RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781182|ref|YP_003065595.1| hypothetical protein CLIBASIA_05445 [Candidatus Liberibacter asiaticus str. psy62] (94 letters) >gnl|CDD|144517 pfam00945, Rhabdo_ncap, Rhabdovirus nucleocapsid protein. The Nucleocapsid (N) Protein is said to have a "tight" structure. The carboxyl end of the N-terminal domain possesses an RNA binding domain. Sequence alignments show 2 regions of reasonable conservation, approx. 64-103 and 201-329. A whole functional protein is required for encapsidation to take place. Length = 406 Score = 25.4 bits (56), Expect = 3.4 Identities = 9/27 (33%), Positives = 11/27 (40%) Query: 11 FEKCGMLSDRTRYLKQHNLIIEEIFEW 37 ++ C L T K L IEE W Sbjct: 214 YKDCSGLVSFTHLCKVTGLSIEEAITW 240 >gnl|CDD|133358 cd04158, ARD1, ARD1 subfamily. ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization. Length = 169 Score = 24.9 bits (54), Expect = 5.6 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 5/57 (8%) Query: 18 SDRTRYLKQHN----LIIEEIFEWSNFVRIEGNKAVHEGQSSIEESDECLEFVNLFC 70 S R R + H+ L+ E+ + + I NK G S+EE E L L C Sbjct: 77 SHRDRVSEAHSELAKLLTEKELRDALLL-IFANKQDVAGALSVEEMTELLSLHKLCC 132 >gnl|CDD|31738 COG1549, COG1549, Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]. Length = 519 Score = 24.5 bits (53), Expect = 7.4 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 2/56 (3%) Query: 31 IEEIFEWSNF--VRIEGNKAVHEGQSSIEESDECLEFVNLFCDIVFTLPALIKEKK 84 +E+F +S + AV S E DE +E PA+ K+ + Sbjct: 4 DQELFGYSRPGEFPEYDSPAVTVLPESYVEVDEIIEKAGKRIPRQLYFPAVKKQSE 59 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 0.319 0.136 0.402 Gapped Lambda K H 0.267 0.0822 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,127,968 Number of extensions: 48204 Number of successful extensions: 108 Number of sequences better than 10.0: 1 Number of HSP's gapped: 108 Number of HSP's successfully gapped: 5 Length of query: 94 Length of database: 6,263,737 Length adjustment: 62 Effective length of query: 32 Effective length of database: 4,923,979 Effective search space: 157567328 Effective search space used: 157567328 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 (21.7 bits) S2: 51 (23.2 bits)