RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780890|ref|YP_003065303.1| hypothetical protein CLIBASIA_03935 [Candidatus Liberibacter asiaticus str. psy62] (104 letters) >gnl|CDD|147763 pfam05788, Orbi_VP1, Orbivirus RNA-dependent RNA polymerase (VP1). This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbiviruses. VP1 may have both enzymatic and structural roles in the virus life cycle. Length = 1301 Score = 27.0 bits (60), Expect = 1.3 Identities = 13/27 (48%), Positives = 17/27 (62%) Query: 39 PNQEIRTKIYIITARIIALIVFREGEK 65 PN E R + I +RI AL++F EG K Sbjct: 460 PNAEKRKEFIRIVSRIKALVIFTEGHK 486 >gnl|CDD|111930 pfam03089, RAG2, Recombination activating protein 2. V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome. Length = 528 Score = 26.7 bits (59), Expect = 1.5 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%) Query: 38 TPNQEIRTKIYIIT--ARIIALIVFREGEKSLIFD 70 TPN E+ +K+YI+T +R + R EK L+ D Sbjct: 98 TPNNELSSKLYIMTVDSRCNKKVTLRCSEKDLVGD 132 >gnl|CDD|176969 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit. Length = 200 Score = 26.7 bits (60), Expect = 1.5 Identities = 10/35 (28%), Positives = 17/35 (48%) Query: 2 FYDSREKEVFLESEVVHNIRLQIEEISAILSKKSR 36 FY+ + E LE+E + +R I + A + K Sbjct: 132 FYEGQASEFVLEAEELLKLRETITRVYAQRTGKPL 166 >gnl|CDD|35684 KOG0463, KOG0463, KOG0463, GTP-binding protein GP-1 [General function prediction only]. Length = 641 Score = 25.0 bits (54), Expect = 5.1 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 3/58 (5%) Query: 43 IRTKIYIITARIIALIVFREGEKSLIFDLLRTNQKTNSSLTQAIIQEIDTLQHQCKSI 100 I+ YI R +VFREG + + + + S +A ++ + S+ Sbjct: 518 IKQPEYI---RPGQRLVFREGRTKAVGTISSVLPQESLSPQRAKPKDGRQKSYGKGSM 572 >gnl|CDD|33103 COG3294, COG3294, Uncharacterized conserved protein [Function unknown]. Length = 269 Score = 24.9 bits (54), Expect = 5.1 Identities = 10/29 (34%), Positives = 14/29 (48%) Query: 2 FYDSREKEVFLESEVVHNIRLQIEEISAI 30 Y EK V + SEV+H I E + + Sbjct: 137 IYPDPEKAVRVRSEVLHAIYCHDENETPL 165 >gnl|CDD|33432 COG3634, AhpF, Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones]. Length = 520 Score = 24.9 bits (54), Expect = 5.5 Identities = 11/37 (29%), Positives = 16/37 (43%) Query: 10 VFLESEVVHNIRLQIEEISAILSKKSRDTPNQEIRTK 46 VFL E R+ +EEI A + + +E K Sbjct: 173 VFLNGEEFGQGRMTLEEILAKIDTGAAKRDAEEFNAK 209 >gnl|CDD|30439 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]. Length = 275 Score = 24.8 bits (54), Expect = 5.5 Identities = 8/14 (57%), Positives = 11/14 (78%) Query: 55 IALIVFREGEKSLI 68 IAL+V+ +GEK I Sbjct: 91 IALVVYEDGEKRYI 104 >gnl|CDD|147664 pfam05622, HOOK, HOOK protein. This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head. Length = 713 Score = 24.0 bits (52), Expect = 8.5 Identities = 16/42 (38%), Positives = 21/42 (50%) Query: 12 LESEVVHNIRLQIEEISAILSKKSRDTPNQEIRTKIYIITAR 53 LE + N+ +I E+ A L KK D E R K Y+ AR Sbjct: 566 LEPDQDQNLSRKIAELEAALQKKDEDMRAMEERYKKYVEKAR 607 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 0.133 0.345 Gapped Lambda K H 0.267 0.0657 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,093,508 Number of extensions: 47617 Number of successful extensions: 105 Number of sequences better than 10.0: 1 Number of HSP's gapped: 105 Number of HSP's successfully gapped: 20 Length of query: 104 Length of database: 6,263,737 Length adjustment: 71 Effective length of query: 33 Effective length of database: 4,729,498 Effective search space: 156073434 Effective search space used: 156073434 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 (21.8 bits) S2: 51 (23.6 bits)