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)