RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy960
(83 letters)
>gnl|CDD|238462 cd00922, Cyt_c_Oxidase_IV, Cytochrome c oxidase subunit IV.
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. Found only in
eukaryotes, subunit IV is the largest of the
nuclear-encoded subunits. It binds ATP at the matrix
side, leading to an allosteric inhibition of enzyme
activity at high intramitochondrial ATP/ADP ratios. In
mammals, subunit IV has a lung-specific isoform and a
ubiquitously expressed isoform.
Length = 136
Score = 55.0 bits (133), Expect = 2e-11
Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 9 FPEKAETLSEEHRQEMLQKMIDLRWNPITGTASKWDY 45
+ K T +EE ++ L++M+D++ NPITG ASKWDY
Sbjct: 100 YGPKPHTFTEEWQEAQLERMLDMKVNPITGYASKWDY 136
>gnl|CDD|202477 pfam02936, COX4, Cytochrome c oxidase subunit IV. 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 IV. The Dictyostelium member of this family is
called COX VI. The yeast protein MTC3 appears to be the
yeast COX IV subunit.
Length = 142
Score = 47.8 bits (114), Expect = 2e-08
Identities = 18/43 (41%), Positives = 29/43 (67%)
Query: 9 FPEKAETLSEEHRQEMLQKMIDLRWNPITGTASKWDYEKNDWK 51
+P +T+++E ++ ++M DL+ NPITG AS +DYE WK
Sbjct: 100 YPPLPKTMNKEWQEAQNERMKDLKINPITGLASGYDYENKVWK 142
>gnl|CDD|183276 PRK11688, PRK11688, hypothetical protein; Provisional.
Length = 154
Score = 27.9 bits (63), Expect = 0.40
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 11 EKAETLSEEHRQEMLQKM--IDLR 32
+ E +SEE ++ L ++ IDLR
Sbjct: 81 ARHEDISEEELRQRLSRLGTIDLR 104
>gnl|CDD|100094 cd05801, PGM_like3, This bacterial PGM-like
(phosphoglucomutase-like) protein of unknown function
belongs to the alpha-D-phosphohexomutase superfamily.
The alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Other
members of this superfamily include phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 522
Score = 26.8 bits (60), Expect = 1.0
Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 4/30 (13%)
Query: 3 EKVKKIFPEKAET-LSEEHRQEMLQKMIDL 31
E V KI+ AE+ LSEEH +++ ++ ++
Sbjct: 495 EDVYKIY---AESFLSEEHLKKIQKEAQEI 521
>gnl|CDD|239472 cd03377, TPP_PFOR_PNO, Thiamine pyrophosphate (TPP family),
PFOR_PNO subfamily, TPP-binding module; composed of
proteins similar to the single subunit pyruvate
ferredoxin oxidoreductase (PFOR) of Desulfovibrio
Africanus, present in bacteria and amitochondriate
eukaryotes. This subfamily also includes proteins
characterized as pyruvate NADP+ oxidoreductase (PNO).
These enzymes are dependent on TPP and a divalent metal
cation as cofactors. PFOR and PNO catalyze the oxidative
decarboxylation of pyruvate to form acetyl-CoA, a
crucial step in many metabolic pathways. Archaea,
anaerobic bacteria and eukaryotes that lack mitochondria
(and therefore pyruvate dehydrogenase) use PFOR to
oxidatively decarboxylate pyruvate, with ferredoxin or
flavodoxin as the electron acceptor. The PFOR from
cyanobacterium Anabaena (NifJ) is required for the
transfer of electrons from pyruvate to flavodoxin, which
reduces nitrogenase. The facultative anaerobic
mitochondrion of the photosynthetic protist Euglena
gracilis oxidizes pyruvate with PNO.
Length = 365
Score = 26.4 bits (59), Expect = 1.8
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 6 KKIFPEKAETLSEEHRQEMLQKMIDLRWN 34
KK PE+AE L E+ LQ R+
Sbjct: 335 KKANPERAEQLFEQ-----LQADAKERYK 358
>gnl|CDD|163472 TIGR03760, ICE_TraI_Pfluor, integrating conjugative element
relaxase, PFL_4751 family. Members of this protein
family are the TraI putative relaxases required for
transfer by a subclass of integrating conjugative
elements (ICE) as found in Pseudomonas fluorescens
Pf-5, and understood from study of two related ICE, SXT
and R391. This model represents the N-terminal domain.
Note that no homology is detected to the similarly
named TraI relaxase of the F plasmid.
