Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF3193 HP15_3135 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Marino:GFF3193 Length = 387 Score = 286 bits (732), Expect = 7e-82 Identities = 152/377 (40%), Positives = 221/377 (58%) Query: 7 FIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYD 66 F+ V GA S N +++G +V+D + G ++ L + I S +Y Sbjct: 11 FVSPEIVFGAGSRKSVANFASNFGARHVFLVSDPGVAAAGWVDEIVTLLTDAGIRSTVYT 70 Query: 67 GTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRS 126 G PNP + V G +L K N CD ++++GGGSP DCAKGI +VA +G I ++EGVD Sbjct: 71 GVSPNPKVDEVMTGAELYKSNECDVIVAIGGGSPMDCAKGIGIVATHGRSILEFEGVDTI 130 Query: 127 AKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKS 186 P P+I I TTAGT++++++F II+D R K +I+ K V P +S+ D + M Sbjct: 131 TNPSPPLILIPTTAGTSADVSQFAIISDPNRRFKFSIISKAVVPDVSLIDPEVTETMDAY 190 Query: 187 LTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYA 246 LTA TG+DAL HAIEAYVS + P+TD AL+A+ +I NL V++ ++ RE + A Sbjct: 191 LTACTGVDALVHAIEAYVSTGSGPLTDTHALEAIRLINRNLEPLVDNTADPYLREQIMLA 250 Query: 247 QFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAA 306 AG+AF+NA LG VHAM+H LGGF +LPHG+CNA+LL HV +N + A R R A A Sbjct: 251 SMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNALLLEHVVAYNFQSAEDRFRRVAEA 310 Query: 307 MGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTN 366 M ++ G E + +N I EL ++V + A L L V D L+ AL+D C TN Sbjct: 311 MDIDTRGMAKPEIKKRLMNRIVELKRRVGLEARLAQLGVSVSDIPHLSGFALQDPCILTN 370 Query: 367 PIQATHEEIVAIYRAAM 383 P +++ ++ +Y A+ Sbjct: 371 PRKSSLRDVQVVYEEAL 387 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: 16 Number of successful extensions: 1 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 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