RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780241|ref|YP_003064654.1| preprotein translocase subunit SecY [Candidatus Liberibacter asiaticus str. psy62] (444 letters) >gnl|CDD|30550 COG0201, SecY, Preprotein translocase subunit SecY [Intracellular trafficking and secretion]. Length = 436 Score = 396 bits (1020), Expect = e-111 Identities = 207/430 (48%), Positives = 285/430 (66%), Gaps = 13/430 (3%) Query: 13 NFASFSRAKDLKSRIVFTIIALIVYRFGTYIPLPSIDFISYSKAFQSKSAGIFGLFNMFS 72 + + +L+ RI+FT+ ALIVYR G++IP+P I+ + S F S+ I LFNMFS Sbjct: 9 VLSPKFKVPELRKRILFTLGALIVYRIGSFIPVPGINPAALSDLFNSQRFLI--LFNMFS 66 Query: 73 GGAVERMAVFSLGIMPYISASIIVQLIAATVPSLENLKKEGEQGRKVINQYTRYATVLLG 132 GGA+ R ++F+LGIMPYI+ASII+QL+ P L+ L KEGE+GR+ I QYTRY T++L Sbjct: 67 GGALSRGSIFALGIMPYITASIIMQLLTVGSPILKKLDKEGEEGRRKIQQYTRYLTLVLA 126 Query: 133 ILQAYGIAVGLKN--GQGIVSDSDYFFVFSTIITLLGGTMFLVWLGEQITMRGIGNGVSL 190 ++QA G+ +G N V + FF I+ L GTMFL+WLGEQIT RGIGNG+SL Sbjct: 127 VIQALGVVLGGNNGGSPSDVGNGGIFFYLLIILQLTAGTMFLMWLGEQITKRGIGNGISL 186 Query: 191 IIFSGIVAGLPSSLVSVLELGRVGS--ISTPLMLLIFSSTVAVIALVIFFERAQRRLLIQ 248 IIF+GIVA LPS++ ++ G+ +S +LL+ T+A+I LV++ E+A+RR+ IQ Sbjct: 187 IIFAGIVASLPSAIFGIIGALPTGALFLSILFLLLLVLLTLAIIFLVVYVEQARRRIPIQ 246 Query: 249 YPKRQVGNRMFQDDVSYLPLKLNTAGVVPSIFASSLLLLPATIMGFIDVSSSP---TWIV 305 Y KRQ ++ SYLPLKLN AGV+P IFASSLLL P+TI F+ + + Sbjct: 247 YAKRQ----SYRGQSSYLPLKLNYAGVIPVIFASSLLLFPSTIAQFLGNGGLAYYLSPLT 302 Query: 306 GLVDSLGHGRSFYMVLYSVFIVFFAFFYTAIVFNPKEAADNLKKHGGFIPGIRPGDRTAL 365 + D+L G Y+ LY V I+FF++FYT I FNP+E A+NLKK GGFIPGIRPG T Sbjct: 303 SISDALSPGSPVYIALYVVLIIFFSYFYTEIQFNPEEIAENLKKSGGFIPGIRPGKDTEK 362 Query: 366 HIDYVLTRVTVVGAGYLVCVCIFPEALIAVTGVPVSLSGTSLLIIVSVVLDTIVQIQGYL 425 +++ V+ R+T +GA +L + I PE L GVP GTSLLI+V V LDT QI+ L Sbjct: 363 YLNRVIPRLTFIGALFLGLIAILPELLGTAGGVPFYFGGTSLLIVVGVALDTYEQIEAEL 422 Query: 426 IAQQYEGVFK 435 + ++Y G+ + Sbjct: 423 LMEKYPGLRR 432 >gnl|CDD|144075 pfam00344, SecY, eubacterial secY protein. Length = 340 Score = 343 bits (883), Expect = 5e-95 Identities = 167/344 (48%), Positives = 226/344 (65%), Gaps = 12/344 (3%) Query: 81 VFSLGIMPYISASIIVQLIAATVPSLENLKKEGEQGRKVINQYTRYATVLLGILQAYGIA 140 +F+LGI PYI+ASII+QL+ P LE L KEGE+GRK I