RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780812|ref|YP_003065225.1| uroporphyrinogen decarboxylase [Candidatus Liberibacter asiaticus str. psy62] (346 letters) >gnl|CDD|178875 PRK00115, hemE, uroporphyrinogen decarboxylase; Validated. Length = 346 Score = 441 bits (1136), Expect = e-124 Identities = 143/343 (41%), Positives = 209/343 (60%), Gaps = 12/343 (3%) Query: 7 KILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRY 66 + L L+G ++ P+W+MRQAGRYLPEYR +R K +FL++C PE E+TLQP+RRY Sbjct: 7 RFLRALRGEPVDRTPVWMMRQAGRYLPEYRALRAKAGSFLELCKNPELAAEVTLQPVRRY 66 Query: 67 NFDAAILFSDILVIADALGRNVRFVENEGPRMD-PITTQE----IYLLNPNIDLFLNYLL 121 DAAILFSDIL DA+G ++ F E EGP D PI T+ + + +P D L Sbjct: 67 GVDAAILFSDILTPPDAMGLDLDFEEGEGPVFDNPIRTEADVEKLPVPDPEED-----LP 121 Query: 122 PIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLL 181 + +++ +LR++L + LIGF GAPWT+A+YM+ GG KD+ + + Y + LL Sbjct: 122 YVLEAVRLLRRELGGEVPLIGFAGAPWTLATYMVEGGGSKDYAKTKAMMYAEPELLHALL 181 Query: 182 DFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK 241 D L+D + YL AQI AG +QIFD+ AG L ++ + + RI++ ++R++P+ Sbjct: 182 DKLADATIAYLNAQIEAGAQAVQIFDSWAGALSPADYREFVLPYMKRIVAELKREHPDVP 241 Query: 242 FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQV 300 I F KGAG +L+ T ++ +GLDW+V L+ A + + +QGNLDP L+ + Sbjct: 242 VILFGKGAGELLEAMAE-TGADVVGLDWTVDLAEARRRVGDKKALQGNLDPAVLLAPPEA 300 Query: 301 MIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343 + + V AILD G IFNLGHGI P+ P+NV LV+ V Sbjct: 301 IEEEVRAILDGGGGPGHIFNLGHGILPETPPENVKALVEAVHE 343 >gnl|CDD|162374 TIGR01464, hemE, uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products. Length = 338 Score = 384 bits (988), Expect = e-107 Identities = 152/342 (44%), Positives = 211/342 (61%), Gaps = 9/342 (2%) Query: 7 KILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRY 66 L +G ++ PP+WLMRQAGRYLPEYR++R K +FL++C P+ VE+TLQPIRR+ Sbjct: 1 LFLRAAKGEEVDRPPVWLMRQAGRYLPEYRELRAKAPDFLELCRNPDLAVEVTLQPIRRF 60 Query: 67 NFDAAILFSDILVIADALGRNVRFVENEGPRM-DPITTQE--IYLLNPNIDLFLNYLLPI 123 DAAILFSDILV ALG +V FVE +GP + +PI T E L + + L Y+ Sbjct: 61 GVDAAILFSDILVPLQALGLDVDFVEGKGPVIPEPIRTPEDVERLKEFDPESELPYV--- 117 Query: 124 FQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDF 183 +++I +LR++LP + LIGF GAPWT+ASYMI GG KD + + F YQ + LL+ Sbjct: 118 YEAIKLLREELPGEVPLIGFAGAPWTLASYMIEGGGSKDFAKAKRFMYQEPEVLHALLNK 177 Query: 184 LSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFI 243 L+D + EYL+ Q+ AG +QIFD+ AG L +FE + + +II V+ + PN I Sbjct: 178 LTDATIEYLVEQVKAGAQAVQIFDSWAGALSPEDFEEFVLPYLKKIIEEVKARLPNVPVI 237 Query: 244 SFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFA-LELQKEGPVQGNLDPMRLVVGNQVMI 302 FAKGAG++L+ ++ +GLDW+V L A + +QGNLDP L + + Sbjct: 238 LFAKGAGHLLEELAETG-ADVVGLDWTVDLKEARKRVGPGVAIQGNLDPAVLYAPEEALE 296 Query: 303 DGVNAILDVL-GSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343 + V IL+ G +IFNLGHGI P P+NV LV+ V S Sbjct: 297 EKVEKILEAFGGKSRYIFNLGHGILPDTPPENVKALVEYVHS 338 >gnl|CDD|178052 PLN02433, PLN02433, uroporphyrinogen