RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7198
(128 letters)
>gnl|CDD|189008 cd09601, M1_APN_2, Peptidase M1 Aminopeptidase N family incudes
tricorn interacting factor F3, Endoplasmic reticulum
aminopeptidase 1 (ERAP1), Aminopeptidase Q (APQ). This
M1 peptidase family includes eukaryotic and bacterial
members: aminopeptidase N (APN), aminopeptidase Q (APQ,
laeverin), endoplasmic reticulum aminopeptidase 1
(ERAP1) as well as tricorn interacting factor F3.
Aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease,
consists of a small N-terminal cytoplasmic domain, a
single transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and is present in a variety
of human tissues and cell types (leukocyte, fibroblast,
endothelial and epithelial cells). APN expression is
dysregulated in inflammatory diseases such as chronic
pain, rheumatoid arthritis, multiple sclerosis, systemic
sclerosis, systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is considered a marker of differentiation since it is
predominantly expressed on stem cells and on cells of
the granulocytic and monocytic lineages at distinct
stages of differentiation. Thus, APN inhibition may lead
to the development of anti-cancer and anti-inflammatory
drugs. ERAP1 also known as endoplasmic reticulum
aminopeptidase associated with antigen processing
(ERAAP), adipocyte derived leucine aminopeptidase
(A-LAP) or aminopeptidase regulating tumor necrosis
factor receptor I (THFRI) shedding (ARTS-1), associates
with the closely related ER aminopeptidase ERAP2, for
the final trimming of peptides within the ER for
presentation by MHC class I molecules. ERAP1 is
associated with ankylosing spondylitis (AS), an
inflammatory arthritis that predominantly affects the
spine. ERAP1 also aids in the shedding of membrane-bound
cytokine receptors. The tricorn interacting factor F3,
together with factors F1 and F2, degrades the tricorn
protease products, producing free amino acids, thus
completing the proteasomal degradation pathway. F3 is
homologous to F2, but not F1, and shows a strong
preference for glutamate in the P1' position. APQ, also
known as laeverin, is specifically expressed in human
embryo-derived extravillous trophoblasts (EVTs) that
invade the uterus during early placentation. It cleaves
the N-terminal amino acid of various peptides such as
angiotensin III, endokinin C, and kisspeptin-10, all
expressed in the placenta in large quantities. APN is a
receptor for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs are also putative Cry toxin
receptors. Cry1 proteins are pore-forming toxins that
bind to the midgut epithelial cell membrane of
susceptible insect larvae, causing extensive damage.
Several different toxins, including Cry1Aa, Cry1Ab,
Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to
bind to APNs; however, a direct role of APN in
cytotoxicity has been yet to be firmly established.
Length = 446
Score = 71.4 bits (176), Expect = 1e-15
Identities = 24/44 (54%), Positives = 32/44 (72%)
Query: 59 RYIIMTKFDPTGARQAFPCFDEPIHKTTFNVSVTHSKKYSFLWN 102
RY+ T+F+PT AR+AFPCFDEP K TF +++TH Y+ L N
Sbjct: 114 RYLAATQFEPTDARRAFPCFDEPAFKATFTITITHPAGYTALSN 157
>gnl|CDD|216501 pfam01433, Peptidase_M1, Peptidase family M1. Members of this
family are aminopeptidases. The members differ widely in
specificity, hydrolysing acidic, basic or neutral
N-terminal residues. This family includes leukotriene-A4
hydrolase, this enzyme also has an aminopeptidase
activity.
Length = 390
Score = 63.1 bits (154), Expect = 1e-12
Identities = 21/44 (47%), Positives = 31/44 (70%)
Query: 59 RYIIMTKFDPTGARQAFPCFDEPIHKTTFNVSVTHSKKYSFLWN 102
+ + T+F+PT AR+AFPCFDEP K TF++++ H Y+ L N
Sbjct: 123 KPMATTQFEPTDARRAFPCFDEPSVKATFDITINHPADYTALSN 166
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 44.8 bits (106), Expect = 2e-06
Identities = 16/56 (28%), Positives = 27/56 (48%)
Query: 60 YIIMTKFDPTGARQAFPCFDEPIHKTTFNVSVTHSKKYSFLWNKNKLGTRLSGKPK 115
++T+ + GAR+ FPC DEP K TF +++ K + N N + +
Sbjct: 134 PYLITQCEAEGARRIFPCIDEPDVKATFTLTIRADKGPKLISNGNLIDGGTLVDGR 189
>gnl|CDD|189010 cd09603, M1_APN_4, Peptidase M1 family Aminopeptidase N. This
family contains mostly bacterial and some archaeal
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 415
Score = 36.4 bits (85), Expect = 0.002
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 68 PTGARQAFPCFDEPIHKTTFNVSVTHSKKYS 98
P GA FPC D P K TF++SVT Y+
Sbjct: 113 PEGASTWFPCNDHPSDKATFDISVTVPAGYT 143
>gnl|CDD|189009 cd09602, M1_APN_3, Peptidase M1 family containing Aminopeptidase N.
