RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4520
(291 letters)
>gnl|CDD|238542 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands.
Length = 271
Score = 155 bits (394), Expect = 6e-46
Identities = 53/217 (24%), Positives = 85/217 (39%), Gaps = 44/217 (20%)
Query: 1 MSEYSLDLALQ-GVTTLWGSFEVQNKRLARIMLQQLVRKPLLDNLDKFDEYSDWFKTLPM 59
+ EY+LDL Q GV S E R AR +L Q K L F
Sbjct: 47 LREYALDLITQHGVRVGTISLEEPVVRTARRLLGQYAGKRLHLPDTVFIYT--------- 97
Query: 60 YFLTFHGPQPLKLVMELVRKPLLDNLDKFDEYSDWFKTLPMYFLTFHGPQ-PLKLVMEAV 118
L++FD D F+ F+ + + V+E V
Sbjct: 98 -------------------------LEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKV 132
Query: 119 EHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQEFRAFASRSHCHVTLVIHPRK 178
+ + H+IIDN+ M+ ++ D D I+ + R FA+ H+TLV H R+
Sbjct: 133 RYMAVSHGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSHLRR 192
Query: 179 --------ENEQLTVNSVFGSAKATQESDNVLIIQQK 207
E +++++ GSA Q +DNV+ +++
Sbjct: 193 PDGDKTHEEGGEVSLSDFRGSAAIGQLADNVIALERN 229
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 47.3 bits (113), Expect = 1e-06
Identities = 14/68 (20%), Positives = 23/68 (33%), Gaps = 9/68 (13%)
Query: 117 AVEHAMYVYDTGHVIIDNVQFMLGL---SDSALDRFYMQDTIIQEFRAFASRSHCHVTLV 173
E + V+ID + +LG ++A+ + A R+ V LV
Sbjct: 93 LGEALEEIEGPDLVVIDPLASLLGGDENDNAAVGAL------LAALDRLARRTGAAVLLV 146
Query: 174 IHPRKENE 181
H K
Sbjct: 147 HHTGKAGG 154
>gnl|CDD|214480 smart00034, CLECT, C-type lectin (CTL) or carbohydrate-recognition
domain (CRD). Many of these domains function as
calcium-dependent carbohydrate binding modules.
Length = 124
Score = 42.6 bits (100), Expect = 3e-05
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 233 PPGSTATYNGKCYIFYNRRPMNLRDSLAFCRSRGGSLVDESNPALQGFIS 282
P G +Y GKCY F D+ AFC+S GG L + A F++
Sbjct: 2 PSGWI-SYGGKCYKFSTE-KKTWEDAQAFCQSLGGHLASIHSEAENDFVA 49
>gnl|CDD|153057 cd00037, CLECT, C-type lectin (CTL)/C-type lectin-like (CTLD)
domain. CLECT: C-type lectin (CTL)/C-type lectin-like
(CTLD) domain; protein domains homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. This group is chiefly comprised of eukaryotic
CTLDs, but contains some, as yet functionally
uncharacterized, bacterial CTLDs. Many CTLDs are
calcium-dependent carbohydrate binding modules; other
CTLDs bind protein ligands, lipids, and inorganic
surfaces, including CaCO3 and ice. Animal C-type
lectins are involved in such functions as extracellular
matrix organization, endocytosis, complement activation,
pathogen recognition, and cell-cell interactions. For
example: mannose-binding lectin and lung surfactant
proteins A and D bind carbohydrates on surfaces (e.g.
pathogens, allergens, necrotic, and apoptotic cells) and
mediate functions associated with killing and
phagocytosis; P (platlet)-, E (endothelial)-, and L
(leukocyte)- selectins (sels) mediate the initial
attachment, tethering, and rolling of lymphocytes on
inflamed vascular walls enabling subsequent lymphocyte
adhesion and transmigration. CTLDs may bind a variety
of carbohydrate ligands including mannose,
N-acetylglucosamine, galactose, N-acetylgalactosamine,
and fucose. Several CTLDs bind to protein ligands, and
only some of these binding interactions are
Ca2+-dependent; including the CTLDs of Coagulation
Factors IX/X (IX/X) and Von Willebrand Factor (VWF)
binding proteins, and natural killer cell receptors.
C-type lectins, such as lithostathine, and some type II
antifreeze glycoproteins function in a Ca2+-independent
manner to bind inorganic surfaces. Many proteins in
this group contain a single CTLD; these CTLDs associate
with each other through several different surfaces to
form dimers, trimers, or tetramers, from which
ligand-binding sites project in different orientations.
