RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780913|ref|YP_003065326.1| cold shock protein [Candidatus Liberibacter asiaticus str. psy62] (78 letters) >gnl|CDD|31469 COG1278, CspC, Cold shock proteins [Transcription]. Length = 67 Score = 73.2 bits (180), Expect = 2e-14 Identities = 30/70 (42%), Positives = 41/70 (58%), Gaps = 5/70 (7%) Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63 G++KW+N KG+GFITPE G DVF+H SA+ AG L EGQ V ++ Q Sbjct: 3 TGTVKWFNATKGFGFITPED---GGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGR--K 57 Query: 64 KYSAENLKLV 73 SA N++ + Sbjct: 58 GPSAANVRAL 67 >gnl|CDD|88424 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.. Length = 65 Score = 71.0 bits (174), Expect = 7e-14 Identities = 26/69 (37%), Positives = 43/69 (62%), Gaps = 5/69 (7%) Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63 G++KW++ +KG+GFITP+ + G+DVF+H SA+ G +L EG V ++ + D Sbjct: 2 TGTVKWFDDEKGFGFITPD---DGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGD--K 56 Query: 64 KYSAENLKL 72 A N++L Sbjct: 57 GPQAVNVRL 65 >gnl|CDD|144050 pfam00313, CSD, 'Cold-shock' DNA-binding domain. Length = 66 Score = 67.2 bits (165), Expect = 8e-13 Identities = 29/70 (41%), Positives = 40/70 (57%), Gaps = 5/70 (7%) Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63 G++KW+N KG+GFITPE DVF+H SA+ G +L EGQ V +D V+ Sbjct: 2 TGTVKWFNAKKGFGFITPED---GDKDVFVHFSAIQGDGFRSLQEGQRVEFDIVEG--TK 56 Query: 64 KYSAENLKLV 73 A N+ L+ Sbjct: 57 GPQAANVTLL 66 >gnl|CDD|38280 KOG3070, KOG3070, KOG3070, Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]. Length = 235 Score = 43.6 bits (102), Expect = 1e-05 Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 7/58 (12%) Query: 5 GSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQ 58 G++KW+N KGYGFIT + +DVF+H+SA+ G +L EG+ V +D + Sbjct: 59 GTVKWFNVGKGYGFITR---DDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQE 113 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 0.312 0.131 0.386 Gapped Lambda K H 0.267 0.0780 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 898,549 Number of extensions: 35355 Number of successful extensions: 48 Number of sequences better than 10.0: 1 Number of HSP's gapped: 44 Number of HSP's successfully gapped: 5 Length of query: 78 Length of database: 6,263,737 Length adjustment: 48 Effective length of query: 30 Effective length of database: 5,226,505 Effective search space: 156795150 Effective search space used: 156795150 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 (21.8 bits) S2: 51 (23.3 bits)