Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase
Query= curated2:Q67N85 (351 letters) >FitnessBrowser__azobra:AZOBR_RS13230 Length = 340 Score = 144 bits (364), Expect = 3e-39 Identities = 100/299 (33%), Positives = 149/299 (49%), Gaps = 8/299 (2%) Query: 1 MAETMRALRKLEAGPGATLQEVPIPTIGPRDVLVKVRAASICGTDYHIYTWDPWSAGRVK 60 MA+TM+A + +++EVP+P +GP +LVK+ A+ +C TD H D W + Sbjct: 1 MAKTMKAAVVRQFKMPLSIEEVPVPEVGPGQILVKIEASGVCHTDLHAADGD-WPV-KPN 58 Query: 61 PPLTIGHELAGEVVAVGREVTACKVGDYVSAE-THIVCNRCPRCHMGEYHLCENTKILGV 119 PP GHE G V AVG VTA K GD V H C C +C G LC+ + G Sbjct: 59 PPFIPGHEGVGTVAAVGTGVTAVKEGDRVGVPWLHTACGHCRQCLAGWETLCDLQQNTGY 118 Query: 120 DTDGAFAEYVAVPEQNIWVNDKDIPFELQSIQEPLGNAVHTALNGDLT--ARSVLITGCG 177 +G FAEY + + +E+ + G V+ L T +V+I+G G Sbjct: 119 SVNGGFAEYTLADPNYVGHLPDRLDWEMAAPILCAGVTVYKGLKETDTKPGDTVVISGIG 178 Query: 178 PIGIMSVPVAKMAGAEIVMAMDINEYRLQLAGQLGADVLINPTKQDPVEVVRSYTRGYGA 237 +G ++V AK G +++ A+DI++ +L LA +GAD IN DPV V++ GA Sbjct: 179 GLGHIAVQYAKAMGLDVI-AVDISDEKLALARAMGADAAINAKTTDPVAEVKALCG--GA 235 Query: 238 DVVLEMSGNPTAIRQGLKAARNGARISLLGLPGRPLELDLAADVIMRGLVLQGITGRRM 296 VL + + A Q L ++L+GLP ELD+ + V+MR + I G R+ Sbjct: 236 QGVLVTAVSRHAFNQALGMLAKRGTMALVGLPPGSFELDIFSTVLMRKTIRGSIVGTRL 294 Lambda K H 0.320 0.137 0.415 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: 307 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: 351 Length of database: 340 Length adjustment: 29 Effective length of query: 322 Effective length of database: 311 Effective search space: 100142 Effective search space used: 100142 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: 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