RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9058
(142 letters)
>gnl|CDD|131494 TIGR02441, fa_ox_alpha_mit, fatty acid oxidation complex, alpha
subunit, mitochondrial. Members represent alpha subunit
of mitochondrial multifunctional fatty acid degradation
enzyme complex. Subunit activities include: enoyl-CoA
hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA
dehydrogenase (EC 1.1.1.35). Some characterization in
human , pig , and rat. The beta subunit has activity:
acetyl-CoA C-acyltransferase (EC 2.3.1.16).
Length = 737
Score = 218 bits (558), Expect = 2e-68
Identities = 88/135 (65%), Positives = 102/135 (75%), Gaps = 2/135 (1%)
Query: 8 GRKSGKGYFVYAKGSKA-RPVNDGALAILKKYSLQPQSAL-KDEDLQLRMVSRFVNEAVL 65
GRKSGKG F+Y +G K + VN A IL +Y L P++ + ED+Q+R+VSRFVNEAVL
Sbjct: 603 GRKSGKGIFIYQEGKKGSKKVNSDADEILAQYKLPPKAEVSSPEDIQIRLVSRFVNEAVL 662
Query: 66 CLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLSYENLYGAPFRPC 125
CLEE IL SP++GD+GAVFGLGFPPF GGPFR+VD YGADKLV KM Y YG F PC
Sbjct: 663 CLEEGILASPSEGDIGAVFGLGFPPFLGGPFRFVDLYGADKLVDKMEKYAAAYGVQFTPC 722
Query: 126 QLLLDHAKDSSKKFY 140
QLLLDHAK KKFY
Sbjct: 723 QLLLDHAKSPGKKFY 737
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 148 bits (377), Expect = 1e-42
Identities = 55/136 (40%), Positives = 83/136 (61%), Gaps = 6/136 (4%)
Query: 8 GRKSGKGYFVYAK--GSKARPVNDGALAILKKYSLQPQSALKDEDLQLRMVSRFVNEAVL 65
GRK+G+G+++Y + + V++ +L + PQS L ++ R V +NEAV
Sbjct: 576 GRKNGRGFYLYGQKGKKSKKQVDESVYPLLG---ITPQSRLSANEIAERCVMLMLNEAVR 632
Query: 66 CLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLSYENLYGAPFRPC 125
CL+E I+ S DGD+GAVFG+GFPPF GGPFR++D GA ++V + YG F PC
Sbjct: 633 CLDEGIIRSARDGDIGAVFGIGFPPFLGGPFRYMDSLGAGEVVAILERLAAQYGDRFTPC 692
Query: 126 QLLLDHAKDSSKKFYP 141
+ L++ A+ + FYP
Sbjct: 693 ERLVEMAE-RGESFYP 707
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 132 bits (334), Expect = 8e-37
Identities = 53/133 (39%), Positives = 83/133 (62%), Gaps = 4/133 (3%)
Query: 8 GRKSGKGYFVYAKGSKARPVNDGALAILKKYSLQPQSALKDEDLQLRMVSRFVNEAVLCL 67
GRK+GKG+++Y +K + V++ ++ ++P + + R V +NEAV CL
Sbjct: 571 GRKNGKGFYLYGAATKKKAVDE---SVYGLLGIKPGVDKEASAVAERCVMLMLNEAVRCL 627
Query: 68 EETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLSYENLYGAPFRPCQL 127
+E ++ SP DGD+GA+FG+GFPPF GGPFR++D GAD +V+ + + YG F PCQ
Sbjct: 628 DEGVIRSPRDGDIGAIFGIGFPPFLGGPFRYIDTLGADNVVKILERLQTQYGDRFTPCQR 687
Query: 128 LLDHAKDSSKKFY 140
L+ A + + FY
Sbjct: 688 LVAMAAE-KQSFY 699
>gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 715
Score = 116 bits (293), Expect = 3e-31
Identities = 50/136 (36%), Positives = 77/136 (56%), Gaps = 4/136 (2%)
Query: 8 GRKSGKGYFVYAKGSKARP--VNDGALAILKKYSLQPQSALKDEDLQLRMVSRFVNEAVL 65
G+K+GKG++ Y + K +P D A+ L +QP+ DE++ RM+ +NE V
Sbjct: 582 GQKNGKGFYRYEEDKKGKPKKEVDPAVYELLAPVVQPKREFSDEEIIARMMIPMINEVVR 641
Query: 66 CLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLSYENLYGAPFRPC 125
CLEE I+ SP + D+ V+GLGFPPF GG FR++D G V Y +L G ++
Sbjct: 642 CLEEGIVASPAEADMALVYGLGFPPFRGGAFRYLDTLGVANYVALADKYAHL-GPLYQVP 700
Query: 126 QLLLDHAKDSSKKFYP 141
+ L + A + + +YP
Sbjct: 701 EGLREMAA-NGESYYP 715
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Activities include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 102 bits (256), Expect = 3e-26
