Align α-hydroxy-γ-carboxymuconate ε-semialdehyde dehydrogenase subunit (EC 1.1.1.312) (characterized)
to candidate WP_011382702.1 AMB_RS01295 gfo/Idh/MocA family oxidoreductase
Query= metacyc::MONOMER-8501 (319 letters) >NCBI__GCF_000009985.1:WP_011382702.1 Length = 320 Score = 489 bits (1260), Expect = e-143 Identities = 238/316 (75%), Positives = 268/316 (84%) Query: 1 MSKTIKVALAGAGAFGIKHLDGIKNIDGVEVVSLVGRRFDQTKEVADKYGIKHVATDLAE 60 MSK + +AL GAGAFG+KHLD + IDG +VVSLV R D+ +E+A KYGI HVA DLAE Sbjct: 1 MSKPVNIALIGAGAFGVKHLDALSVIDGAQVVSLVSRPEDKPEEIAAKYGIPHVAHDLAE 60 Query: 61 SLALPEVDAVILCTPTQMHAEQAIACMKAGKHVQVEIPLADALKDAQEVAELQKQTGLVA 120 SLALP VDAVIL TPTQ+HA QA+AC+KAGKHV VEIP+AD L DA+ + LQK+TGLVA Sbjct: 61 SLALPHVDAVILTTPTQLHASQAMACLKAGKHVMVEIPMADNLADAEALVALQKKTGLVA 120 Query: 121 MVGHTRRFNPSHQWVHKKIEAGEFNIQQMDVQTYFFRRTNMNALGQARSWTDHLLWHHAA 180 M GHTRRFNPSHQWVH KI G FNIQQMDVQTYFFRRTN+NALGQ R WTDHLLWHHAA Sbjct: 121 MCGHTRRFNPSHQWVHNKITGGGFNIQQMDVQTYFFRRTNINALGQPRCWTDHLLWHHAA 180 Query: 181 HTVDLFAYQAGSPIVKANAVQGPIHKDLGIAMDMSIQLKAANGAICTLSLSFNNDGPLGT 240 HTVDLFAYQ G IV AN +QGPIH DLGIAMDMSIQLK++ GAICTLSLSFNN+GPLGT Sbjct: 181 HTVDLFAYQTGGEIVAANVLQGPIHPDLGIAMDMSIQLKSSTGAICTLSLSFNNEGPLGT 240 Query: 241 FFRYIGDTGTYVARYDDLFNGKEEKIDVSQVDVSMNGIELQDREFFAAIRERPRTNSSVQ 300 FFRYIGD+GTY+ARYDDLF+GK++ IDV++VDVSMNGIELQDREF AAIRE N+SV Sbjct: 241 FFRYIGDSGTYIARYDDLFDGKDQPIDVTKVDVSMNGIELQDREFLAAIREGREPNASVA 300 Query: 301 QVFNCYKVLHDLEQQL 316 +V CY+ LH LEQQL Sbjct: 301 KVLPCYRTLHALEQQL 316 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: 402 Number of extensions: 7 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: 319 Length of database: 320 Length adjustment: 28 Effective length of query: 291 Effective length of database: 292 Effective search space: 84972 Effective search space used: 84972 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: 48 (23.1 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