QYTRY T++L ++QA GI Sbjct: 2 IFALGIGPYITASIIMQLLTVVGPKLEKLDKEGEEGRKKIQQYTRYLTLVLALIQAIGIV 61 Query: 141 VGLKN----GQGIVSDSDYFFVFSTIITLLGGTMFLVWLGEQITMRGIGNGVSLIIFSGI 196 +GL + GIV + + ++ L GTMFL+WLGE IT GIGNG+SLIIF+GI Sbjct: 62 LGLGSYGAFSNGIVLGVGFLNLLLIVLQLTAGTMFLMWLGELITKYGIGNGISLIIFAGI 121 Query: 197 VAGLPSSLVSVLELGRVGS--ISTPLMLLIFSSTVAVIALVIFFERAQRRLLIQYPKRQV 254 V+ +P +++++ L G +S +LL+ +T+AVI LV++ + A+RR+ IQY KR V Sbjct: 122 VSSIPWAIINLFSLLSSGGGLLSILYLLLLLIATLAVILLVVYLQEARRRIPIQYAKRVV 181 Query: 255 GNRMFQDDVSYLPLKLNTAGVVPSIFASSLLLLPATIMGFIDVSSSPTWIVGLVDSLGHG 314 G + SYLP+KLN AGV+P IFASSLL P TI F+ S + GL L G Sbjct: 182 GGG--RGQSSYLPIKLNYAGVIPIIFASSLLANPQTIAQFLGSSFPLWPVSGLAYYLPIG 239 Query: 315 RSFYMVLYSVFIVFFAFFYTAIVFNPKEAADNLKKHGGFIPGIRPGDRTALHIDYVLTRV 374 Y++ Y V I+FF++FYTAI FNPK+ A+NLKK GGFIPGIRPG T +++ V+ R+ Sbjct: 240 SPVYILFYIVLIIFFSYFYTAIGFNPKDIAENLKKSGGFIPGIRPGKSTEKYLNRVIPRL 299 Query: 375 TVVGAGYLVCVCIFPEALIAVTGVPVSLSGTSLLIIVSVVLDTI 418 T +GA +L + + P+ L A+ G GTSLLI V V LDT Sbjct: 300 TFIGAIFLGLLAVLPDLLGALGG----FGGTSLLIAVGVALDTY 339 >gnl|CDD|177074 CHL00161, secY, preprotein translocase subunit SecY; Validated. Length = 417 Score = 299 bits (769), Expect = 7e-82 Identities = 164/420 (39%), Positives = 250/420 (59%), Gaps = 15/420 (3%) Query: 21 KDLKSRIVFTIIALIVYRFGTYIPLPSIDFISYSKAFQSKSAGIFGLFNMFSGGAVERMA 80 +L +R++FT+ L++ R GT+IP+P ID + + + L N FSGG + Sbjct: 8 DELLNRLLFTLGLLLLIRLGTFIPVPGIDHTQLYPSLSNNP--LLNLLNTFSGGGFFVIG 65 Query: 81 VFSLGIMPYISASIIVQLIAATVPSLENLKKE-GEQGRKVINQYTRYATVLLGILQAYGI 139 +F+LGI+PYI+ASII+QL+ + +PSLE L+KE GE GR+ INQYTRY T+ I+Q+ GI Sbjct: 66 LFALGILPYINASIIIQLLTSIIPSLEKLQKEEGEAGRRKINQYTRYLTLGWAIIQSIGI 125 Query: 140 AVGLKNGQGIVSDSDYFFVFSTIITLLGGTMFLVWLGEQITMRGIGNGVSLIIFSGIVAG 199 + LK + + + ++ L G+M ++WL E IT +G+GNG SL+IF IV+ Sbjct: 126 SFWLKP---YLFNWNLLLALEIVLALTSGSMIVLWLSELITEKGLGNGSSLLIFFNIVSN 182 Query: 200 LPSSLVSVLELGRVGSISTPLMLLIFSSTVAVIAL--VIFFERAQRRLLIQYPKRQVGNR 257 LP L L S + ++ ++ + I L +IF + A R++ + K Q+G Sbjct: 183 LPKLL---QSLLFSLSANITILSILLLLFLFFITLIGIIFLQEAIRKIPLISAK-QLGKS 238 Query: 258 MFQDDVSYLPLKLNTAGVVPSIFASSLLLLPATIMGFIDVSSSPTWIVGLVDSLGHGRSF 317 SYLPL+LN AGV+P IFAS+LL+LP + I ++ ++ L L + Sbjct: 239 