RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy669
(248 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 = 97.8 bits (244), Expect = 3e-26
Identities = 41/100 (41%), Positives = 59/100 (59%), Gaps = 2/100 (2%)
Query: 54 VYYAQIVENQSGILPIVQLAASDGDLDPDQRISYKISAGNPESYFNIDIGSGLISTTGRK 113
Y + EN ++ ++A+D D + ++Y I +GN + F+ID +G I+T +
Sbjct: 1 SYEVSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTA-KP 59
Query: 114 LDRENQAEHVLEVTVTDDGAPAPLSSTTRVIISVEDVNDN 153
LDRE Q+ + L VT TD G P PLSST V I+V DVNDN
Sbjct: 60 LDREEQSSYTLTVTATDGGGP-PLSSTATVTITVLDVNDN 98
Score = 51.5 bits (124), Expect = 8e-09
Identities = 21/46 (45%), Positives = 26/46 (56%)
Query: 1 NIRTSTILDVETKTHYWLTVFAQDHGVVPLHARTDVYIQVQNVNDN 46
I T+ LD E ++ Y LTV A D G PL + V I V +VNDN
Sbjct: 53 EITTAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVNDN 98
>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 = 87.0 bits (216), Expect = 2e-22
Identities = 41/82 (50%), Positives = 53/82 (64%), Gaps = 2/82 (2%)
Query: 74 ASDGDLDPDQRISYKISAGNPESYFNIDIGSGLISTTGRKLDRENQAEHVLEVTVTDDGA 133
A+D D + +++Y I +GN + F+ID +G I+TT LDRE Q E+ L V TD G
Sbjct: 2 ATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTTKP-LDREEQPEYTLTVEATDGGG 60
Query: 134 PAPLSSTTRVIISVEDVNDNAP 155
P PLSST V I+V DVNDNAP
Sbjct: 61 P-PLSSTATVTITVLDVNDNAP 81
Score = 51.2 bits (123), Expect = 7e-09
Identities = 22/47 (46%), Positives = 26/47 (55%)
Query: 2 IRTSTILDVETKTHYWLTVFAQDHGVVPLHARTDVYIQVQNVNDNVP 48
I T+ LD E + Y LTV A D G PL + V I V +VNDN P
Sbjct: 35 ITTTKPLDREEQPEYTLTVEATDGGGPPLSSTATVTITVLDVNDNAP 81
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 76.6 bits (189), Expect = 3e-18
Identities = 42/94 (44%), Positives = 54/94 (57%), Gaps = 2/94 (2%)
Query: 55 YYAQIVENQSGILPIVQLAASDGDLDPDQRISYKISAGNPESYFNIDIGSGLISTTGRKL 114
Y A + EN ++ + A+D DL P+ RI Y I G P +F ID +G +STT L
Sbjct: 1 YSASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKP-L 59
Query: 115 DRENQAEHVLEVTVTDDGAPAPLSSTTRVIISVE 148
DRE+ E+ L V TD G P PLSSTT V I+V
Sbjct: 60 DRESIGEYELTVLATDSGGP-PLSSTTTVTITVL 92
Score = 32.3 bits (74), Expect = 0.044
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 2 IRTSTILDVETKTHYWLTVFAQDHGVVPLHARTDVYIQVQ 41
+ T+ LD E+ Y LTV A D G PL + T V I V
Sbjct: 53 LSTTKPLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
>gnl|CDD|206635 cd00031, CA_like, Cadherin repeat-like 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. This
family also includes the cadherin-like repeats of
extracellular alpha-dystroglycan.
Length = 98
Score = 36.6 bits (84), Expect = 0.002
Identities = 31/98 (31%), Positives = 44/98 (44%), Gaps = 8/98 (8%)
Query: 59 IVENQSGILPIVQLAASDGDLDPDQRISYKISA-GN--PESYFNIDIGSGLISTTGRKLD 115
VE +S V + DL KISA G S+ + + SG++ KLD
Sbjct: 6 AVEGRSRGSFRVSIPT---DLIASSGEIIKISAAGKEALPSWLHWEPHSGILEGL-EKLD 61
Query: 116 RENQAEHVLEVTVTDDGAPAPLSSTTRVIISVEDVNDN 153
RE++ H + V+ GA P +S + I V D NDN
Sbjct: 62 REDKGVHYISVSAASLGANVPQTS-SVFSIEVYDENDN 98
>gnl|CDD|220006 pfam08758, Cadherin_pro, Cadherin prodomain like. Cadherins are a
family of proteins that mediate calcium dependent
cell-cell adhesion. They are activated through cleavage
of a prosequence in the late Golgi. This domain
corresponds to the folded region of the prosequence, and
is termed the prodomain. The prodomain shows structural
resemblance to the cadherin domain, but lacks all the
features known to be important for cadherin-cadherin
interactions.
Length = 90
Score = 32.2 bits (74), Expect = 0.052
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 155 PEFEQNFYHVNIPETRHRDEPLSQVSLISTTGRK 188
P F + Y +P +PL +V GR+
Sbjct: 4 PGFSEEVYTFLVPRRLEEGQPLGRVKFNDCKGRR 37
>gnl|CDD|214999 smart01055, Cadherin_pro, Cadherin prodomain like. Cadherins are a
family of proteins that mediate calcium dependent
cell-cell adhesion. They are activated through cleavage
of a prosequence in the late Golgi. This domain
corresponds to the folded region of the prosequence, and
is termed the prodomain. The prodomain shows structural
resemblance to the cadherin domain, but lacks all the
features known to be important for cadherin-cadherin
interactions.
