Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BWI76_RS20780 BWI76_RS20780 alcohol dehydrogenase EutG
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Koxy:BWI76_RS20780 Length = 395 Score = 238 bits (607), Expect = 2e-67 Identities = 137/378 (36%), Positives = 200/378 (52%), Gaps = 6/378 (1%) Query: 5 TFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVI 64 TF +P V + G +L+ G ++ D+ L + G+ + ++L + + + Sbjct: 23 TFSVPPVTLCGLGALSACGQEAQARGVNHLFVMVDSFLHQAGLTAGLARSLAVKGVAMTV 82 Query: 65 YDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD 124 + P +V A + L+E CD V++ GGGS D AK +AL+ N Sbjct: 83 WPCPPGEPCVTDVCAAVAQLREAKCDGVVAFGGGSVLDAAKAVALLVTNPEQTLSEMTES 142 Query: 125 RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMP 184 +P+LP+IA+ TTAGT SE T +I D K + + P +++ D++L G+P Sbjct: 143 SVLRPRLPLIAVPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVP 202 Query: 185 KSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMA 244 +TA TG+DALTHA+EAY ++ ATP TD+ AL A+ MI + LP AV G + ARE+M Sbjct: 203 PQVTAMTGIDALTHAVEAYSALNATPFTDSLALGAIAMIGQALPKAVGYGHDLAARESML 262 Query: 245 YAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCA 304 A +AGMAF++A LG HAMAHQ G ++PHG NA+LLP V FN V R R Sbjct: 263 LASCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGQANAMLLPTVMAFNRMVCRERFRQIG 322 Query: 305 AAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGF 364 A+ T ++A I A+ L +V + L D K E F+ A A +D C Sbjct: 323 RALIAKKTDDHEA------IAAVEALIAEVGLSKRLSDAGAKPEHFSAWAQAAQEDICLR 376 Query: 365 TNPIQATHEEIVAIYRAA 382 NP AT E+I+ +Y AA Sbjct: 377 ANPRTATREQIIDLYAAA 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: 349 Number of extensions: 18 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