SRLASNSYLPLRLNQAGVMPIIFASALLVLPGYL-TNILLNQFLLPLLSLFLQLASFKIL 297 Query: 318 YMVLYSVFIVFFAFFYTAIVFNPKEAADNLKKHGGFIPGIRPGDRTALHIDYVLTRVTVV 377 Y+VLY V I+FF++FY+ IV NPK+ ++NL+K IPGIRPG T ++ L R+T++ Sbjct: 298 YLVLYFVLILFFSYFYSTIVLNPKDISENLQKMAVSIPGIRPGKATTKYLKKTLNRLTLL 357 Query: 378 GAGYLVCVCIFPEALIAVTGVPV--SLSGTSLLIIVSVVLDTIVQIQGYLIAQQYEGVFK 435 GA +L + + P + +V + V L TSLLI+V V +DT QIQ YLI+ YE ++ Sbjct: 358 GALFLAFIALLPNLIESVLNLSVFKGLGTTSLLILVGVAIDTSRQIQTYLISNNYENMYD 417 >gnl|CDD|36587 KOG1373, KOG1373, KOG1373, Transport protein Sec61, alpha subunit [Intracellular trafficking, secretion, and vesicular transport, Posttranslational modification, protein turnover, chaperones]. Length = 476 Score = 39.1 bits (91), Expect = 0.002 Identities = 37/175 (21%), Positives = 78/175 (44%), Gaps = 15/175 (8%) Query: 23 LKSRIVFTIIALIVYRFGTYIPLPSIDFISYSKAFQSKSAGIFGLFNMFSGGAVERMAVF 82 + ++++T I+L+++ + IPL I S + M A R + Sbjct: 29 FREKLLWTAISLLIFLVCSQIPLYGI----------MSSDTADPFYWMRVILASNRGTLM 78 Query: 83 SLGIMPYISASIIVQLIAATVPSLENLKKEGEQGRKVINQYTRYATVLLGILQAYGIAVG 142 LGI P +++ +I+QL+A + + + ++ R++ N + +++ + QA + Sbjct: 79 ELGISPIVTSGLIMQLLAGS--KIIEVNFNIKEDRELFNGAQKLFAIIITVGQA--VVYV 134 Query: 143 LKNGQGIVSDSDYFFVFSTIITLLGGTMFLVWLGEQITM-RGIGNGVSLIIFSGI 196 + G SD I+ L + ++ L E + G+G+G+SL I + I Sbjct: 135 MTGMYGSPSDLGVGICLLIILQLFFAGIIVILLDELLQKGYGLGSGISLFIATNI 189 >gnl|CDD|30450 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]. Length = 266 Score = 32.2 bits (73), Expect = 0.27 Identities = 13/43 (30%), Positives = 18/43 (41%) Query: 1 MASAVEQFVSNLNFASFSRAKDLKSRIVFTIIALIVYRFGTYI 43 M A + + +F SF +A V TI + V R G I Sbjct: 140 MREAAKLLLGTHDFTSFRKAGCQSKSPVRTIYRIDVSRDGDLI 182 >gnl|CDD|144263 pfam00606, Glycoprotein_B, Herpesvirus Glycoprotein B. This family of proteins contains a transmembrane region. Length = 711 Score = 29.1 bits (66), Expect = 2.3 Identities = 21/65 (32%), Positives = 27/65 (41%), Gaps = 11/65 (16%) Query: 182 RGIGNGVSLIIFSGIVAGLPSSLVSVLELGRVGSISTPL-MLLIFSSTVAVIALVIFFER 240 + +GN V VAG S+VS G V + P LLI +A + V R Sbjct: 637 KAVGNVV------SGVAGAVGSIVS----GVVSFLKNPFGGLLIILLVLAGLVAVFLAYR 686 Query: 241 AQRRL 245 RRL Sbjct: 687 RVRRL 691 >gnl|CDD|31311 COG1114, BrnQ, Branched-chain