Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_037448983.1 N825_RS07075 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_000576635.1:WP_037448983.1 Length = 387 Score = 251 bits (642), Expect = 2e-71 Identities = 150/381 (39%), Positives = 211/381 (55%), Gaps = 5/381 (1%) Query: 4 STFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSV 63 +T +P + +IG S+ + +A G R LIVTD + G + L I Sbjct: 3 ATIAMPKLMLIGGGSIAQVADTLAKLGIKRPLIVTDPFMRDSGAIAKLTDPLTAAGIPFD 62 Query: 64 IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGV 123 ++ T P+PTTE V AG ++L + D +I+LGGGSP D AK + ++AAN G +RDY+ Sbjct: 63 VFADTVPDPTTEVVYAGARMLSDGGFDGMIALGGGSPIDTAKAMGVMAANPGKMRDYKVP 122 Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 + LP++AI TTAGT SE T+F +ITD KM I V P ++ D L + Sbjct: 123 NPIPNESLPLLAIPTTAGTGSEATKFTVITDTETDEKMLIAGAGVIPQGAIVDFELTLSC 182 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 P LTA TG+D LTHAIEAYVS A P +D+ AL A+ +A++L A + N +ARE M Sbjct: 183 PFRLTADTGIDTLTHAIEAYVSRKANPFSDSMALAAMARVAKHLRTACFEPGNREAREQM 242 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 A AG+AF+NAS+ VH M+ +G +++PHG+ NA+LLP V F+ A AR DC Sbjct: 243 MLAANQAGIAFSNASVALVHGMSRPIGAHFHVPHGLSNAMLLPAVTAFSLPTATARYADC 302 Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363 A AMG G +D A ++A+ L + +P + + E F L T + A G Sbjct: 303 ARAMGACAPGTDDETAGVALLDALNALNADLKVPTP-QAYGIDEGRFMGLLTLMAEQALG 361 Query: 364 F----TNPIQATHEEIVAIYR 380 NP T EEIV++YR Sbjct: 362 SGSPGNNPRVPTAEEIVSLYR 382 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: 389 Number of extensions: 13 Number of successful extensions: 2 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: 387 Length adjustment: 30 Effective length of query: 353 Effective length of database: 357 Effective search space: 126021 Effective search space used: 126021 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