Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate Echvi_4494 Echvi_4494 Hemoglobin-like flavoprotein
Query= reanno::WCS417:GFF4631 (335 letters) >FitnessBrowser__Cola:Echvi_4494 Length = 402 Score = 70.9 bits (172), Expect = 5e-17 Identities = 57/182 (31%), Positives = 86/182 (47%), Gaps = 15/182 (8%) Query: 133 DFLPGQYARL--SVPGTDSW--RSYSFANLPGNHLQFLVRLLPD-----GVMSNYLRERC 183 +F PGQY L S+PGTD R+YS ++ GN + + + G++SNYL ++ Sbjct: 184 EFTPGQYISLTLSIPGTDHLHTRNYSLSDY-GNKEALRISVKRESGKYKGLVSNYLHDQV 242 Query: 184 QVGDELLMEAPLGAFYLRHVTQPLVLVAGGTGLSALLGMLDQLAANGCEQPVHLYYGVRG 243 GD L + P G FYL PLV +A G G++ L+ M L G E+ + + Sbjct: 243 GEGDILSLGMPSGEFYLNSNKGPLVFLAAGVGITPLISMYKSL--KGSEREIVFVQCAKN 300 Query: 244 AEDLCEAARIRAYAAKIPNLRYTEVLSAP-SEEWSGKRGYLTEHFDLAELRDGSADMYLC 302 +E A R + K N+ + P S + +GYLT L +D+Y+C Sbjct: 301 SES--HAFRNEIESQKTDNVTSVVIYEEPLSNDIFDFKGYLTSKVLNDILPSSPSDVYMC 358 Query: 303 GP 304 GP Sbjct: 359 GP 360 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: 290 Number of extensions: 16 Number of successful extensions: 2 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: 402 Length adjustment: 30 Effective length of query: 305 Effective length of database: 372 Effective search space: 113460 Effective search space used: 113460 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