RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780775|ref|YP_003065188.1| undecaprenyl diphosphate synthase [Candidatus Liberibacter asiaticus str. psy62] (243 letters) >1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW fold for isoprenoid synthase, peptidoglycan synthesis, transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1 Length = 249 Score = 283 bits (726), Expect = 2e-77 Identities = 103/229 (44%), Positives = 147/229 (64%) Query: 11 PDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRR 70 P HI IIMDGNGRWA + +PR GH +G++ +I A+++G+K LT++AFS NW R Sbjct: 21 PKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENWSR 80 Query: 71 PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGL 130 P E++ L+KL FL L + N+KV IG L D + EA+++T+ NTGL Sbjct: 81 PKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGL 140 Query: 131 NLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGG 190 L A NY R EI A++ I + +SG + ++ + +YL T+++PDP+L+IRT G Sbjct: 141 TLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSG 200 Query: 191 EKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGGL 239 E+RLS+FL+WQ +YSEFVFI E+WPDF+ E ++ Y R RRFGGL Sbjct: 201 EERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNRHRRFGGL 249 >1ueh_A Undecaprenyl pyrophosphate synthase; parallel alpha-beta, rossmann-like fold, transferase; HET: OXN; 1.73A {Escherichia coli} SCOP: c.101.1.1 PDB: 1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A* 2e9c_A* 2e9d_A* 1x09_A* 1x08_A* Length = 253 Score = 222 bits (566), Expect = 7e-59 Identities = 89/233 (38%), Positives = 141/233 (60%) Query: 6 MSSSPPDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSI 65 + + H+ IIMDGNGRWA +G R GH+ G + V+ AA GI+ LT++AFS Sbjct: 13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSS 72 Query: 66 NNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTR 125 NW RP E+S L++L L SL ++N+++R+IG+ + + ++++E T Sbjct: 73 ENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTA 132 Query: 126 LNTGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLI 185 NTGL L IA NY R +I + ++ + + ++ G++ +D ++ +++ ++ DL+ Sbjct: 133 GNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLV 192 Query: 186 IRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGG 238 IRTGGE R+S+FLLWQ+AY+E F WPDF + F ALN + R+RRFGG Sbjct: 193 IRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRFGG 245 >2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL biogenesis/degradation, cell cycle, cell shape, cell division; HET: GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A* 2vg4_A Length = 284 Score = 219 bits (558), Expect = 5e-58 Identities = 88/228 (38%), Positives = 138/228 (60%) Query: 11 PDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRR 70 P+H+ I+MDGNGRWA RGL R GH+ G V +I A E+GIK L+++AFS NW+R Sbjct: 56 PNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKR 115 Query: 71 PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGL 130 E+ L+ + +++ +LKK +++R +G+R L ++ L AE+ T+ N + Sbjct: 116 SPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVI 175 Query: 131 NLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGG 190 + NY R EI+ A + I +++ +G + + S IA++L D+PD DL +RT G Sbjct: 176 TINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSG 235 Query: 191 EKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGG 238 E+R S+F+LWQ AY+E++F + WPD+ R + A +Y R RRFG Sbjct: 236 EQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGS 283 >2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A Length = 245 Score = 213 bits (543), Expect = 3e-56 Identities = 88/245 (35%), Positives = 140/245 (57%), Gaps = 10/245 (4%) Query: 5 MMSS---------SPPDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGI 55 M+S+ S H+ IIMDGNGRWA + R GH+KG++ +I A + Sbjct: 1 MLSATQPLSEKLDSTLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKL 60 Query: 56 KNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILC 115 + LT++AFS NW+RP SE+ L+K++K +LK + NNI+ R IG+ ++ Sbjct: 61 ECLTLYAFSTENWKRPKSEVDFLMKMLKKYLKDERSTYLDNNIRFRAIGDLEGFSKELRD 120 Query: 116 VLKEAEDQTRLNTGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLD 175 + + E+ TR +A NY S++E+SRA K++ + S +++ + LD Sbjct: 121 TILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPSNISLLESLENEIS-NRLD 179 Query: 176 TSDVPDPDLIIRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRR 235 T ++P+ DL++RTGGE RLS+FLLWQ +Y+E F P WPDF+ + + ++ + R R+ Sbjct: 180 TRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRVRK 239 Query: 236 FGGLS 240 FG L Sbjct: 240 FGELK 244 >2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan synthesis, cell WALL biogenesis/degradation, secreted, cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis} PDB: 2vfw_A* 2vg1_A* Length = 227 Score = 182 bits (463), Expect = 5e-47 Identities = 73/227 (32%), Positives = 113/227 (49%), Gaps = 7/227 (3%) Query: 11 PDHIGIIMDGNGRWAAARGLPRCA-GHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWR 69 P HI ++ DGN RWA + G + G+R G E++ E GI+ T++ S N + Sbjct: 3 PRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQ 62 Query: 70 RPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTG 129 R E++ L+++I +++ N+ VR +G+ + ++ L+ A + T Sbjct: 63 RDPDELAALIEIITDVVEE--ICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVAS 120 Query: 130 LNLFIAFNYSSRDEISRAIKNIFQDIESG----SVCSHDVDSSLIAKYLDTSDVPDPDLI 185 ++ +A Y R EI A++ + + V I++ L TS PDPDL+ Sbjct: 121 FHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLV 180 Query: 186 IRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLR 232 IRT GE+RLS FLLWQ AYSE F +WP F F AL Y+ R Sbjct: 181 IRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 227 >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 = 38.8 bits (90), Expect = 0.001 Identities = 50/274 (18%), Positives = 73/274 (26%), Gaps = 120/274 (43%) Query: 7 SSSPPDHIGIIMD----GNGRWA---AARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLT 59 +S PP I+ D G + + L + + N + A +V I Sbjct: 317 TSLPPS---ILEDSLENNEGVPSPMLSISNLTQEQVQ-DYVNKTNSHLPAGKQVEI---- 368 Query: 60 IFAFSINNWRR-------PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDD 112 S+ N + P S L Y L N+ +R L Sbjct: 369 ----SLVNGAKNLVVSGPPQS----L------------YGL---NLTLRKAKAPSGL--- 402 Query: 113 ILCVLKEAEDQTRLNTGLNLFIAFNYSSRD-EIS----------------RAIKNIFQDI 155 DQ+R I F S R + S A I +D+ Sbjct: 403 ---------DQSR--------IPF--SERKLKFSNRFLPVASPFHSHLLVPASDLINKDL 443 Query: 156 ESGSVCSHDVD---SSL-IAKYLDTSDVPDPDLIIRTGGEKRLSDFLLWQVAYSEFVFIP 211 ++V + I Y DT D D +R ++ + V Sbjct: 444 V-----KNNVSFNAKDIQIPVY-DTFDGSD----LRVLSGSISER-IVDCII-RLPVK-- 489 Query: 212 EYWPDFSRELFF---HALNQYNLRDRRF--GGLS 240 W F H L D F GG S Sbjct: 490 --WE---TTTQFKATHIL------D--FGPGGAS 510 Score = 36.1 bits (83), Expect = 0.008 Identities = 33/183 (18%), Positives = 58/183 (31%), Gaps = 37/183 (20%) Query: 73 SEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDIL-CVLKEAEDQTRLNTGLN 131 E + +L+ FL G+ + V +++ D +L L E E+ ++ Sbjct: 52 DEPTTPAELVGKFL--GY-------VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH 102 Query: 132 LFIAFNYSSRD----EISRAIKNIFQDIE-SGSVCSHDVDSSLIAKYLDTSDVPDPDLII 186 A D + IKN + +S+L V + + + Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF------RAVGEGNAQL 156 Query: 187 RT--GGEKRLSDFL-----LWQVAYSEFV--FIPEYWPDFSRELFFHALNQYNLRDRRFG 237 GG+ D+ L+Q Y V I FS E + ++ F Sbjct: 157 VAIFGGQGNTDDYFEELRDLYQT-YHVLVGDLI-----KFSAETLSELIRTTLDAEKVFT 210 Query: 238 -GL 239 GL Sbjct: 211 QGL 213 >2hj0_A Putative citrate lyase, ALFA subunit; alpha beta protein., structural genomics, PSI-2, protein structure initiative; HET: CIT; 2.70A {Streptococcus mutans UA159} Length = 519 Score = 36.0 bits (83), Expect = 0.009 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 3/53 (5%) Query: 37 RKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSEISE---LVKLIKSFL 86 R+G V N ++ A++GIK+++I SI N P+ + + + + S L Sbjct: 74 REGDYVMNMVLDEIAKMGIKDISIAPSSIANVHEPLIDHIKNGVVTNITSSGL 126 >1xr4_A Putative citrate lyase alpha chain/citrate-ACP transferase; the midwest center for structural genomics, MCSG, structural genomics; 2.37A {Salmonella typhimurium LT2} SCOP: c.124.1.2 c.124.1.2 Length = 509 Score = 34.1 bits (78), Expect = 0.028 Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%) Query: 37 RKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKS 84 R G +V N ++A AE+G ++LT+ + S+ + L++ IK+ Sbjct: 71 RGGDKVVNMVMAKLAEMGFRDLTLASSSLID------AHWPLIEHIKN 112 >1yj5_A 5' polynucleotide kinase-3' phosphatase catalytic domain; beta sandwich, P-loop, transferase; 2.80A {Mus musculus} SCOP: c.108.1.9 c.37.1.1 Length = 383 Score = 30.8 bits (69), Expect = 0.31 Identities = 21/168 (12%), Positives = 51/168 (30%), Gaps = 10/168 (5%) Query: 40 