Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_037461509.1 N825_RS34055 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_000576635.1:WP_037461509.1 Length = 377 Score = 194 bits (494), Expect = 3e-54 Identities = 126/355 (35%), Positives = 187/355 (52%), Gaps = 17/355 (4%) Query: 26 MADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLK 85 +A+ G + LI+ D + K G+ G + AL E + ++ T NPT E V L + + Sbjct: 24 LAELGIAKPLIIADEGVAKAGIVGQIT-ALLEGSASPPVFTRTPTNPTEEAVEDALAVYR 82 Query: 86 ENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYE----GVDRSAKPQLPMIAINTTAG 141 E+ CD +I++GGGSP D AKG+AL+AA+ G + Y G+ R P+IA+ TTAG Sbjct: 83 EHGCDGLIAVGGGSPIDLAKGVALLAAHDGPLERYAAIRGGIPRITAAVAPVIAVPTTAG 142 Query: 142 TASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIE 201 T SE+ R +IT K+ + H+ P +V D L +G+P+ LTAATGMDA+TH +E Sbjct: 143 TGSEVGRASLITLRDGR-KLGFISPHLIPKRAVCDPELTLGLPRWLTAATGMDAVTHCVE 201 Query: 202 AYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGY 261 Y+S P +A AL + +N+ A +GS+ AR M A G+ F LG Sbjct: 202 TYLSPRDNPPAEAIALDGLKRAVDNIEKAAANGSDRDARHQMMMAALEGGLTFQK-GLGA 260 Query: 262 VHAMAHQLGGF--YNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEG 319 VHA++H LGG +L HG NAV+LP FN A A+ A +G+ DA+ Sbjct: 261 VHALSHPLGGLKDLSLHHGTLNAVILPVTLRFNQSHAEAKYAVIRATLGLAA----DADL 316 Query: 320 AEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNPIQATHEE 374 A+ L+ ++ +P L ++ V +A A++D TN AT E+ Sbjct: 317 AD----YFERLSGRLGLPKNLAEMGVTRAIVPAIARAAIEDHSHATNARPATVED 367 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: 355 Number of extensions: 24 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 377 Length adjustment: 30 Effective length of query: 353 Effective length of database: 347 Effective search space: 122491 Effective search space used: 122491 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 24 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