This family contains bacterial and eukaryotic
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 438
Score = 34.9 bits (81), Expect = 0.006
Identities = 17/36 (47%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 60 YIIMTKFDPTGARQAFPCFDEPIHKTTFNVSVTHSK 95
Y+ T+F+P AR+ FPCFD+P K F ++VT K
Sbjct: 110 YLY-TQFEPDDARRVFPCFDQPDLKAPFTLTVTAPK 144
>gnl|CDD|233857 TIGR02412, pepN_strep_liv, aminopeptidase N, Streptomyces lividans
type. This family is a subset of the members of the
zinc metallopeptidase family M1 (pfam01433), with a
single member characterized in Streptomyces lividans 66
and designated aminopeptidase N. The spectrum of
activity may differ somewhat from the aminopeptidase N
clade of E. coli and most other Proteobacteria, well
separated phylogenetically within the M1 family. The M1
family also includes leukotriene A-4
hydrolase/aminopeptidase (with a bifunctional active
site).
Length = 831
Score = 33.6 bits (77), Expect = 0.017
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 64 TKFDPTGARQAFPCFDEPIHKTTFNVSVT 92
T+F+P AR+ F FD+P K F SV
Sbjct: 122 TQFEPADARRVFAVFDQPDLKANFKFSVK 150
>gnl|CDD|233856 TIGR02411, leuko_A4_hydro, leukotriene A-4
hydrolase/aminopeptidase. Members of this family
represent a distinctive subset within the zinc
metallopeptidase family M1 (pfam01433). The majority of
the members of pfam01433 are aminopeptidases, but the
sequences in this family for which the function is known
are leukotriene A-4 hydrolase. A dual epoxide hydrolase
and aminopeptidase activity at the same active site is
indicated. The physiological substrate for
aminopeptidase activity is not known.
Length = 602
Score = 30.9 bits (70), Expect = 0.16
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 71 ARQAFPCFDEPIHKTTFNVSVTH 93
AR FPC D P K+T+ V
Sbjct: 135 ARSLFPCQDTPSVKSTYTAEVES 157
>gnl|CDD|240316 PTZ00216, PTZ00216, acyl-CoA synthetase; Provisional.
Length = 700
Score = 30.3 bits (69), Expect = 0.21
Identities = 20/59 (33%), Positives = 22/59 (37%), Gaps = 15/59 (25%)
Query: 25 DRQVDLTGG--PDEVYLSGLPDREWLALDFHLAHHFRYIIMTKFDPTGARQAFPCFDEP 81
DR DL G DE Y S LP LAH + + F AR A F P
Sbjct: 298 DRLNDLIGPPEEDETYCSYLP----------LAHIMEFGVTNIF---LARGALIGFGSP 343
>gnl|CDD|189006 cd09599, M1_LTA4H, Peptidase M1 family contains leukotriene A4
hydrolase. This family includes leukotriene A4
hydrolase (LTA4H; E.C. 3.3.2.6) and the close homolog
cold-active aminopeptidase (Colwellia
psychrerythraea-type peptidase; ColAP), both members of
the aminopeptidase M1 family. LTA4H, is a bifunctional
enzyme possessing an aminopeptidase as well as an
epoxide hydrolase activity. The two activities occupy
different, but overlapping sites. The activity and
physiological relevance of the aminopeptidase is as yet
unknown while the epoxide hydrolase converts leukotriene
A4 (LTA4) into leukotriene B4 (LTB4), a potent
chemotaxin that is fundamental to the inflammatory
response of mammals. It accepts a variety of substrates,
including some opioid, di- and tripeptides, as well as
chromogenic aminoacyl-p-nitroanilide derivatives. The
aminopeptidase activity of LTA4H is possibly involved in
the processing of peptides related to inflammation and
host defense. Kinetic analysis shows that LTA4H
hydrolyzes arginyl tripeptides with high efficiency and
specificity, indicating its function as an arginyl
aminopeptidase. LTA4H is overexpressed in certain human
cancers, and has been identified as a functionally
important target for mediating anticancer properties of
resveratrol, a well known red wine polyphenolic compound
with cancer chemopreventive activity.
