Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_029549136.1 SWIT_RS23900 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000016765.1:WP_029549136.1 Length = 430 Score = 615 bits (1586), Expect = 0.0 Identities = 315/430 (73%), Positives = 359/430 (83%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M++PLRVALAGLGTVGAGV++LID N LI RRAGRPIEIVAVSARDR++DRGVD++RF Sbjct: 1 MSQPLRVALAGLGTVGAGVVKLIDENRALIERRAGRPIEIVAVSARDRSRDRGVDLSRFA 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 WVDD T LA DVVVEL+GGSDGPAL LAR TL AGK VTANKAMIAHHGLELA++ Sbjct: 61 WVDDATTLAASGDVDVVVELVGGSDGPALTLARDTLGAGKPFVTANKAMIAHHGLELAEL 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE+ +K+EAAVAGG+PVIKGLREGAAAN I V+GILNGTCN+IL++ME +G DF E Sbjct: 121 AEQKGVALKYEAAVAGGIPVIKGLREGAAANVISHVFGILNGTCNYILTEMEEKGSDFAE 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 VLAEAQ G+AEADPSFDIDG+DAAHKLSIL+S+AFGT F + + GIRH++AADIAE Sbjct: 181 VLAEAQRLGYAEADPSFDIDGIDAAHKLSILSSLAFGTAVDFDSIEVTGIRHIIAADIAE 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 AAALG+R+RL+G + S GLFQRVHP LVPLSHPLAHV G NAVVA GNFVGRL FQG Sbjct: 241 AAALGFRVRLVGHGEESAKGLFQRVHPCLVPLSHPLAHVSGSLNAVVAHGNFVGRLFFQG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 GAG+GPTASAVVADLIDIAR E GP +AMP +LA AP G+RRGRAYLRFTVAD+ Sbjct: 301 RGAGEGPTASAVVADLIDIARGETGPAFAMPVAALAKPATAPAGDRRGRAYLRFTVADRP 360 Query: 361 GVLAEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAG 420 GVLAEI AAMRDAGVSIESLIQRG DG+VL+A+VTH PER++A AL++L GS SLAG Sbjct: 361 GVLAEITAAMRDAGVSIESLIQRGVADDGNVLIAMVTHVGPERAVADALDRLAGSQSLAG 420 Query: 421 EPMWMHILGE 430 PM MHIL E Sbjct: 421 TPMLMHILDE 430 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: 614 Number of extensions: 20 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: 430 Length of database: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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