RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4323
(191 letters)
>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 = 49.9 bits (119), Expect = 3e-08
Identities = 24/120 (20%), Positives = 47/120 (39%), Gaps = 14/120 (11%)
Query: 56 EVDWLDARNICRRHCMDAVSLETPQENEFVKQRITRGNVRYIWTSGRKCNFNGCDRPDLQ 115
++ W +A+ CR S+ + +EN+F+ + + + +W + G
Sbjct: 9 KLTWEEAQEYCRSLGGHLASIHSEEENDFLASLLKKSSSSDVWIGLNDLSSEG------- 61
Query: 116 PANVNGWFWSGSGAKIGPTTQRNTGDWSATGGFGQAQPDNREAAQ-HDVACHHLKPFVCE 174
W WS G+ + T G+ + G + + +DV+C PF+CE
Sbjct: 62 -----TWKWS-DGSPLVDYTNWAPGEPNPGGSEDCVVLSSSSDGKWNDVSCSSKLPFICE 115
>gnl|CDD|215684 pfam00059, Lectin_C, Lectin C-type domain. This family includes
both long and short form C-type.
Length = 108
Score = 45.8 bits (109), Expect = 5e-07
Identities = 23/129 (17%), Positives = 43/129 (33%), Gaps = 39/129 (30%)
Query: 59 WLDARNICRRHCMDAVSLETPQENEFVKQRITRGNVRYIWTSGRKCNFNGCDRPDLQPAN 118
W +A C++ VS+++ +E +F+ + N Y W N G
Sbjct: 5 WAEAEAACQKLGGHLVSIQSAEEQDFLTSLVKASNT-YAWIGLTDINTEG---------- 53
Query: 119 VNGWFWSGSGAKIGPTTQRNTGDWSATGGFGQAQPDNREAAQH-------------DVAC 165
W W+ + N +W+ +P+N+ + D C
Sbjct: 54 --TWVWTDG-------SPVNYTNWA------PGEPNNKGGNEDCVEIYTDTNGKWNDEPC 98
Query: 166 HHLKPFVCE 174
+ +VCE
Sbjct: 99 GSKRLYVCE 107
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 27/118 (22%), Positives = 43/118 (36%), Gaps = 17/118 (14%)
Query: 59 WLDARNICRRHCMDAVSLETPQENEFVKQRITR-GNVRYIWTSGRKCNFNGCDRPDLQPA 117
W DA+ C+ S+ + EN+FV + G+ Y W +
Sbjct: 22 WEDAQAFCQSLGGHLASIHSEAENDFVASLLKNSGSSDYYWIGLSDPD------------ 69
Query: 118 NVNGWFWS-GSGAKIGPTTQRNTGDWSATGGFGQAQPDNREAAQHDVACHHLKPFVCE 174
+ W WS GSG + +++G + +DV+C PFVCE
Sbjct: 70 SNGSWQWSDGSGPVSY-SNWAPGEPNNSSGDCVVLSTSGGKW--NDVSCTSKLPFVCE 124
>gnl|CDD|153072 cd03602, CLECT_1, C-type lectin (CTL)/C-type lectin-like (CTLD)
domain subgroup 1; a subgroup of protein domains
homologous to the carbohydrate-recognition domains
(CRDs) of the C-type lectins. CLECT_1: C-type lectin
(CTL)/C-type lectin-like (CTLD) domain subgroup 1; a
subgroup of protein domains homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. 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. CTLDs may bind a variety of
carbohydrate ligands including mannose,
N-acetylglucosamine, galactose, N-acetylgalactosamine,
and fucose. CTLDs associate with each other through
several different surfaces to form dimers, trimers, or
tetramers from which ligand-binding sites project in
different orientations. In some CTLDs a loop extends to
the adjoining domain to form a loop-swapped dimer.
Length = 108
Score = 35.4 bits (82), Expect = 0.003
Identities = 24/125 (19%), Positives = 41/125 (32%), Gaps = 36/125 (28%)
Query: 59 WLDARNICRRHCMDAVSLETPQENEFVKQRITRGNVRYIWTSGRKCNFNGCDRPDLQPAN 118
W +A+ CR + D +++ ++N + N W + +
Sbjct: 12 WSEAQQYCRENYTDLATVQNQEDNALLSNLSRVSNS-AAWIGLYR--------------D 56
Query: 119 VNGWFWSGSGAKIGPTTQRNTGDWSATGGFGQAQPDNREA--------AQHDVACHHLKP 170
V+ W WS ++ RN W QP + + C LKP
Sbjct: 57 VDSWRWSDG----SESSFRN---W------NTFQPFGQGDCATMYSSGRWYAALCSALKP 103
Query: 171 FVCED 175
F+C D
Sbjct: 104 FICYD 108
>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 = 31.2 bits (71), Expect = 0.10
Identities = 11/47 (23%), Positives = 21/47 (44%)
Query: 59 WLDARNICRRHCMDAVSLETPQENEFVKQRITRGNVRYIWTSGRKCN 105
+ +A C+ D V+++ +EN + + N+ Y W G N
Sbjct: 12 FNEAVKYCKSRGTDLVAIQNAEENALLNGFALKYNLGYYWIDGNDIN 58
>gnl|CDD|222742 pfam14415, DUF4424, Domain of unknown function (DUF4424). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 310 and 361 amino
acids in length.
