Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF2304 PGA1_c23360 putative iron containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Phaeo:GFF2304 Length = 381 Score = 191 bits (485), Expect = 3e-53 Identities = 120/376 (31%), Positives = 178/376 (47%), Gaps = 13/376 (3%) Query: 9 PSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGT 68 P+ GA + + A G + L+VTD L L + LE + ++ Sbjct: 10 PTAIKFGAGRIRELAEACATAGMKKPLLVTDKGLADLPVTQSTLDILEAAGLGRAMFCEV 69 Query: 69 QPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD---- 124 PNP +N+ AG+ K + D VI+ GGGS D K +A + + D+E + Sbjct: 70 DPNPNEKNLEAGVAAYKAGDHDGVIAFGGGSGLDLGKMVAFMCGQNRPVWDFEDIGDWWT 129 Query: 125 -RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 A P+IA+ TTAGT SE+ R +ITD H K I V P + + D L +GM Sbjct: 130 RADADAIAPIIAVPTTAGTGSEVGRASVITDSVTHQKKIIFHPKVLPTVVICDPELTVGM 189 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 PK +TA TG+DA H +EA+ S P++ AL+ + ++ E LP A DG++ +AR M Sbjct: 190 PKFITAGTGLDAFAHCVEAFSSPHYHPMSQGIALEGMRLVKEYLPRAYADGTDIEARAQM 249 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 A + AF LG +HAM+H +G +N HG NAV + V FN+ A R + Sbjct: 250 MSAAAMGATAFQK-GLGAIHAMSHPIGALFNTHHGTTNAVCMLAVLAFNAPEIADRFKTA 308 Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363 A +G++ G E ++EL + IP GL +L V E L AL D Sbjct: 309 ADYLGID-------GGFEGVCAYVQELNDSLGIPRGLSELGVTEAAIPELVKGALIDPSC 361 Query: 364 FTNPIQATHEEIVAIY 379 NP+ + ++ Sbjct: 362 GGNPVVLDQANLTQLF 377 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: 386 Number of extensions: 23 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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