decarboxylase. Length = 345 Score = 281 bits (722), Expect = 2e-76 Identities = 119/331 (35%), Positives = 186/331 (56%), Gaps = 10/331 (3%) Query: 20 PPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILV 79 PP+WLMRQAGRY+ EYR++ KK+ +F + TP+ VE++LQP R + D ILFSDIL Sbjct: 13 PPVWLMRQAGRYMKEYRELCKKYPSFRERSETPDLAVEISLQPWRAFKPDGVILFSDILT 72 Query: 80 IADALGRNVRFVENEGPR-MDPITTQE-IYLLNPNIDLFLNYLLPIFQSISILRKKLPNH 137 A+G V+ +GP +PI ++E + L+P L + +++ ILRK++ N Sbjct: 73 PLPAMGIPFDIVKGKGPVIPNPIRSEEDVKRLHPLD--PEEKLPFVGEALKILRKEVGNE 130 Query: 138 ITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIH 197 ++GF GAPWT+A+Y++ GG K++ + A+ + LLD L+D EY+ QI Sbjct: 131 AAVLGFVGAPWTLATYIVEGGSSKNYKVIKKMAFTAPEVLHALLDKLTDAVIEYVDYQID 190 Query: 198 AGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYR 257 AG V+QIFD+ AG L +FE ++ + +I+ V+ ++P+ I +A G+G +L+ Sbjct: 191 AGAQVVQIFDSWAGHLSPVDFEEFSKPYLEKIVDEVKARHPDVPLILYANGSGGLLE--- 247 Query: 258 RLTDSNA--IGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGS 314 RL + IGLDW+V ++ A L + VQGN+DP L + + V ++ G Sbjct: 248 RLAGTGVDVIGLDWTVDMADARRRLGSDVAVQGNVDPAVLFGSKEAIEKEVRDVVKKAGP 307 Query: 315 GPFIFNLGHGITPQVDPKNVLDLVKTVRSEK 345 I NLGHG+ +NV R + Sbjct: 308 QGHILNLGHGVLVGTPEENVAHFFDVARELR 338 >gnl|CDD|180490 PRK06252, PRK06252, methylcobalamin:coenzyme M methyltransferase; Validated. Length = 339 Score = 55.7 bits (135), Expect = 2e-08 Identities = 87/382 (22%), Positives = 143/382 (37%), Gaps = 89/382 (23%) Query: 5 KQKILEVLQGNVINPPP---------IWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYT 55 K+++L L+G ++ P + LM G Y PE PE Sbjct: 6 KERLLNALKGKEVDRVPVICVTQTGTVELMDITGAYWPEAH-------------SDPEKM 52 Query: 56 VELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEG-----PRM--DPITTQEIYL 108 +L + F+A + + V A+A+G V + G P + PI Y Sbjct: 53 ADLAIAGYEVAGFEAVRVPFCMTVEAEAMGCEV----DMGTKDRQPSVTKYPIKKDVEYR 108 Query: 109 LNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISG--GFIKDHGQN 166 P+ L + + ++I IL++K+ + +I P ++AS + G F+K + Sbjct: 109 KLPDDLLEEGRIPTVLEAIKILKEKVGEEVPIIAGLTGPISLAS-SLMGPKNFLKWLIKK 167 Query: 167 RVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAG--CLGEHEFENYAAR 224 A++ LDF++D EY AQ+ AG DVI I D A LG FE + Sbjct: 168 PELAHE-------FLDFVTDFCIEYAKAQLEAGADVICIADPSASPELLGPKMFEEFVLP 220 Query: 225 SVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTD---------SNAIGLDWSVPLSF 275 + +II V KG +L LT + I +D V + Sbjct: 221 YLNKIIDEV-------------KGLPTILHICGDLTSILEEMADCGFDGISIDEKVDVKT 267 Query: 276 ALE-LQKEGPVQGNLDPMRLV----------VGNQVMIDGVNAILDVLGSGPFIFNLGHG 324 A E + + GN+ + + + DGV D+L P G G Sbjct: 268 AKENVGDRAALIGNVSTSFTLLNGTPEKVKAEAKKCLEDGV----DIL--AP-----GCG 316 Query: 325 ITPQVDPKNVLDLVKTVRSEKI 346 I P+ +N+ +V+ + Sbjct: 317 IAPKTPLENIKAMVEARKEYYA 338 >gnl|CDD|130530 TIGR01463, mtaA_cmuA, methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein. Length = 340 Score = 49.5 bits (118), Expect = 1e-06 Identities = 46/195 (23%), Positives = 73/195 (37%), Gaps = 32/195 (16%) Query: 24 LMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADA 83 LMR+ G PE E L + ++ +A D+ A+ Sbjct: 34 LMRECGATWPEAH-------------RDGEAMAHLAIAAYEKFGGEAVRPPFDLTTEAEC 80 Query: 84 LGRNVRFVENEGPRMDPITTQEIYLLNP-NIDLFLNYLLP------IFQSISILRKKLPN 136 +G + + GP P T+ N + NYLL + ++I ILR++ + Sbjct: 81 VGCEL----DYGPYAQPSVTKHPTPTNLADYRYPENYLLKPGRIPVVLEAIKILRERYGD 136 Query: 137 HITLIGFCGAPWTVASYMISG-GFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQ 195 +IG G P+T+A MI F+ + + +L+ D Y A Sbjct: 137 THPIIGPMGGPFTLAQLMIGVSEFLS-------WISTDPDYAKAVLELALDFVIAYAKAM 189 Query: 196 IHAGVDVIQIFDTHA 210 + AG DVI I D A Sbjct: 190 VEAGADVIAIADPFA 204 >gnl|CDD|163134 TIGR03098, ligase_PEP_1, acyl-CoA ligase (AMP-forming), exosortase system type 1 associated. This group of proteins contains an AMP-binding domain (pfam00501) associated with acyl CoA-ligases. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present next to a decarboxylase enzyme. A number of sequences from Burkholderia species also hit this model, but the genomic context is obviously different. The hypothesis of a constant substrate for this family is only strong where the exosortase context is present. Length = 515 Score = 29.0 bits (65), Expect = 1.8 Identities = 13/44 (29%), Positives = 20/44 (45%) Query: 78 LVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLL 121 L ++ ++R++ N G M T + PN LFL Y L Sbjct: 266 LDWPESAAPSLRYLTNSGGAMPRATLSRLRSFLPNARLFLMYGL 309 >gnl|CDD|181678 PRK09177, PRK09177, xanthine-guanine phosphoribosyltransferase; Validated. Length = 156 Score = 28.3 bits (64), Expect = 2.9 Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%) Query: 227 GRIISAVRRKYPNAKFIS-FAKGAG 250 G AVR YP A F + +AK AG Sbjct: 97 GGTARAVREMYPKAHFATVYAKPAG 121 >gnl|CDD|178627 PLN03078, PLN03078, Putative tRNA pseudouridine synthase; Provisional. Length = 513 Score = 27.9 bits (62), Expect = 3.6 Identities = 15/39 (38%), Positives = 17/39 (43%) Query: 214 GEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYM 252 GEH F NY ARS R + K N AK + M Sbjct: 234 GEHPFHNYTARSKYRKKLPGKHKQRNGAVSRRAKSSKEM 272 >gnl|CDD|184142 PRK13558, PRK13558, bacterio-opsin activator; Provisional. Length = 665 Score = 27.9 bits (62), Expect = 4.1 Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 2/25 (8%) Query: 82 DALGRNVRFVENEGPRMDPITTQEI 106 + LGRN RF+ +G + E+ Sbjct: 190 EVLGRNCRFL--QGEDTNEERVAEL 212 >gnl|CDD|130457 TIGR01390, CycNucDiestase, 2',3'-cyclic-nucleotide 2'-phosphodiesterase. 2',3'-cyclic-nucleotide 2'-phosphodiesterase is a bifunctional enzyme localized to the periplasm of Gram-negative bacteria. 2',3'-cyclic-nucleotide 2'-phosphodiesters are intermediates formed during the hydrolysis of RNA by the ribonuclease I, which is also found to the periplasm, and other enzymes of the RNAse T2 family. Bacteria are unable to transport 2',3'-cyclic-nucleotides into the cytoplasm. 