Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_015929850.1 MNOD_RS15400 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000022085.1:WP_015929850.1 Length = 440 Score = 362 bits (930), Expect = e-104 Identities = 196/437 (44%), Positives = 273/437 (62%), Gaps = 10/437 (2%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 MT+ LR+ +AGLGTVG+ V+R+++ A + AGRPI + AVSARDR +DRG+ + Sbjct: 1 MTQSLRLGVAGLGTVGSAVVRMVERRAATLTDAAGRPIRVTAVSARDRTRDRGLALADVA 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W +D LAR + D VVELIGG++G A A A LAAGK +VTANKA++A HG LA+ Sbjct: 61 WFEDPVALARSGEVDCVVELIGGAEGAARATVEAALAAGKHVVTANKALLARHGAALARA 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE + + FEA+ AGG+PV+K LRE A N+I R+YGILNGTCN+ILS+ME EG F Sbjct: 121 AEAAGVALAFEASAAGGIPVVKTLREALAGNRISRIYGILNGTCNYILSRMELEGLTFEA 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 L +AQA G+AEADP+FD++G D AHKL++L S+AFG++ V++ GI + D+ Sbjct: 181 CLKDAQALGYAEADPTFDVEGYDTAHKLALLTSLAFGSEIDADGVSVEGISAITPLDLRM 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 A LGYRI+LLG+A+ + G+ QRVHP +VP S +A V+G TNAV + + + L G Sbjct: 241 ADELGYRIKLLGVAETTPAGIEQRVHPTMVPKSSAIAQVMGVTNAVTIDTDALRELTLIG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 GAG TASAVVAD+ D+A P + PA +L A G Y+R TV D+ Sbjct: 301 PGAGGEATASAVVADIADVAAGRLVPAFGRPAAALVHPRRAEMQRHEGGYYIRLTVHDRP 360 Query: 361 GVLAEIAAAMRDAGVSIESLIQR----GAMADG------SVLVAIVTHEVPERSIAQALE 410 GV A +A M + +S+ES++QR A D V + ++T+ E +I +L+ Sbjct: 361 GVAAGVATRMAERDISLESILQRRSENAAQQDPHGRSGVPVPLVLITYAATEAAIRASLD 420 Query: 411 KLRGSPSLAGEPMWMHI 427 + L+ P + I Sbjct: 421 AMAADGLLSEPPQVIRI 437 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: 486 Number of extensions: 14 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: 440 Length adjustment: 32 Effective length of query: 398 Effective length of database: 408 Effective search space: 162384 Effective search space used: 162384 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