RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16571
(150 letters)
>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat.
Length = 60
Score = 44.5 bits (106), Expect = 3e-07
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 11 LKRLEITGASNLTRVRKGAFADNLNLETLTLNKNPKLKIIEEDALVGLPNLYHLNLKEN 69
LK L+++ + LT + GAF NL+ L L+ N L I +A GLP+L L+L N
Sbjct: 2 LKSLDLSN-NRLTVIPDGAFKGLPNLKVLDLSGN-NLTSISPEAFSGLPSLRSLDLSGN 58
Score = 38.7 bits (91), Expect = 5e-05
Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 35 NLETLTLNKNPKLKIIEEDALVGLPNLYHLNLKENAFTSFSESMLA-WPELRTIDIAENP 93
NL++L L+ N +L +I + A GLPNL L+L N TS S + P LR++D++ N
Sbjct: 1 NLKSLDLSNN-RLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNN 59
Query: 94 I 94
+
Sbjct: 60 L 60
Score = 24.8 bits (55), Expect = 5.5
Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 6 KGLSYLKRLEITGASNLTRVRKGAFADNLNLETLTLNKNP 45
KGL LK L+++G +NLT + AF+ +L +L L+ N
Sbjct: 21 KGLPNLKVLDLSG-NNLTSISPEAFSGLPSLRSLDLSGNN 59
>gnl|CDD|188093 TIGR00864, PCC, polycystin cation channel protein. The Polycystin
Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a
huge protein of 4303aas. Its repeated leucine-rich (LRR)
segment is found in many proteins. It contains 16
polycystic kidney disease (PKD) domains, one
LDL-receptor class A domain, one C-type lectin family
domain, and 16-18 putative TMSs in positions between
residues 2200 and 4100. Polycystin-L has been shown to
be a cation (Na+, K+ and Ca2+) channel that is activated
by Ca2+. Two members of the PCC family (polycystin 1 and
2) are mutated in autosomal dominant polycystic kidney
disease, and polycystin-L is deleted in mice with renal
and retinal defects. Note: this model is restricted to
the amino half for technical reasons.
Length = 2740
Score = 41.2 bits (96), Expect = 8e-05
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 84 LRTIDIAENPIECGCNIL----WLREMLVR-RNTSAVFCNSPAPLKYKSLISLSAEDLG 137
L ID++ NP EC C + W E V+ R A C P L + L+ + D G
Sbjct: 21 LSEIDLSGNPFECDCGLARLPRWAEEKGVKVRQPEAALCAGPGALAGQPLLGIPLLDSG 79
>gnl|CDD|205486 pfam13306, LRR_5, Leucine rich repeats (6 copies). This family
includes a number of leucine rich repeats. This family
contains a large number of BSPA-like surface antigens
from Trichomonas vaginalis.
Length = 128
Score = 36.4 bits (85), Expect = 0.001
Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 6 KGLSYLKRLEITGASNLTRVRKGAFADNLNLETLTLNKNPKLKIIEEDALVGLPNLYHLN 65
G + LK + + S+LT + AF + +L ++T+ + L I E A +L +
Sbjct: 31 SGCTSLKSITLP--SSLTSIGSYAFYNCSSLTSITIPSS--LTSIGEYAFSNCSSLTSIT 86
Query: 66 LKENAFTSFSESMLAWPELRTIDIAEN 92
+ N T+ + L++I I +
Sbjct: 87 IPSN-LTTIGSYAFSNCSLKSITIPSS 112
Score = 30.2 bits (69), Expect = 0.20
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 20 SNLTRVRKGAFADNLNLETLTLNKNPKLKIIEEDALVGLPNLYHLNLKENAFTSFSESML 79
S++T + + AF+ +L+++TL + L I A +L + + + TS E
Sbjct: 20 SSVTSIGEYAFSGCTSLKSITLPSS--LTSIGSYAFYNCSSLTSITIPSS-LTSIGEYAF 76
Query: 80 AW-PELRTIDIAEN 92
+ L +I I N
Sbjct: 77 SNCSSLTSITIPSN 90
>gnl|CDD|214507 smart00082, LRRCT, Leucine rich repeat C-terminal domain.
Length = 51
Score = 30.5 bits (69), Expect = 0.041
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 92 NPIECGCNILWLREMLVRR----NTSAVFCNSPAPLK 124
NP C C + WL L + + C SP+ L+
Sbjct: 1 NPFICDCELRWLLRWLQANEHLQDPVDLRCASPSSLR 37
>gnl|CDD|205079 pfam12799, LRR_4, Leucine Rich repeats (2 copies). Leucine rich
repeats are short sequence motifs present in a number
of proteins with diverse functions and cellular
locations. These repeats are usually involved in
protein-protein interactions. Each Leucine Rich Repeat
is composed of a beta-alpha unit. These units form
elongated non-globular structures. Leucine Rich Repeats
are often flanked by cysteine rich domains.