amino acid permeases [Amino acid transport and metabolism]. Length = 431 Score = 27.8 bits (62), Expect = 5.7 Identities = 13/42 (30%), Positives = 23/42 (54%) Query: 196 IVAGLPSSLVSVLELGRVGSISTPLMLLIFSSTVAVIALVIF 237 I+ L S LV+ L L ++ IS P++ I+ +A++ L Sbjct: 318 IIFTLISFLVANLGLEQIIKISVPVLTAIYPIAIALVLLSFA 359 >gnl|CDD|146013 pfam03176, MMPL, MMPL family. Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport. Length = 332 Score = 27.6 bits (62), Expect = 6.5 Identities = 22/125 (17%), Positives = 44/125 (35%), Gaps = 20/125 (16%) Query: 127 ATVLLGILQAYGIAVGLKNGQGIVSDSDYFFVFSTIITLLGGT---MFLV---------- 173 TV L + A G+ L + GI S + ++ + GT +FLV Sbjct: 174 LTVGLSLGAAQGLVAILAHILGI-GLSTFALNLLVVLLIAVGTDYALFLVSRYREELRAG 232 Query: 174 ---WLGEQITMRGIGNGVSLIIFSGIVAGLPSSLVSVLELGRVGSISTPLMLLIFSSTVA 230 +RG G ++ +G+ + +S L + + + + +A Sbjct: 233 EDREEAVIRAVRGTG---KVVTAAGLTVAIAMLALSFARLPVFAQVGPTIAIGVLVDVLA 289 Query: 231 VIALV 235 + L+ Sbjct: 290 ALTLL 294 >gnl|CDD|133025 cd04182, GT_2_like_f, GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. Length = 186 Score = 27.1 bits (61), Expect = 9.3 Identities = 6/22 (27%), Positives = 10/22 (45%) Query: 80 AVFSLGIMPYISASIIVQLIAA 101 + L P ++A + LI A Sbjct: 94 VLILLADQPLVTAETLRALIDA 115 >gnl|CDD|30020 cd02570, PseudoU_synth_EcTruA, PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.. Length = 239 Score = 27.0 bits (60), Expect = 9.9 Identities = 14/43 (32%), Positives = 18/43 (41%) Query: 1 MASAVEQFVSNLNFASFSRAKDLKSRIVFTIIALIVYRFGTYI 43 M A + + +F+SF A V TI VYR G I Sbjct: 135 MQEAAKLLLGTHDFSSFRAAGCQSKSTVRTIYRADVYREGDLI 177 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 0.326 0.142 0.403 Gapped Lambda K H 0.267 0.0746 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,294,196 Number of extensions: 306647 Number of successful extensions: 1370 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1337 Number of HSP's successfully gapped: 109 Length of query: 444 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 347 Effective length of database: 4,167,664 Effective search space: 1446179408 Effective search space used: 1446179408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 59 (26.5 bits)