RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11061
(212 letters)
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 73.9 bits (182), Expect = 2e-17
Identities = 36/95 (37%), Positives = 51/95 (53%), Gaps = 4/95 (4%)
Query: 75 EYNVSLRDDIQTTTAFAVVLATDRDSDRFGTISYKIVTGKDANLFRIDRSSGELFVTRGN 134
Y VS+ ++ T V ATD DS G ++Y IV+G + LF ID S+GE+ +
Sbjct: 1 SYEVSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTAKP- 59
Query: 135 FLSR--SNSYHINVSAMDGGGNKCSQDAQVNINII 167
L R +SY + V+A DGGG S A V I ++
Sbjct: 60 -LDREEQSSYTLTVTATDGGGPPLSSTATVTITVL 93
Score = 68.1 bits (167), Expect = 3e-15
Identities = 31/68 (45%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 2 VNYTLGESPSRTNHFYMKSVSGEICIAQDLDFESRSSYEFPVVATDRGG--LSTTAMVRI 59
V Y++ S + F + +GEI A+ LD E +SSY V ATD GG LS+TA V I
Sbjct: 32 VTYSI-VSGNEDGLFSIDPSTGEITTAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTI 90
Query: 60 QITDVNDN 67
+ DVNDN
Sbjct: 91 TVLDVNDN 98
Score = 27.3 bits (61), Expect = 2.2
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 180 TYSFVVPEDVFKNSIVGTIKAATSDSGKFTEFS 212
+Y VPE+ ++V T+ A DSG+ E +
Sbjct: 1 SYEVSVPENAPPGTVVLTVSATDPDSGENGEVT 33
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 67.4 bits (165), Expect = 3e-15
Identities = 29/71 (40%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 1 MVNYTLGESPSRTNHFYMKSVSGEICIAQDLDFESRSSYEFPVVATDRGG--LSTTAMVR 58
V Y++ S + F + +GEI + LD E + Y V ATD GG LS+TA V
Sbjct: 12 KVTYSI-LSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDGGGPPLSSTATVT 70
Query: 59 IQITDVNDNEP 69
I + DVNDN P
Sbjct: 71 ITVLDVNDNAP 81
Score = 58.9 bits (143), Expect = 5e-12
Identities = 32/82 (39%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 95 ATDRDSDRFGTISYKIVTGKDANLFRIDRSSGELFVTRGNFLSR--SNSYHINVSAMDGG 152
ATD DS G ++Y I++G D LF ID +GE+ T+ L R Y + V A DGG
Sbjct: 2 ATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTTKP--LDREEQPEYTLTVEATDGG 59
Query: 153 GNKCSQDAQVNINI--INSHMP 172
G S A V I + +N + P
Sbjct: 60 GPPLSSTATVTITVLDVNDNAP 81
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 64.6 bits (158), Expect = 5e-14
Identities = 31/94 (32%), Positives = 42/94 (44%), Gaps = 4/94 (4%)
Query: 76 YNVSLRDDIQTTTAFAVVLATDRDSDRFGTISYKIVTGKDANLFRIDRSSGELFVTRGNF 135
Y+ S+ ++ T V ATD D G I Y I+ G FRID +G+L T+
Sbjct: 1 YSASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTK--P 58
Query: 136 LSR--SNSYHINVSAMDGGGNKCSQDAQVNINII 167
L R Y + V A D GG S V I ++
Sbjct: 59 LDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
Score = 48.1 bits (115), Expect = 8e-08
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 9 SPSRTNHFYMKSVSGEICIAQDLDFESRSSYEFPVVATDRG--GLSTTAMVRIQIT 62
F + +G++ + LD ES YE V+ATD G LS+T V I +
Sbjct: 37 GGGPGGWFRIDPDTGDLSTTKPLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
>gnl|CDD|214795 smart00736, CADG, Dystroglycan-type cadherin-like domains.
Cadherin-homologous domains present in metazoan
dystroglycans and alpha/epsilon sarcoglycans, yeast
Axl2p and in a very large protein from magnetotactic
bacteria. Likely to bind calcium ions.
Length = 97
Score = 30.4 bits (69), Expect = 0.18
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 38 SYEFPVVATDRGGLSTTAMVRIQITDVNDN 67
S V ATD G S + I + + ND
Sbjct: 68 SLSLKVTATDSSGASASDTFTITVVNTNDA 97
>gnl|CDD|199905 cd10317, RGL4_C, C-terminal domain of rhamnogalacturonan lyase, a
family 4 polysaccharide lyase. The rhamnogalacturonan
lyase of the polysaccharide lyase family 4 (RGL4) is
involved in the degradation of RG (rhamnogalacturonan)
type-I, an important pectic plant cell wall
polysaccharide, by cleaving the alpha-1,4 glycoside bond
between L-rhamnose and D-galacturonic acids in the
backbone of RG type-I through a beta-elimination
reaction. RGL4 consists of three domains, an N-terminal
catalytic domain, a middle domain with a FNIII type fold
and a C-terminal domain with a jelly roll fold. Both
the middle and the C-terminal domain are putative
carbohydrate binding modules. There are two types of RG
lyases, which both cleave the alpha-1,4 bonds of the
RG-I main chain (RG chain) through the beta-elimination
reaction, but belong to two structurally unrelated
polysaccharide lyase (PL) families, 4 and 11.
Length = 161
Score = 28.8 bits (65), Expect = 1.5
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 2 VNYTLGESPSRTNHFYMKSVSGEICIAQDLDFESRSSYEFPVVATDRGGL-STTAMVRIQ 60
+ YT+G S S + +Y +SV+G I DL + AT R L +A R Q
Sbjct: 35 LTYTVGSSDSDFDWYYAQSVNGPWTIRFDLTAVQATG-----GATLRIALAGASAGGRPQ 89
Query: 61 ITDVNDNEPIFNP 73
+ VNDN P+
Sbjct: 90 VR-VNDNGPLLPT 101
>gnl|CDD|216843 pfam02010, REJ, REJ domain. The REJ (Receptor for Egg Jelly)
domain is found in PKD1, and the sperm receptor for egg
jelly. The function of this domain is unknown. The
domain is 600 amino acids long so is probably composed
of multiple structural domains. There are six completely
conserved cysteine residues that may form disulphide
bridges. This region contains tandem PKD-like domains.
Length = 436
Score = 28.2 bits (63), Expect = 3.2
Identities = 25/138 (18%), Positives = 39/138 (28%), Gaps = 30/138 (21%)
Query: 33 FESRSSYEFPVVATDRGGLSTTAMVRIQITDVNDNEPIF------------NPVEYNVSL 80
++ ++Y F + + S + I I V N P NP + L
Sbjct: 159 LKAGTTYTFKLTVSKDSRRSASTEQTILI--VEGNPPEVIISCISNCNQKVNPSSR-LVL 215
Query: 81 R-----DDIQTTTAFAVVLATDRDSDRFGTISYKIVTGKDANLFRIDRSSGELFVTRGNF 135
R D + L + S + TG SG V R
Sbjct: 216 RANCLNCDSSDNVTYRWSLLESDSNLTLTDWSSETTTG----------LSGPNLVIRAGV 265
Query: 136 LSRSNSYHINVSAMDGGG 153
L Y +++ D G
Sbjct: 266 LEPGVEYRFSLTVTDTSG 283
>gnl|CDD|221214 pfam11769, DUF3313, Protein of unknown function (DUF3313). This a
bacterial family of proteins which are annotated as
putative lipoproteins.
Length = 202
Score = 27.7 bits (62), Expect = 4.0
Identities = 28/114 (24%), Positives = 40/114 (35%), Gaps = 23/114 (20%)
Query: 33 FESRSSYEFPVVATDRGGLSTTAMVRIQITDVNDNEPIFNPVEYNVSLRDDIQTTTAFAV 92
+ S FP+V G T VR+ IT V+ + P E I A
Sbjct: 87 LKEELSKRFPLVDAPGPG---TLRVRVAITGVDTSTPDLKAYEV-------IPIGLVIAG 136
Query: 93 VLATDRDSDRFGTISYKIVTGKDANLFRIDRSSGEL-----FVTRGNFLSRSNS 141
V A D G+++ ++ +D +GEL GN L S S
Sbjct: 137 VKAATGTRDGSGSVAVEVEL--------LDAQTGELLAAVVDKRYGNKLENSAS 182
>gnl|CDD|215164 PLN02290, PLN02290, cytokinin trans-hydroxylase.
Length = 516
Score = 27.9 bits (62), Expect = 4.3
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 113 GKDANLFRIDRSSGELFVTRGNFL 136
GKDAN F DR +G F +F+
Sbjct: 430 GKDANEFNPDRFAGRPFAPGRHFI 453
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 28.0 bits (63), Expect = 4.5
Identities = 13/35 (37%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 172 PIPLFQQST--YSFVVPEDVFKNSIVGTIKAATSD 204
PI F + VV EDV IV IK A
Sbjct: 556 PISKFPAVRRDIALVVDEDVPAGDIVKAIKKAGGK 590
>gnl|CDD|100093 cd05800, PGM_like2, This PGM-like (phosphoglucomutase-like) protein
of unknown function belongs to the
alpha-D-phosphohexomutase superfamily and is found in
both archaea and bacteria. 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 structural domains (subdomains)
with a centrally located active site formed by four
loops, one from each subdomain. All four subdomains are
included in this alignment model.
Length = 461
Score = 27.9 bits (63), Expect = 4.8
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 72 NPVEYNVSLRDDIQTTTAFAVVLATDRDSDRFGTI 106
P+E N+ + + LATD D+DR G +
Sbjct: 217 EPIEKNLGELAEAVKEGGADLGLATDGDADRIGAV 251
>gnl|CDD|100092 cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and
PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2
is thought to be a phosphopentomutase that catalyzes the
conversion of the nucleoside breakdown products,
ribose-1-phosphate and deoxyribose-1-phosphate to the
corresponding 5-phosphopentoses. PGM2L1 is thought to
catalyze the 1,3-bisphosphoglycerate-dependent synthesis
of glucose 1,6-bisphosphate and other
aldose-bisphosphates that serve as cofactors for several
sugar phosphomutases and possibly also as regulators of
glycolytic enzymes. PGM2 and PGM2L1 belong to the
alpha-D-phosphohexomutase superfamily which includes
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 = 487
Score = 27.1 bits (61), Expect = 7.7
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 92 VVLATDRDSDRFG 104
++LATD D+DR G
Sbjct: 255 LILATDPDADRLG 267
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
0.317 0.132 0.372
Gapped
Lambda K H
0.267 0.0879 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,232,379
Number of extensions: 918881
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 684
Number of HSP's successfully gapped: 24
Length of query: 212
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 119
Effective length of database: 6,812,680
Effective search space: 810708920
Effective search space used: 810708920
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: 57 (25.5 bits)