Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate WP_078210972.1 BXU11_RS03085 SDR family oxidoreductase
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >NCBI__GCF_002017945.1:WP_078210972.1 Length = 328 Score = 111 bits (277), Expect = 2e-29 Identities = 86/280 (30%), Positives = 131/280 (46%), Gaps = 31/280 (11%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVD--VKPADSFGDSLRATYGDRVLTVS 61 RL+ KV I+TGAA GIG A A R EGA V+ D K + ++ A G +VL V Sbjct: 49 RLKGKVIIITGAARGIGRATAIRASKEGASVVIADWLEKEGMATAKTIEAN-GGKVLFVK 107 Query: 62 ADVTRRDDIQRIVASTLERFGQIDILFNNAALFD--------------------MRPILE 101 D+ +D ++VA T+++FG++D NA + D + + Sbjct: 108 TDIRSTEDCNKLVAETIKKFGKLDGAVLNAGVMDGIHSGDPLDYDKQTALLPAAVDAATD 167 Query: 102 ESWDVFDRLFAVNVKGMFFLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKA 161 E WD + VN G F M++V ++++++G GG ++ + S AG G A Y A+K Sbjct: 168 EYWDF---VIDVNTTGTFKSMRSVLKQLLKEGKGGALVTVGSIAGLTGLAGNPAYVASKY 224 Query: 162 AVLSYTQSAALALAPHKINVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVP 221 AV T+SAA+ AP I VN + TPM ++ + R + E++ Sbjct: 225 AVNGLTKSAAIDYAPFGIRVNSVNMAATKTPMTDKAFEFVKEVKKRGITGMGGAKTESLL 284 Query: 222 L-----GRMGVPDDLTGAALFLASADADYITAQTLNVDGG 256 + RM P + LFL S +A +T T DGG Sbjct: 285 MLNDSKHRMSTPWEQASVILFLLSDEASNLTGGTYATDGG 324 Lambda K H 0.321 0.135 0.393 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: 176 Number of extensions: 7 Number of successful extensions: 3 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: 260 Length of database: 328 Length adjustment: 26 Effective length of query: 234 Effective length of database: 302 Effective search space: 70668 Effective search space used: 70668 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 (21.9 bits) S2: 48 (23.1 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