Identities = 49/129 (37%), Positives = 70/129 (54%), Gaps = 5/129 (3%)
Query: 8 GRKSGKGYFVYAKGSKARP---VNDGALAILKKYSLQPQSALKDEDLQLRMVSRFVNEAV 64
G+K+GKG++ Y K +P V+ L +LK Q DE++ RM+ +NE V
Sbjct: 582 GQKNGKGFYAYEADKKGKPKKLVDSSVLELLKPVV-YEQRDFDDEEIIARMMIPMINETV 640
Query: 65 LCLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLSYENLYGAPFRP 124
CLEE I+ + + D+G V+GLGFPPF GG FR++D G V Y L GA ++
Sbjct: 641 RCLEEGIVATAAEADMGLVYGLGFPPFRGGAFRYLDSIGVANFVALADQYAEL-GALYQV 699
Query: 125 CQLLLDHAK 133
L + AK
Sbjct: 700 TAKLREMAK 708
>gnl|CDD|216084 pfam00725, 3HCDH, 3-hydroxyacyl-CoA dehydrogenase, C-terminal
domain. This family also includes lambda crystallin.
Some proteins include two copies of this domain.
Length = 97
Score = 44.1 bits (105), Expect = 9e-07
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 54 RMVSRFVNEAVLCLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLS 113
R+++ +NEA+ +EE + +P D D GLG P GPF D G D +
Sbjct: 6 RLLAPLLNEAIRLVEEGVA-TPEDIDAAMRLGLGLPM---GPFELSDLVGLDVGYHILEV 61
Query: 114 YENLYGAP-FRPCQLLLDHAKD------SSKKFY 140
+G +RP LL + + K FY
Sbjct: 62 LAEEFGDRAYRPSPLLEKLVEAGRLGRKTGKGFY 95
>gnl|CDD|224170 COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism].
Length = 307
Score = 38.8 bits (91), Expect = 3e-04
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 54 RMVSRFVNEAVLCLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLS 113
R+++ +NEA+ LEE + +P + D GLG P GPF D G D ++ M
Sbjct: 191 RLLAALLNEAIRLLEEGVA-TPEEIDAAMRQGLGLP---MGPFELADLIGLDVMLHIMKV 246
Query: 114 YENLYGAP--FRPCQLL 128
G +RP LL
Sbjct: 247 LNETLGDDPYYRPPPLL 263
Score = 27.6 bits (62), Expect = 2.1
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 8 GRKSGKGYFVY-AKGSKARPVNDGALAIL 35
GRKSGKG++ Y + K P N+ A ++
Sbjct: 273 GRKSGKGFYDYRGEAIKPLP-NEAARCLI 300
>gnl|CDD|236434 PRK09260, PRK09260, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 288
Score = 33.6 bits (77), Expect = 0.020
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 4/80 (5%)
Query: 54 RMVSRFVNEAVLCLEETILNSPTDGDVGAVFGLGFPPFSGGPFRWVDWYGADKLVQKMLS 113
R+ + NEA L+E + + D D GL FP GP D G D + +
Sbjct: 190 RISALVGNEAFYMLQEG-VATAEDIDKAIRLGLNFPM---GPLELGDLVGLDTRLNNLKY 245
Query: 114 YENLYGAPFRPCQLLLDHAK 133
G +RP LL + K
Sbjct: 246 LHETLGEKYRPAPLLEKYVK 265
>gnl|CDD|143342 cd07837, STKc_CdkB_plant, Catalytic domain of the
Serine/Threonine Kinase, Plant B-type Cyclin-Dependent
protein Kinase. Serine/Threonine Kinases (STKs), Plant
B-type Cyclin-Dependent protein Kinase (CdkB)
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
CdkB subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. CDKs belong to a large
family of STKs that are regulated by their cognate
cyclins. Together, they are involved in the control of
cell-cycle progression, transcription, and neuronal
function. The plant-specific B-type CDKs are expressed
from the late S to the M phase of the cell cycle. They
are characterized by the cyclin binding motif
PPT[A/T]LRE. They play a role in controlling mitosis
and integrating developmental pathways, such as stomata
and leaf development. CdkB has been shown to associate
with both cyclin B, which controls G2/M transition, and
cyclin D, which acts as a mediator in linking
extracellular signals to the cell cycle.
