RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780122|ref|YP_003064535.1| hypothetical protein
CLIBASIA_00005 [Candidatus Liberibacter asiaticus str. psy62]
(123 letters)
>gnl|CDD|146857 pfam04425, Bul1_N, Bul1 N terminus. This family contains the N
terminus of Saccharomyces cerevisiae Bul1. Bul1 binds
the ubiquitin ligase Rsp5, via an N terminal PPSY motif.
The complex containing Bul1 and Rsp5 is involved in
intracellular trafficking of the general amino acid
permease Gap1, degradation of Rog1 in cooperation with
Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may
contain HEAT repeats.
Length = 432
Score = 29.2 bits (66), Expect = 0.31
Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 10/85 (11%)
Query: 19 HSHPNADPDISIEMQISENQRYLDEEISQCNAVVDVFKRSDSTILDKLDAMDDLKT---- 74
S P+ + E E + D SD+TILD L + L +
Sbjct: 76 SSLSLESPNTTEASNSPEETHLNIENNEHNTPIEDDLNDSDNTILDNLYKLPKLTSSPIE 135
Query: 75 ---YIS--LLQATAKN-LKSLLKEY 93
++ + + K ++S+LKEY
Sbjct: 136 IDIRVTKHVPKPGEKPEIESILKEY 160
>gnl|CDD|145547 pfam02465, FliD_N, Flagellar hook-associated protein 2
C-terminus. The flagellar hook-associated protein 2
(HAP2 or FliD) forms the distal end of the flagella,
and plays a role in mucin specific adhesion of the
bacteria. This alignment covers the N-terminal region
of this family of proteins.
Length = 99
Score = 26.7 bits (60), Expect = 1.8
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 60 STILDKLDAMDDLKTYISLLQATAKNLKS 88
+ + KL A LK+ +S LQ NL S
Sbjct: 29 TKLEAKLSAYGQLKSALSTLQDALSNLSS 57
>gnl|CDD|35477 KOG0256, KOG0256, KOG0256, 1-aminocyclopropane-1-carboxylate
synthase, and related proteins [Signal transduction
mechanisms].
Length = 471
Score = 26.4 bits (58), Expect = 2.4
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 9/85 (10%)
Query: 9 HDEINENFYFHS-------HPNADPDISIEMQISENQRY--LDEEISQCNAVVDVFKRSD 59
H E + FY P +P I+M ++ENQ L E N R
Sbjct: 48 HGEDSSYFYGWKAYEKNPYDPIKNPLGIIQMGLAENQLCFDLIESWLSKNPEASNCTREG 107
Query: 60 STILDKLDAMDDLKTYISLLQATAK 84
+ D+L D S QA A+
Sbjct: 108 QSSFDELAMFQDYHGLPSFRQAVAE 132
>gnl|CDD|133293 cd01893, Miro1, Miro1 subfamily. Miro (mitochondrial Rho)
proteins have tandem GTP-binding domains separated by a
linker region containing putative calcium-binding EF
hand motifs. Genes encoding Miro-like proteins were
found in several eukaryotic organisms. This CD
represents the N-terminal GTPase domain of Miro
proteins. These atypical Rho GTPases have roles in
mitochondrial homeostasis and apoptosis. Most Rho
proteins contain a lipid modification site at the
C-terminus; however, Miro is one of few Rho subfamilies
that lack this feature.
Length = 166
Score = 25.8 bits (57), Expect = 3.0
Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 22 PNADPDIS----IEMQISENQR-YLDEEISQCNAVVDVFKRSDSTILDKL 66
+ P+ ++ R L EI + N + V+ + L+++
Sbjct: 40 ADVTPERVPTTIVDTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERI 89
>gnl|CDD|144834 pfam01387, Synuclein, Synuclein. There are three types of
synucleins in humans, these are called alpha, beta and
gamma. Alpha synuclein has been found mutated in
families with autosomal dominant Parkinson's disease. A
peptide of alpha synuclein has also been found in
amyloid plaques in Alzheimer's patients.
Length = 132
Score = 25.7 bits (56), Expect = 3.1
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 84 KNLKSLLKEYWEESLDGEDDEEIYEHPDQE 113
KN + +E EE E D E YE P +E
Sbjct: 102 KNEEEAPQEGIEEDKPVEPDNEAYEMPSEE 131
>gnl|CDD|114252 pfam05520, Citrus_P18, Citrus tristeza virus P18 protein.
Length = 167
Score = 25.8 bits (56), Expect = 3.4
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 45 ISQCNAVVD---VFKRSDSTILDKLDAMDDLKTYISLLQAT 82
IS C + D + K D+T++D+L++M+ L + L + T
Sbjct: 54 ISNCTIIADGSALLK--DNTVVDRLESMNPLAYLLKLAKTT 92
>gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding
protein [Defense mechanisms].
