Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_043919311.1 jaqu_RS12410 L-iditol 2-dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000877395.1:WP_043919311.1 Length = 256 Score = 145 bits (365), Expect = 1e-39 Identities = 89/252 (35%), Positives = 139/252 (55%), Gaps = 6/252 (2%) Query: 5 TGRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVT 64 TGRL GK LIT AA+GIGRA E + REGA+V DI + + A+ G ++DVT Sbjct: 2 TGRLRGKGALITGAARGIGRAFAEAYIREGAQVCIADIDRDAVIGTANEIGASPIVMDVT 61 Query: 65 DDDAIKALV----AKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 D D+I A +G +++L N A A +++ D + F++N + T++AV Sbjct: 62 DQDSIDAATDAAEENLGGIEILINNAALFTADPLVDIDRADYARVFDVNVAGVLFTMQAV 121 Query: 121 LPGMLAK-KAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAI 179 M+A + G I+N+AS A +G Y ASKAAV+ LT+S + + GI NAI Sbjct: 122 ARRMIAAGRRGRIINMASQAGR-RGEPLVAVYCASKAAVISLTQSAGLNLIEHGINVNAI 180 Query: 180 CPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESN 239 PG ++ + + A+ G + E +A A P GR+G+A ++ +A++LASDE++ Sbjct: 181 APGVVDGAHWDGVDAQFARLEGLAPGEKKAQVGASVPYGRMGRASDLTGMAVFLASDEAD 240 Query: 240 FTTGSIHMIDGG 251 + + +DGG Sbjct: 241 YIVAQCYNVDGG 252 Lambda K H 0.316 0.129 0.359 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: 152 Number of extensions: 9 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: 254 Length of database: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 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