Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate PP_0808 PP_0808 Flavohemoprotein
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__Putida:PP_0808 Length = 392 Score = 70.5 bits (171), Expect = 7e-17 Identities = 59/200 (29%), Positives = 89/200 (44%), Gaps = 7/200 (3%) Query: 136 PGQYA--RLSVPGTDSWRSYSFANL-PGNHLQFLVRLLPDGVMSNYLRERCQVGDELLME 192 PGQY +L + G + R+YS + L G + V+ G +SNYL + +VGD L + Sbjct: 188 PGQYIGLKLDIDGAEQRRNYSLSALCDGKEYRISVKREAGGKVSNYLHDELKVGDTLQLF 247 Query: 193 APLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRGAEDLCEAAR 252 P G F L +PLVL++GG G++ L ML AA + VH + R Sbjct: 248 PPAGDFTLAASDKPLVLISGGVGITPTLAMLQ--AALQTRREVHFIHCARNGAVHAFRDW 305 Query: 253 IRAYAAKIPNLRYTEVLSAPSEEWSGKRGYLTEHFDLAEL--RDGSADMYLCGPPPMVES 310 I AA+ P L+ + P + L LAE ++ D Y GP + + Sbjct: 306 IDGLAARHPQLKRFYCYAEPEGGAAADAVGLLSEDLLAEWLPQERDVDAYFLGPKGFMAA 365 Query: 311 IQQWLADQALDGVQLYYEKF 330 +++ L + Q YE F Sbjct: 366 VKRQLKGLGVPEQQSRYEFF 385 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: 341 Number of extensions: 17 Number of successful extensions: 1 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: 392 Length adjustment: 29 Effective length of query: 306 Effective length of database: 363 Effective search space: 111078 Effective search space used: 111078 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