Length = 442
Score = 30.2 bits (69), Expect = 0.27
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 71 ARQAFPCFDEPIHKTTFNVSVTHSK 95
AR FPC D P K+T++ +VT K
Sbjct: 136 ARSLFPCQDTPSVKSTYSATVTVPK 160
>gnl|CDD|224012 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
outer membrane].
Length = 329
Score = 28.7 bits (65), Expect = 0.73
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 46 EWLALDFHLAHHFRYIIMTKFDPTGA 71
E + D A+ F+ +I+ F+ GA
Sbjct: 150 EEILRDAAKANPFKVVILRYFNVAGA 175
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 28.6 bits (65), Expect = 1.0
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 35 DEVYLSGLPDREWLALDFHLAHH 57
+VYL+ PDRE A+ +HLAH
Sbjct: 75 KKVYLATDPDREGEAIAWHLAHI 97
>gnl|CDD|239008 cd02053, alpha2AP, Alpha2-antiplasmin (alpha2AP) is the primary
inhibitor of plasmin, a proteinase that digests fibrin,
the main component of blood clots. Alpha2-Antiplasmin
forms an inactive 1 : 1 stoichiometric complex with
plasmin. It also rapidly crosslinks to fibrin during
blood clotting by activated coagulation factor XIII, and
as a consequence fibrin becomes more resistant to
fibrinolysis. Therefore alpha2AP is important in
modulating the effectiveness and persistence of fibrin
with respect to its susceptibility to digestion and
removal by plasmin. This subgroup corresponds to clade
F2 of the serpin superfamily.
Length = 351
Score = 28.2 bits (63), Expect = 1.1
Identities = 22/74 (29%), Positives = 29/74 (39%), Gaps = 7/74 (9%)
Query: 29 DLTGGPDEVYLSGLPDREWLALDFHLAHHFRYIIMTKFDPT-GARQAFPCFDEPIHKTTF 87
+ T G +LS LP L L A HF+ KFDP+ R AF T
Sbjct: 129 EATEGQIPNFLSDLPHDTVLLL--LNAIHFKGFWRNKFDPSLTQRDAF----HLDDDFTV 182
Query: 88 NVSVTHSKKYSFLW 101
+V + + Y W
Sbjct: 183 SVEMMQASTYPLRW 196
>gnl|CDD|189002 cd09595, M1, Peptidase M1 family contains aminopeptidase N and
leukotriene A4 hydrolase. M1 Peptidase family includes
aminopeptidase N (APN) and leukotriene A4 hydrolase
(LTA4H). All peptidases in this family bind a single
catalytic zinc ion which is tetrahedrally co-ordinated
by three amino acid ligands and a water molecule that
forms the nucleophile on activation during catalysis.
APN consists of a small N-terminal cytoplasmic domain, a
single transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and is present in a variety
of human tissues and cell types. APN expression is
dysregulated in many inflammatory diseases and is
enhanced in numerous tumor cells, making it a lead
target in the development of anti-cancer and
anti-inflammatory drugs. LTA4H is a bifunctional enzyme,
possessing an aminopeptidase as well as an epoxide
hydrolase activity. The two activities occupy different,
but overlapping sites. The activity and physiological
relevance of the aminopeptidase in LTA4H is as yet
unknown while the epoxide hydrolase converts leukotriene
A4 (LTA4) into leukotriene B4 (LTB4), a potent
chemotaxin that is fundamental to the inflammatory
response of mammals.