Length = 625
Score = 24.9 bits (54), Expect = 5.1
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 1 MGALKNHFHDEINENFYFHSHP-NADPDIS----IEMQISENQR-YLDEEISQCNAVVDV 54
M L+ F D + P + P+ ++ + R L +EI + + + V
Sbjct: 27 MSLLEEEFVDAVPRRLPRILIPADVTPENVPTSIVDTSSDSDDRLCLRKEIRKADVICLV 86
Query: 55 FKRSDSTILDKL 66
+ D + +D++
Sbjct: 87 YAVDDESTVDRI 98
>gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family
helicases are composed of four structural domains. The
Rep family function as dimers. REP helicases catalyse
ATP dependent unwinding of double stranded DNA to single
stranded DNA. Bacillus subtilis addA and Escherichia
coli exodeoxyribonuclease V beta have large insertions
near to the carboxy-terminus relative to other members
of the family.
Length = 494
Score = 25.0 bits (55), Expect = 5.7
Identities = 11/70 (15%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 40 YLDEEISQCNAVVDVFKRSDSTI-LDKLDAMDDLKTYISLLQATAKNLKSLLKEYWEESL 98
+ +E+ Q + ++ K+ + L + +LK IS + + + L + + +
Sbjct: 105 SILDELDQLALLKEILKKDRLDLDSKLLRPLLELKELISKAKNELLSPEELQQASYAATP 164
Query: 99 DGEDDEEIYE 108
+ E Y+
Sbjct: 165 RDKLAAEFYQ 174
>gnl|CDD|163698 cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A
deubiquitinase. This family includes histone H2A
deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM
and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or
KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases
(DUBs), with possible Zn2+-dependent ubiquitin
isopeptidase activity. It contains the SWIRM (Swi3p,
Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR,
TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain
can bind directly to DNA. 2A-DUB is specific for
monoubiquitinated H2A (uH2A), regulating transcription
by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. 2A-DUB interacts
with p/CAF (p300/CBP-associated factor) in a
co-regulatory protein complex, where the status of
acetylation of nucleosomal histones modulates its
deubiquitinase activity. 2A-DUB is a positive regulator
of androgen receptor (AR) transactivation activity on a
reporter gene; it participates in transcriptional
regulation events in androgen receptor-dependent gene
activation. In prostate tumors, the levels of uH2A are
dramatically decreased, thus 2A-DUB serving as a
cancer-related marker.
Length = 187
Score = 24.9 bits (55), Expect = 6.4
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 3/19 (15%)
Query: 18 FHSHPNADPDIS---IEMQ 33
+HSHP P+ S I+ Q
Sbjct: 85 YHSHPTFPPNPSLRDIDTQ 103
>gnl|CDD|34147 COG4469, CoiA, Competence protein [General function prediction
only].
Length = 342
Score = 24.5 bits (53), Expect = 6.8
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 4 LKNHFHDEINENFYFHSHPNADPDISIEMQISEN----QRYLDEEIS 46
++ F+ FY+ +++ I E+ +YL E+S
Sbjct: 151 QQSFFYFSFINGFYYWELDFYAQKTRLKLLIHEDLRGKHKYLASEVS 197
>gnl|CDD|173804 cd07478, Peptidases_S8_CspA-like, Peptidase S8 family domain in
CspA-like proteins. GSP (germination-specific protease)
converts the spore peptidoglycan hydrolase (SleC)
precursor to an active enzyme during germination of
Clostridium perfringens S40 spores. Analysis of an
enzyme fraction of GSP showed that it was composed of a
gene cluster containing the processed forms of products
of cspA, cspB, and cspC which are positioned in a tandem
array just upstream of the 5' end of sleC. The amino
acid sequences deduced from the nucleotide sequences of
the csp genes showed significant similarity and showed a
high degree of homology with those of the catalytic
domain and the oxyanion binding region of
subtilisin-like serine proteases. Members of the
peptidases S8 and S35 clan include endopeptidases,
exopeptidases and also a tripeptidyl-peptidase. The S8
family has an Asp/His/Ser catalytic triad similar to
that found in trypsin-like proteases, but do not share
their three-dimensional structure and are not homologous
to trypsin. The S53 family contains a catalytic triad
Glu/Asp/Ser. The stability of these enzymes may be
enhanced by calcium, some members have been shown to
bind up to 4 ions via binding sites with different
affinity. Some members of this clan contain disulfide
bonds. These enzymes can be intra- and extracellular,
some function at extreme temperatures and pH values.
Length = 455
Score = 24.5 bits (54), Expect = 7.7
Identities = 4/29 (13%), Positives = 12/29 (41%)
Query: 17 YFHSHPNADPDISIEMQISENQRYLDEEI 45
+ ++E+ + E ++ + EI
Sbjct: 200 HSGGIVPNGETKTVELNVGEGEKGFNLEI 228
>gnl|CDD|30789 COG0440, IlvH, Acetolactate synthase, small (regulatory) subunit
[Amino acid transport and metabolism].
Length = 163
Score = 24.4 bits (53), Expect = 8.3
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 25 DPDIS-IEMQISENQRYLDEEISQCNAVVDVFKRSDST 61
P +S I + +S +++ L++ I Q N ++DV K D T
Sbjct: 42 TPGLSRITIVVSGDEQVLEQIIKQLNKLIDVLKVLDLT 79
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.313 0.132 0.377
Gapped
Lambda K H
0.267 0.0526 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,556,275
Number of extensions: 70552
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 245
Number of HSP's successfully gapped: 43
Length of query: 123
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,491,799
Effective search space: 184163759
Effective search space used: 184163759
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 (21.9 bits)
S2: 51 (23.9 bits)