Align α-hydroxy-γ-carboxymuconate ε-semialdehyde dehydrogenase subunit (EC 1.1.1.312) (characterized)
to candidate WP_011426140.1 RHE_RS14800 Gfo/Idh/MocA family oxidoreductase
Query= metacyc::MONOMER-8501 (319 letters) >NCBI__GCF_000092045.1:WP_011426140.1 Length = 353 Score = 70.1 bits (170), Expect = 8e-17 Identities = 52/171 (30%), Positives = 76/171 (44%), Gaps = 12/171 (7%) Query: 3 KTIKVALAGAGAFGIKHLDGIKNIDGVEVVSLVGRRFDQTKEVADKYGIKHVATDLAESL 62 K I+V +AG G G H N G E++ LV R + + Y + D +L Sbjct: 5 KPIRVLVAGLGNMGRSHALAYHNDPGFEIIGLVNRSLAKLEPELRAYTVH---PDFMTAL 61 Query: 63 ALPEVDAVILCTPTQMHAEQAIACMKAGKHVQVEIPLADALKDAQEVAELQKQTGLVAMV 122 A + D + T + HA+ A+A +AG HV VE PLA + DA+ V K+ G ++ Sbjct: 62 AELKPDLCSINTYSDSHADYAVAAFEAGCHVFVEKPLATTVADAERVVAAAKKAGRKLVI 121 Query: 123 GHTRRFNPSHQWVHKKIEAGEFNIQQMDVQTYFFRRTNMNALGQARSWTDH 173 G+ R +PS W EA + Y F R N+N +W H Sbjct: 122 GYILRHHPS--WTKLIEEARKLG------PPYVF-RMNLNQQSSGPTWATH 163 Lambda K H 0.320 0.134 0.392 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: 231 Number of extensions: 11 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: 319 Length of database: 353 Length adjustment: 28 Effective length of query: 291 Effective length of database: 325 Effective search space: 94575 Effective search space used: 94575 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 Apr 09 2024. 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