Length = 407
Score = 28.2 bits (63), Expect = 1.4
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 8/58 (13%)
Query: 40 SGLPDREWLALDFHLAHHFRYIIMTKFDPTGARQAFPCFDEPIHKTTFNVSVTHSKKY 97
GL + A L ++ + GAR FPC D P T+ +VT K
Sbjct: 93 MGLGWQTAGAEGAFLF--------SQGEAIGARSWFPCQDRPDSVATYYTTVTVPDKT 142
>gnl|CDD|187558 cd05247, UDP_G4E_1_SDR_e, UDP-glucose 4 epimerase, subgroup 1,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 323
Score = 27.5 bits (62), Expect = 1.7
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 46 EWLALDFHLAHHFRYIIMTKFDPTGA 71
E + D A Y+I+ F+P GA
Sbjct: 152 EQILRDLAKAPGLNYVILRYFNPAGA 177
>gnl|CDD|130009 TIGR00934, 2a38euk, potassium uptake protein, Trk family. The
proteins of the Trk family are derived from
Gram-negative and Gram-positive bacteria, yeast and
wheat. The proteins of E. coli K12 TrkH and TrkG as well
as several yeast proteins have been functionally
characterized.The E. coli TrkH and TrkG proteins are
complexed to two peripheral membrane proteins, TrkA, an
NAD-binding protein, and TrkE, an ATP-binding protein.
This complex forms the potassium uptake system. This
family is specific for the eukaryotic Trk system
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 800
Score = 27.6 bits (61), Expect = 2.2
Identities = 19/114 (16%), Positives = 31/114 (27%)
Query: 15 FFLILQKRSHDRQVDLTGGPDEVYLSGLPDREWLALDFHLAHHFRYIIMTKFDPTGARQA 74
F + + +D D L D E + D AHH + +
Sbjct: 296 SFDKAVRLRRSKTIDRAEACDLEELDRAKDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRK 355
Query: 75 FPCFDEPIHKTTFNVSVTHSKKYSFLWNKNKLGTRLSGKPKSLKDSEPSISQCH 128
F + + + S SF + L + + P K E S
Sbjct: 356 ASRFPKDSDRNYEDNGNHLSASSSFGSEEPSLSSEENLYPTYNKKREDSRHTLS 409
>gnl|CDD|173783 cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to Escherichia coli DNA topoisomerase I. Type
IA DNA topoisomerases remove (relax) negative
supercoils in the DNA by: cleaving one strand of the
DNA duplex, covalently linking to the 5' phosphoryl end
of the DNA break and, allowing the other strand of the
duplex to pass through the gap. The TOPRIM domain has
two conserved motifs, one of which centers at a
conserved glutamate and the other one at two conserved
aspartates (DxD). For topoisomerases the conserved
glutamate is believed to act as a general base in
strand joining and, as a general acid in strand
cleavage. The DXD motif may co-ordinate Mg2+, a
cofactor required for full catalytic function.
Length = 123
Score = 26.8 bits (60), Expect = 2.3
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 29 DLTGGPDEVYLSGLPDREWLALDFHLA 55
L DE+YL+ PDRE A+ +HLA
Sbjct: 68 KLAKKADEIYLATDPDREGEAIAWHLA 94
>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events [DNA metabolism, DNA replication, recombination,
and repair].
Length = 610
Score = 27.3 bits (61), Expect = 2.6
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 35 DEVYLSGLPDREWLALDFHLAH 56
DEVYL+ PDRE A+ +HLA
Sbjct: 71 DEVYLATDPDREGEAIAWHLAE 92
>gnl|CDD|143434 cd07116, ALDH_ACDHII-AcoD, Ralstonia eutrophus NAD+-dependent
acetaldehyde dehydrogenase II-like. Included in this CD
is the NAD+-dependent, acetaldehyde dehydrogenase II
(AcDHII, AcoD, EC=1.2.1.3) from Ralstonia (Alcaligenes)
eutrophus H16 involved in the catabolism of acetoin and
ethanol, and similar proteins, such as, the dimeric
dihydrolipoamide dehydrogenase of the acetoin
dehydrogenase enzyme system of Klebsiella pneumonia.
Also included are sequences similar to the
NAD+-dependent chloroacetaldehyde dehydrogenases (AldA
and AldB) of Xanthobacter autotrophicus GJ10 which are
involved in the degradation of 1,2-dichloroethane. These
proteins apparently require RpoN factors for expression.
