RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780812|ref|YP_003065225.1| uroporphyrinogen decarboxylase [Candidatus Liberibacter asiaticus str. psy62] (346 letters) >1r3s_A URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyrinogen decarboxylase coproporphyrinogen, X-RAY crystallography, lyase; HET: 1CP; 1.65A {Homo sapiens} (A:) Length = 367 Score = 250 bits (639), Expect = 2e-67 Identities = 124/346 (35%), Positives = 181/346 (52%), Gaps = 9/346 (2%) Query: 5 KQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIR 64 L G + P+W MRQAGRYLPE+R+ R +F C +PE ELTLQP+R Sbjct: 16 NDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAAQ-DFFSTCRSPEACCELTLQPLR 74 Query: 65 RYNFDAAILFSDILVIADALGRNVRFVENEGPRM-DPITTQEIYLLNPNIDLFLNYLLPI 123 R+ DAAI+FS ILV+ ALG V V +GP +P+ ++ + ++ + L + Sbjct: 75 RFPLDAAIIFSGILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYV 134 Query: 124 FQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDF 183 FQ+I++ R++L + LIGF GAPWT+ +YM+ GG Q + + YQ +A + LL Sbjct: 135 FQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRI 194 Query: 184 LSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK-- 241 L+D YL+ Q+ AG +Q+F++HAG LG F +A + + V+ + A Sbjct: 195 LTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLA 254 Query: 242 ---FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALEL-QKEGPVQGNLDPMRLVVG 297 I FAK + L +GLDW+V A E K +QGNLDP L Sbjct: 255 PVPMIIFAKDGHFAL-EELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYAS 313 Query: 298 NQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343 + + V +LD G +I NLGHG+ P +DP++V V V Sbjct: 314 EEEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHK 359 >2eja_A URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.90A {Aquifex aeolicus} (A:) Length = 338 Score = 246 bits (628), Expect = 3e-66 Identities = 112/341 (32%), Positives = 187/341 (54%), Gaps = 12/341 (3%) Query: 5 KQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIR 64 +L L+G I P+WLMRQAGRY+PEYR+IR + KNFL++C + E++L P++ Sbjct: 4 NDLLLRSLRGEPIGRFPVWLMRQAGRYMPEYRKIRNRVKNFLELCKNVDLATEISLLPLK 63 Query: 65 RYNFDAAILFSDILVIADALGRNVRFVENEGPRM-DPITTQEIYLLNPNIDLFLNYLLPI 123 DA I+FSDILV + LG V FVE EGP++ ++ +P+ + Sbjct: 64 ILGVDAIIIFSDILVPLEPLGVKVEFVEGEGPKLSWSGKVSDLKKYDPSQ------NAYV 117 Query: 124 FQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDF 183 ++ I ++ + + + +IGF GAP+T+ SY+I GG KD ++F ++N + + L+D Sbjct: 118 YEIIKRVK-EAQDEVPVIGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDI 176 Query: 184 LSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFI 243 L++ YL QI AG DV+QIFD+ L ++ Y V +IS + + + + I Sbjct: 177 LTETVLAYLKEQIKAGADVVQIFDSWVNNLSLEDYGEYVYPYVNYLISEL-KDFSDTPVI 235 Query: 244 SFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMID 303 F +G+ + + ++A+ +DWSV + ++ QGNL+P L +V+ + Sbjct: 236 YFFRGSSSFI-DLAVDYRADALSVDWSVDIPELFKIYD-KGFQGNLEPAVLYASEEVIEE 293 Query: 304 GVNAILDVLGSGP-FIFNLGHGITPQVDPKNVLDLVKTVRS 343 +L + ++FNLGHG+ P ++ + V LV V+S Sbjct: 294 KTLGLLRRIPVKTRYVFNLGHGLAPDMELEKVKYLVDLVKS 334 >1j93_A UROD, uroporphyrinogen decarboxylase; beta barrel, plastidial enzyme, crystallographic dimer, lyase; 2.30A {Nicotiana tabacum} (A:) Length = 353 Score = 243 bits (620), Expect = 3e-65 Identities = 98/345 (28%), Positives = 177/345 (51%), Gaps = 4/345 (1%) Query: 1 MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTL 60 +N + +L+ ++G + PP+WLMRQAGRY+ Y+ + +K+ F D + VE++L Sbjct: 8 INATQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISL 67 Query: 61 QPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMD-PITTQEIYLLNPNIDLFLNY 119 QP + + D ILFSDIL + ++ +GP + P+ T + + Sbjct: 68 QPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAA-DVEKVREFIPEKS 126 Query: 120 LLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNW 179 + + ++++ILRK++ N ++GF GAP+T+ASY++ GG K+ + + A+ + + Sbjct: 127 VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 186 Query: 180 LLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPN 239 LL + A+Y+ Q +G +QIFD+ A L +FE ++ + +I+ +V+ +PN Sbjct: 187 LLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN 246 Query: 240 AKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALEL-QKEGPVQGNLDPMRLVVGN 298 I +A G+G + LT + + LDW+V ++ +QGN+DP L Sbjct: 247 LPLILYASGSGGL-LERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSK 305 Query: 299 QVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343 + + + +N + G G I NLGHGI +N + + Sbjct: 306 EFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG 350 >2inf_A URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel, eight parallel beta strands surrounded by eight alpha helices, lyase; 2.30A {Bacillus subtilis} (A:1-330) Length = 330 Score = 241 bits (615), Expect = 1e-64 Identities = 108/325 (33%), Positives = 167/325 (51%), Gaps = 12/325 (3%) Query: 5 KQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIR 64 + L+ +G + P+W MRQAGR PEYR++++K+ ++ + PE +T P+ Sbjct: 14 NETFLKAARGEKADHTPVWYMRQAGRSQPEYRKLKEKY-GLFEITHQPELCAYVTRLPVE 72 Query: 65 RYNFDAAILFSDILVIADALGRNVRFVENEGPRMD-PITTQEIY--LLNPNIDLFLNYLL 121 +Y DAAIL+ DI+ ++G +V GP +D PI + L + + + Y Sbjct: 73 QYGVDAAILYKDIMTPLPSIGVDVEIKNGIGPVIDQPIRSLADIEKLGQIDPEQDVPY-- 130 Query: 122 PIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLL 181 + ++I +L + N + LIGF GAP+T+ASYM GG K++ + + F Y A+N L+ Sbjct: 131 -VLETIKLLVNEQLN-VPLIGFSGAPFTLASYMTEGGPSKNYNKTKAFMYSMPDAWNLLM 188 Query: 182 DFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK 241 L+D+ Y+ AQI AG IQIFD+ G L + ++ Y + RI S + N Sbjct: 189 SKLADMIIVYVKAQIKAGAKAIQIFDSWVGALNQADYRTYIKPVMNRIFSEL--AKENVP 246 Query: 242 FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVM 301 I F GA ++ + +GLDW + + A VQGNLDP L+ +V+ Sbjct: 247 LIMFGVGASHLAG-DWHDLPLDVVGLDWRLGIDEARSKGITKTVQGNLDPSILLAPWEVI 305 Query: 302 IDGVNAILDVLGSGP-FIFNLGHGI 325 ILD FIFNLGHG+ Sbjct: 306 EQKTKEILDQGMESDGFIFNLGHGV 330 >3cyv_A URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta barrel, cytoplasm, lyase, porphyrin biosynthesis; 2.80A {Shigella flexneri} (A:) Length = 354 Score = 234 bits (598), Expect = 1e-62 Identities = 115/343 (33%), Positives = 176/343 (51%), Gaps = 3/343 (0%) Query: 4 RKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPI 63 + + L L ++ P+W+MRQAGRYLPEY+ R + +F+ +C E E+TLQP+ Sbjct: 5 KNDRYLRALLRQPVDVTPVWMMRQAGRYLPEYKATRAQAGDFMSLCKNAELACEVTLQPL 64 Query: 64 RRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPI 123 RRY DAAILFSDIL + DA+G + F EGPR T + + I + L + Sbjct: 65 RRYPLDAAILFSDILTVPDAMGLGLYFEAGEGPRFTSPVTCKADVDKLPIPDPEDELGYV 124 Query: 124 FQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDF 183 ++ +R +L + LIGF G+PWT+A+YM+ GG K + Y + +A + LLD Sbjct: 125 MNAVRTIRHELKGEVPLIGFSGSPWTLATYMVEGGSSKAFTVIKKMMYADPQALHALLDK 184 Query: 