Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_038858435.1 AFK65_RS00460 L-threonine dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_001277175.1:WP_038858435.1 Length = 383 Score = 585 bits (1509), Expect = e-172 Identities = 284/383 (74%), Positives = 332/383 (86%) Query: 1 MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60 M AS F+IP++N+IG +SL +A+ +YG+ LIVTD ML+ LGMAG +++ L ++ I Sbjct: 1 MTASVFYIPAINMIGMNSLDEALKTACEYGYRNALIVTDGMLSALGMAGQLKEMLAQKGI 60 Query: 61 FSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY 120 SV++DGT PNPTTENV AGL +L+ + CD VISLGGGSPHDCAKGIALVAANGGDIRDY Sbjct: 61 HSVVFDGTHPNPTTENVEAGLSMLRAHRCDCVISLGGGSPHDCAKGIALVAANGGDIRDY 120 Query: 121 EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLM 180 EGVDRS KPQLPMIAINTTAGTASEMTRFCIITD+ RH+KMAIVDKHVTP++SVND +LM Sbjct: 121 EGVDRSRKPQLPMIAINTTAGTASEMTRFCIITDQERHVKMAIVDKHVTPVMSVNDPALM 180 Query: 181 IGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAR 240 +GMPKSLTAATGMDALTHAIEAYVS AATP+TDACALKA+ MIA+ LP AVE+G N AR Sbjct: 181 MGMPKSLTAATGMDALTHAIEAYVSTAATPVTDACALKAIAMIAQTLPQAVEEGDNVAAR 240 Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARL 300 EAMA+AQF+AGMAFNNASLGYVHAMAHQLGGFY+LPHGVCNA+LLPHVQ FNS A RL Sbjct: 241 EAMAWAQFMAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNAILLPHVQRFNSAAAGHRL 300 Query: 301 RDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKD 360 RDCA AMGV+V+G +DAEGA ACI AI LA+++ IPAGLR+L V+E+D + LA NALKD Sbjct: 301 RDCAQAMGVDVSGMSDAEGANACIAAICALARRIHIPAGLRELRVREDDISELAENALKD 360 Query: 361 ACGFTNPIQATHEEIVAIYRAAM 383 ACGFTNP+QA+H EI+AIYRAA+ Sbjct: 361 ACGFTNPVQASHAEIMAIYRAAL 383 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: 570 Number of extensions: 17 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: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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