Length = 43
Score = 30.2 bits (69), Expect = 0.055
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 35 NLETLTLNKNPKLKIIEEDALVGLPNLYHLNLKENAFTSFSE 76
NLETL L+ N +I + L LPNL L+L N T S
Sbjct: 2 NLETLDLSNN---QITDLPPLSNLPNLETLDLSGNKITDLSP 40
Score = 26.3 bits (59), Expect = 1.5
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 59 PNLYHLNLKENAFTSFSESMLAWPELRTIDIAENPIE 95
NL L+L N T + P L T+D++ N I
Sbjct: 1 TNLETLDLSNNQITDLPP-LSNLPNLETLDLSGNKIT 36
>gnl|CDD|238064 cd00116, LRR_RI, Leucine-rich repeats (LRRs), ribonuclease
inhibitor (RI)-like subfamily. LRRs are 20-29 residue
sequence motifs present in many proteins that
participate in protein-protein interactions and have
different functions and cellular locations. LRRs
correspond to structural units consisting of a beta
strand (LxxLxLxxN/CxL conserved pattern) and an alpha
helix. This alignment contains 12 strands corresponding
to 11 full repeats, consistent with the extent observed
in the subfamily acting as Ran GTPase Activating
Proteins (RanGAP1).
Length = 319
Score = 30.0 bits (68), Expect = 0.46
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 29 AFADNLNLETLTLNKN---PKLKIIEEDALVGLPNLYHLNLKENAFTS-----FSESMLA 80
N NLE L LN N + + L L +L LNL +N T + ++L+
Sbjct: 188 GLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNNLTDAGAAALASALLS 247
Query: 81 W-PELRTIDIAENPIEC 96
L T+ ++ N I
Sbjct: 248 PNISLLTLSLSCNDITD 264
>gnl|CDD|227348 COG5015, COG5015, Uncharacterized conserved protein [Function
unknown].
Length = 132
Score = 27.5 bits (61), Expect = 1.7
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 24 RVR-KGAFADNLNLETLTLNKNPKLK-IIEED 53
R+R + F +N+ L+ L L P LK I D
Sbjct: 72 RLRGRAEFVENIELKKLALEIYPVLKEIYPTD 103
>gnl|CDD|217648 pfam03632, Glyco_hydro_65m, Glycosyl hydrolase family 65 central
catalytic domain. This family of glycosyl hydrolases
contains vacuolar acid trehalase and maltose
phosphorylase.Maltose phosphorylase (MP) is a dimeric
enzyme that catalyzes the conversion of maltose and
inorganic phosphate into beta-D-glucose-1-phosphate and
glucose. The central domain is the catalytic domain,
which binds a phosphate ion that is proximal the the
highly conserved Glu. The arrangement of the phosphate
and the glutamate is thought to cause nucleophilic
attack on the anomeric carbon atom. The catalytic domain
also forms the majority of the dimerisation interface.
Length = 370
Score = 28.1 bits (63), Expect = 1.7
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 59 PNLYHLNLKENAFTSFSESMLAWPELRTIDIAENPIECGCNILWLRE 105
P+ YH N+ NA+T+ M W ++ E G L + E
Sbjct: 163 PDEYHNNVNNNAYTNL---MAKWNLEYALEALR---ELGEEKLGVDE 203
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 28.0 bits (63), Expect = 2.0
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 13/60 (21%)
Query: 7 GLSYLKRLEITGAS-----NLTRVRKGA----FADNLNLE----TLTLNKNPKLKIIEED 53
G SY+KR +TG + +LT+ G+ F+ N N E T+TL N ++K ++ D
Sbjct: 571 GPSYIKRFNVTGVTRDKEYDLTQGTPGSKVLYFSANPNGEAEVVTVTLKPNGRIKKLKFD 630
>gnl|CDD|185268 PRK15370, PRK15370, E3 ubiquitin-protein ligase SlrP; Provisional.