Various vertebrate type 1 transmembrane proteins
including macrophage mannose receptor, endo180,
phospholipase A2 receptor, and dendritic and epithelial
cell receptor (DEC205) have extracellular domains
containing 8 or more CTLDs; these CTLDs remain in the
parent model. In some members (IX/X and VWF binding
proteins), a loop extends to the adjoining domain to
form a loop-swapped dimer. A similar conformation is
seen in the macrophage mannose receptor CRD4's putative
non-sugar bound form of the domain in the acid
environment of the endosome. Lineage specific
expansions of CTLDs have occurred in several animal
lineages including Drosophila melanogaster and
Caenorhabditis elegans; these CTLDs also remain in the
parent model.
Length = 116
Score = 37.6 bits (87), Expect = 0.001
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 243 KCYIFYNRRPMNLRDSLAFCRSRGGSLVDESNPALQGFIS 282
CY F + ++ +CRS GG L + F++
Sbjct: 1 SCYKFSTE-KLTWEEAQEYCRSLGGHLASIHSEEENDFLA 39
>gnl|CDD|153061 cd03591, CLECT_collectin_like, C-type lectin-like domain (CTLD) of
the type found in human collectins including lung
surfactant proteins A and D, mannose- or mannan binding
lectin (MBL), and CL-L1 (collectin liver 1).
CLECT_collectin_like: C-type lectin-like domain (CTLD)
of the type found in human collectins including lung
surfactant proteins A and D, mannose- or mannan binding
lectin (MBL), and CL-L1 (collectin liver 1). CTLD
refers to a domain homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. The CTLDs of these collectins bind
carbohydrates on surfaces (e.g. pathogens, allergens,
necrotic, or apoptotic cells) and mediate functions
associated with killing and phagocytosis. MBPs
recognize high mannose oligosaccharides in a calcium
dependent manner, bind to a broad range of pathogens,
and trigger cell killing by activating the complement
pathway. MBP also acts directly as an opsonin. SP-A
and SP-D in addition to functioning as host defense
components, are components of pulmonary surfactant which
play a role in surfactant homeostasis. Pulmonary
surfactant is a phospholipid-protein complex which
reduces the surface tension within the lungs. SP-A
binds the major surfactant lipid:
dipalmitoylphosphatidylcholine (DPPC). SP-D binds two
minor components of surfactant that contain sugar
moieties: glucosylceramide and phosphatidylinositol
(PI). MBP and SP-A, -D monomers are homotrimers with an
N-terminal collagen region and three CTLDs. Multiple
homotrimeric units associate to form supramolecular
complexes. MBL deficiency results in an increased
susceptibility to a large number of different infections
and to inflammatory disease, such as rheumatoid
arthritis.
Length = 114
Score = 36.1 bits (84), Expect = 0.004
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 5/46 (10%)
Query: 246 IFY-NRRPMNLRDSLAFCRSRGGSLV----DESNPALQGFISWELS 286
IF N N D+ C GG+L N A+ ++ +
Sbjct: 3 IFVTNGEEKNFDDAQKLCSEAGGTLAMPRNAAENAAIASYVKKGNT 48
>gnl|CDD|153060 cd03590, CLECT_DC-SIGN_like, C-type lectin-like domain (CTLD) of
the type found in human dendritic cell (DC)-specific
intercellular adhesion molecule 3-grabbing non-integrin
(DC-SIGN) and the related receptor, DC-SIGN receptor
(DC-SIGNR). CLECT_DC-SIGN_like: C-type lectin-like
domain (CTLD) of the type found in human dendritic cell
(DC)-specific intercellular adhesion molecule 3-grabbing
non-integrin (DC-SIGN) and the related receptor, DC-SIGN
receptor (DC-SIGNR). This group also contains proteins
similar to hepatic asialoglycoprotein receptor (ASGP-R)
and langerin in human. These proteins are type II
membrane proteins with a CTLD ectodomain. CTLD refers
to a domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. DC-SIGN is
thought to mediate the initial contact between dendritic
cells and resting T cells, and may also mediate the
rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind
to oligosaccharides present on human tissues, as well
as, on pathogens including parasites, bacteria, and
viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing
viral infection of T cells. DC-SIGN and DC-SIGNR are
homotetrameric, and contain four CTLDs stabilized by a
coiled coil of alpha helices. The hepatic ASGP-R is an
endocytic recycling receptor which binds and
internalizes desialylated glycoproteins having a
terminal galactose or N-acetylgalactosamine residues on
their N-linked carbohydrate chains, via the
clathrin-coated pit mediated endocytic pathway, and
delivers them to lysosomes for degradation. It has been
proposed that glycoproteins bearing terminal Sia (sialic
acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are
endogenous ligands for ASGP-R and that ASGP-R
participates in regulating the relative concentration of
serum glycoproteins bearing alpha 2,6-linked Sia. The
human ASGP-R is a hetero-oligomer composed of two
subunits, both of which are found within this group.
