365 VHGGSGYTREYPIEQYYRDARITTIYEGTTGIQALDLIGR 404
Score = 55.1 bits (133), Expect = 1e-10
Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 40 IVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAII 83
I V GG+G+ +YP+E+ RDA+I IYEGT IQ L + I
Sbjct: 363 IQVHGGSGYTREYPIEQYYRDARITTIYEGTTGIQALDLIGRKI 406
>gnl|CDD|215284 PLN02519, PLN02519, isovaleryl-CoA dehydrogenase.
Length = 404
Score = 52.6 bits (126), Expect = 1e-09
Identities = 19/41 (46%), Positives = 32/41 (78%)
Query: 40 IVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSR 80
I GGNG+ ++YP +L+RDAK+Y+I GT++I+R+++ R
Sbjct: 358 IQCLGGNGYINEYPTGRLLRDAKLYEIGAGTSEIRRMLIGR 398
Score = 49.1 bits (117), Expect = 2e-08
Identities = 17/35 (48%), Positives = 30/35 (85%)
Query: 7 GGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
GGNG+ ++YP +L+RDAK+Y+I GT++I+R+++
Sbjct: 362 GGNGYINEYPTGRLLRDAKLYEIGAGTSEIRRMLI 396
>gnl|CDD|173843 cd01154, AidB, Proteins involved in DNA damage response, similar to
the AidB gene product. AidB is one of several genes
involved in the SOS adaptive response to DNA alkylation
damage, whose expression is activated by the Ada
protein. Its function has not been entirely elucidated;
however, it is similar in sequence and function to
acyl-CoA dehydrogenases. It has been proposed that aidB
directly destroys DNA alkylating agents such as
nitrosoguanidines (nitrosated amides) or their reaction
intermediates.
Length = 418
Score = 49.3 bits (118), Expect = 1e-08
Identities = 20/41 (48%), Positives = 29/41 (70%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAI 82
VFGGNG+ ++PV +L R+A++ I+EGT IQ L V R +
Sbjct: 376 VFGGNGYLEEWPVARLHREAQVTPIWEGTGNIQALDVLRVL 416
Score = 47.4 bits (113), Expect = 9e-08
Identities = 19/38 (50%), Positives = 28/38 (73%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVV 42
VFGGNG+ ++PV +L R+A++ I+EGT IQ L V+
Sbjct: 376 VFGGNGYLEEWPVARLHREAQVTPIWEGTGNIQALDVL 413
>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 = 48.2 bits (115), Expect = 4e-08
Identities = 18/45 (40%), Positives = 32/45 (71%)
Query: 40 IVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAIIE 84
I + GG GF +Y VE+++RD +I++I+EGT +I RL ++ ++
Sbjct: 362 IQIHGGMGFMREYGVERVLRDLRIFRIFEGTNEILRLFIALTGLQ 406
Score = 47.5 bits (113), Expect = 8e-08
Identities = 18/41 (43%), Positives = 29/41 (70%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVVFGG 45
+ GG GF +Y VE+++RD +I++I+EGT +I RL + G
Sbjct: 364 IHGGMGFMREYGVERVLRDLRIFRIFEGTNEILRLFIALTG 404
>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 = 44.0 bits (104), Expect = 1e-06
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAII 83
+ GG G+ +YP+ + RDA++ IY GT +I + ++SR ++
Sbjct: 331 LHGGWGYMREYPIARAYRDARVQPIYGGTTEIMKELISRQMV 372
Score = 39.0 bits (91), Expect = 7e-05
Identities = 13/37 (35%), Positives = 24/37 (64%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GG G+ +YP+ + RDA++ IY GT +I + ++
Sbjct: 331 LHGGWGYMREYPIARAYRDARVQPIYGGTTEIMKELI 367
>gnl|CDD|185635 PTZ00456, PTZ00456, acyl-CoA dehydrogenase; Provisional.
