Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_012757284.1 RLEG_RS08600 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000023185.1:WP_012757284.1 Length = 441 Score = 379 bits (973), Expect = e-109 Identities = 201/434 (46%), Positives = 275/434 (63%), Gaps = 7/434 (1%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M + L++ +AGLGTVGA ++R+I + +A GRPI I AVSARD+A+DRG+D++ Sbjct: 1 MADALKIGIAGLGTVGASLVRIIQQKSNELAVTCGRPITITAVSARDKARDRGIDLSAVT 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W D ELA DV VEL+GG++G A R L G +VTANKA++A+HG+ELA + Sbjct: 61 WFDRPEELAEKGDIDVFVELMGGAEGAANISVRTALQRGLHVVTANKALLAYHGVELATI 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE+ + + FEAAVAGG+PVIK LRE N + R+YGI+NGTCN+IL+KME EG F E Sbjct: 121 AEEKGSLLNFEAAVAGGIPVIKALRESLTGNSVSRIYGIMNGTCNYILTKMEKEGLSFAE 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 L EAQ G+AEADP+FDI+G D AHKLSIL ++AFG Q A D+ + GI ++ DI Sbjct: 181 CLKEAQRLGYAEADPAFDIEGNDTAHKLSILTTLAFGNQIAADDIYLEGITNISIEDIHA 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 AA LGYRI+LLG+A + G+ QRVHP +VP+ +A V G TNAV E + +G LL G Sbjct: 241 AAELGYRIKLLGVAQRTDTGIEQRVHPTMVPVDSVIAQVDGVTNAVAIESDVLGELLMVG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFG----PPYAMPATSLAAEPVAPTGERRGRAYLRFTV 356 GAG TAS+V+ D+ DIA+++ G P PAT+L A G ++R TV Sbjct: 301 PGAGGNATASSVLGDIADIAKSQPGAQRVPVLGHPATTLEPYRKAQMQSHEGGYFIRLTV 360 Query: 357 ADKVGVLAEIAAAMRDAGVSIESLIQRGAM---ADGSVLVAIVTHEVPERSIAQALEKLR 413 D+ GV A +A M + +S+ES++QR + +VTH E S+ +A+ ++ Sbjct: 361 LDRTGVFASVATRMAENNISLESIVQRSKQHLAPSHHQTIILVTHATTEDSVRKAVASIK 420 Query: 414 GSPSLAGEPMWMHI 427 L GEP + I Sbjct: 421 SEGYLFGEPQVIRI 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: 456 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: 430 Length of database: 441 Length adjustment: 32 Effective length of query: 398 Effective length of database: 409 Effective search space: 162782 Effective search space used: 162782 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 10 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