Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate Ac3H11_2497 Alcohol dehydrogenase (EC 1.1.1.1)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2497 Length = 378 Score = 194 bits (494), Expect = 3e-54 Identities = 133/355 (37%), Positives = 187/355 (52%), Gaps = 23/355 (6%) Query: 30 GFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSV-IYDGTQPNPTTENVAAGLKLLKENN 88 G TR LIVTD + AG +QKAL+ +V ++D T NPT V A +++ K Sbjct: 28 GITRPLIVTD---PGVKAAGVLQKALDALPGMTVAVFDQTPSNPTEAAVRAAVEMYKAQG 84 Query: 89 CDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD----RSAKPQLPMIAINTTAGTAS 144 CD +I++GGGS DCAKGIA+ A + G + Y ++ R P+IA+ TT+GT S Sbjct: 85 CDGLIAVGGGSAIDCAKGIAIAATHEGPLTHYATIEGGSPRITDRAAPLIAVPTTSGTGS 144 Query: 145 EMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYV 204 E+ R II + H K+ ++ P ++ D L +G+P LTAATGMDA+ H +E ++ Sbjct: 145 EVARGAIIIVDD-HRKLGFHSWNLVPKTAICDPELTLGLPPMLTAATGMDAIAHCMETFM 203 Query: 205 SIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHA 264 S A P D AL +T N+ A ++GS+ AR M A MAF LG VH+ Sbjct: 204 SAAFNPPADGIALDGLTRGWANIEQATKNGSDRDARLHMMSASMQGAMAFQK-GLGAVHS 262 Query: 265 MAHQLGGFY-NLPHGVCNAVLLPHVQVFNSKVAAA----RLRDCAAAMGVNVTGKNDAEG 319 ++H LGG L HG NA+ LP V FN++ + RL A AMG+ G Sbjct: 263 LSHSLGGVNPRLHHGTLNAMFLPAVVRFNAQAESVQKEKRLERMAHAMGLASAGD----- 317 Query: 320 AEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNPIQATHEE 374 AIR++ ++ +P GL + V E F + A+ D C TNP AT EE Sbjct: 318 ---IPEAIRDMNARLGLPTGLAAMGVNEAMFDDIIKGAMADHCHKTNPRIATPEE 369 Lambda K H 0.318 0.131 0.373 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: 365 Number of extensions: 25 Number of successful extensions: 7 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: 383 Length of database: 378 Length adjustment: 30 Effective length of query: 353 Effective length of database: 348 Effective search space: 122844 Effective search space used: 122844 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 (21.8 bits) S2: 50 (23.9 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