Length = 218
Score = 25.7 bits (57), Expect = 3.0
Identities = 8/20 (40%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 10 PEKAET-LSEEHRQEMLQKM 28
P A LS RQ++LQ++
Sbjct: 6 PLSASDLLSTPRRQQLLQQL 25
>gnl|CDD|235046 PRK02507, PRK02507, proton extrusion protein PcxA; Provisional.
Length = 422
Score = 25.7 bits (57), Expect = 3.1
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 1 MEEKVKKIFPEKAETLSEEHRQEMLQ 26
+EEK+K EKAE L+EE R E L
Sbjct: 277 IEEKLK----EKAEELAEEARYESLN 298
>gnl|CDD|179310 PRK01622, PRK01622, OxaA-like protein precursor; Validated.
Length = 256
Score = 25.5 bits (56), Expect = 3.3
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 11/47 (23%)
Query: 1 MEEKVKKIFPE---------KAETLSE--EHRQEMLQKMIDLRWNPI 36
M+EK+ + PE + L + E+++EM++ NP+
Sbjct: 89 MQEKMAVMKPELDKIQAKLKVTKDLEKQKEYQKEMMELYKSGNINPL 135
>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
Length = 974
Score = 25.5 bits (56), Expect = 4.0
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 1 MEEKVKKIFPEKAETLSEEHRQEMLQKMIDLRWNPIT 37
M+E + + LSEE +Q+ L ++ + I
Sbjct: 483 MDEICEYLGLGNYSELSEEEKQDFLLDILPSKRPLIP 519
>gnl|CDD|223985 COG1057, NadD, Nicotinic acid mononucleotide adenylyltransferase
[Coenzyme metabolism].
Length = 197
Score = 24.6 bits (54), Expect = 7.0
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 9 FPEKAETLSEEHRQEMLQKMI 29
+K E S EHR ML+ I
Sbjct: 45 HKKKKELASAEHRLAMLELAI 65
>gnl|CDD|171876 PRK13152, hisH, imidazole glycerol phosphate synthase subunit
HisH; Provisional.
Length = 201
Score = 24.4 bits (53), Expect = 7.7
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 9 FPEKAETLSEEHRQEMLQKMIDLRWNPITGTA------SKWDYE 46
F E + L E E L++ + ++ PI G + YE
Sbjct: 49 FKEAMKNLKELGFIEALKEQVLVQKKPILGICLGMQLFLERGYE 92
>gnl|CDD|185680 cd02165, NMNAT, Nicotinamide/nicotinate mononucleotide
adenylyltransferase. Nicotinamide/nicotinate
mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT).
NMNAT represents the primary bacterial and eukaryotic
adenylyltransferases for nicotinamide-nucleotide and
for the deamido form, nicotinate nucleotide. It is an
indispensable enzyme in the biosynthesis of NAD(+) and
NADP(+). Nicotinamide-nucleotide adenylyltransferase
synthesizes NAD via the salvage pathway, while
nicotinate-nucleotide adenylyltransferase synthesizes
the immediate precursor of NAD via the de novo pathway.
Human NMNAT displays unique dual substrate specificity
toward both NMN and NaMN, and can participate in both
de novo and salvage pathways of NAD synthesis.
Length = 192
Score = 24.5 bits (54), Expect = 7.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 12 KAETLSEEHRQEMLQKMID 30
+ S EHR EML+ I+
Sbjct: 43 PPKPASFEHRLEMLKLAIE 61
>gnl|CDD|238849 cd01751, PLAT_LH2, PLAT/ LH2 domain of plant lipoxygenase related
proteins. Lipoxygenases are nonheme, nonsulfur iron
dioxygenases that act on lipid substrates containing one
or more (Z,Z)-1,4-pentadiene moieties. In plants, the
immediate products are involved in defense mechanisms
against pathogens and may be precursors of metabolic
regulators. The generally proposed function of PLAT/LH2
domains is to mediate interaction with lipids or
membrane bound proteins.
Length = 137
Score = 24.2 bits (53), Expect = 8.5
Identities = 12/35 (34%), Positives = 13/35 (37%), Gaps = 4/35 (11%)
Query: 19 EHRQEMLQKMIDLR----WNPITGTASKWDYEKND 49
EH E K I L IT + W Y K D
Sbjct: 93 EHHSEFFLKSITLEGFGGSGTITFVCNSWVYPKKD 127
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
0.313 0.127 0.385
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,075,960
Number of extensions: 301261
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 330
Number of HSP's successfully gapped: 28
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)