184 LSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK-F 242 L+ YL AQI AG + IFDT G L +++ ++ + +I+ + R+ + Sbjct: 185 LAKSVTLYLNAQIKAGAQAVMIFDTWGGVLTGRDYQQFSLYYMHKIVDGLLRENDGRRVP 244 Query: 243 ISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEG-PVQGNLDPMRLVVGNQVM 301 ++ G T +A+GLDW+ ++ A +QGN+DP L + Sbjct: 245 VTLFTKGGGQWLEAMAETGCDALGLDWTTDIADARRRVGNKVALQGNMDPSMLYAPPARI 304 Query: 302 IDGVNAILDVLGSGP-FIFNLGHGITPQVDPKNVLDLVKTVRS 343 + V IL G G +FNLGHGI V P++ V+ V Sbjct: 305 EEEVATILAGFGHGEGHVFNLGHGIHQDVPPEHAGVFVEAVHR 347 >1t7l_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; TIM barrel, methyltetrahydrofolate, zinc; 2.00A {Thermotoga maritima} PDB: 3bq5_A 3bq6_A 1xdj_A 1xr2_A* 1xpg_A* (A:392-766) Length = 375 Score = 126 bits (316), Expect = 4e-30 Identities = 36/363 (9%), Positives = 89/363 (24%), Gaps = 36/363 (9%) Query: 1 MNERKQKILE-VLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNF------LDMCYTPE 53 R+++ E P++ G + + + K + + Sbjct: 22 SFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIK 81 Query: 54 YTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNI 113 ++ ++ D + ++ P I Sbjct: 82 EQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPII 141 Query: 114 DLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQN 173 + P+ I + + G P T+ S+ I + Sbjct: 142 YGTVTRPEPMTLKE-ITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPERE--------- 191 Query: 174 SRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHE---FENYAARSVGRII 230 + ++ E + AG+ ++QI + + + Y ++ Sbjct: 192 ------IAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFN 245 Query: 231 SAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEG------P 284 A + + Y + + I ++ S + + Sbjct: 246 LAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQI 305 Query: 285 VQGNLDPMRLVVGN-QVMIDGVNAILDVLGSGPFIFNLGHGI---TPQVDPKNVLDLVKT 340 G D V + M + V +L VL N G+ ++ ++V Sbjct: 306 GVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVAL 365 Query: 341 VRS 343 + Sbjct: 366 AKE 368 >1u1j_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; methionine, synthase, methyltetrahydrofolate; HET: C2F; 2.40A {Arabidopsis thaliana} (A:1-10,A:129-393) Length = 275 Score = 124 bits (313), Expect = 1e-29 Identities = 22/227 (9%), Positives = 51/227 (22%), Gaps = 21/227 (9%) Query: 122 PIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLL 181 + + + P + + + + LL Sbjct: 18 KAVNEYKEAKAL---GVDTVPVLVGPVSYLLLSKAAKGVDK--------SFELLS---LL 63 Query: 182 DFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK 241 + + E + AG IQ+ + E + + + S + Sbjct: 64 PKILPIYKEVITELKAAGATWIQLDEPVLVXDLEGQKLQAFTGAYAELESTLSGLNVLV- 122 Query: 242 FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGP-----VQGNLDPMRLVV 296 FA K L A G D ++ P G +D + Sbjct: 123 ETYFADIPAEAYKTLTSLKGVTAFGFDLVRGTKTLDLVKAGFPEGKYLFAGVVDGRNIWA 182 Query: 297 GNQVMI-DGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVR 342 + + A+ ++G + + + + Sbjct: 183 NDFAASLSTLQALEGIVGKDKLVVSTSCSLLHTAVDLINETKLDDEI 229 >2nq5_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans} (A:1-66,A:130-390) Length = 327 Score = 121 bits (305), Expect = 1e-28 Identities = 27/228 (11%), Positives = 52/228 (22%), Gaps = 32/228 (14%) Query: 122 PIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLL 181 + R+ + + P T + ++ A + Sbjct: 73 RLLDLYLEAREVVGD--KAKPVITGPITYVALS--------------TGVEDFTA---AV 