RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy516
(80 letters)
>gnl|CDD|238467 cd00927, Cyt_c_Oxidase_VIc, Cytochrome c oxidase subunit VIc.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is
a multi-chain transmembrane protein located in the
inner membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in
bacteria and up to 13 in mammalian mitochondria.
Subunits I, II, and III of mammalian CcO are encoded
within the mitochondrial genome and the remaining 10
subunits are encoded within the nuclear genome. The VIc
subunit is found only in eukaryotes and its specific
function remains unclear. It has been reported that the
relative concentrations of some nuclear encoded CcO
subunits, including subunit VIc, compared to those of
the mitochondrial encoded subunits, are altered
significantly during the progression of prostate
cancer.
Length = 70
Score = 82.4 bits (204), Expect = 7e-23
Identities = 38/68 (55%), Positives = 49/68 (72%)
Query: 9 KLPKPQLRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTYDGEKDFER 68
L KPQ+R LL S IK L+ V++ G A A+K L+ +P KKA ++FYKTYD KDFER
Sbjct: 1 ALAKPQMRGLLASRIKRHLIVAFVLSLGAAAAYKFLVNEPRKKAYADFYKTYDAMKDFER 60
Query: 69 MKKAGLFE 76
M+KAGLF+
Sbjct: 61 MRKAGLFQ 68
>gnl|CDD|145867 pfam02937, COX6C, Cytochrome c oxidase subunit VIc. Cytochrome c
oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the
terminal oxidase in the mitochondrial electron
transport chain. This family is composed of cytochrome
c oxidase subunit VIc.
Length = 73
Score = 79.0 bits (195), Expect = 2e-21
Identities = 33/70 (47%), Positives = 47/70 (67%)
Query: 7 TGKLPKPQLRNLLQSSIKVALVQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTYDGEKDF 66
LPKPQ+R LL ++ +V V++ G A A+K + +P K+A ++FYK YD KDF
Sbjct: 1 PELLPKPQMRGLLAKRLRRHIVGAFVLSLGVAAAYKFGVAEPRKRAYADFYKNYDAMKDF 60
Query: 67 ERMKKAGLFE 76
ERM+KAGLF+
Sbjct: 61 ERMRKAGLFQ 70
>gnl|CDD|236220 PRK08290, PRK08290, enoyl-CoA hydratase; Provisional.
Length = 288
Score = 27.2 bits (61), Expect = 0.77
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 10/32 (31%)
Query: 10 LPKPQLRNLLQSSIKVALVQGAVIAFGTAVAW 41
LPKP +A VQGA IA G +AW
Sbjct: 117 LPKPT----------IAQVQGACIAGGLMLAW 138
>gnl|CDD|237190 PRK12755, PRK12755, phospho-2-dehydro-3-deoxyheptonate aldolase;
Provisional.
Length = 353
Score = 26.4 bits (59), Expect = 1.7
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 37 TAVAWKVLIMDPH 49
T V WK LI DPH
Sbjct: 101 TTVGWKGLINDPH 113
>gnl|CDD|129145 TIGR00034, aroFGH, phospho-2-dehydro-3-deoxyheptonate aldolase.
[Amino acid biosynthesis, Aromatic amino acid family].
Length = 344
Score = 25.8 bits (57), Expect = 2.7
Identities = 8/13 (61%), Positives = 8/13 (61%)
Query: 37 TAVAWKVLIMDPH 49
T V WK LI DP
Sbjct: 95 TTVGWKGLINDPD 107
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 25.7 bits (56), Expect = 3.3
Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 28 VQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTYDGEKD 65
++G +++ GT V + I+DP K+ I+ + +DG K+
Sbjct: 177 IKGNLLS-GTCVGKHMHIIDPRKQEIASSFHIHDGGKN 213
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated
NodG, as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 25.5 bits (56), Expect = 3.7
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 24 KVALVQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTYDGEKDFERMKKAGLFEEY 78
++ALV G + GTA+ + L D + + + + + + + + A F+
Sbjct: 1 RIALVTGGMGGIGTAIC-QRLAKDGY-RVAANCGPNEERAEAWLQEQGALGFDFR 53
>gnl|CDD|217042 pfam02449, Glyco_hydro_42, Beta-galactosidase. This group of
beta-galactosidase enzymes belong to the glycosyl
hydrolase 42 family. The enzyme catalyzes the
hydrolysis of terminal, non-reducing terminal
beta-D-galactosidase residues.
