Align Protein dhs-3; Alcohol dehydrogenase dhs-3; EC 1.1.1.1 (characterized)
to candidate WP_011384968.1 AMB_RS13020 KR domain-containing protein
Query= SwissProt::A5JYX5 (309 letters) >NCBI__GCF_000009985.1:WP_011384968.1 Length = 256 Score = 91.7 bits (226), Expect = 2e-23 Identities = 60/189 (31%), Positives = 88/189 (46%), Gaps = 7/189 (3%) Query: 39 VSGQTVLITGSGSGLGRLMAFEFGKLGARLVLWDINEQGNKETLKELEAMGVEAKAYTVD 98 ++G+ L+TG G G+G +A + LGA + + G + + A + A +D Sbjct: 7 LAGRHALVTGGGRGIGAAIARQMLALGAVVTI-----TGRDQGRLDAAATSLGCSAVAMD 61 Query: 99 LSEYKEINRTADLVKSEVGKVDILVNNAGIVTGKKLLQCPDELMVKTVSVNTNALFFTTK 158 +++ I G + ILVNNAGI + L + + F T+ Sbjct: 62 VTDAPAIQNGFARAAQVQGPITILVNNAGIAKAAPFAKTDLGLWDDILRTDLTGAFLCTQ 121 Query: 159 NFLPGMLESNKGHIVTIASMAGKCGVAGLVDYCASKHGAVGFNDSLASELYALKKDVKTT 218 LPGMLE+ G +V +AS AG G+A YCA+KHG +G +LA EL K V Sbjct: 122 AALPGMLEAGWGRVVNVASTAGLTGLAYCAAYCAAKHGLIGLTRALAVEL--ASKPVTVN 179 Query: 219 VVCPIYINT 227 VCP Y T Sbjct: 180 AVCPGYTET 188 Lambda K H 0.320 0.137 0.401 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: 184 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: 309 Length of database: 256 Length adjustment: 26 Effective length of query: 283 Effective length of database: 230 Effective search space: 65090 Effective search space used: 65090 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: 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