Length = 295
Score = 27.9 bits (62), Expect = 1.9
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 10 KSGKGYFVYAKGSKARPVNDGALAILKKYSLQ------PQSALKDEDLQLRMVSRFVNEA 63
K G+G Y K KAR N G L LKK L+ P +AL++ L L+M+S +
Sbjct: 8 KIGEG--TYGKVYKARDKNTGKLVALKKTRLEMDEEGIPPTALREISL-LQMLSESIYIV 64
Query: 64 -VLCLEETILNSP 75
+L +E +
Sbjct: 65 RLLDVEHVEEKNG 77
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 27.9 bits (63), Expect = 1.9
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 8 GRKSGKGYFVYAKGSKARP 26
GRKSG+G++ YA G+K P
Sbjct: 277 GRKSGQGFYRYADGAKQPP 295
>gnl|CDD|237329 PRK13278, purP,
5-formaminoimidazole-4-carboxamide-1-(beta)-D-
ribofuranosyl 5'-monophosphate synthetase; Provisional.
Length = 358
Score = 27.6 bits (62), Expect = 2.1
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 6 PPGRKSGKGYFVYAKGSK------ARPVNDGALAILKKYSLQ 41
PG K G+GYF+ AK + + + G + +++ +Q
Sbjct: 156 LPGAKGGRGYFI-AKSPEEFKEKIDKLIERGLITEVEEAIIQ 196
>gnl|CDD|238597 cd01192, INT_P22_C, P22-like integrases, site-specific
recombinases, DNA breaking-rejoining enzymes,
C-terminal catalytic domain. This CD includes various
bacterial and phage integrases, including those similar
to phage P22-like integrases, DLP12 and APSE-1.
Length = 177
Score = 27.0 bits (60), Expect = 3.0
Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 2/21 (9%)
Query: 19 AKGSKAR--PVNDGALAILKK 37
+KG +A P+ND AL +LK+
Sbjct: 62 SKGGRAIRVPLNDEALQVLKR 82
>gnl|CDD|180269 PRK05808, PRK05808, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 282
Score = 26.8 bits (60), Expect = 3.5
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 8 GRKSGKGYFVY 18
GRK+G+G++ Y
Sbjct: 272 GRKTGRGFYDY 282
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 26.2 bits (58), Expect = 6.3
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 8 GRKSGKGYFVYAKGSKARPV 27
GRKSG+G + Y + P
Sbjct: 273 GRKSGRGVYHYDGKKRGDPP 292
>gnl|CDD|180289 PRK05851, PRK05851, long-chain-fatty-acid--[acyl-carrier-protein]
ligase; Validated.
Length = 525
Score = 26.3 bits (58), Expect = 6.7
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 91 FSGGPFRWVDW 101
FS PFRW+ W
Sbjct: 230 FSASPFRWLSW 240
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
0.320 0.140 0.447
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,347,064
Number of extensions: 654094
Number of successful extensions: 547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 540
Number of HSP's successfully gapped: 26
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
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: 54 (24.5 bits)