Length = 622
Score = 42.9 bits (101), Expect = 3e-06
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 32 GTAQIQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRL 76
G R + V+GG+G+ +E+++RDA+I +YEGT IQ L
Sbjct: 427 GVEAASRCLQVWGGHGYIKGNGMEQILRDARIGTLYEGTTGIQAL 471
Score = 39.5 bits (92), Expect = 5e-05
Identities = 16/35 (45%), Positives = 25/35 (71%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRL 39
V+GG+G+ +E+++RDA+I +YEGT IQ L
Sbjct: 437 VWGGHGYIKGNGMEQILRDARIGTLYEGTTGIQAL 471
>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 = 39.6 bits (93), Expect = 4e-05
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAI 82
+ GGNG + +Y + + M + + YEGT I LI+ RAI
Sbjct: 340 MLGGNGISDEYHIIRHMVNLESVNTYEGTHDIHALILGRAI 380
Score = 33.5 bits (77), Expect = 0.006
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GGNG + +Y + + M + + YEGT I LI+
Sbjct: 340 MLGGNGISDEYHIIRHMVNLESVNTYEGTHDIHALIL 376
>gnl|CDD|185640 PTZ00461, PTZ00461, isovaleryl-CoA dehydrogenase; Provisional.
Length = 410
Score = 37.6 bits (87), Expect = 2e-04
Identities = 17/31 (54%), Positives = 22/31 (70%)
Query: 40 IVVFGGNGFNSDYPVEKLMRDAKIYQIYEGT 70
I V GG G++ D PVE+L RDAK+ +I GT
Sbjct: 363 IQVMGGMGYSRDMPVERLWRDAKLLEIGGGT 393
Score = 37.2 bits (86), Expect = 3e-04
Identities = 16/29 (55%), Positives = 21/29 (72%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGT 33
V GG G++ D PVE+L RDAK+ +I GT
Sbjct: 365 VMGGMGYSRDMPVERLWRDAKLLEIGGGT 393
>gnl|CDD|183454 PRK12341, PRK12341, putative acyl-CoA dehydrogenase; Provisional.
Length = 381
Score = 37.4 bits (87), Expect = 2e-04
Identities = 18/62 (29%), Positives = 28/62 (45%)
Query: 24 AKIYQIYEGTAQIQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAII 83
AK+Y I I + GG G+ + V + RD + +I GT +I I R I+
Sbjct: 318 AKLYCARTAMEVIDDAIQIMGGLGYTDEARVSRFWRDVRCERIGGGTDEIMIYIAGRQIL 377
Query: 84 ER 85
+
Sbjct: 378 KD 379
Score = 31.2 bits (71), Expect = 0.040
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQI 36
+ GG G+ + V + RD + +I GT +I
Sbjct: 336 IMGGLGYTDEARVSRFWRDVRCERIGGGTDEI 367
>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 = 36.8 bits (85), Expect = 5e-04
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 36 IQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSR 80
I + ++ G G++ +E+ +RD +QI +GTAQI + I++R
Sbjct: 326 IHQCLLTHGHGGYDRG-DMEQRLRDVLGFQIGDGTAQIMKTIIAR 369
Score = 32.2 bits (73), Expect = 0.020
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 6 FGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
G G++ +E+ +RD +QI +GTAQI + I+
Sbjct: 333 HGHGGYDRG-DMEQRLRDVLGFQIGDGTAQIMKTII 367
>gnl|CDD|219705 pfam08028, Acyl-CoA_dh_2, Acyl-CoA dehydrogenase, C-terminal
domain.
Length = 134
Score = 35.0 bits (81), Expect = 0.001
Identities = 12/50 (24%), Positives = 18/50 (36%)
Query: 21 MRDAKIYQIYEGTAQIQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGT 70
R A + RL GG+ D P+++ RDA + G
Sbjct: 83 ARRDAALAAELAVAAVDRLFRAAGGSALFKDSPLQRFWRDAHAGAAHAGL 132
Score = 30.7 bits (70), Expect = 0.036
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGT 33
GG+ D P+++ RDA + G
Sbjct: 104 AAGGSALFKDSPLQRFWRDAHAGAAHAGL 132
>gnl|CDD|178141 PLN02526, PLN02526, acyl-coenzyme A oxidase.
