Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 16552 b2453 ethanolamine utilization; homolog of Salmonella enzyme, similar to iron-containing alcohol dehydrogenase (VIMSS)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Keio:16552 Length = 395 Score = 240 bits (613), Expect = 4e-68 Identities = 140/378 (37%), Positives = 202/378 (53%), Gaps = 6/378 (1%) Query: 5 TFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVI 64 TF +P V + G S++ G ++ D+ L + GM + ++L + I + Sbjct: 23 TFSVPPVTLCGPGSVSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLTVKGIAMTL 82 Query: 65 YDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD 124 + P +V A + L+E+ CD VI+ GGGS D AK + L+ N Sbjct: 83 WPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGGSVLDAAKAVTLLVTNPDSTLAEMSET 142 Query: 125 RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMP 184 +P+LP+IAI TTAGT SE T +I D K + + P +++ D++L G+P Sbjct: 143 SVLQPRLPLIAIPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVP 202 Query: 185 KSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMA 244 +TA TG+DALTHAIEAY ++ ATP TD+ A+ A+ MI ++LP AV G + ARE+M Sbjct: 203 SHVTAMTGIDALTHAIEAYSALNATPFTDSLAIGAIAMIGKSLPKAVGYGHDLAARESML 262 Query: 245 YAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCA 304 A +AGMAF++A LG HAMAHQ G ++PHG+ NA+LLP V FN V R Sbjct: 263 LASCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGLANAMLLPTVMEFNRMVCRERFSQIG 322 Query: 305 AAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGF 364 A+ + DA INA+ EL +V I L D+ + A AL+D C Sbjct: 323 RALRTKKSDDRDA------INAVSELIAEVGIGKRLGDVGATSAHYGAWAQAALEDICLR 376 Query: 365 TNPIQATHEEIVAIYRAA 382 +NP A+ E+IV +Y AA Sbjct: 377 SNPRTASLEQIVGLYAAA 394 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: 368 Number of extensions: 21 Number of successful extensions: 3 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: 395 Length adjustment: 30 Effective length of query: 353 Effective length of database: 365 Effective search space: 128845 Effective search space used: 128845 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