Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate HSERO_RS00730 HSERO_RS00730 4-hydroxybutyrate dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__HerbieS:HSERO_RS00730 Length = 379 Score = 191 bits (486), Expect = 2e-53 Identities = 123/360 (34%), Positives = 195/360 (54%), Gaps = 14/360 (3%) Query: 30 GFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNC 89 G + L+VTD + G+ V L+E + +V+YD T PNP V A + L +++ C Sbjct: 28 GIKKPLVVTDMGIRNAGLLDKVLGQLKE-GVGAVVYDQTPPNPNEGAVRAAVALFRQHGC 86 Query: 90 DSVISLGGGSPHDCAKGIALVAANGGDIRDYE----GVDRSAKPQLPMIAINTTAGTASE 145 D ++++GGGS D AKG+A+ + G ++ + G+ P+IAI TTAGT SE Sbjct: 87 DGIVAVGGGSSIDLAKGVAVCGTHEGPLKSFALIEGGLANITAKTAPVIAIPTTAGTGSE 146 Query: 146 MTRFCI-ITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYV 204 + R I I D+ R K+ I+ ++ P L++ D L +G+P +TAATGMDA+ H +E ++ Sbjct: 147 VGRGAILILDDGR--KVGIISPYLVPKLAICDPELTLGLPPLMTAATGMDAIAHCLETFM 204 Query: 205 SIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHA 264 + + P D AL + ++ A + + +AR M A MAF LG VH+ Sbjct: 205 APSFNPPADGIALDGLWRAWAHIERATREPGDREARLNMMSASMQGAMAFQK-GLGCVHS 263 Query: 265 MAHQLGGFY-NLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEGAEAC 323 ++H LGG L HG NA+ LP + FN AA+ ++D A + G GAE Sbjct: 264 LSHSLGGINPRLHHGTLNAIFLPAIIAFNES-AASMVKDNKMARMAHAMGL--GSGAEIG 320 Query: 324 INAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNPIQATHEEIVAIYRAAM 383 AIRE+++++ +PAGL +L V E F + AL D TNP +A+ ++ + + + +M Sbjct: 321 -PAIREMSRRLGLPAGLGELGVTESMFPQIIQGALADHSHKTNPREASEQDYLHMLQQSM 379 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: 322 Number of extensions: 17 Number of successful extensions: 6 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: 379 Length adjustment: 30 Effective length of query: 353 Effective length of database: 349 Effective search space: 123197 Effective search space used: 123197 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