Align BadH (characterized)
to candidate WP_077275131.1 BW732_RS01515 glucose 1-dehydrogenase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_001998885.1:WP_077275131.1 Length = 261 Score = 137 bits (346), Expect = 2e-37 Identities = 87/252 (34%), Positives = 135/252 (53%), Gaps = 6/252 (2%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAEAVRC 62 L K AVITGG GIG A R +E K+ V + + A + A++ AGG AV+ Sbjct: 5 LNGKVAVITGGSKGIGTAISERLGKEKMKVVVNYHSDEAGANQAVEAVKAAGGDGIAVQA 64 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 ++ V + + G +D+ +NNAG + K +WER+I +NLTG Sbjct: 65 NVGSEEGVQKLVDVALSEYGTLDLWINNAGMENQCETHKLPLEDWERVINVNLTGVFLGT 124 Query: 123 HAVLPGMVER-RHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVN 181 A L VE + G I+NI+S ++ A Y+A KGG+ ++T+A E+A I VN Sbjct: 125 KAALSYFVENNKKGNIINISSVHEQIPWPTFAHYSASKGGVKLLTETVAMEYANRNIRVN 184 Query: 182 VVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFIT 241 + PG T + A+ A+PE+L + + IP+ R+G P+++A A A+ SD+A ++T Sbjct: 185 NIGPGAIKTPINAEKF---ADPEQL-QTTKETIPMQRIGNPEEVAAAAAWLASDEASYVT 240 Query: 242 GQVLSVSGGLTM 253 G L V GG+T+ Sbjct: 241 GITLFVDGGMTL 252 Lambda K H 0.318 0.135 0.398 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: 164 Number of extensions: 9 Number of successful extensions: 5 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: 255 Length of database: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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