Langerin is expressed in a subset of dendritic
leukocytes, the Langerhans cells (LC). Langerin induces
the formation of Birbeck Granules (BGs) and associates
with these BGs following internalization. Langerin
binds, in a calcium-dependent manner, to
glyco-conjugates containing mannose and related sugars
mediating their uptake and degradation. Langerin
molecules oligomerize as trimers with three CTLDs held
together by a coiled-coil of alpha helices.
Length = 126
Score = 34.6 bits (80), Expect = 0.013
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 240 YNGKCYIFYNRRPMNLRDSLAFCRSRGGSLVDESNPALQGFISWELS-------GLPDS 291
+ CY F++ + +S FC G LV ++ Q FIS LS GL D
Sbjct: 8 FQSSCY-FFSTEKKSWEESRQFCEDMGAHLVIINSQEEQEFISKILSGNRSYWIGLSDE 65
>gnl|CDD|153064 cd03594, CLECT_REG-1_like, C-type lectin-like domain (CTLD) of the
type found in Human REG-1 (lithostathine), REG-4, and
avian eggshell-specific proteins: ansocalcin,
structhiocalcin-1(SCA-1), and -2(SCA-2).
CLECT_REG-1_like: C-type lectin-like domain (CTLD) of
the type found in Human REG-1 (lithostathine), REG-4,
and avian eggshell-specific proteins: ansocalcin,
structhiocalcin-1(SCA-1), and -2(SCA-2). CTLD refers to
a domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. REG-1 is a
proliferating factor which participates in various kinds
of tissue regeneration including pancreatic beta-cell
regeneration, regeneration of intestinal mucosa,
regeneration of motor neurons, and perhaps in tissue
regeneration of damaged heart. REG-1 may play a role on
the pathophysiology of Alzheimer's disease and in the
development of gastric cancers. Its expression is
correlated with reduced survival from early-stage
colorectal cancer. REG-1 also binds and aggregates
several bacterial strains from the intestinal flora and
it has been suggested that it is involved in the control
of the intestinal bacterial ecosystem. Rat
lithostathine has calcium carbonate crystal inhibitor
activity in vitro. REG-IV is unregulated in pancreatic,
gastric, hepatocellular, and prostrate adenocarcinomas.
REG-IV activates the EGF receptor/Akt/AP-1 signaling
pathway in colorectal carcinoma. Ansocalcin, SCA-1 and
-2 are found at high concentration in the calcified egg
shell layer of goose and ostrich, respectively and tend
to form aggregates. Ansocalcin nucleates calcite
crystal aggregates in vitro.
Length = 129
Score = 31.6 bits (72), Expect = 0.21
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 233 PPGSTATYNGKCYIFYNRRPMNLRDSLAFCRSRGGS 268
P G Y G CY ++ R+P++ D+ FC+ G
Sbjct: 2 PKGWLP-YKGNCYGYF-RQPLSWSDAELFCQKYGPG 35
>gnl|CDD|236719 PRK10576, PRK10576, iron-hydroxamate transporter substrate-binding
subunit; Provisional.
Length = 292
Score = 31.9 bits (73), Expect = 0.35
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 14/54 (25%)
Query: 1 MSEYSLDLALQGVTTLWGSFEVQNKRLARI--------------MLQQLVRKPL 40
+ E ++ A QG T WGS V +RLA +QQL+ PL
Sbjct: 198 LDELGIENAWQGETNFWGSTVVGIERLAAYKDADVICFDHGNSKDMQQLMATPL 251
>gnl|CDD|215684 pfam00059, Lectin_C, Lectin C-type domain. This family includes
both long and short form C-type.
Length = 108
Score = 30.0 bits (68), Expect = 0.52
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 252 PMNLRDSLAFCRSRGGSLVDESNPALQGFIS 282
++ A C+ GG LV + Q F++
Sbjct: 2 SKTWAEAEAACQKLGGHLVSIQSAEEQDFLT 32
>gnl|CDD|238573 cd01168, adenosine_kinase, Adenosine kinase (AK) catalyzes the
phosphorylation of ribofuranosyl-containing nucleoside
analogues at the 5'-hydroxyl using ATP or GTP as the
phosphate donor.The physiological function of AK is
associated with the regulation of extracellular
adenosine levels and the preservation of intracellular
adenylate pools. Adenosine kinase is involved in the
purine salvage pathway. .