Length = 479
Score = 27.4 bits (61), Expect = 2.6
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 36 EVYLSGLPDREWLALDFHLA-HHFRY 60
E + +G P RE LA D LA HFRY
Sbjct: 84 ETWDNGKPVRETLAADIPLAIDHFRY 109
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion
protein; Validated.
Length = 860
Score = 27.1 bits (60), Expect = 3.1
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 35 DEVYLSGLPDREWLALDFHLA 55
D VYLS PDRE A+ +H+A
Sbjct: 75 DVVYLSPDPDREGEAIAWHIA 95
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 26.7 bits (59), Expect = 3.2
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 20 QKRSHDRQVDLTGGPDEVY---LSGLP 43
+ R H ++VD G PDEVY L L
Sbjct: 165 EARGHLKRVDGLGTPDEVYARILKALG 191
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional
gluaredoxin/ribonucleoside-diphosphate reductase subunit
beta; Provisional.
Length = 410
Score = 26.9 bits (59), Expect = 3.4
Identities = 21/67 (31%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 41 GLPDREWLALDFHLAHHFRYIIMTKFDPTGARQAFPCFDEPIHKTTFNVSVTHSKKYSFL 100
GLPD E+ A + A + M DPT R C + KT FN V ++ L
Sbjct: 204 GLPDSEYHAFLEYKAMTDKIDFMMDADPTTRRGLGLC----LAKTVFNEGVALFASFAML 259
Query: 101 WNKNKLG 107
N + G
Sbjct: 260 LNFQRFG 266
>gnl|CDD|235965 PRK07205, PRK07205, hypothetical protein; Provisional.
Length = 444
Score = 26.6 bits (59), Expect = 4.3
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 49 ALDFHLAHHFRYIIMTKFDPTGARQAFPCFDEPIHKTTFNVS-VTHSKKYSF 99
ALDF LA+ D TG DEP K +FN++ +T +K+ S
Sbjct: 276 ALDF-LANVI------GEDATGLNIFGDIEDEPSGKLSFNIAGLTITKEKSE 320
>gnl|CDD|236215 PRK08276, PRK08276, long-chain-fatty-acid--CoA ligase; Validated.
Length = 502
Score = 26.4 bits (59), Expect = 5.1
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 29 DLTGGPDEVYLSGLPDREWLALDF-----HLAHHFRYIIMTKFDPTGA 71
+ GGPD VYLS P L F L ++M KFD A
Sbjct: 181 GMYGGPDSVYLSPAPLYHTAPLRFGMSALALGG--TVVVMEKFDAEEA 226
>gnl|CDD|224252 COG1333, ResB, ResB protein required for cytochrome c biosynthesis
[Posttranslational modification, protein turnover,
chaperones].
Length = 478
Score = 26.2 bits (58), Expect = 5.1
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 12 LWGFFLILQKRSHDRQVDL--TGGPDEVYLSGLPDREWLALDFHLAH 56
+ G L+ R+V L G EV + GL + +W +F
Sbjct: 408 MVG--LVQSLYWRHRRVWLRSLDGTREVEVGGLTNTDWSGGEFERVL 452
>gnl|CDD|130321 TIGR01254, sfuA, ABC transporter periplasmic binding protein, thiB
subfamily. The model describes thiamine ABC
transporter, periplasmic protein in bacteria and archae.
The protein belongs to the larger ABC transport system.
It consists of at least three components: the thiamine
binding periplasmic protein; an inner membrane permease;
an ATP-binding subunit. It has been experimentally
demonstrated that the mutants in the various steps in
the de novo synthesis of the thiamine and the
biologically active form, namely thiamine pyrophosphate
can be exogenously supplemented with thiamine, thiamine
monophosphate (TMP) or thiamine pyrophosphate (TPP)
[Transport and binding proteins, Other].
Length = 304
Score = 25.6 bits (56), Expect = 8.2
Identities = 9/23 (39%), Positives = 15/23 (65%), Gaps = 4/23 (17%)
Query: 97 YSFLWNKNKLGTRLSGKPKSLKD 119
+F+++KNKL P+SLK+
Sbjct: 107 VAFVYDKNKL----QNPPQSLKE 125
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
0.324 0.139 0.450
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,612,747
Number of extensions: 583740
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 507
Number of HSP's successfully gapped: 36
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.2 bits)