Length = 754
Score = 28.1 bits (62), Expect = 2.0
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 10/84 (11%)
Query: 50 IEEDALVGLPNLYHLNLK-----ENAFTSFSESMLAWPELRTIDIAENPIECGCNIL--W 102
++ ++L LP LK ENA TS S+ PEL+ +D+++N I L
Sbjct: 311 VQSNSLTALPETLPPGLKTLEAGENALTSLPASLP--PELQVLDVSKNQITVLPETLPPT 368
Query: 103 LREMLVRRNT-SAVFCNSPAPLKY 125
+ + V RN + + N PA L+
Sbjct: 369 ITTLDVSRNALTNLPENLPAALQI 392
>gnl|CDD|238690 cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and MBD4 are members
of a protein family that share the methyl-CpG-binding
domain (MBD). The MBD, consists of about 70 residues and
is defined as the minimal region required for binding to
methylated DNA by a methyl-CpG-binding protein which
binds specifically to methylated DNA. The MBD can
recognize a single symmetrically methylated CpG either
as naked DNA or within chromatin. MeCP2, MBD1 and MBD2
(and likely MBD3) form complexes with histone
deacetylase and are involved in histone
deacetylase-dependent repression of transcription. MBD4
is an endonuclease that forms a complex with the DNA
mismatch-repair protein MLH1.
Length = 77
Score = 26.2 bits (58), Expect = 2.6
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 102 WLREMLVRRNTSA----VFCNSPAPLKYKSLISL 131
W RE++ R++ SA V+ SP K++S + L
Sbjct: 11 WKRELVPRKSGSAGKFDVYYISPTGKKFRSKVEL 44
>gnl|CDD|237601 PRK14076, pnk, inorganic polyphosphate/ATP-NAD kinase; Provisional.
Length = 569
Score = 27.4 bits (61), Expect = 4.0
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 12 KRLEITGASNLTRVRKGAFADNLNLETLTLNKNPKLKIIEEDALVGLPNLYHLNLKENAF 71
K++EI+ SNL G FA L+L+TL K+ K++ I + L Y + +AF
Sbjct: 162 KKIEISNISNLKDASIGLFAYGLSLDTLKFIKDRKVRRIRLFGSIALEMCYVASGALDAF 221
Query: 72 TSFSESMLAWPELRTIDIA 90
+ +E+ R DIA
Sbjct: 222 INVNETT------RLCDIA 234
>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function
unknown].
Length = 394
Score = 26.9 bits (59), Expect = 4.6
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 4/94 (4%)
Query: 2 EKEVKGLSYLKRLEITGASNLTRVRKGAFADNLNLETLTLNKNPKLKIIEEDALVGLPNL 61
K + LS L L+++G N LE L L+ N ++++ +L L NL
Sbjct: 179 PKLLSNLSNLNNLDLSG--NKISDLPPEIELLSALEELDLSNNSIIELL--SSLSNLKNL 234
Query: 62 YHLNLKENAFTSFSESMLAWPELRTIDIAENPIE 95
L L N ES+ L T+D++ N I
Sbjct: 235 SGLELSNNKLEDLPESIGNLSNLETLDLSNNQIS 268
>gnl|CDD|224471 COG1554, ATH1, Trehalose and maltose hydrolases (possible
phosphorylases) [Carbohydrate transport and metabolism].
Length = 772
Score = 26.5 bits (59), Expect = 6.0
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 59 PNLYHLNLKENAFTSFSESMLAWPELRTIDIAE 91
P+ YH ++ NAFT+ M AW ++I E
Sbjct: 492 PDEYHNHVNNNAFTNL---MAAWNLEYALEILE 521
>gnl|CDD|238069 cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and
BAZ2A-like proteins constitute a family of proteins that
share the methyl-CpG-binding domain (MBD). The MBD
consists of about 70 residues and is defined as the
minimal region required for binding to methylated DNA by
a methyl-CpG-binding protein which binds specifically to
methylated DNA. The MBD can recognize a single
symmetrically methylated CpG either as naked DNA or
within chromatin. MeCP2, MBD1 and MBD2 (and likely
MBD3) form complexes with histone deacetylase and are
involved in histone deacetylase-dependent repression of
transcription. MBD4 is an endonuclease that forms a
complex with the DNA mismatch-repair protein MLH1. The
MBDs present in putative chromatin remodelling subunit,
BAZ2A, and putative histone methyltransferase, CLLD8,
represent two phylogenetically distinct groups within
the MBD protein family.
Length = 62
Score = 25.0 bits (55), Expect = 6.4
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 91 ENPIECGCNILWLREMLVRRNTSA----VFCNSPAPLKYKSLISL 131
+P+ G W RE+++R++ SA V+ SP K +S +
Sbjct: 3 RDPLPPG----WKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEV 43
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
0.318 0.134 0.385
Gapped
Lambda K H
0.267 0.0671 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,601,587
Number of extensions: 677997
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 25
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
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: 54 (24.7 bits)