Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF1423 HP15_1388 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Marino:GFF1423 Length = 395 Score = 197 bits (502), Expect = 3e-55 Identities = 125/386 (32%), Positives = 199/386 (51%), Gaps = 9/386 (2%) Query: 6 FFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI-FSVI 64 FF P + G +L + R +IVTD + G+ V A EE + + I Sbjct: 8 FFCPVKVIAGKAALEHIPYELTGMAAKRPMIVTDKGVRAAGLLEPVIAACEESGLEITTI 67 Query: 65 YDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGD-IRDYEGV 123 YD P+ +T V + ++ CDS+I++GGGS D K + ++ + GGD I Y G Sbjct: 68 YDDVPPDSSTTVVRDIAGIYRQEKCDSIIAVGGGSAIDTGKAVNILVSEGGDDIAKYSGA 127 Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 P P + TTAGT SE+T +ITDEA+ +K+ + P ++ D + + + Sbjct: 128 GVLKHPLKPFFVVPTTAGTGSEVTSVAVITDEAKGVKLPFTSSFLLPNAAIIDPRMTLTL 187 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 P +TAAT MDA+THA EA+ +A P++DA A A+ I+++L +++ ++ R + Sbjct: 188 PPHITAATAMDAMTHATEAFTCMAKNPLSDAYATAAIKKISQSLLQVMDNPKDSDGRLEL 247 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 A A +AG+AF+N+ +G VHA+ H G +LPHG+C ++ LP+ +N + L + Sbjct: 248 AQASTMAGIAFSNSMVGLVHALGHATGAVCHLPHGLCMSLYLPYALEYNLETIREPLGEL 307 Query: 304 AAAM-GVNVTGKNDA-EGAEACINAIRELA----KKVDIPAGLRDL-NVKEEDFAVLATN 356 + G V A AEA I+AIR+L K+ +P L++ V E +A Sbjct: 308 LLYLEGPEVFAATPASRRAEASISAIRKLRDALYKRCQLPRTLKETGKVTEAQLDHIAEM 367 Query: 357 ALKDACGFTNPIQATHEEIVAIYRAA 382 AL D NP + T E+ ++ R A Sbjct: 368 ALDDGSIMFNPKEVTLEDARSVLRRA 393 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: 377 Number of extensions: 17 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