Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_012384384.1 BIND_RS07040 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000019845.1:WP_012384384.1 Length = 433 Score = 409 bits (1050), Expect = e-118 Identities = 213/430 (49%), Positives = 289/430 (67%), Gaps = 3/430 (0%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M PLRV +AGLGTVGA VI+L+D AE +A R GR + + VSARD+ K+RG+D++RF Sbjct: 1 MQRPLRVGIAGLGTVGAAVIKLLDRQAEALASRVGRAVIVTGVSARDKTKERGIDLSRFV 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W DD LAR + D+ VELIGG+DG ALA A LA+GK +VTANKA++A HG+ LA + Sbjct: 61 WFDDPVALARSEEIDLFVELIGGADGTALAGAEQALASGKPVVTANKALLARHGMRLATL 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE+ + FEA+VAGG+P++K LREG A N I+RVYGILNGTCN+ILS+ME EG F Sbjct: 121 AEEMSLALAFEASVAGGIPIVKTLREGLAGNSIERVYGILNGTCNYILSRMETEGLSFEA 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 LAEAQ G+AEADP+FDI G D AHKL+ILAS+AFGT +++ GI + AD+ Sbjct: 181 CLAEAQKLGYAEADPTFDIGGFDTAHKLAILASLAFGTAVDPEGISVEGIESISLADLQA 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 A LGYR++LLG+A S +G+ QRVHP +VP + +A V+G TNAV + + V L G Sbjct: 241 ADELGYRVKLLGVAQRSADGIEQRVHPSMVPKTSAIAQVMGVTNAVTIDADAVHELTLAG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 GAG TASA+VAD+ DIAR P+ +P +L + P P +G Y+R +V D+ Sbjct: 301 PGAGGEATASAIVADIADIARGVRSAPFGLPVAALTSLPRPPMRLHQGGYYIRLSVEDRP 360 Query: 361 GVLAEIAAAMRDAGVSIESLIQR---GAMADGSVLVAIVTHEVPERSIAQALEKLRGSPS 417 G A IA M + +S+ES++QR G +A G+V V +VT+ E+++ +AL+ + Sbjct: 361 GAAAAIAKRMAEREISLESIVQRRRPGTIASGAVPVILVTYATHEQTVREALDAVVADGY 420 Query: 418 LAGEPMWMHI 427 LA +P + I Sbjct: 421 LAAKPQLIRI 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: 509 Number of extensions: 24 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: 433 Length adjustment: 32 Effective length of query: 398 Effective length of database: 401 Effective search space: 159598 Effective search space used: 159598 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