Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate SMc00293 SMc00293 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >FitnessBrowser__Smeli:SMc00293 Length = 440 Score = 375 bits (962), Expect = e-108 Identities = 203/434 (46%), Positives = 275/434 (63%), Gaps = 7/434 (1%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M + L++ +AGLGTVGA ++R++ E +A GR IEI AV+ARDR+KDRGV +T Sbjct: 1 MADALKIGIAGLGTVGASLVRILQDRHETMATTCGRAIEITAVAARDRSKDRGVKLTGIA 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W +D LA DV VEL+GG+ PA + +A L G +VTANKA++A HG+ELA++ Sbjct: 61 WFEDAVSLASEADVDVFVELMGGAGDPAYSCVKAALTRGVHVVTANKALLAAHGIELAEI 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE+ + +EAAVAGG+PVIK LRE N I RVYGI+NGTCN+IL+KME EG F E Sbjct: 121 AEQHGALLNYEAAVAGGIPVIKALRESMTGNTISRVYGIMNGTCNYILTKMEKEGLSFEE 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 L EAQ G+AEADP+FDI+G D AHKLSIL S+AFGT A D+ + GI ++ DI Sbjct: 181 CLKEAQRLGYAEADPAFDIEGNDTAHKLSILTSLAFGTAIAADDIYLEGITNISIEDIQA 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 A+ LGYRI+LLG+A + +G+ QRVHP +VP +A V G TNAV E + +G LL G Sbjct: 241 ASDLGYRIKLLGVAQRTDSGIEQRVHPTMVPHDTVIAQVDGVTNAVAIESDILGELLMVG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFG----PPYAMPATSLAAEPVAPTGERRGRAYLRFTV 356 GAG TASAV+ D+ DIA++ G P + PA +L A G ++R V Sbjct: 301 PGAGGDATASAVLGDIADIAKSRPGAQHVPAFGRPAKALLPYKRARMQSHEGGYFIRLKV 360 Query: 357 ADKVGVLAEIAAAMRDAGVSIESLIQRGA-MADGS--VLVAIVTHEVPERSIAQALEKLR 413 D+ GV A +A M + +S+ES++Q AD + + +VTH E S+ +A+ ++ Sbjct: 361 VDRTGVFANVAKHMAENDISLESIMQHSKHYADPAEPKTIILVTHATSEASVRKAIVSIK 420 Query: 414 GSPSLAGEPMWMHI 427 G L GEP + I Sbjct: 421 GEGYLVGEPQVIRI 434 Lambda K H 0.319 0.136 0.388 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: 466 Number of extensions: 11 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: 430 Length of database: 440 Length adjustment: 32 Effective length of query: 398 Effective length of database: 408 Effective search space: 162384 Effective search space used: 162384 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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