RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780914|ref|YP_003065327.1| hypothetical protein CLIBASIA_04065 [Candidatus Liberibacter asiaticus str. psy62] (408 letters) >gnl|CDD|177239 MTH00191, CYTB, cytochrome b; Provisional. Length = 365 Score = 29.5 bits (67), Expect = 1.8 Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 10/46 (21%) Query: 210 TLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREY 255 T++ N LS IPY ++ W G +SVDN T TR + Sbjct: 141 TVITNLLSAIPYIG--------DDLVQWLWGG--FSVDNATLTRFF 176 >gnl|CDD|35313 KOG0090, KOG0090, KOG0090, Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]. Length = 238 Score = 29.1 bits (65), Expect = 2.4 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 11/93 (11%) Query: 31 SSFVAIVDVVVDQVTVMQKTAWLQEVLDHVIYRTSPK----------NLYDLREAGRDNF 80 + + VVD T ++ + E L ++ + K N DL A Sbjct: 106 NYSAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNKQDLFTAKTAEK 165 Query: 81 IRHQIEKALNTYN-SRDLSNIGSIESIVKDAVI 112 IR Q+EK ++ SR S E I KD + Sbjct: 166 IRQQLEKEIHKLRESRSALRSISDEDIAKDFTL 198 >gnl|CDD|39700 KOG4500, KOG4500, KOG4500, Rho/Rac GTPase guanine nucleotide exchange factor smgGDS/Vimar [Signal transduction mechanisms]. Length = 604 Score = 28.5 bits (63), Expect = 3.7 Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 5/53 (9%) Query: 283 FGDGQVLTNTNHCFPHGASQNKYMLMLAIGNQLSRSS-----VEKEKIEKVLQ 330 D Q L F S M LAIGN R V+K+ + K++ Sbjct: 311 HADPQFLDFLESWFRSDDSNLITMGSLAIGNFARRDDICIQLVQKDFLNKLIS 363 >gnl|CDD|133316 cd04116, Rab9, Rab9 subfamily. Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 170 Score = 27.9 bits (62), Expect = 4.7 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 9/66 (13%) Query: 242 LTYSVDNKTTTREY--YKDP--YYA---TWDHFPYSFIKNVFDMTSNQFG--DGQVLTNT 292 LT++VD+ + + +K YYA + FP+ + N D+ Q + Q Sbjct: 83 LTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIPERQVSTEEAQAWCRE 142 Query: 293 NHCFPH 298 N +P+ Sbjct: 143 NGDYPY 148 >gnl|CDD|177109 MTH00034, CYTB, cytochrome b; Validated. Length = 379 Score = 27.7 bits (62), Expect = 5.3 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 18/63 (28%) Query: 210 TLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPY 269 T++ N +S +PY + I+ W G +SVDN T TR ++A HF + Sbjct: 144 TVITNLVSAVPYIG--------TDIVQWIWGG--FSVDNATLTR------FFAF--HFLF 185 Query: 270 SFI 272 FI Sbjct: 186 PFI 188 >gnl|CDD|35436 KOG0215, KOG0215, KOG0215, RNA polymerase III, second largest subunit [Transcription]. Length = 1153 Score = 27.2 bits (60), Expect = 7.4 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 16/77 (20%) Query: 331 DCHYMHKRHRTGRDAITIFSVGFSP-------------DQDTRYTLRQCASDPSKYYEIN 377 D Y R + + I G P D++ L +C DP Y+ + Sbjct: 137 DIEYTRGRQIIAKRDVII---GRMPIMLRSSKCVLRGKDEEELARLNECPLDPGGYFIVK 193 Query: 378 SDENVMPIAKSLARNVI 394 E V+ I + L++N I Sbjct: 194 GTEKVILIQEQLSKNRI 210 >gnl|CDD|35549 KOG0328, KOG0328, KOG0328, Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]. Length = 400 Score = 27.2 bits (60), Expect = 9.4 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%) Query: 334 YMHKRHRTGRDAITIFSVGFSPDQDTRYTLRQCASDPSKYYEINSDENVMPIAKSL 389 Y+H+ R+GR ++ F D R D +YY DE M +A + Sbjct: 350 YIHRIGRSGRFGRKGVAINFVKSDDLRILR-----DIEQYYSTQIDEMPMNVADLI 400 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 0.321 0.134 0.402 Gapped Lambda K H 0.267 0.0740 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,909,533 Number of extensions: 256460 Number of successful extensions: 560 Number of sequences better than 10.0: 1 Number of HSP's gapped: 553 Number of HSP's successfully gapped: 17 Length of query: 408 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 312 Effective length of database: 4,189,273 Effective search space: 1307053176 Effective search space used: 1307053176 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 (21.9 bits) S2: 59 (26.5 bits)