2',3'-cyclic-nucleotide 2'-phosphodiesterase contains 2 active sites which catalyze the reactions that convert the 2',3'-cyclic-nucleotide into a 3'-nucleotide, which is then converted into nucleic acid and phosphate. Both final products can be transported into the cytoplasm. Thus, it has been suggested that 2',3'-cyclic-nucleotide 2'-phosphodiesterase has a 'scavenging' function. Experimental evidence indicates that 2',3'-cyclic-nucleotide 2'-phosphodiesterase enables Yersinia enterocolitica O:8 to grow on 2'3'-cAMP as a sole source of carbon and energy (PubMed:11160814). Length = 626 Score = 27.5 bits (61), Expect = 5.3 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%) Query: 195 QIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFI 243 Q+H + + G LG HEF NY + + I+A + NA + Sbjct: 75 QMHPVYKAMNLLKYDVGNLGNHEF-NYGLPFLKQAIAAAKFPIVNANVV 122 >gnl|CDD|152330 pfam11894, DUF3414, Protein of unknown function (DUF3414). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 764 to 2011 amino acids in length. This protein has a conserved LLG sequence motif. Length = 1611 Score = 27.3 bits (61), Expect = 6.1 Identities = 24/124 (19%), Positives = 42/124 (33%), Gaps = 22/124 (17%) Query: 6 QKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRR 65 +K L+ + G I+ P L A ++ +C P T TL+ +R Sbjct: 991 EKSLDSISGLNIDEAPPRLAELA-------------YQLLQKLCSNP-LTSGPTLRYLRS 1036 Query: 66 YNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQ 125 +F L S + + L + F + + I FLN + Q Sbjct: 1037 NDFLFRHLASLPFIDPNTLWDGLSFAADNKFFLSSSIGALIS--------FLNQRSWLLQ 1088 Query: 126 SISI 129 ++I Sbjct: 1089 YLAI 1092 >gnl|CDD|184632 PRK14336, PRK14336, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional. Length = 418 Score = 26.8 bits (59), Expect = 7.8 Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 3/27 (11%) Query: 226 VGRIISAVRRKYPNAKFISFAKGAGYM 252 VG+ IS +R+K+P F+ + G G M Sbjct: 83 VGQDISLIRKKFP---FVDYIFGPGSM 106 >gnl|CDD|178282 PLN02678, PLN02678, seryl-tRNA synthetase. Length = 448 Score = 26.6 bits (59), Expect = 9.3 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 8/60 (13%) Query: 130 LRKKLPNHITLIGFCGAPWTVASYMISGG---FIKDHGQNRVFAYQNSRAFNWLLDFLSD 186 KL NH+ L+ G T ++GG ++K G N N+ L FL Sbjct: 136 QEPKLKNHVDLVELLGIVDTERGADVAGGRGYYLKGAG-----VLLNQALINFGLAFLRK 190 >gnl|CDD|180592 PRK06498, PRK06498, isocitrate lyase; Provisional. Length = 531 Score = 26.5 bits (59), Expect = 9.6 Identities = 10/24 (41%), Positives = 14/24 (58%) Query: 160 IKDHGQNRVFAYQNSRAFNWLLDF 183 I++ N Y NS +FNW L+F Sbjct: 368 IREVVPNAKLVYNNSPSFNWTLNF 391 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.324 0.142 0.428 Gapped Lambda K H 0.267 0.0744 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,968,528 Number of extensions: 400947 Number of successful extensions: 837 Number of sequences better than 10.0: 1 Number of HSP's gapped: 824 Number of HSP's successfully gapped: 25 Length of query: 346 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 252 Effective length of database: 3,963,321 Effective search space: 998756892 Effective search space used: 998756892 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: 58 (26.1 bits)