Length = 412
Score = 34.1 bits (78), Expect = 0.004
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAI 82
+ GGNG +D+ V K D + YEGT I L+ R I
Sbjct: 356 LLGGNGILADFLVAKAFCDLEPIYTYEGTYDINALVTGREI 396
Score = 30.2 bits (68), Expect = 0.083
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
+ GGNG +D+ V K D + YEGT I L+
Sbjct: 356 LLGGNGILADFLVAKAFCDLEPIYTYEGTYDINALVT 392
>gnl|CDD|173841 cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar
to fadE6, fadE17, and fadE26. Putative acyl-CoA
dehydrogenases (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 = 380
Score = 32.7 bits (75), Expect = 0.013
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 44 GGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAI 82
G E ++ IY GT++IQR I++ +
Sbjct: 340 PAPGAELAGRWEADYLRSRATTIYGGTSEIQRNIIAERL 378
Score = 30.8 bits (70), Expect = 0.053
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 7 GGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIV 41
G E ++ IY GT++IQR I+
Sbjct: 340 PAPGAELAGRWEADYLRSRATTIYGGTSEIQRNII 374
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 27.6 bits (62), Expect = 0.66
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 57 LMRDAKIYQIYEGTAQI---QRLIVSRAI 82
L R+A +Y + E +A + QR+IV++ I
Sbjct: 470 LSREADLYLLDEPSAYLDVEQRIIVAKVI 498
>gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 343
Score = 27.4 bits (61), Expect = 0.76
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 12 NSDYPVEKLMRDAKIYQIYEGTAQIQRLIVVFGGNGFNSD-YPVEKLMRDAKIY 64
N Y +E+++ KIYQ G I++ G N D + +L++ K++
Sbjct: 229 NKKYSIEEIINAVKIYQKKTGNRVTIEYILIKGFNDEIEDAKKLAELLKGLKVF 282
Score = 24.7 bits (54), Expect = 8.4
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 49 NSDYPVEKLMRDAKIYQ 65
N Y +E+++ KIYQ
Sbjct: 229 NKKYSIEEIINAVKIYQ 245
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 27.5 bits (62), Expect = 0.76
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 57 LMRDAKIYQIYEGTAQI---QRLIVSRAI 82
L RDA +Y + E +A + QRL V++AI
Sbjct: 468 LSRDADLYLLDEPSAHLDVEQRLAVAKAI 496
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 27.4 bits (61), Expect = 0.93
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 57 LMRDAKIYQIYEGTAQI---QRLIVSRAI 82
L +DA IY + E +A + QRL+ S+ I
Sbjct: 130 LSKDADIYLLDEPSAYLDVEQRLMASKVI 158
>gnl|CDD|234249 TIGR03538, DapC_gpp, succinyldiaminopimelate transaminase. This
family of succinyldiaminopimelate transaminases (DapC)
includes the experimentally characterized enzyme from
Bordatella pertussis. The majority of genes in this
family are proximal to genes encoding components of the
lysine biosynthesis via diaminopimelate pathway
(GenProp0125).
Length = 393
Score = 26.2 bits (58), Expect = 2.0
Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 27 YQIYEGTAQIQRLIVVF----GGNGFNSDY 52
YQIYEG A + F NGF D+
Sbjct: 126 YQIYEGAALLAGAEPYFLNCTAENGFLPDF 155
>gnl|CDD|239002 cd02047, HCII, Heparin cofactor II (HCII) inhibits thrombin, the
final protease of the coagulation cascade. HCII is
allosterically activated by binding to cell surface
glycosaminoglycans (GAGs). The specificity of HCII for
thrombin is conferred by a highly acidic hirudin-like
N-terminal tail, which becomes available after GAG
binding for interaction with the anion-binding exosite
I of thrombin. This subgroup corresponds to clade D of
the serpin superfamily.
Length = 436
Score = 26.3 bits (58), Expect = 2.2
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 13 SDYPVEKLMRDAKIYQIYEGTAQIQRLIVVFGGNGFN 49
S P + ++ I +++ G +IQRL ++ GFN
Sbjct: 39 SVSPTDSEIQQGNILELFHGKTRIQRLNILNANFGFN 75
>gnl|CDD|179566 PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated.
