Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate AO353_24520 AO353_24520 short-chain dehydrogenase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24520 Length = 249 Score = 119 bits (298), Expect = 6e-32 Identities = 84/254 (33%), Positives = 137/254 (53%), Gaps = 17/254 (6%) Query: 12 GLRVLISGAAA--GIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGV-ADVSD 68 G +I+GAA+ GIG A A F GA V I D+D +A A + + H G+ A+V+D Sbjct: 5 GKVAIITGAASARGIGRATATTFAQQGARVVILDLDESAARDAAASLGEGHLGIGANVAD 64 Query: 69 CAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKA 128 QV + + G +D+LINNAGI P + D+ P+++++ + +L + Sbjct: 65 ELQVRQAVAKIIEHFGRIDILINNAGITQPLKTL-DIRPSDYDKVLDVSLRGTLLMSQAV 123 Query: 129 VPLLKETSANPGIIAMASV-AGRLGYAFRTP-YAASKWAIVGMVKSLAIELGPNNVRVNA 186 +P +++ S+ I+ M+SV A R G F P Y+A+K ++G+ K++A ELGP+ VRVN+ Sbjct: 124 IPTMRQQSSG-SIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLAKAMARELGPDKVRVNS 182 Query: 187 ILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAG 246 I PG++ + G+ D+ + + I L R+ DVA ALFLAS Sbjct: 183 IAPGLIHTDITG----------GLMQDERRHAIIDGIPLGRLGEAQDVANAALFLASDLS 232 Query: 247 QNISGQAISVDGNV 260 ++G + V+G + Sbjct: 233 SYLTGITLDVNGGM 246 Lambda K H 0.320 0.136 0.391 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: 139 Number of extensions: 6 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: 263 Length of database: 249 Length adjustment: 24 Effective length of query: 239 Effective length of database: 225 Effective search space: 53775 Effective search space used: 53775 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