RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780817|ref|YP_003065230.1| preprotein translocase subunit SecB [Candidatus Liberibacter asiaticus str. psy62] (152 letters) >gnl|CDD|145603 pfam02556, SecB, Preprotein translocase subunit SecB. This family consists of preprotein translocase subunit SecB. SecB is required for the normal export of envelope proteins out of the cell cytoplasm. Length = 147 Score = 163 bits (416), Expect = 1e-41 Identities = 54/136 (39%), Positives = 87/136 (63%), Gaps = 2/136 (1%) Query: 5 QKQAFTILNQYIKDFSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSFDI 64 + F I QY+KD SFE+PNAP F ++ QP + + + VNA ++ ++V+L+ + Sbjct: 9 PQPQFQIQRQYVKDLSFENPNAPAIF--LEEWQPEVNVQLNVNARKLAENVYEVVLTVTV 66 Query: 65 EAKNNDKVIFRLELAYSGILRILDCPQEHISQILFVECPQLLFPFVRQIISNTIRDGGFP 124 AKN +K F +E+ +GI I + P+E + L +ECP +LFP+ R+IIS+ R GGFP Sbjct: 67 TAKNEEKTAFLVEVKQAGIFTIRNVPEEQLHPFLGIECPNILFPYAREIISDLTRRGGFP 126 Query: 125 PLVIDTIDFLKLFQQE 140 PL++ I+F L++Q+ Sbjct: 127 PLMLAPINFDALYEQQ 142 >gnl|CDD|32135 COG1952, SecB, Preprotein translocase subunit SecB [Intracellular trafficking and secretion]. Length = 157 Score = 149 bits (378), Expect = 3e-37 Identities = 54/147 (36%), Positives = 90/147 (61%), Gaps = 2/147 (1%) Query: 3 KKQKQAFTILNQYIKDFSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSF 62 + +F I Y+KD SFE+PNAPH F ++ QP + +++ NAN ++ F+V+L+ Sbjct: 7 PTGQPSFNIQRIYVKDLSFEAPNAPHIF--QKDWQPEVNLDLNTNANQLAENVFEVVLTV 64 Query: 63 DIEAKNNDKVIFRLELAYSGILRILDCPQEHISQILFVECPQLLFPFVRQIISNTIRDGG 122 + AK +K F E+ +GI RI P+E ++ +L +ECP +LFP+ R++IS+ GG Sbjct: 65 TVTAKLGEKTAFLCEVQQAGIFRIAGIPEEQMAHLLGIECPNILFPYARELISDLTARGG 124 Query: 123 FPPLVIDTIDFLKLFQQEKSLIKNKEG 149 FPPL++ I+F L+ Q + + +E Sbjct: 125 FPPLMLAPINFDALYAQRLAEQQAEEV 151 >gnl|CDD|29643 cd00557, Translocase_SecB, Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent polypeptides across the cytoplasmic membrane. SecB has been shown to function as export-specific molecular chaperone that selectively binds preproteins, maintains them in a translocation competent state and delivers them to SecA, the membrane-bound ATPase, that drives the translocation reaction. In solution, SecB exists as homotetramer, which is organized as a dimer of dimers.. Length = 131 Score = 92.3 bits (229), Expect = 5e-20 Identities = 40/131 (30%), Positives = 70/131 (53%), Gaps = 4/131 (3%) Query: 9 FTILNQYIKDFSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGAD-FDVILSFDIEAK 67 I Y+KD SFE+PNAPH F ++ +P + +++ + + ++V+L+ AK Sbjct: 1 LQIQRIYVKDISFEAPNAPHLF--QKDWKPRLNLDLDTEITQLKNDNKYEVVLNITAGAK 58 Query: 68 NND-KVIFRLELAYSGILRILDCPQEHISQILFVECPQLLFPFVRQIISNTIRDGGFPPL 126 K F E+ +G+ I+ + ++ L + CP +LFP+ R++IS+ FPPL Sbjct: 59 LEFAKSAFYCEVKQAGVFEIIGIEIDQMAHCLEINCPAILFPYARELISSITARATFPPL 118 Query: 127 VIDTIDFLKLF 137 + I+F LF Sbjct: 119 NLPPINFDALF 129 >gnl|CDD|34525 COG4916, COG4916, Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]. Length = 329 Score = 26.9 bits (59), Expect = 2.6 Identities = 10/50 (20%), Positives = 16/50 (32%) Query: 19 FSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSFDIEAKN 68 + + F + I+ V S D +SF EA+N Sbjct: 141 RTVPDASLRRDLFTFETILLREPIHATVTVVDSSEKPVDSGISFAGEARN 190 >gnl|CDD|144627 pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD. Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains. Length = 177 Score = 26.5 bits (59), Expect = 3.4 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 8/67 (11%) Query: 18 DFSFE-SPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSFDIEAKN-NDKVIFR 75 +FE CF++ + + + QV ISG D+ F + + N VI+ Sbjct: 1 ALTFELPAGEKECFYEEVPKGTLVTGSYQV----ISGGGLDI--DFTVTDPDGNGNVIYS 54 Query: 76 LELAYSG 82 + G Sbjct: 55 KKRKSEG 61 >gnl|CDD|145140 pfam01819, Levi_coat, Levivirus coat protein. The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication. Length = 129 Score = 25.2 bits (55), Expect = 6.9 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 10/56 (17%) Query: 34 QNQQPTIKINVQ-VNANTISGADF---------DVILSFDIEAKNNDKVIFRLELA 79 ++ TIK+ V V T++G + DV L+ I + ++ R ELA Sbjct: 55 NRRKYTIKLEVPKVTTQTVNGVELPVVARTSYADVDLTIPIFSTTKERAFIRKELA 110 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 0.325 0.142 0.411 Gapped Lambda K H 0.267 0.0700 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,836,298 Number of extensions: 92004 Number of successful extensions: 279 Number of sequences better than 10.0: 1 Number of HSP's gapped: 276 Number of HSP's successfully gapped: 15 Length of query: 152 Length of database: 6,263,737 Length adjustment: 85 Effective length of query: 67 Effective length of database: 4,426,972 Effective search space: 296607124 Effective search space used: 296607124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (24.3 bits)