Length = 312
Score = 30.3 bits (69), Expect = 1.2
Identities = 16/82 (19%), Positives = 27/82 (32%), Gaps = 25/82 (30%)
Query: 101 YFLTFHGPQPLKLVMEAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQD------- 153
Y LT P + ++ A EHA + V+ L LS + + + +
Sbjct: 154 YLLTV----PPEAILLAAEHA-----KEN----GVKIALNLSAPFIVQRFKEALLELLPY 200
Query: 154 -TII----QEFRAFASRSHCHV 170
I+ +E A A
Sbjct: 201 VDILFGNEEEAEALAEAETTDD 222
>gnl|CDD|153062 cd03592, CLECT_selectins_like, C-type lectin-like domain (CTLD) of
the type found in the type 1 transmembrane proteins:
P(platlet)-, E(endothelial)-, and L(leukocyte)-
selectins (sels). CLECT_selectins_like: C-type
lectin-like domain (CTLD) of the type found in the type
1 transmembrane proteins: P(platlet)-, E(endothelial)-,
and L(leukocyte)- selectins (sels). CTLD refers to a
domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. P- E- and L-sels
are cell adhesion receptors that mediate the initial
attachment, tethering, and rolling of lymphocytes on
inflamed vascular walls enabling subsequent lymphocyte
adhesion and transmigration. L- sel is expressed
constitutively on most leukocytes. P-sel is stored in
the Weibel-Palade bodies of endothelial cells and in the
alpha granules of platlets. E- sels are present on
endothelial cells. Following platelet and/or
endothelial cell activation P- sel is rapidly
translocated to the cell surface and E-sel expression is
induced. The initial step in leukocyte migration
involves interactions of selectins with fucosylated,
sialylated, and sulfated carbohydrate moieties on target
ligands displayed on glycoprotein scaffolds on
endothelial cells and leucocytes. A major ligand of P-
E- and L-sels is PSGL-1 (P-sel glycoprotein ligand).
Interactions of E- and P- sels with tumor cells may
promote extravasation of cancer cells. Regulation of
L-sel and P-sel function includes proteolytic shedding
of the most extracellular portion (containing the CTLD)
from the cell surface. Increased levels of the soluble
form of P-sel in the plasma have been found in a number
of diseases including coronary disease and diabetes. E-
and P- sel also play roles in the development of
synovial inflammation in inflammatory arthritis.
Platelet P-sel, but not endothelial P-sel, plays a role
in the inflammatory response and neointimal formation
after arterial injury. Selectins may also function as
signal-transducing receptors.
Length = 115
Score = 28.5 bits (64), Expect = 1.5
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 246 IFYNRRPMNLRDSLAFCRSRGGSLV----DESNPALQGFI 281
Y+ M +++ +C+SRG LV E N L GF
Sbjct: 3 YHYSTEKMTFNEAVKYCKSRGTDLVAIQNAEENALLNGFA 42
>gnl|CDD|224877 COG1966, CstA, Carbon starvation protein, predicted membrane
protein [Signal transduction mechanisms].
Length = 575
Score = 28.8 bits (65), Expect = 3.5
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 8 LALQGVTTLWGSFEVQNKRLARIMLQQLVRKPLLDNLDKFDEYSDWFKTLPMYFLTF 64
L+L G+ LW F + N+ LA I L L + + W +P F+ F
Sbjct: 456 LSLGGINVLWPLFGIANQMLAGIAL-LTAAVVLARMGRRRRYH--WITLIPAAFVLF 509
>gnl|CDD|163666 cd07423, MPP_PrpE, Bacillus subtilis PrpE and related proteins,
metallophosphatase domain. PrpE (protein phosphatase E)
is a bacterial member of the PPP (phosphoprotein
phosphatase) family of serine/threonine phosphatases and
a key signal transduction pathway component controlling
the expression of spore germination receptors GerA and
GerK in Bacillus subtilis. PrpE is closely related to
ApaH (also known symmetrical Ap(4)A hydrolase and
bis(5'nucleosyl)-tetraphosphatase). PrpE has
specificity for phosphotyrosine only, unlike the
serine/threonine phosphatases to which it is related.
The Bacilli members of this family are single domain
proteins while the other members have N- and C-terminal
domains in addition to this phosphatase domain. The PPP
(phosphoprotein phosphatase) family, to which PrpE
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpA/PrpB, and ApA4
hydrolase. The PPP catalytic domain is defined by three
conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The
PPP enzyme family is ancient with members found in all
eukaryotes, and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 234
Score = 28.0 bits (63), Expect = 5.7
Identities = 17/79 (21%), Positives = 26/79 (32%), Gaps = 16/79 (20%)
Query: 106 HGPQPLKLVMEAVEH--AMYV----------YDTGHVIIDNVQFMLGLSDSALDRFYMQD 153
P+ L+LVM V A+ V G NV+ GL ++ +
Sbjct: 53 DSPEVLRLVMSMVAAGAALCVPGNHDNKLYRKLQGR----NVKITHGLEETVAQLEAESE 108
Query: 154 TIIQEFRAFASRSHCHVTL 172
+E F H+ L
Sbjct: 109 EFKEEVIEFYESLPSHLVL 127
>gnl|CDD|213269 cd03369, ABCC_NFT1, ATP-binding cassette domain 2 of NFT1,
subfamily C. Domain 2 of NFT1 (New full-length MRP-type
transporter 1). NFT1 belongs to the MRP (multidrug
resistance-associated protein) family of ABC
transporters. Some of the MRP members have five
additional transmembrane segments in their N-terminus,
but the function of these additional membrane-spanning
domains is not clear. The MRP was found in the
multidrug-resisting lung cancer cell in which
p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions such as
glutathione, glucuronate, and sulfate.
Length = 207
Score = 27.8 bits (62), Expect = 5.8
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 13/48 (27%)
Query: 18 GSFEVQNKRLARIMLQQLVRK-------PLL------DNLDKFDEYSD 52
G E+ ++ I L+ L P L NLD FDEYSD
Sbjct: 63 GKIEIDGIDISTIPLEDLRSSLTIIPQDPTLFSGTIRSNLDPFDEYSD 110
>gnl|CDD|153071 cd03601, CLECT_TC14_like, C-type lectin-like domain (CTLD) of the
type found in lectins TC14, TC14-2, TC14-3, and TC14-4
from the budding tunicate Polyandrocarpa misakiensis and
PfG6 from the Acorn worm. CLECT_TC14_like: C-type
lectin-like domain (CTLD) of the type found in lectins
TC14, TC14-2, TC14-3, and TC14-4 from the budding
tunicate Polyandrocarpa misakiensis and PfG6 from the
Acorn worm. CTLD refers to a domain homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. TC14 is homodimeric. The CTLD of TC14 binds
D-galactose and D-fucose. TC14 is expressed
constitutively by multipotent epithelial and mesenchymal
cells and plays in role during budding, in inducing the
aggregation of undifferentiated mesenchymal cells to
give rise to epithelial forming tissue. TC14-2 and
TC14-3 shows calcium-dependent galactose binding
activity. TC14-3 is a cytostatic factor which blocks
cell growth and dedifferentiation of the atrial
epithelium during asexual reproduction. It may also act
as a differentiation inducing factor. Galactose
inhibits the cytostatic activity of TC14-3. The gene
for Acorn worm PfG6 is gill-specific; PfG6 may be a
secreted protein.
Length = 119
Score = 26.7 bits (59), Expect = 6.6
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 246 IFYNRRPMNLRDSLAFCRSRGGSLVDESNP 275
I + MN + AFCRSRG L +
Sbjct: 3 ILCSDETMNYAKAGAFCRSRGMRLASLAMR 32
>gnl|CDD|222710 pfam14363, AAA_assoc, Domain associated at C-terminal with AAA.
This domain is found in association with the AAA family,
pfam00004.
Length = 100
Score = 26.4 bits (59), Expect = 8.7
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 160 RAFASRSHCHVTLVIHPRKENEQLTVNSVFGSAKA 194
R F SR ++T+VI E + + N ++ +A+A
Sbjct: 16 RLFGSRFSPYLTIVID---EYDGFSRNQLYDAAEA 47
>gnl|CDD|118156 pfam09621, LcrR, Type III secretion system regulator (LcrR). This
family of proteins are encoded within type III secretion
operons and have been characterized in Yersinia as a
regulator of the Low-Calcium Response (LCR).
Length = 139
Score = 26.6 bits (59), Expect = 9.0
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 119 EHAMYVYDTGHVIIDNVQFMLG--LSDSALDRFY 150
E A+ V V+ NV + G LS L RFY
Sbjct: 74 EAALAVLGPDWVLYGNVDVLRGSPLSSQRLARFY 107
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
0.323 0.138 0.421
Gapped
Lambda K H
0.267 0.0597 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,991,770
Number of extensions: 1417413
Number of successful extensions: 1164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1158
Number of HSP's successfully gapped: 22
Length of query: 291
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 195
Effective length of database: 6,679,618
Effective search space: 1302525510
Effective search space used: 1302525510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.8 bits)