Length = 376
Score = 24.9 bits (55), Expect = 4.9
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 63 EKDFERMKKAGL 74
E+D MK+AG+
Sbjct: 13 EEDIRLMKEAGV 24
>gnl|CDD|223794 COG0722, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP)
synthase [Amino acid transport and metabolism].
Length = 351
Score = 24.9 bits (55), Expect = 5.5
Identities = 8/13 (61%), Positives = 8/13 (61%)
Query: 37 TAVAWKVLIMDPH 49
T V WK LI DP
Sbjct: 100 TTVGWKGLINDPD 112
>gnl|CDD|216231 pfam00995, Sec1, Sec1 family.
Length = 554
Score = 24.5 bits (54), Expect = 8.4
Identities = 7/19 (36%), Positives = 10/19 (52%), Gaps = 1/19 (5%)
Query: 41 WKVLIMDPH-KKAISEFYK 58
WKVL++D K +S
Sbjct: 1 WKVLVLDKETTKILSSVLT 19
>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
Family 4; Alpha-glucosidases and alpha-galactosidases.
Glucosidases cleave glycosidic bonds to release glucose
from oligosaccharides. Alpha-glucosidases and
alpha-galactosidases release alpha-D-glucose and
alpha-D-galactose, respectively, via the hydrolysis of
alpha-glycopyranoside bonds. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases such as the
alpha-glucosidases. Other organsisms (such as archaea
and Thermotoga maritima) lack the PEP-PTS system, but
have several enzymes normally associated with the
PEP-PTS operon. Alpha-glucosidases and
alpha-galactosidases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 423
Score = 24.4 bits (54), Expect = 8.4
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 8 GKLPKPQLRNLLQSSIKVALVQG-AVIAFGTA---VAWKVLIMDPHKKA 52
G LP PQL L++ I VQ AV A T + ++ L++DP KA
Sbjct: 364 GPLP-PQLAALIRPRI---NVQELAVEAALTGDRELLYQALMLDPLTKA 408
>gnl|CDD|130318 TIGR01251, ribP_PPkin, ribose-phosphate pyrophosphokinase.
Alternate name: phosphoribosylpyrophosphate synthetase
In some systems, close homologs lacking enzymatic
activity exist and perform regulatory functions. The
model is designated subfamily rather than equivalog for
this reason [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 308
Score = 24.2 bits (53), Expect = 8.5
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 35 FGTAVAWKVLIMDPHKKAISEFYKTY 60
TA A +VL +D H I F+
Sbjct: 114 LETAGADRVLTVDLHSPQIQGFFDVP 139
>gnl|CDD|233832 TIGR02353, NRPS_term_dom, non-ribosomal peptide synthetase terminal
domain of unknown function. This domain is found
exclusively in non-ribosomal peptide synthetases and
always as the final domain in the polypeptide. This
domain is roughly 700 amino acids in size and is found
in polypeptides roughly twice that size.
Length = 695
Score = 24.3 bits (53), Expect = 8.6
Identities = 8/36 (22%), Positives = 13/36 (36%)
Query: 25 VALVQGAVIAFGTAVAWKVLIMDPHKKAISEFYKTY 60
+ L+ V AF V K L+ K + +
Sbjct: 525 LILMAVGVGAFLILVERKWLVFGRLKPQEHPLWSPF 560
>gnl|CDD|236435 PRK09261, PRK09261, phospho-2-dehydro-3-deoxyheptonate aldolase;
Validated.
Length = 349
Score = 24.4 bits (54), Expect = 9.0
Identities = 8/13 (61%), Positives = 8/13 (61%)
Query: 37 TAVAWKVLIMDPH 49
T V WK LI DP
Sbjct: 100 TTVGWKGLINDPD 112
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
0.318 0.133 0.380
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: 4,140,873
Number of extensions: 324251
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 444
Number of HSP's successfully gapped: 20
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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 (24.3 bits)