RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9061
(99 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 = 98.0 bits (244), Expect = 2e-25
Identities = 41/71 (57%), Positives = 52/71 (73%), Gaps = 2/71 (2%)
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 CLEETILNSPA 76
CLEE IL SP+
Sbjct: 663 CLEEGILASPS 673
>gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 715
Score = 58.7 bits (143), Expect = 1e-11
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 2/71 (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 CLEETILNSPA 76
CLEE I+ SPA
Sbjct: 642 CLEEGIVASPA 652
>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 = 57.9 bits (140), Expect = 3e-11
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
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 LCLEETILNSPA 76
CLEE I+ + A
Sbjct: 641 RCLEEGIVATAA 652
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 56.1 bits (136), Expect = 1e-10
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 8 GRKSGKGYFVYAK--GSKARPVNDGALAILKKYSLQPQSALKDEDLQLRMVSRFVNEAVL 65
GRK+G+G+++Y + + V++ +L + PQS L ++ R V +NEAV
Sbjct: 576 GRKNGRGFYLYGQKGKKSKKQVDESVYPLLG---ITPQSRLSANEIAERCVMLMLNEAVR 632
Query: 66 CLEETILNSP 75
CL+E I+ S
Sbjct: 633 CLDEGIIRSA 642
>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 = 56.0 bits (135), Expect = 1e-10
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 8 GRKSGKGYFVYAKGSKARPVNDGALAILKKYSLQPQSALKDEDLQLRMVSRFVNEAVLCL 67
GRK+GKG+++Y +K + V++ ++ ++P + + R V +NEAV CL
Sbjct: 571 GRKNGKGFYLYGAATKKKAVDE---SVYGLLGIKPGVDKEASAVAERCVMLMLNEAVRCL 627
Query: 68 EETILNSP 75
+E ++ SP
Sbjct: 628 DEGVIRSP 635
>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 = 29.8 bits (67), Expect = 0.15
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
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 -VLCLEETILNSPASPVY 80
+L +E + +Y
Sbjct: 65 RLLDVEHVEEKNGKPSLY 82
>gnl|CDD|237329 PRK13278, purP,
5-formaminoimidazole-4-carboxamide-1-(beta)-D-
ribofuranosyl 5'-monophosphate synthetase; Provisional.
Length = 358
Score = 27.9 bits (63), Expect = 0.65
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|224170 COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism].
Length = 307
Score = 28.0 bits (63), Expect = 0.70
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|184102 PRK13511, PRK13511, 6-phospho-beta-galactosidase; Provisional.
Length = 469
Score = 28.0 bits (63), Expect = 0.74
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 8/64 (12%)
Query: 42 PQSALKDED-LQLRMVSRFVNEAVLCLEE-------TILNSPASPVYDHHLDGNLEPGHS 93
P++ + D L + FV A C EE T N +L G PG
Sbjct: 120 PEALHSNGDWLNRENIDHFVRYAEFCFEEFPEVKYWTTFNEIGPIGDGQYLVGKFPPGIK 179
Query: 94 RHVT 97
+
Sbjct: 180 YDLA 183
>gnl|CDD|236211 PRK08268, PRK08268, 3-hydroxy-acyl-CoA dehydrogenase; Validated.
Length = 507
Score = 27.9 bits (63), Expect = 0.82
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 8 GRKSGKGYFVYAKGSKARP 26
GRKSG+G++ YA G+K P
Sbjct: 277 GRKSGQGFYRYADGAKQPP 295
>gnl|CDD|180269 PRK05808, PRK05808, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 282
Score = 27.2 bits (61), Expect = 1.5
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 = 3.0
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 8 GRKSGKGYFVYAKGSKARPV 27
GRKSG+G + Y + P
Sbjct: 273 GRKSGRGVYHYDGKKRGDPP 292
>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 = 25.8 bits (57), Expect = 3.6
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|222890 PHA02584, 34, long tail fiber, proximal subunit; Provisional.
Length = 1229
Score = 25.9 bits (57), Expect = 4.6
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 8 GRKSGKGYFVYAKGSKARPVNDG 30
R SG G+F++ K V DG
Sbjct: 277 SRTSGDGFFIFDSTEKLWRVWDG 299
>gnl|CDD|238328 cd00585, Peptidase_C1B, Peptidase C1B subfamily (MEROPS database
nomenclature); composed of eukaryotic bleomycin
hydrolases (BH) and bacterial aminopeptidases C (pepC).
The proteins of this subfamily contain a large insert
relative to the C1A peptidase (papain) subfamily. BH is
a cysteine peptidase that detoxifies bleomycin by
hydrolysis of an amide group. It acts as a
carboxypeptidase on its C-terminus to convert itself
into an aminopeptidase and peptide ligase. BH is found
in all tissues in mammals as well as in many other
eukaryotes. Bleomycin, a glycopeptide derived from the
fungus Streptomyces verticullus, is an effective
anticancer drug due to its ability to induce DNA strand
breaks. Human BH is the major cause of tumor cell
resistance to bleomycin chemotherapy, and is also
genetically linked to Alzheimer's disease. In addition
to its peptidase activity, the yeast BH (Gal6) binds DNA
and acts as a repressor in the Gal4 regulatory system.
BH forms a hexameric ring barrel structure with the
active sites imbedded in the central channel. The
bacterial homolog of BH, called pepC, is a cysteine
aminopeptidase possessing broad specificity. Although
its crystal structure has not been solved, biochemical
analysis shows that pepC also forms a hexamer. .
