Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate 3608881 Dshi_2273 Homoserine dehydrogenase (RefSeq)
Query= reanno::Korea:Ga0059261_2711 (430 letters) >FitnessBrowser__Dino:3608881 Length = 428 Score = 408 bits (1048), Expect = e-118 Identities = 217/427 (50%), Positives = 287/427 (67%), Gaps = 2/427 (0%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M+ PLR+ +AGLGTVGAGV+++I EL+A RAGRPIE+ AVSAR R KDRGVD++ + Sbjct: 1 MSSPLRLGIAGLGTVGAGVVKIISRKQELLAARAGRPIEVTAVSARSRDKDRGVDMSTYG 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W +D LAR DV VEL+GG DGPA A LAAGK +VTANKAM+AHHG LA Sbjct: 61 WENDPVALARRDDVDVFVELMGGEDGPARNATEAALAAGKDVVTANKAMLAHHGQALAMA 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE + ++FEAAVAGG+PVIK L EG A N+I RV G++NGTCN+IL++MEAEG + Sbjct: 121 AEDAGRVIRFEAAVAGGIPVIKALTEGLAGNEITRVMGVMNGTCNYILTRMEAEGLGYNI 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 + EA G+ EADP+ D+ G+DAAHKL++LASIAFGT+ F V + GI + DI Sbjct: 181 LFEEAGKLGYLEADPTLDVGGIDAAHKLALLASIAFGTKVDFDGVELEGIEQVTLEDIRH 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 AA +G+RI+LLG+A SG GL QR+ P LVP S PL + G TN VV EG+ VG+++ +G Sbjct: 241 AADMGFRIKLLGVAQRSGRGLEQRMRPCLVPASSPLGQLEGGTNMVVIEGDQVGQVVLRG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 AGAG+GPTASAV++D++DIAR + + PA+ L P+ YLR + DK Sbjct: 301 AGAGEGPTASAVLSDIMDIARGDRISTFGQPASGLVT-PIRAQSAVAAPYYLRMELEDKP 359 Query: 361 GVLAEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAG 420 G LA++A + D+GVSI+ + Q G S V IVTH+ ++ ALE L + + G Sbjct: 360 GALAKVATVLGDSGVSIDRMRQYG-HESSSAPVLIVTHKAARNAVDAALEALPKTGVVLG 418 Query: 421 EPMWMHI 427 P+ + I Sbjct: 419 TPVALRI 425 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: 476 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: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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