Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__azobra:AZOBR_RS13230 Length = 340 Score = 144 bits (362), Expect = 4e-39 Identities = 108/343 (31%), Positives = 165/343 (48%), Gaps = 15/343 (4%) Query: 10 KAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILG 69 KAA++++F PLSIE+V +PE ++L++I +GVC TDL G + P I G Sbjct: 6 KAAVVRQFKMPLSIEEVPVPEVGPGQILVKIEASGVCHTDLHAADGDWPVKP-NPPFIPG 64 Query: 70 HENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCRE---GKFNICKNQIIPGQTTNG 125 HE GT+ VG + VK+GD V V W C +CR+ G +C Q G + NG Sbjct: 65 HEGVGTVAAVGTGVTAVKEGDRVGV--PWLHTACGHCRQCLAGWETLCDLQQNTGYSVNG 122 Query: 126 GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIG 185 GF+EY L + + L AAP+ AG T +++ V+++GIG Sbjct: 123 GFAEYTLADPNYVGHLPDRLDWEMAAPILCAGVTVYKGLKET----DTKPGDTVVISGIG 178 Query: 186 GLAVYTIQILKALMKNITIVGISRSKKHRDFALELGADYVSEMKDAESLIN-KLTDGLGA 244 GL +Q KA+ ++ V IS K A +GAD K + + K G Sbjct: 179 GLGHIAVQYAKAMGLDVIAVDISDEKLA--LARAMGADAAINAKTTDPVAEVKALCGGAQ 236 Query: 245 SIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSLND 304 + + V LG +LA+ G + LVG+ L+ F T + K + GS G+ D Sbjct: 237 GVLVTAVSRHAFNQALG-MLAKRGTMALVGLPPGSFELDIFSTVLMRKTIRGSIVGTRLD 295 Query: 305 LEDVVRLSESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVI 347 L + ++ + GK+K + LD+IN F+ + +DGR V+ Sbjct: 296 LAECLQFAGDGKVKVHYSVEHLDNINNVFSRMRNNEIDGRVVM 338 Lambda K H 0.317 0.136 0.389 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: 292 Number of extensions: 17 Number of successful extensions: 5 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: 349 Length of database: 340 Length adjustment: 29 Effective length of query: 320 Effective length of database: 311 Effective search space: 99520 Effective search space used: 99520 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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