Length = 437
Score = 25.6 bits (57), Expect = 4.9
Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 26 PVNDG-----ALAILKKYSLQPQSALKD 48
P NDG + +++KY L P+S + +
Sbjct: 131 PQNDGGQWDMLVNLIEKYGLVPKSVMPE 158
>gnl|CDD|177990 PLN02361, PLN02361, alpha-amylase.
Length = 401
Score = 25.5 bits (56), Expect = 5.0
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 5/22 (22%)
Query: 4 WCPPGRK-----SGKGYFVYAK 20
WCP GR+ SG Y V+ K
Sbjct: 380 WCPSGREWTLATSGHRYAVWHK 401
>gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 639
Score = 25.4 bits (55), Expect = 6.1
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 21 GSKARPVNDGALAILKKYSLQPQSALKDEDLQLRMV 56
GS+ VN + ++++QPQ DED +L V
Sbjct: 491 GSRKEVVNAREEGVEFQFNVQPQYIACDEDGRLTAV 526
>gnl|CDD|220735 pfam10408, Ufd2P_core, Ubiquitin elongating factor core. This is
the most conserved part of the core region of Ufd2P
ubiquitin elongating factor or E4, running from helix
alpha-11 to alpha-38. It consists of 31 helices of
variable length connected by loops of variable size
forming a compact unit; the helical packing pattern of
the compact unit consists of five structural repeats
that resemble tandem Armadillo (ARM) repeats. This
domain is involved in ubiquitination as it binds Cdc48p
and escorts ubiquitinated proteins from Cdc48p to the
proteasome for degradation. The core is structurally
similar to the nuclear transporter protein
importin-alpha. The core is associated with the U-box at
the C-terminus, pfam04564, which has ligase activity.
Length = 625
Score = 25.3 bits (56), Expect = 6.3
Identities = 6/31 (19%), Positives = 18/31 (58%)
Query: 43 QSALKDEDLQLRMVSRFVNEAVLCLEETILN 73
+ + ++ D +R ++ +N+A L+E++
Sbjct: 425 KESKENNDFFVRFINLLLNDATYLLDESLSY 455
>gnl|CDD|225406 COG2850, COG2850, Uncharacterized conserved protein [Function
unknown].
Length = 383
Score = 25.0 bits (55), Expect = 7.9
Identities = 17/67 (25%), Positives = 22/67 (32%), Gaps = 3/67 (4%)
Query: 6 PPGRKSGKGYFVYAKGSKARPVNDGALAILKKYSLQPQSALKDEDLQ---LRMVSRFVNE 62
R G V+A G K N AL L K +L L +++ VN
Sbjct: 317 GGLRLLYSGDRVFANGEKFDLPNLKALLALLKNALLTAENQGAALEDPSLLDLLAALVNS 376
Query: 63 AVLCLEE 69
LE
Sbjct: 377 GYWFLEG 383
>gnl|CDD|213070 cd11754, GH94N_CBP_like, N-terminal domain of cellobiose
phosphorylase (CBP) and similar proteins. The glycoside
hydrolase family 94 (previously known as
glycosyltransferase family 36) includes cellobiose
phosphorylase (EC:2.4.1.20) or cellobiose:phosphate
alpha-D-glucosyltransferase, or CepA. This N-terminal
domain is involved in oligomerization and may play a
role in catalysis, but it is separate from the catalytic
domain [an (alpha/alpha)(6) barrel]. Cellobiose
phosphorylase participates in the degradation of
cellulose, it catalyzes the phosphate dependent
hydrolysis of cellobiose into
alpha-D-glucose-1-phosphate and D-glucose, a reversible
reaction.
Length = 303
Score = 24.9 bits (55), Expect = 8.0
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 73 NSPA---SPVYDHHLDGNLEPGHSR 94
NS A SP+ HH++ L PG S+
Sbjct: 232 NSVAHGWSPIGSHHVELTLAPGESK 256
>gnl|CDD|184517 PRK14117, gpmA, phosphoglyceromutase; Provisional.
Length = 230
Score = 25.0 bits (54), Expect = 8.4
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 1 MPFW---CPPGRKSGKGYFVYAKGSKAR 25
+PFW P K GK FV A G+ R
Sbjct: 160 LPFWEDKIAPALKDGKNVFVGAHGNSIR 187
>gnl|CDD|225157 COG2248, COG2248, Predicted hydrolase (metallo-beta-lactamase
superfamily) [General function prediction only].
Length = 304
Score = 24.7 bits (54), Expect = 8.6
Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 9/84 (10%)
Query: 12 GKGYFVYAKGSKARPVNDGALAILKKYSLQPQSALKDEDLQLRMVSRF----VNEAVLCL 67
GK V+A + P+ND AL + + P + + R + + + L
Sbjct: 175 GKSSIVFASDVQG-PINDEALEFILEKR--PDVLIIGGPPTYLLGYRVGPKSLEKGIRNL 231
Query: 68 EETILNSPASPVYDHHL--DGNLE 89
E I + A+ V DHHL D N
Sbjct: 232 ERIIEETNATLVIDHHLLRDKNYR 255
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
0.317 0.135 0.417
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,989,871
Number of extensions: 405235
Number of successful extensions: 297
Number of sequences better than 10.0: 1
Number of HSP's gapped: 291
Number of HSP's successfully gapped: 26
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)