Align Anthranilate 3-monooxygenase oxygenase component; 4-hydroxyphenylacetate 3-monooxygenase oxygenase component; 4 HPA 3-hydroxylase; Anthranilate 3-hydroxylase; Anthranilate hydroxylase; EC 1.14.14.8; EC 1.14.14.9 (characterized)
to candidate BWI76_RS15105 BWI76_RS15105 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
Query= SwissProt::A4IT51 (494 letters) >FitnessBrowser__Koxy:BWI76_RS15105 Length = 504 Score = 232 bits (591), Expect = 3e-65 Identities = 148/459 (32%), Positives = 235/459 (51%), Gaps = 13/459 (2%) Query: 3 MGIRTGAQYISGLKSRKPEIWLSGRRVINVCEEPVFKQPIREIARLYDMQHDPEYQDKIT 62 + + TG +++GL + EIW G +V NV P F+ IA+LYD HD +YQ +T Sbjct: 6 VSLPTGNDFLAGLNDGR-EIWAYGEKVDNVITHPAFRNSALSIAKLYDALHDEKYQAILT 64 Query: 63 HIC-TETGERVSNAFLVPKSREDLLARRALFEVWARATFGLMGRTPDFLNVVLTSLYSNA 121 C T +G F VP S +DL+ R WAR ++G +GR+PDF LT+L +N Sbjct: 65 TPCDTGSGGVTHPFFRVPHSVDDLIRDRDAIAQWARLSYGWLGRSPDFKASFLTTLGANP 124 Query: 122 SFLEKYNPQWAENIRAYYRYVRDNDLFLTHAIINPQNDRSKPSHEQQDTFTHLGVVRETP 181 E Y ++A+N R +Y+ ++ L+ HAIINP DR+ P + +D H V +E Sbjct: 125 ---EAYG-EYADNARHWYKRSQEELLYWNHAIINPPIDRNLPPDQIEDICIH--VEKECD 178 Query: 182 EGLIVRGAKMLATLAPITDEVIIYTFPGYKPGDERYAVSFAIPIDTPGLRILCREPMQDG 241 +G+IV GAK++AT + +T I + G +A+ +P++ PGL+++CR Sbjct: 179 DGVIVSGAKVVATGSALTHYNFIAHY-GLPVKKREFALVCTLPMNAPGLKLVCRPSYSLA 237 Query: 242 TRPL---FDHPLASRFEEMDALLVFNDVLVPWDRVFIYNNVEAANLLYPKTGIAQQPAHQ 298 + FD+PL+SR++E D + + + V +PW+ +FIY + A P +G + Sbjct: 238 AEKIGSPFDYPLSSRYDENDMIFILDKVKIPWENIFIYGDTAKAATFLPSSGFLHRSTFH 297 Query: 299 TGVRGLIKLQFATEVAIRLADSIGVDVYLNVQNDLGELLQSVEAIRALLHLAEHELEVLP 358 R +K+ F + I+ ++ GV + +Q +GE+L A+ Sbjct: 298 GVTRLAVKIDFICGLFIKGVEATGVADFRGIQTRVGEMLAWRNLFWAISDAMAKSPNPWH 357 Query: 359 SGEVMPGWVPLETIRGLLPKLYPRAVEVL-QIIGAGGLLMSPTGADFANPELAADMEKYY 417 +G ++P R + YPR E++ Q +G+ + ++ DFA PEL ++KY Sbjct: 358 NGALLPNLDYGLAYRWFMSLGYPRIREIIEQDLGSALIYINSHAKDFAAPELEPYLKKYM 417 Query: 418 AGRIGVGGEERVRLFKLAWDLCGEAFGQRLLQYERFYTG 456 G G+ ERV+L KL WD G F R YER YTG Sbjct: 418 RGSNGMDAVERVKLMKLIWDSVGTEFASRHELYERNYTG 456 Lambda K H 0.322 0.139 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 559 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 494 Length of database: 504 Length adjustment: 34 Effective length of query: 460 Effective length of database: 470 Effective search space: 216200 Effective search space used: 216200 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory