Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 207896 DVU2405 alcohol dehydrogenase, iron-containing
Query= ecocyc::EG12293-MONOMER (383 letters) >MicrobesOnline__882:207896 Length = 393 Score = 401 bits (1030), Expect = e-116 Identities = 210/384 (54%), Positives = 264/384 (68%), Gaps = 6/384 (1%) Query: 6 FFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIY 65 FFIP V +IG + + G ++ LIVTD + K G+ + L+ + +Y Sbjct: 10 FFIPRVTLIGIGASKAIPEKIKALGGSKPLIVTDMGIVKAGILKQITDLLDAAKMAYSVY 69 Query: 66 DGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDR 125 D T PNPT +NV G+ + K+N CDS+I+LGGGS HDC KGI LV ANGG I D+EGVD+ Sbjct: 70 DETIPNPTDDNVHKGVDVYKKNKCDSLITLGGGSSHDCGKGIGLVVANGGKIHDFEGVDK 129 Query: 126 SAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPK 185 S + P +A+NTTAGTASEMTRFCIITD +R +KMAIVD VTP ++++D LM+GMP Sbjct: 130 STQRMPPYLAVNTTAGTASEMTRFCIITDTSRKVKMAIVDWRVTPNIALDDPLLMLGMPP 189 Query: 186 SLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAY 245 +LTAATGMDALTHA+EAYVS ATP+TDACA +A+T+IA L AV +G + +ARE M + Sbjct: 190 ALTAATGMDALTHAVEAYVSTIATPMTDACAEQAITLIATFLRRAVANGQDLEARERMCF 249 Query: 246 AQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAA 305 AQ+LAGMAFNNASLG+VHAMAHQLGGFY+LPHG CNA+LLPHV FN R A Sbjct: 250 AQYLAGMAFNNASLGHVHAMAHQLGGFYDLPHGECNAILLPHVSKFNLIAKLDRYARIAQ 309 Query: 306 AMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDL------NVKEEDFAVLATNALK 359 MG N+ G + E AE I+AI+ L+ V IPAGL L +VK D A++ NA K Sbjct: 310 LMGENIAGLSTREAAERAISAIKCLSTDVGIPAGLVALGKRYGKDVKAADIAIMTKNAQK 369 Query: 360 DACGFTNPIQATHEEIVAIYRAAM 383 DACG TNP T ++ AIY AA+ Sbjct: 370 DACGLTNPRCPTDADVAAIYEAAL 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: 440 Number of extensions: 19 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: 393 Length adjustment: 30 Effective length of query: 353 Effective length of database: 363 Effective search space: 128139 Effective search space used: 128139 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