RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780690|ref|YP_003065103.1| flagellar biosynthesis protein FlhB [Candidatus Liberibacter asiaticus str. psy62] (354 letters) >2jlj_A YSCU, YOP proteins translocation protein U; cell membrane, transmembrane, yersinia pesits, protein transport, type III secretion system, plasmid; 1.3A {Yersinia pestis} PDB: 2jlh_A* 2v5g_A 2w0r_A Length = 144 Score = 164 bits (417), Expect = 2e-41 Identities = 39/130 (30%), Positives = 71/130 (54%) Query: 221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALR 280 +LKMSK EIK E K+ G+P IK++++ + M E R+++++ TH A+ + Sbjct: 3 ELKMSKDEIKREYKEMEGSPEIKSKRRQFHQEIQSRNMRENVKRSSVVVAAATHIAIGIL 62 Query: 281 YIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYK 340 Y + E P++ K + + +RKIA E +PI + LAR+L+ ++ IP + Sbjct: 63 YKRGETPLPLVTFKYTDAQVQTVRKIAEEEGVPILQRIPLARALYWDALVDHYIPAEQIE 122 Query: 341 AVAQLIYKIY 350 A A+++ + Sbjct: 123 ATAEVLRWLE 132 >2jli_A YSCU, YOP proteins translocation protein; cell membrane, transmembrane, protein transport, type III secretion system, plasmid, membrane; 1.13A {Yersinia pestis} Length = 123 Score = 155 bits (394), Expect = 1e-38 Identities = 36/119 (30%), Positives = 66/119 (55%) Query: 228 EIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTEND 287 EIK E K+ G+P IK++++ + M E R+++++ NPTH A+ + Y + E Sbjct: 1 EIKREYKEMEGSPEIKSKRRQFHQEIQSRNMRENVKRSSVVVANPTHIAIGILYKRGETP 60 Query: 288 APVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLI 346 P++ K + + +RKIA E +PI + LAR+L+ ++ IP +A A+++ Sbjct: 61 LPLVTFKYTDAQVQTVRKIAEEEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVL 119 >3bzs_A ESCU; auto cleavage protein, intein, T3SS, TTSS, asparagine cyclization, membrane, membrane protein, protein transport; 1.48A {Escherichia coli} PDB: 3bzr_A 3bzp_A 3bzt_A 3c03_A Length = 137 Score = 153 bits (388), Expect = 6e-38 Identities = 42/130 (32%), Positives = 70/130 (53%) Query: 221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALR 280 MSK E+K E K + GNP IK ++ + + ++T+I+ +PTH A+ L Sbjct: 4 MASMSKDEVKREAKDTDGNPEIKGERRRLHSEIQSGSLANNIKKSTVIVKDPTHIAICLY 63 Query: 281 YIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYK 340 Y E P+++ G++ A ++ K+A ++IP+ E+ LARSL+K + I F++ Sbjct: 64 YKLGETPLPLVIETGKDAKALQIIKLAELYDIPVIEDIPLARSLYKNIHKGQYITEDFFE 123 Query: 341 AVAQLIYKIY 350 VAQLI Sbjct: 124 PVAQLIRIAI 133 >3bzy_B ESCU; auto cleavage protein, flagella, intein, T3SS, membrane, membrane protein, protein transport; 1.20A {Escherichia coli} SCOP: d.367.1.1 PDB: 3c00_B 3bzl_C 3bzo_B 3bzv_B 3c03_C 3bzz_B 3bzx_B Length = 83 Score = 100 bits (250), Expect = 6e-22 Identities = 28/79 (35%), Positives = 44/79 (55%) Query: 272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPIN 331 PTH A+ L Y E P+++ G++ A ++ K+A ++IP+ E+ LARSL K + Sbjct: 1 PTHIAICLYYKLGETPLPLVIETGKDAKALQIIKLAELYDIPVIEDIPLARSLDKNIHKG 60 Query: 332 SAIPPVFYKAVAQLIYKIY 350 I F++ VAQLI Sbjct: 61 QYITEDFFEPVAQLIRIAI 79 >2vt1_B Surface presentation of antigens protein SPAS; specificity switch, virulence, transmembrane, inner membrane, FLHB, YSCU, T3SS, plasmid; 2.0A {Shigella flexneri} SCOP: d.367.1.1 Length = 93 Score = 98.4 bits (245), Expect = 2e-21 Identities = 23/79 (29%), Positives = 33/79 (41%) Query: 272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPIN 331 PTH A+ + + AP + N A +RK A E IP + LAR L+K Sbjct: 1 PTHIAIGIYFNPEIAPAPFISLIETNQCALAVRKYANEVGIPTVRDVKLARKLYKTHTKY 60 Query: 332 SAIPPVFYKAVAQLIYKIY 350 S + V +LI + Sbjct: 61 SFVDFEHLDEVLRLIVWLE 79 >3c01_E Surface presentation of antigens protein SPAS; auto cleavage protein, flagella, ESCU, YSCU, intein, T3SS, membrane, inner membrane; 2.60A {Salmonella typhimurium} SCOP: d.367.1.1 Length = 98 Score = 95.3 bits (237), Expect = 2e-20 Identities = 18/79 (22%), Positives = 32/79 (40%) Query: 272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPIN 331 PTH + + + P++ N A +R A + +P+ + LARSLFK Sbjct: 1 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRY 60 Query: 332 SAIPPVFYKAVAQLIYKIY 350 + V +L+ + Sbjct: 61 DLVSLEEIDEVLRLLVWLE 79 >3bzy_A ESCU; auto cleavage protein, flagella, intein, T3SS, membrane, membrane protein, protein transport; 1.20A {Escherichia coli} SCOP: d.367.1.1 PDB: 3bzl_A 3bzv_A 3bzx_A 3bzo_A 3bzz_A 3c03_B 3c00_A Length = 54 Score = 74.3 bits (183), Expect = 4e-14 Identities = 15/51 (29%), Positives = 25/51 (49%) Query: 221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN 271 MSK E+K E K + GNP IK ++ + + ++T+I+ N Sbjct: 4 MASMSKDEVKREAKDTDGNPEIKGERRRLHSEIQSGSLANNIKKSTVIVKN 54 >2vt1_A Surface presentation of antigens protein SPAS; specificity switch, virulence, transmembrane, inner membrane, FLHB, YSCU, T3SS, plasmid; 2.0A {Shigella flexneri} SCOP: d.367.1.1 Length = 52 Score = 73.5 bits (181), Expect = 7e-14 Identities = 11/50 (22%), Positives = 24/50 (48%) Query: 222 LKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN 271 + M KQEIK E + G+ K+R++ + + + + +++ N Sbjct: 3 MMMDKQEIKREYIEQEGHFETKSRRRELHIEILSEQTKSDIRNSKLVVMN 52 >3c01_A Surface presentation of antigens protein SPAS; auto cleavage protein, flagella, ESCU, YSCU, intein, T3SS, membrane, inner membrane; 2.60A {Salmonella typhimurium} SCOP: d.367.1.1 Length = 48 Score = 70.4 bits (173), Expect = 6e-13 Identities = 12/48 (25%), Positives = 28/48 (58%) Query: 224 MSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN 271 M K+E+K E+K+ GNP +K++++ + + ++ + +I+ N Sbjct: 1 MDKEEVKREMKEQEGNPEVKSKRREVHMEILSEQVKSDIENSRLIVAN 48 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 64.6 bits (157), Expect = 3e-11 Identities = 69/484 (14%), Positives = 128/484 (26%), Gaps = 201/484 (41%) Query: 2 SENDAPDNKTEAPSSKKIE----------DALNEGNAPISREASLFSSILACLIYLLFF- 50 +E A D++ P++ E + + F +L L F Sbjct: 45 TEGFAADDE---PTTP-AELVGKFLGYVSSLVEPS------KVGQFDQVLNLC--LTEFE 92 Query: 51 --FSPGIYSVTSDLHVLLAS------ATQRKLEDISHIVFLLTHLSLSASRLVIPGLL-- 100 + G +D+H L A T K +++ ++ L Sbjct: 93 NCYLEG-----NDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR 147 Query: 101 --------LFMMFG----IGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNF 148 L +FG Y F+ LR+ +Y Sbjct: 148 AVGEGNAQLVAIFGGQGNTDDY----------------FE--ELRD----LYQT------ 179 Query: 149 MKSFVKIILVGTIITI--SLTEN------YFTM-LDFIS--ANPHSI------------- 184 V L+ L FT L+ + NP + Sbjct: 180 YHVLVGD-LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC 238 Query: 185 -------LYHAFFTVR-KVL--------------------IMILLFIAT----------- 205 L H + V K+L ++ + IA Sbjct: 239 PLIGVIQLAH--YVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSV 296 Query: 206 ---LTVL-DIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPI----IKNRQKSIARSRIRHK 257 +TVL IG ++ Y + ++D ++ + G P I N + + ++ Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN----LTQEQV-QD 351 Query: 258 MMEAT----------------SRATIIITNPT----HYALALRYIQ--TENDAPVLVAKG 295 + T ++++ P L LR + + D Sbjct: 352 YVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD-------- 403 Query: 296 QNLIAKKMRKIAYEHN-IPI---FEEPSL--ARSLFKQ--VPINSAIPPVFYKAVAQLIY 347 Q+ I RK+ + + +P+ F L A L + V N + + Sbjct: 404 QSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA------KDIQI 457 Query: 348 KIYH 351 +Y Sbjct: 458 PVYD 461 Score = 47.6 bits (113), Expect = 4e-06 Identities = 37/175 (21%), Positives = 61/175 (34%), Gaps = 59/175 (33%) Query: 10 KTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHV-LLAS 68 K +APS L++ P S FS+ F P V S H LL Sbjct: 395 KAKAPSG------LDQSRIPFSERKLKFSNR----------FLP----VASPFHSHLLVP 434 Query: 69 ATQRKLEDISHIVFLLTHLSLSASRLVIPGLLLFMMF-G-----IGSYLIQRI------- 115 A+ +D + ++S +A + IP ++ F