Length = 380
Score = 26.3 bits (58), Expect = 2.2
Identities = 12/62 (19%), Positives = 31/62 (50%)
Query: 24 AKIYQIYEGTAQIQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAII 83
K + + + V GG G ++ + + RD ++ ++ G+ ++Q L + RA++
Sbjct: 317 CKYFCANAAFEVVDSAMQVLGGVGIAGNHRISRFWRDLRVDRVSGGSDEMQILTLGRAVL 376
Query: 84 ER 85
++
Sbjct: 377 KQ 378
>gnl|CDD|212675 cd10233, HSPA1-2_6-8-like_NBD, Nucleotide-binding domain of
HSPA1-A, -B, -L, HSPA-2, -6, -7, -8, and similar
proteins. This subfamily includes human HSPA1A (70-kDa
heat shock protein 1A, also known as HSP72; HSPA1;
HSP70I; HSPA1B; HSP70-1; HSP70-1A), HSPA1B (70-kDa heat
shock protein 1B, also known as HSPA1A; HSP70-2;
HSP70-1B), and HSPA1L (70-kDa heat shock protein 1-like,
also known as HSP70T; hum70t; HSP70-1L; HSP70-HOM). The
genes for these three HSPA1 proteins map in close
proximity on the major histocompatibility complex (MHC)
class III region on chromosome 6, 6p21.3. This subfamily
also includes human HSPA8 (heat shock 70kDa protein 8,
also known as LAP1; HSC54; HSC70; HSC71; HSP71; HSP73;
NIP71; HSPA10; the HSPA8 gene maps to 11q24.1), human
HSPA2 (70-kDa heat shock protein 2, also known as
HSP70-2; HSP70-3, the HSPA2 gene maps to 14q24.1), human
HSPA6 (also known as heat shock 70kDa protein 6
(HSP70B') gi 94717614, the HSPA6 gene maps to 1q23.3),
human HSPA7 (heat shock 70kDa protein 7 , also known as
HSP70B; the HSPA7 gene maps to 1q23.3) and Saccharmoyces
cerevisiae Stress-Seventy subfamily B/Ssb1p. This
subfamily belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs).
Associations of polymorphisms within the MHC-III HSP70
gene locus with longevity, systemic lupus erythematosus,
Meniere's disease, noise-induced hearing loss,
high-altitude pulmonary edema, and coronary heart
disease, have been found. HSPA2 is involved in cancer
cell survival, is required for maturation of male
gametophytes, and is linked to male infertility. The
induction of HSPA6 is a biomarker of cellular stress.
HSPA8 participates in the folding and trafficking of
client proteins to different subcellular compartments,
and in the signal transduction and apoptosis process; it
has been shown to protect cardiomyocytes against
oxidative stress partly through an interaction with
alpha-enolase. S. cerevisiae Ssb1p, is part of the
ribosome-associated complex (RAC), it acts as a
chaperone for nascent polypeptides, and is important for
translation fidelity; Ssb1p is also a [PSI+]
prion-curing factor.
Length = 376
Score = 26.2 bits (58), Expect = 2.4
Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 10/46 (21%)
Query: 16 PVEKLMRDAKIYQIYEGTAQIQRLIVVFGGNGFNSDYP-VEKLMRD 60
PVEK++RDAK+ +QI IV+ GG ++ P V+KL++D
Sbjct: 311 PVEKVLRDAKL-----DKSQIHD-IVLVGG---STRIPKVQKLLQD 347
Score = 24.6 bits (54), Expect = 7.8
Identities = 8/11 (72%), Positives = 11/11 (100%)
Query: 53 PVEKLMRDAKI 63
PVEK++RDAK+
Sbjct: 311 PVEKVLRDAKL 321
>gnl|CDD|173038 PRK14574, hmsH, outer membrane protein; Provisional.
Length = 822
Score = 26.2 bits (57), Expect = 2.9
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 14 DYPVEKLMRDAKIYQIYEGTAQIQRLIVVFGGNGFNSDYPVEKLMRDAKI 63
D P ++L R K++ +YE R+I N DY VE L+ I
Sbjct: 517 DIPSQELDRQRKVHNMYELRVSGNRVISSNSPVSGNKDYGVETLLYSPPI 566
>gnl|CDD|183199 PRK11561, PRK11561, isovaleryl CoA dehydrogenase; Provisional.
