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_RS03830 BWI76_RS03830 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component
Query= SwissProt::A4IT51 (494 letters) >FitnessBrowser__Koxy:BWI76_RS03830 Length = 520 Score = 233 bits (594), Expect = 1e-65 Identities = 155/486 (31%), Positives = 248/486 (51%), Gaps = 17/486 (3%) Query: 7 TGAQYISGLKSRKPEIWLSGRRVINVCEEPVFKQPIREIARLYDMQHDPEYQDKITH-IC 65 TG +Y+ L+ + EI++ G RV +V P F+ +A++YD H PE QD + Sbjct: 15 TGEEYLKSLQDGR-EIYIYGERVKDVTTHPAFRNAAASVAQMYDALHKPELQDTLCWGTD 73 Query: 66 TETGERVSNAFLVPKSREDLLARRALFEVWARATFGLMGRTPDFLNVVLTSLYSNASFLE 125 T +G F V KS +DL +R W+R ++G MGRTPD+ +L +N F Sbjct: 74 TGSGGYTHKFFRVAKSADDLRQQRDAIAEWSRLSYGWMGRTPDYKAAFGCALGANPGFYG 133 Query: 126 KYNPQWAENIRAYYRYVRDNDLFLTHAIINPQNDRSKPSHEQQDTFTHLGVVRETPEGLI 185 Q+ +N R +Y +++ L+ HAI+NP DR KP+ E +D + L +ET G+I Sbjct: 134 ----QFEQNARDWYTRIQETGLYFNHAIVNPPIDRHKPADEVKDVYIKLE--KETDAGII 187 Query: 186 VRGAKMLATLAPITDEVIIYTFPGYKPGDER-YAVSFAIPIDTPGLRILCR---EPMQDG 241 V GAK++AT + +T +I G+ +A+ F P+D G++++ R E + Sbjct: 188 VSGAKVVATNSALTHYNMIGFGSAQVMGENPDFALMFVAPMDAEGVKLISRASYELVAGA 247 Query: 242 TRPLFDHPLASRFEEMDALLVFNDVLVPWDRVFIYNNVEAANLLYPKTGIAQQPAHQTGV 301 T +D+PL+SRF+E DA+LV ++VL+PW+ V IY + + + G A+ Q V Sbjct: 248 TGSPYDYPLSSRFDENDAILVMDNVLIPWENVLIYRDFDRCRRWTMEGGFARMYPLQACV 307 Query: 302 RGLIKLQFATEVAIRLADSIGVDVYLNVQNDLGELLQSVEAIRALLHLAEHELEVLPSGE 361 R +KL F T + R + G + VQ +LGE++ AL E +G Sbjct: 308 RLAVKLDFITALLKRSLECTGTLEFRGVQAELGEVVAWRNMFWALSDSMCAEATPWVNGA 367 Query: 362 VMPGWVPLETIRGLLPKLYPRAVEVLQIIGAGGLLMSPTGA-DFANPELAADMEKYYAGR 420 +P L+T R + P Y + +++ GL+ P+ A D NP++ + KY G Sbjct: 368 YLPDHAALQTYRVMAPMAYAKIKNIIERSVTSGLIYLPSSARDLNNPQINEYLAKYVRGS 427 Query: 421 IGVGGEERVRLFKLAWDLCGEAFGQRLLQYERFYTG--DPIRKRAI--FYNNIKRERTLV 476 G+ ER+++ KL WD G FG R YE Y+G D IR + + ++ ++ + Sbjct: 428 NGMDHVERIKILKLMWDAIGSEFGGRHELYEINYSGSQDEIRLQCLRQAQSSGNMDKMMA 487 Query: 477 MVDEAL 482 MVD L Sbjct: 488 MVDRCL 493 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: 586 Number of extensions: 41 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: 520 Length adjustment: 34 Effective length of query: 460 Effective length of database: 486 Effective search space: 223560 Effective search space used: 223560 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