Length = 87
Score = 30.3 bits (69), Expect = 0.18
Identities = 8/35 (22%), Positives = 14/35 (40%)
Query: 155 PEFEQNFYHVNIPETRHRDEPLSQVSLISTTGRKL 189
P F + Y ++P +PL +V+ G
Sbjct: 3 PGFSEEKYTFHVPSHLEAGQPLGRVNFEECLGSAR 37
>gnl|CDD|219122 pfam06650, DUF1162, Protein of unknown function (DUF1162). This
family represents a conserved region within several
hypothetical eukaryotic proteins. Family members might
be vacuolar protein sorting related-proteins.
Length = 271
Score = 29.2 bits (66), Expect = 2.1
Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 20/84 (23%)
Query: 85 ISYKISAGNPESYFNI-DIGSGLISTTGRKLDRENQAEHVLEVTVTDDGAPAPLSSTTRV 143
++ K S FNI D+G+ + KL REN + +L V + +GA T
Sbjct: 168 VNSKWSGP-----FNISDVGTTYV-----KLRRENSRQGLLRVEIILEGA------TI-- 209
Query: 144 IISVEDVNDNAPEFE-QNFYHVNI 166
I+ D +DN F +NF V I
Sbjct: 210 FITFSDADDNPWPFSIRNFSDVEI 233
>gnl|CDD|163693 cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in 19S
proteasomal subunits Rpn7 and Rpn8. This family
includes lid subunits of the 26 S proteasome regulatory
particles, Rpn7 (PSMD7; proteasome 26S non-ATPase
subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S
non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be
critical for the integrity of the 26 S proteasome
complex by establishing a correct lid structure. It is
necessary for the incorporation/anchoring of Rpn3 and
Rpn12 to the lid and essential for viability and normal
mitosis. Rpn7 and Rpn8 are ATP-independent components of
the 19S regulator subunit, and contain the MPN
structural motif on its N-terminal region. However,
while they show a typical MPN metalloprotease fold, they
lack the canonical JAMM motif, and therefore do not show
catalytic isopeptidase activity. It is suggested that
Rpn7 function is primarily structural.
Length = 280
Score = 29.1 bits (66), Expect = 2.2
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 126 VTVTDDGAPAPLSSTTRVIISVEDVNDNAPEFEQNFYHV 164
V V D P L T I+VE+V+D+ + F HV
Sbjct: 113 VLVIIDVRPKDLGLPTEAYIAVEEVHDDGTPTSKTFVHV 151
>gnl|CDD|132924 cd07013, S14_ClpP, Caseinolytic protease (ClpP) is an
ATP-dependent, highly conserved serine protease. Clp
protease (caseinolytic protease; ClpP; Peptidase S14) is
a highly conserved serine protease present throughout in
bacteria and eukaryota, but seems to be absent in
archaea, mollicutes and some fungi. Clp proteases are
involved in a number of cellular processes such as
degradation of misfolded proteins, regulation of
short-lived proteins and housekeeping removal of
dysfunctional proteins. Additionally, they are
implicated in the control of cell growth, targeting
DNA-binding protein from starved cells. ClpP has also
been linked to the tight regulation of virulence genes
in the pathogens Listeria monocytogenes and Salmonella
typhimurium. This enzyme belong to the family of
ATP-dependent proteases; the functional Clp protease is
comprised of two components: a proteolytic component and
one of several regulatory ATPase components, both of
which are required for effective levels of protease
activity in the presence of ATP, although the
proteolytic subunit alone does possess some catalytic
activity. Active site consists of the triad Ser, His and
Asp; some members have lost all of these active site
residues and are therefore inactive, while others may
have one or two large insertions. ClpP seems to prefer
hydrophobic or non-polar residues at P1 or P1' positions
in its substrate. The protease exists as a tetradecamer
made up of two heptameric rings stacked back-to-back
such that the catalytic triad of each subunit is located
at the interface between three monomers, thus making
oligomerization essential for function.
Length = 162
Score = 27.2 bits (60), Expect = 6.5
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 184 TTGRKLDRENQAEHVLETGSGESEATLETGSGESEATLEVLFENSTWENFHET 236
T G D A+ +L+ G + +G+SE L E TW + E
Sbjct: 102 TLGDATDMRIYADLLLKV-EGNLVSAYAHKTGQSEEELHADLERDTWLSAREA 153
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 27.5 bits (61), Expect = 8.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 132 GAPAPLSSTTRVIISVEDVNDNAPEFEQN 160
G L + V++SVEDV + PEFE+
Sbjct: 16 GESEYLQAVKEVLLSVEDVYNQHPEFEKA 44
>gnl|CDD|177178 MTH00117, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 227
Score = 27.2 bits (61), Expect = 8.1
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 136 PLSSTTRVIISVEDV 150
P+ S R++I+ EDV
Sbjct: 145 PMESPIRILITAEDV 159
>gnl|CDD|239970 cd04597, CBS_pair_DRTGG_assoc2, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with a DRTGG domain upstream. The
function of the DRTGG domain, named after its conserved
residues, is unknown. CBS is a small domain originally
identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The
interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is
unknown.
Length = 113
Score = 26.2 bits (58), Expect = 9.9
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 19 TVFAQDH-GVVPLHARTDVYIQVQNVNDNVPMTL---DPVYYA--QIVENQSGILPIV 70
T + ++ G+ P DV+ +V++V + P+T DP+ A + E+ LP+V
Sbjct: 38 TRYVLEYLGIEPPILLADVHPRVRDVINRKPVTARPNDPLREALNLMHEHNIRTLPVV 95
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
0.312 0.130 0.368
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,418,031
Number of extensions: 1154968
Number of successful extensions: 661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 25
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
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 (21.8 bits)
S2: 58 (26.1 bits)