Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate H281DRAFT_01077 H281DRAFT_01077 benzoate/toluate 1,2-dioxygenase reductase subunit
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__Burk376:H281DRAFT_01077 Length = 340 Score = 238 bits (608), Expect = 1e-67 Identities = 131/334 (39%), Positives = 202/334 (60%), Gaps = 8/334 (2%) Query: 2 NHKVAFSFADGKTLFFPVGANEILLDAALRNGIKIPLDCREGVCGTCQGRCESGDYS--Q 59 ++ +A +F DG T F A E +LDAA R I +P+DC +GVCGTC+ R ESG Y Sbjct: 3 SYNIALNFEDGVTRFVECKAGEKVLDAAFRARINLPMDCSDGVCGTCKCRAESGRYDLGD 62 Query: 60 DYVDEEALSSLDLQQRKMLSCQTRVKSDATFYFDFDSSLCNAPGPVQVKGTVSAVEQVSA 119 DY+ E+AL+ + Q +L+CQ +SD S+ C + TV+ VE+ + Sbjct: 63 DYI-EDALTDDEKQSGLVLTCQMVPESDCVIAVPASSTACKTEQS-KFAATVTKVEKHND 120 Query: 120 STAILQVQLDQALD-FLPGQYARLSVPGTDSWRSYSFANLPG-NHLQFLVRLLPDGVMSN 177 + +L++ +D FL GQY + VPG+ RSYSF++LPG + + FL++ + GVMS Sbjct: 121 AAVVLEMDVDGTPPVFLAGQYVNIDVPGSGQHRSYSFSSLPGESKICFLIKKISGGVMST 180 Query: 178 YLRERCQVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHL 237 +L E Q G+++ + P+G FYLR V +PL+ +AGGTGL+ L ML+ LA +Q VHL Sbjct: 181 WL-ESAQPGNKVQLTGPMGTFYLRAVERPLLFLAGGTGLAPFLSMLEVLARANSQQKVHL 239 Query: 238 YYGVRGAEDLCEAARIRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAELRDGSA 297 YGV DL I+AY ++PN ++ V++A +E ++G++T+H + DG Sbjct: 240 IYGVTRDLDLVLVEDIQAYTLRLPNFTFSTVVAA-TESVHPRKGWVTQHMPAECINDGDV 298 Query: 298 DMYLCGPPPMVESIQQWLADQALDGVQLYYEKFT 331 D+YLCGPPPMV++++Q+ + ++ +YEKFT Sbjct: 299 DVYLCGPPPMVDAVRQYFDENGVEPASFHYEKFT 332 Lambda K H 0.320 0.136 0.412 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: 319 Number of extensions: 11 Number of successful extensions: 5 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: 335 Length of database: 340 Length adjustment: 28 Effective length of query: 307 Effective length of database: 312 Effective search space: 95784 Effective search space used: 95784 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 (21.8 bits) S2: 49 (23.5 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