Length = 248
Score = 29.3 bits (66), Expect = 0.90
Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 20/105 (19%)
Query: 39 VTHSYFFSWEHAPTRSLEVDWLDARNICRRHCMDAVSLETPQENEFVKQRITRGNVRYIW 98
+ HSY P+ V +R+C+DA + Q+ + ++ Y+
Sbjct: 143 IEHSY------TPSVGGGVLASLLEEYAKRYCIDAAFKKALQKRG--AGGLGERDLDYVL 194
Query: 99 TSGRKCNFNGC--------DRPDLQPANVNGWFWSGSGAKIGPTT 135
T+G N+ G D+ P N+ + + G+ KI PTT
Sbjct: 195 TTGA--NWAGPIGDFTLTIDKGA--PDNLVSFCFDGNLKKINPTT 235
>gnl|CDD|153058 cd03588, CLECT_CSPGs, C-type lectin-like domain (CTLD) of the type
found in chondroitin sulfate proteoglycan core proteins.
CLECT_CSPGs: C-type lectin-like domain (CTLD) of the
type found in chondroitin sulfate proteoglycan core
proteins (CSPGs) in human and chicken aggrecan, frog
brevican, and zebra fish dermacan. CTLD refers to a
domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. In cartilage,
aggrecan forms cartilage link protein stabilized
aggregates with hyaluronan (HA). These aggregates
contribute to the tissue's load bearing properties.
Aggregates having other CSPGs substituting for aggrecan
may contribute to the structural integrity of many
different tissues. Xenopus brevican is expressed in the
notochord and the brain during early embryogenesis.
Zebra fish dermacan is expressed in dermal bones and may
play a role in dermal bone development. CSPGs do
contain LINK domain(s) which bind HA. These LINK
domains are considered by one classification system to
be a variety of CTLD, but are omitted from this
hierarchical classification based on insignificant
sequence similarity.
Length = 124
Score = 28.7 bits (64), Expect = 1.1
Identities = 36/142 (25%), Positives = 50/142 (35%), Gaps = 42/142 (29%)
Query: 45 FSWEHAPTRSLEVDWLDARNICRRHCMDAVSLETPQENEFVKQ------------RITRG 92
+ H P R W DA CR S+ TP+E EFV R G
Sbjct: 11 HCYRHFPDRE---TWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEG 67
Query: 93 NVRYIWTSGRKCNFNGCDRPDLQPANVNGWFWSGSGAKIGPTTQRNTGDWSATGGFGQAQ 152
+ R W+ G F RP+ QP N +F +G + G+W+
Sbjct: 68 DFR--WSDGHPLQFENW-RPN-QPDN---FFATGEDCVV--MIWHEEGEWN--------- 109
Query: 153 PDNREAAQHDVACHHLKPFVCE 174
DV C++ PF C+
Sbjct: 110 ---------DVPCNYHLPFTCK 122
>gnl|CDD|133138 cd05471, pepsin_like, Pepsin-like aspartic proteases, bilobal
enzymes that cleave bonds in peptides at acidic pH.
Pepsin-like aspartic proteases are found in mammals,
plants, fungi and bacteria. These well known and
extensively characterized enzymes include pepsins,
chymosin, renin, cathepsins, and fungal aspartic
proteases. Several have long been known to be medically
(renin, cathepsin D and E, pepsin) or commercially
(chymosin) important. Structurally, aspartic proteases
are bilobal enzymes, each lobe contributing a catalytic
Aspartate residue, with an extended active site cleft
localized between the two lobes of the molecule. The N-
and C-terminal domains, although structurally related by
a 2-fold axis, have only limited sequence homology
except the vicinity of the active site. This suggests
that the enzymes evolved by an ancient duplication
event. Most members of the pepsin family specifically
cleave bonds in peptides that are at least six residues
in length, with hydrophobic residues in both the P1 and
P1' positions. The active site is located at the groove
formed by the two lobes, with an extended loop
projecting over the cleft to form an 11-residue flap,
which encloses substrates and inhibitors in the active
site. Specificity is determined by nearest-neighbor
hydrophobic residues surrounding the catalytic
aspartates, and by three residues in the flap.The
enzymes are mostly secreted from cells as inactive
proenzymes that activate autocatalytically at acidic pH.
This family of aspartate proteases is classified by
MEROPS as the peptidase family A1 (pepsin A, clan AA).
Length = 283
Score = 28.5 bits (64), Expect = 1.8
Identities = 13/55 (23%), Positives = 18/55 (32%), Gaps = 3/55 (5%)
Query: 96 YIWTSGRKCNFNGCDRPDLQPANVNGWFWSGSGAKIGPTTQRNTGDWSATGGFGQ 150
+W C C + + + S + G T GD S TGG G
Sbjct: 24 LLWVPSSNCTSCSCQKHPRFKYDSSK---SSTYKDTGCTFSITYGDGSVTGGLGT 75
>gnl|CDD|237304 PRK13206, ureC, urease subunit alpha; Reviewed.
Length = 573
Score = 27.0 bits (60), Expect = 7.4
Identities = 12/22 (54%), Positives = 12/22 (54%), Gaps = 4/22 (18%)
Query: 165 CHHLKPFVCEDSDELLNFVRSR 186
CHHL P V ED L F SR
Sbjct: 326 CHHLNPAVPED----LAFAESR 343
>gnl|CDD|237305 PRK13207, ureC, urease subunit alpha; Reviewed.
Length = 568
Score = 26.7 bits (60), Expect = 8.4
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 7/29 (24%)
Query: 163 VACHHLKPFVCEDSDELLNFVRSRNPGIR 191
+ CHHL P + ED + F SR IR
Sbjct: 318 MVCHHLDPSIPED----VAFAESR---IR 339
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
0.321 0.134 0.456
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,766,315
Number of extensions: 848363
Number of successful extensions: 637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 632
Number of HSP's successfully gapped: 19
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.4 bits)