Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate WP_011384968.1 AMB_RS13020 KR domain-containing protein
Query= CharProtDB::CH_091826 (259 letters) >NCBI__GCF_000009985.1:WP_011384968.1 Length = 256 Score = 104 bits (260), Expect = 2e-27 Identities = 78/255 (30%), Positives = 130/255 (50%), Gaps = 11/255 (4%) Query: 5 AVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDATD 64 A+V GGG+ +GA + + G V + ++ + A ++ A +D TD Sbjct: 12 ALVTGGGRGIGAAIARQMLALGAVVTITGRDQGRLDAAATSLGCSAVA-------MDVTD 64 Query: 65 EASVE-ALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSREF 123 +++ ARA + G +LV +AG+AKAAP + L +D L+ +L G FLC++ Sbjct: 65 APAIQNGFARAA-QVQGPITILVNNAGIAKAAPFAKTDLGLWDDILRTDLTGAFLCTQAA 123 Query: 124 SKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLM 183 M+ G GR++ + S +G G + + Y AAK G +GLT++LA++LA +TV+++ Sbjct: 124 LPGMLEAGW-GRVVNVASTAGLTGLAYCAAYCAAKHGLIGLTRALAVELASKPVTVNAVC 182 Query: 184 LGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDKAA 243 G ++ + + K G TPEE V P KR ++V + + +A Sbjct: 183 PG-YTETDIVADTIANIVAKTGRTPEEALAGLVAANPQKRLIKPEEVAEAVAWLCLPGSA 241 Query: 244 YCTGQSINVTGGQVM 258 TGQSI V GG++M Sbjct: 242 SITGQSIAVAGGELM 256 Lambda K H 0.319 0.136 0.387 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: 183 Number of extensions: 11 Number of successful extensions: 4 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: 259 Length of database: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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 (21.7 bits) S2: 47 (22.7 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