Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_036261267.1 DL86_RS10930 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000746085.1:WP_036261267.1 Length = 435 Score = 402 bits (1032), Expect = e-116 Identities = 211/432 (48%), Positives = 285/432 (65%), Gaps = 5/432 (1%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M PLR+ +AGLGTVGA VI+++D A+ +A R GR + + VSARD K+RG+D+ RF Sbjct: 1 MLSPLRIGIAGLGTVGAAVIKMLDRQADALANRTGRQVSVAGVSARDAGKERGIDLARFG 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W DD +LA+ D+ VELIGG G ALA A A L AGK +VTANKA++A HG+ LA + Sbjct: 61 WFDDPVDLAKSGDIDLFVELIGGEGGVALAAAEAALGAGKSVVTANKALLARHGMRLAHL 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE+ + FEA+VAGG+P++K LREG A N I+RVYGILNGTCN+IL++ME EG F + Sbjct: 121 AEEKCVALAFEASVAGGIPIVKTLREGLAGNSIERVYGILNGTCNYILTRMELEGLSFAK 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 L+EAQ+ G+AEADP+FDI G D AHKL+IL S+AFGT +A+ GI + AD+ Sbjct: 181 CLSEAQSLGYAEADPTFDIGGFDTAHKLAILTSLAFGTVIDAEAIAVEGISSITLADLEA 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 AA LGYR++LLG+A + +G+ QRVHP +V S +A V+G TNAV + + V L G Sbjct: 241 AAELGYRVKLLGVAQRTPDGIEQRVHPTMVAKSSAIAQVMGVTNAVTIDADAVHELTLVG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 GAG TASA+VAD+ DIAR P+ +PA SL P AP +G Y+R +V D+ Sbjct: 301 PGAGGQATASAIVADIADIARGVRSAPFGLPAASLVKAPHAPMQLHKGGYYVRLSVFDRP 360 Query: 361 GVLAEIAAAMRDAGVSIESLIQR---GAMAD--GSVLVAIVTHEVPERSIAQALEKLRGS 415 G A IA M + +S+ES++QR GA D G V ++T+ E++I QAL+ + Sbjct: 361 GAAAAIATRMAEREISLESIVQRRRPGANGDAPGVAPVILITYATHEKTIRQALDAIVAD 420 Query: 416 PSLAGEPMWMHI 427 LA +P + I Sbjct: 421 GFLADKPQVIRI 432 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: 499 Number of extensions: 15 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: 435 Length adjustment: 32 Effective length of query: 398 Effective length of database: 403 Effective search space: 160394 Effective search space used: 160394 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