Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate GFF1141 Psest_1174 Hemoglobin-like flavoprotein
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__psRCH2:GFF1141 Length = 392 Score = 77.8 bits (190), Expect = 4e-19 Identities = 68/211 (32%), Positives = 101/211 (47%), Gaps = 21/211 (9%) Query: 132 LDFLPGQYA--RLSVPGTDSWRSYSF-ANLPGNHLQFLVRLLPDGVMSNYLRERCQVGDE 188 +DF+PGQY RL + G + R+YS A G + V+ P GV+SN L + + G Sbjct: 184 MDFVPGQYIGLRLEIDGKEVRRNYSLSAASNGREYRISVKREPGGVVSNALHDMPK-GAT 242 Query: 189 LLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRGAEDLC 248 L + AP G F L+ +PLVL++GG G++ L ML+Q A+ +PVH + R A Sbjct: 243 LELFAPAGEFTLQPGDKPLVLISGGVGITPTLAMLEQALASA--RPVHFIHCARNAGVHA 300 Query: 249 EAARIRAYAAKIPNLR-------YTEVLSAPSEEWSGKRGYLTEHFDLAEL--RDGSADM 299 + A A + L+ ++ SAP G L+E LAE D D Sbjct: 301 FRRSVDALAERHAQLKRFYCYEEHSNTASAPDAV-----GRLSER-QLAEWLPADRDVDA 354 Query: 300 YLCGPPPMVESIQQWLADQALDGVQLYYEKF 330 Y GP P + ++++ L + Q YE F Sbjct: 355 YFLGPKPFMAAVRRQLKALGVPEQQTRYEFF 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: 318 Number of extensions: 18 Number of successful extensions: 3 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