RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7090
(253 letters)
>gnl|CDD|220670 pfam10274, ParcG, Parkin co-regulated protein. This family of
proteins is transcribed anti-sense along the DNA to the
Parkin gene product and the two appear to be transcribed
under the same promoter. The protein has predicted
alpha-helical and beta-sheet domains which suggest its
function is in the ubiquitin/proteasome system.
Mutations in parkin are the genetic cause of early-onset
and autosomal recessive juvenile parkinsonism.
Length = 183
Score = 284 bits (729), Expect = 3e-98
Identities = 115/185 (62%), Positives = 140/185 (75%), Gaps = 3/185 (1%)
Query: 62 SMFRTYYSRGDFPIAMEFKSVGNKISWKEDIKTLNYQYYLPIFFDGLRETEYPYKFFASK 121
+ FR Y RGD P + S NKI WK D + L+Y YLP FFDGLRET++PY+F A
Sbjct: 1 TSFRYVYDRGDIPCRINHGSGKNKIQWKVDPEQLDYDPYLPTFFDGLRETKHPYRFVARN 60
Query: 122 GIHDLLEN-GKDKIVPVLPHLILPIKNALSTRNPEVICETLKVLQHLVTSSSMVGEALVP 180
GI DLLE G +KI+PVLP LILP+K AL+TR+PEV C LKVLQ LV SS ++GEALVP
Sbjct: 61 GIIDLLEAGGGEKILPVLPQLILPLKAALNTRDPEVFCVALKVLQQLVKSSPLIGEALVP 120
Query: 181 YYKQILPHLNMYKDLNKNTGDAIDYSQMKRENIGDLVQETLQILERHGGEDACIYIKYMI 240
YY+Q+LP LN++K+ N N GD IDY K++NIGDL+QETL++LER+GG DA I IKYMI
Sbjct: 121 YYRQLLPVLNLFKNKNVNLGDRIDY--RKKKNIGDLIQETLELLERNGGPDALINIKYMI 178
Query: 241 PTYES 245
PTYES
Sbjct: 179 PTYES 183
>gnl|CDD|214825 smart00802, UME, Domain in UVSB PI-3 kinase, MEI-41 and ESR-1.
Characteristic domain in UVSP PI-3 kinase, MEI-41 and
ESR-1. Found in nucleolar proteins. Associated with FAT,
FATC, PI3_PI4_kinase modules.
Length = 107
Score = 27.6 bits (62), Expect = 2.9
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 110 ETEYPYKFFASKGIHDLLENGKDKIVPVLPHLILPIKNALSTRNPEVICETLKVLQHLVT 169
+ Y K A + I L++ I LP ++ +++AL PE+ L+ L+
Sbjct: 26 KKPYNEKKRALRSIGFLIKLMGKHISSALPQIMACLQSAL--EIPELRSLALRCWHVLIK 83
Query: 170 S 170
+
Sbjct: 84 T 84
>gnl|CDD|191935 pfam08064, UME, UME (NUC010) domain. This domain is characteristic
of UVSB PI-3 kinase, MEI-41 and ESR1.
Length = 107
Score = 27.2 bits (61), Expect = 3.7
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 106 DGLRETEYPYKFFASKGIHDLLENGKDKIVPVLPHLILPIKNALSTRNPEVICETLKVLQ 165
D K A + I +L++ G I P ++ +++AL PE+ E L+
Sbjct: 22 DSKGRKPIFEKKRALRSIEELIKLGGKHISSARPQIMACLQSAL--EIPELRSEALRCWH 79
Query: 166 HLVTS 170
+ S
Sbjct: 80 VFIKS 84
>gnl|CDD|240011 cd04640, CBS_pair_27, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. 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 and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 126
Score = 26.9 bits (60), Expect = 5.4
Identities = 9/27 (33%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 201 DAIDYSQMKRENIGDLVQETLQILERH 227
A+D +++ ++GD+V ETL+ R
Sbjct: 77 KALDLEELENASVGDVV-ETLKASGRQ 102
>gnl|CDD|189054 cd09884, PIN_Smg5, PIN domain of human telomerase-binding protein
EST1, Smg5, and other similar eukaryotic homologs.
Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are
essential to the post-transcriptional regulatory
pathway, NMD, which recognizes recognizes and rapidly
degrades mRNAs containing premature translation
termination codons. These PIN (PilT N terminus) domains
are structural homologs of flap endonuclease-1
(FEN1)-like PIN domains, but lack the extensive
arch/clamp region and the H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region,
seen in FEN1-like PIN domains. Point mutation studies
of the conserved aspartate residues in the catalytic
center of the Smg6 PIN domain revealed that Smg6 is the
endonuclease involved in human NMD. However, Smg5 lacks
several of these key catalytic residues and does not
degrade single-stranded RNA, in vivo. Eukaryotic Smg5
PIN domains are present at the C-terminal end of the
telomerase activating proteins, Est1.
Length = 160
Score = 27.0 bits (60), Expect = 8.2
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 155 EVICETLKVLQHLVTSSSMVGEALVPYYKQILPHLNMYKDLNKNTGDAIDY--SQMKREN 212
+ +CE L +++ LVTS + ++P + ++ L+ K ++ DAI + + K+ N
Sbjct: 8 KALCEYLGIVKQLVTSGKFI--VIIP--RAVVDGLDDLKKESEGARDAIRWLEVEFKKGN 63
>gnl|CDD|236811 PRK10987, PRK10987, regulatory protein AmpE; Provisional.
Length = 284
Score = 27.2 bits (61), Expect = 9.1
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 80 KSVGNKISWKEDIKTLNYQYYL-PIFF 105
+ + + W +NY+YYL P+F+
Sbjct: 130 RELQQALLW------INYRYYLAPLFW 150
>gnl|CDD|215619 PLN03185, PLN03185, phosphatidylinositol phosphate kinase;
Provisional.
Length = 765
Score = 27.1 bits (60), Expect = 9.8
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 95 LNYQYYL-PIFFDG-LRETEYPYKFFASKGIHD 125
LNY +YL P + D LR+ E KF ++ I D
Sbjct: 554 LNYSFYLEPSWRDALLRQIEIDSKFLEAQRIMD 586
>gnl|CDD|176517 cd08575, GDPD_GDE4_like, Glycerophosphodiester phosphodiesterase
domain of mammalian glycerophosphodiester
phosphodiesterase GDE4-like proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in mammalian
GDE4 (also known as glycerophosphodiester
phosphodiesterase domain-containing protein 1 (GDPD1))
and similar proteins. Mammalian GDE4 is a transmembrane
protein whose cellular function is not elucidated. It is
expressed widely, including in placenta, liver, kidney,
pancreas, spleen, thymus, ovary, small intestine and
peripheral blood leukocytes. It is also expressed in the
growth cones in neuroblastoma Neuro2a cells, which
suggests mammalian GDE4 may play some distinct role from
other members of mammalian GDEs family. Also included in
this subfamily are uncharacterized mammalian
glycerophosphodiester phosphodiesterase
domain-containing protein 3 (GDPD3) and similar proteins
which display very high sequence homology to mammalian
GDE4.
Length = 264
Score = 26.8 bits (60), Expect = 9.9
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 208 MKRENIGDLVQETLQILERHGGEDACIY 235
+K + +L+ L +LE++ ED ++
Sbjct: 116 IKSPDAEELIAAVLDLLEKYKREDRTVW 143
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
0.322 0.139 0.422
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,125,800
Number of extensions: 1236221
Number of successful extensions: 1052
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1050
Number of HSP's successfully gapped: 16
Length of query: 253
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 158
Effective length of database: 6,723,972
Effective search space: 1062387576
Effective search space used: 1062387576
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: 58 (26.0 bits)