G + + +RI Sbjct: 435 ASDLINKD-----LVKNNVSFNAKDIQIP---VYDTFDGSDLRVLSGSISERIVDCIIRL 486 Query: 116 PV-----LNLN--HVKPSFKRVSLREGIKRIYSINNLVNFMK--SFVKIILVGTI 161 PV H+ L G + L + K + V++I+ GT+ Sbjct: 487 PVKWETTTQFKATHI--------LDFGPGGASGLGVLTHRNKDGTGVRVIVAGTL 533 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 30.0 bits (66), Expect = 0.77 Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 6/24 (25%) Query: 278 ALRYIQT------ENDAPVLVAKG 295 AL+ +Q ++ AP L K Sbjct: 21 ALKKLQASLKLYADDSAPALAIKA 44 Score = 27.7 bits (60), Expect = 3.7 Identities = 7/29 (24%), Positives = 18/29 (62%), Gaps = 4/29 (13%) Query: 12 EAPSSKKIEDALN---EGNAP-ISREASL 36 E + KK++ +L + +AP ++ +A++ Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATM 46 >2ctw_A DNAJ homolog subfamily C member 5; J-domain, chaperone, helix-turn-helix, structural genomics, NPPSFA; NMR {Mus musculus} Length = 109 Score = 28.6 bits (63), Expect = 2.4 Identities = 13/56 (23%), Positives = 22/56 (39%) Query: 218 WYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPT 273 Y L + K D+IK+SY +K + + + A I+T+ T Sbjct: 19 LYHVLGLDKNATSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHAILTDAT 74 >2qx2_A Sex pheromone staph-CAM373; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 1.90A {Staphylococcus aureus subsp} Length = 344 Score = 28.2 bits (63), Expect = 2.6 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 21/79 (26%) Query: 276 ALALR---YIQTENDAP---------VLVAKGQ---NLIAKKMRKIAYEHNIPIFEEPSL 320 LA+ Y + E D P + +G+ + I ++R+ +IPI Sbjct: 135 GLAMNSVYYYKKEKDGPTFSKKLDDSEVKKQGKQMASEILSRLRENDDLKDIPIH----- 189 Query: 321 ARSLFKQVPINSAIPPVFY 339 +++KQ +S P F Sbjct: 190 -FAIYKQSSEDSITPGEFI 207 >2csu_A 457AA long hypothetical protein; structural genomics, PH0766, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.20A {Pyrococcus horikoshii OT3} SCOP: c.2.1.8 c.23.4.1 c.23.4.1 Length = 457 Score = 28.2 bits (62), Expect = 2.7 Identities = 9/46 (19%), Positives = 21/46 (45%) Query: 276 ALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLA 321 + + N+ PVL +++K +++ ++ IP +E P Sbjct: 392 GIIRAVKEVNNEKPVLAMFMAGYVSEKAKELLEKNGIPTYERPEDV 437 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 27.9 bits (61), Expect = 3.8 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%) Query: 203 IAT--LTVLDIG-WSYHQWYSKLKMSKQ-----EIKDEIKQSYGNPIIKNRQK 247 +AT LT+ D+G S+H +K + E+ + +S GNP+I QK Sbjct: 1327 LATYGLTIDDLGVASFHGTSTKANDKNESATINEMMKHLGRSEGNPVIGVFQK 1379 >1q3q_A Thermosome alpha subunit; chaperone, chaperonin; HET: ANP; 2.30A {Thermococcus SP} SCOP: a.129.1.2 c.8.5.2 d.56.1.2 PDB: 1q2v_A* 1q3s_A* 1q3r_A Length = 548 Score = 26.9 bits (59), Expect = 7.6 Identities = 24/134 (17%), Positives = 48/134 (35%), Gaps = 23/134 (17%) Query: 233 IKQSYGNPIIKNRQKSIARS-RIRH---KMMEATSRAT-----------IIITNPTHYAL 277 + S G+ ++ N +I ++H KMM ++ ++I L Sbjct: 52 LVDSLGDIVVTNDCATILDKIDLQHPAAKMMVEVAKTQDKEAGDGTTTAVVIAG----EL 107 Query: 278 ---ALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAI 334 A + +N P ++ KG L A+K ++I E I + + I Sbjct: 108 LRKAEELL-DQNIHPSIITKGYALAAEKAQEILDEIAIRVDPDDEETLLKIAATSITGKN 166 Query: 335 PPVFYKAVAQLIYK 348 + +A+L + Sbjct: 167 AESHKELLAKLAVE 180 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.324 0.137 0.389 Gapped Lambda K H 0.267 0.0670 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,884,987 Number of extensions: 130547 Number of successful extensions: 614 Number of sequences better than 10.0: 1 Number of HSP's gapped: 599 Number of HSP's successfully gapped: 35 Length of query: 354 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 261 Effective length of database: 3,438,538 Effective search space: 897458418 Effective search space used: 897458418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 57 (25.9 bits)