IEVFNEIVAA-AAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNI 98 EVF V A ++G+ + A R+P + + ++ + + Sbjct: 89 AEVFKGKVEAVLEKLGVPFQVLVATHAGLNRKP------VSGMWDHLQEQANEGIPISVE 142 Query: 99 KVRVIGNRLS-LDDDILCVLKEAEDQTRLNTGLNLFIAFNYSSRDEISRAIKNIFQDIES 157 +G+ L + K+ LN+ + F +E ++ + Sbjct: 143 DSVFVGDAAGRLANWAPGRKKKDFSCADRLFALNVGLPFATP--EEFFLKWPAARFELPA 200 Query: 158 GSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGGEKRLSDFLLWQVAYS 205 + L + P+P++++ G + + S Sbjct: 201 FDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVS 248 >3h4p_a Proteasome subunit beta; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii} Length = 219 Score = 28.8 bits (64), Expect = 1.2 Identities = 0/80 (0%), Positives = 0/80 (0%), Gaps = 8/80 (10%) Query: 50 AAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGN---- 105 A E + + ++ Sbjct: 166 AMERDTFSGNGISLAVITKDGVKIF- 224 Query: 106 --RLSLDDDILCVLKEAEDQ 123 Sbjct: 225 - 243 >1h0b_A Cellulase; endoglucanase, hydrolase; HET: EPE; 1.8A {Rhodothermus marinus} SCOP: b.29.1.11 Length = 256 Score = 28.7 bits (64), Expect = 1.3 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 6/54 (11%) Query: 24 WAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIF------AFSINNWRRP 71 A ARG R + +E E+ A + + ++ A I +P Sbjct: 186 DAVARGYIRPEWYLHAVETGFELWEGGAGLRSADFSVTVQKLAAALEIKRASQP 239 >1i60_A IOLI protein; beta barrel, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Bacillus subtilis} SCOP: c.1.15.4 PDB: 1i6n_A Length = 278 Score = 28.2 bits (62), Expect = 1.8 Identities = 9/59 (15%), Positives = 21/59 (35%), Gaps = 7/59 (11%) Query: 34 AGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSIN-------NWRRPVSEISELVKLIKSF 85 GH + I F ++ +G+K + + V ++EL + + + Sbjct: 77 KGHNEIITEFKGMMETCKTLGVKYVVAVPLVTEQKIVKEEIKKSSVDVLTELSDIAEPY 135 >2g8y_A Malate/L-lactate dehydrogenases; NAD, E.coli, structural genomics, PSI, protein structure initiative, midwest center for structural genomics; HET: NAD 1PE; 2.15A {Escherichia coli K12} Length = 385 Score = 27.4 bits (60), Expect = 2.7 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 9/68 (13%) Query: 1 MVASMMSSSPPDHIGIIMDGNGRWAAARGLPRCAGHRKGI----EVFNEIVAAAAEVGIK 56 + +S D I++ G R ++GI + I AA ++G+ Sbjct: 316 FAEWVKASPHDDDKPILLPGEWEVNTRR-----ERQKQGIPLDAGSWQAICDAARQIGMP 370 Query: 57 NLTIFAFS 64 T+ AF Sbjct: 371 EETLQAFC 378 >2v1l_A Hypothetical protein; pathogenicity island, unknown function; 2.13A {Vibrio cholerae} Length = 148 Score = 27.4 bits (61), Expect = 3.3 Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 1/32 (3%) Query: 199 LWQVAY-SEFVFIPEYWPDFSRELFFHALNQY 229 W + Y ++F ++ ++P+ R L F Sbjct: 71 QWCIEYITDFAYVGNHFPELERCLDFDFQRGD 102 >2w56_A VC0508; unknown function; 1.90A {Vibrio cholerae} PDB: 2w56_B Length = 147 Score = 27.2 bits (60), Expect = 3.5 Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 1/31 (3%) Query: 200 WQVAY-SEFVFIPEYWPDFSRELFFHALNQY 229 W + Y ++F ++ Y+P+ R L F Sbjct: 72 WSIEYITDFAYMGNYYPELERNLDFDFRVGQ 102 >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 = 27.3 bits (59), Expect = 3.6 Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 13/34 (38%) Query: 121 EDQT--RLNTGLNLFIAFNYSSRDEISR---AIK 149 E Q +L L L Y+ D+ S AIK Sbjct: 18 EKQALKKLQASLKL-----YA--DD-SAPALAIK 43 >3krb_A Aldose reductase; ssgcid, SBRI, emerald biostructures, university of washington, NIH, niaid, oxidoreductase, structural genomics; HET: NAP; 1.75A {Giardia lamblia atcc 50803} Length = 334 Score = 26.5 bits (57), Expect = 6.1 Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 3/48 (6%) Query: 118 KEAEDQTR--LNTGLNLF-IAFNYSSRDEISRAIKNIFQDIESGSVCS 162 + + L TG A+ Y + + I RA IF+D SG Sbjct: 38 EAVQTAVETALMTGYRHIDCAYVYQNEEAIGRAFGKIFKDASSGIKRE 85 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 0.322 0.139 0.413 Gapped Lambda K H 0.267 0.0442 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,214,894 Number of extensions: 104551 Number of successful extensions: 345 Number of sequences better than 10.0: 1 Number of HSP's gapped: 342 Number of HSP's successfully gapped: 29 Length of query: 243 Length of database: 5,693,230 Length adjustment: 90 Effective length of query: 153 Effective length of database: 3,511,270 Effective search space: 537224310 Effective search space used: 537224310 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: 55 (25.7 bits)