113 Query: 182 DFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK 241 L + + + AG IQ+ + ++ A V K Sbjct: 114 KSLLPLYKQVFTELVKAGASYIQVDEPIFVTDEGKDYLQAAKAVYAYFAKEVPDA----K 169 Query: 242 FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKE------GPVQGNLDPMRLV 295 FI G + +A GLD+ L LE K G +D + Sbjct: 170 FIFQTYFEGLIDSQVLSQLPVDAFGLDFVYGLEENLEAIKTGAFKGKEIFAGVIDGRNIW 229 Query: 296 VGNQVMIDGVNAILDVLGSGP-FIFNLGHGITPQVDPKNVLDLVKTVR 342 + V + + + + V Sbjct: 230 SSDFVKT--SALLETIEEQSAALTIQPSCSLLHVPVTTKNETDLDPVL 275 >2nq5_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans} (A:415-755) Length = 341 Score = 116 bits (291), Expect = 4e-27 Identities = 44/332 (13%), Positives = 98/332 (29%), Gaps = 36/332 (10%) Query: 32 LPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFV 91 P+ R+IR+ + + + I R+ L D+LV + ++ Sbjct: 11 FPQSREIRRTRLAWKRGDISDAEYKQFIQAEIERWIRIQEDLDLDVLVHGEFERVDMVEF 70 Query: 92 ENEGPRMDPITTQEI-------YLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFC 144 + T + P I + +L PI ++ + L + + G Sbjct: 71 FGQKLAGFTTTKFGWVQSYGSRAVKPPIIYGDVQHLEPITVEETVYAQSLTDR-PVKGML 129 Query: 145 GAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQ 204 P T+ ++ I L + + + + +AG+ +IQ Sbjct: 130 TGPITITNWSFERTDIPRDQ---------------LFNQIGLAIKDEIKLLENAGIAIIQ 174 Query: 205 IFDTHAGCLGE---HEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYM-LKNYRRLT 260 + + + + Y +V A + + + + + + R Sbjct: 175 VDEAALREGLPLRKSKQKAYLDDAVHAFHIATSSVKDETQIHTHMCYSKFDEIIDAIRAL 234 Query: 261 DSNAIGLDWSVPLSFALELQKEGP-----VQGNLDPMRLVVGN-QVMIDGVNAILDVLGS 314 D++ I ++ S +E + G D V + ++ + L L Sbjct: 235 DADVISIETSRSHGDIIESFETAVYPLGIGLGVYDIHSPRVPTKEEVVANIERPLRQLSP 294 Query: 315 GPFIFNLGHGI---TPQVDPKNVLDLVKTVRS 343 F N G+ + LV + Sbjct: 295 TQFWVNPDCGLKTRQEPETIAALKVLVAATKE 326 >2ash_A Queuine tRNA-ribosyltransferase; TM1561, tRNA-guanine, structural genomics, joint center for structural genomics, JCSG; 1.90A {Thermotoga maritima} (A:1-102,A:135-381) Length = 349 Score = 26.8 bits (59), Expect = 4.6 Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 3/51 (5%) Query: 178 NWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGR 228 W L+D + QI G D+ +FD C + R Sbjct: 93 GWKRPILTDSPEISMEVQIALGSDICMVFD---HCPVPDADYEEVKEATER 140 >2bh9_A G6PD, glucose-6-phosphate 1-dehydrogenase; oxidoreductase, oxidoreductase (CHOH(D)-NADP), carbohydrate metabolism, glucose metabolism; HET: NAP; 2.5A {Homo sapiens} PDB: 2bhl_A* 1qki_A* (A:1-178) Length = 178 Score = 26.0 bits (57), Expect = 7.7 Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 1/40 (2%) Query: 114 DLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASY 153 DL + P + LP + ++G+ + TVA Sbjct: 16 DLAKKKIYPTIWWL-FRDGLLPENTFIVGYARSRLTVADI 54 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.324 0.142 0.428 Gapped Lambda K H 0.267 0.0480 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 2,747,089 Number of extensions: 130151 Number of successful extensions: 325 Number of sequences better than 10.0: 1 Number of HSP's gapped: 302 Number of HSP's successfully gapped: 17 Length of query: 346 Length of database: 4,956,049 Length adjustment: 89 Effective length of query: 257 Effective length of database: 1,947,404 Effective search space: 500482828 Effective search space used: 500482828 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: 41 (22.0 bits) S2: 55 (25.6 bits)