Length = 538
Score = 25.5 bits (56), Expect = 3.8
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 42 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVSRAI 82
V GG G+ + + +L R+ + I+EG+ I L V R +
Sbjct: 399 VLGGIGYCEESELPRLYREMPVNSIWEGSGNIMCLDVLRVL 439
>gnl|CDD|182448 PRK10423, PRK10423, transcriptional repressor RbsR; Provisional.
Length = 327
Score = 25.4 bits (56), Expect = 4.0
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 56 KLMRDAKIYQIYEGTAQIQRLIVSRAIIERNS 87
+L D I+++ + T Q QRL ++ ++ER S
Sbjct: 295 ELAIDVLIHRMAQPTLQQQRLQLTPELMERGS 326
>gnl|CDD|151371 pfam10924, DUF2711, Protein of unknown function (DUF2711). Some
members in this family of proteins are annotated as ywbB
however currently there is no known function.
Length = 217
Score = 24.7 bits (54), Expect = 6.9
Identities = 10/35 (28%), Positives = 13/35 (37%)
Query: 36 IQRLIVVFGGNGFNSDYPVEKLMRDAKIYQIYEGT 70
+ L+ V G G S Y E + QI E
Sbjct: 118 LPNLLKVLGSKGAKSIYYSEPIYDTRGSLQINETA 152
>gnl|CDD|180281 PRK05839, PRK05839, hypothetical protein; Provisional.
Length = 374
Score = 24.6 bits (54), Expect = 7.2
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 27 YQIYEGTAQIQRLIVVF 43
YQIYEG A R V+
Sbjct: 119 YQIYEGAAIASRAKVLL 135
Score = 24.6 bits (54), Expect = 7.3
Identities = 11/18 (61%), Positives = 11/18 (61%), Gaps = 5/18 (27%)
Query: 64 YQIYEGTAQIQRLIVSRA 81
YQIYEG A I SRA
Sbjct: 119 YQIYEGAA-----IASRA 131
>gnl|CDD|236393 PRK09147, PRK09147, succinyldiaminopimelate transaminase;
Provisional.
Length = 396
Score = 24.4 bits (54), Expect = 8.2
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 27 YQIYEGTA 34
YQIYEG A
Sbjct: 127 YQIYEGAA 134
Score = 24.4 bits (54), Expect = 8.2
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 64 YQIYEGTA 71
YQIYEG A
Sbjct: 127 YQIYEGAA 134
>gnl|CDD|100031 cd02195, SelD, Selenophosphate synthetase (SelD) catalyzes the
conversion of selenium to selenophosphate which is
required by a number of bacterial, archaeal and
eukaryotic organisms for synthesis of Secys-tRNA, the
precursor of selenocysteine in selenoenzymes. The
N-terminal domain of SelD is related to the ATP-binding
domains of hydrogen expression/formation protein HypE,
the AIR synthases, and FGAM synthase and is thought to
bind ATP.
Length = 287
Score = 24.4 bits (54), Expect = 8.8
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 23 DAKIYQIYEGTAQIQ 37
DA +Y++ G A +Q
Sbjct: 43 DAAVYRLPGGLALVQ 57
Score = 24.4 bits (54), Expect = 8.8
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 60 DAKIYQIYEGTAQIQ 74
DA +Y++ G A +Q
Sbjct: 43 DAAVYRLPGGLALVQ 57
>gnl|CDD|217190 pfam02698, DUF218, DUF218 domain. This large family of proteins
contains several highly conserved charged amino acids,
suggesting this may be an enzymatic domain (Bateman A
pers. obs). The family includes SanA, which is involved
in Vancomycin resistance. This protein may be involved
in murein synthesis.
Length = 148
Score = 24.2 bits (53), Expect = 9.3
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 5 VFGGNGFNSDYPVEKLMRDAKIYQIYEGTAQIQRLIVVFGGNGFNSDYPVEKLMRDA 61
V GG S +L A++Y+ A I+V GG G ++MR
Sbjct: 7 VLGGG---SPALAARLDAAAELYR-----AGPAPRIIVSGGAGGGEPVSEAEVMRRY 55
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
0.321 0.140 0.398
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,649,544
Number of extensions: 386968
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 416
Number of HSP's successfully gapped: 62
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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 (24.3 bits)