Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_059152026.1 V474_RS13885 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_001046635.1:WP_059152026.1 Length = 435 Score = 567 bits (1460), Expect = e-166 Identities = 298/434 (68%), Positives = 346/434 (79%), Gaps = 5/434 (1%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M EPL +ALAGLGTVG+GV+RLI+ NAELIARRA RPI I AVSARDR KDRGVD++R+D Sbjct: 1 MVEPLNIALAGLGTVGSGVVRLIETNAELIARRARRPIRIAAVSARDRTKDRGVDLSRYD 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W DD LA DVVVE++GGSDGPALALAR +A GKGLVTANKAMIAHHGLELA Sbjct: 61 WEDDTAALAARADVDVVVEMVGGSDGPALALARNAIAGGKGLVTANKAMIAHHGLELAAA 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE + +KFEAAVAGG+PVIKGL EGAAAN I+RVYGILNGTCN+ILS ME GRDF + Sbjct: 121 AEAAGVALKFEAAVAGGIPVIKGLSEGAAANAIERVYGILNGTCNYILSTMEDTGRDFAD 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 VLA+AQ G+AEADP+FDI+G+DAAHKLSILA+IAFGT+ F V GI + AADI + Sbjct: 181 VLADAQRMGYAEADPTFDIEGIDAAHKLSILAAIAFGTRLRFDAVETMGISRVKAADIEQ 240 Query: 241 AAALGYRIRLLGIADLSG-NG---LFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRL 296 A ALGY IRL+G+A + G NG LFQRV PHLVP+ HPLAHV G TNAVVAEGNF+GRL Sbjct: 241 ARALGYVIRLIGMAGIDGTNGSARLFQRVRPHLVPIDHPLAHVDGATNAVVAEGNFMGRL 300 Query: 297 LFQGAGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTV 356 LFQGAGAGDGPTASAVVAD+IDIA+ E GP +AMPA L A A +G R G +Y+RFTV Sbjct: 301 LFQGAGAGDGPTASAVVADIIDIAKGEKGPAFAMPAAELEAMEPASSGHRVGSSYIRFTV 360 Query: 357 ADKVGVLAEIAAAMRDAGVSIESLIQRG-AMADGSVLVAIVTHEVPERSIAQALEKLRGS 415 D+ GVLA+I AAMRDAGVSIESLIQ+G DG V++A+VTH PE ++ +A+ L GS Sbjct: 361 PDRPGVLADITAAMRDAGVSIESLIQKGDPDQDGEVILAVVTHPGPESAVTEAMRILDGS 420 Query: 416 PSLAGEPMWMHILG 429 SLAG P+ M I+G Sbjct: 421 DSLAGRPLVMQIIG 434 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: 613 Number of extensions: 20 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: 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 Jul 26 2024. The underlying query database was built on Jul 25 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