Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_027722491.1 H589_RS0113380 homoserine dehydrogenase
Query= reanno::Miya:8500664 (436 letters) >NCBI__GCF_000425265.1:WP_027722491.1 Length = 429 Score = 466 bits (1198), Expect = e-136 Identities = 237/423 (56%), Positives = 308/423 (72%), Gaps = 1/423 (0%) Query: 15 IGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPRAWPVPQGATLTADP 74 + +AGFGTVG+GLAR+++EN+ I R G+ + ++LVRD+ K R + TADP Sbjct: 6 LAIAGFGTVGTGLARIIEENKDVILARCGKNFKLTSVLVRDINKKRDFLPGPEVKFTADP 65 Query: 75 AVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAEDGYDLYRLAEQKNV 134 T +P++D++VELMGGI I+ +AL+AGKHVVTANK LLA G +L+R+A + V Sbjct: 66 DEFTSNPDVDIVVELMGGITVAKEIVIKALKAGKHVVTANKHLLAVHGIELFRVAAENKV 125 Query: 135 GLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMTSNGLDFATALAQAQ 194 GL++EASVAGGIPI+Q++KESLA NRI S+VGILNGTANYILSEM++NGL+F TAL QA+ Sbjct: 126 GLYYEASVAGGIPIIQSIKESLAANRIKSIVGILNGTANYILSEMSTNGLEFDTALNQAK 185 Query: 195 ELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAGIDRMDIEFARELGF 254 ELGYAEADPT DIEG D AHK+V+L R+AYG DYP ELP++GI ++ DI FARE G+ Sbjct: 186 ELGYAEADPTFDIEGIDAAHKVVVLARIAYGQDYPLDELPIEGITKVEGQDIRFAREFGY 245 Query: 255 RIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNAVGPVFLHGLGAGSL 314 RIKL+ QVR+V GKLEAGVFP LVK+T L+ARVGG YNAIR+EGNAVGP F HG GAGSL Sbjct: 246 RIKLIGQVRDVGGKLEAGVFPALVKYTLLLARVGGNYNAIRVEGNAVGPAFFHGQGAGSL 305 Query: 315 PTASAVLADLMTVARGAAPHNTGFQRQVPPRADILPPADAESSYYVRAMVPDNPGVLRDL 374 PT SAVLAD+M +++ P NTGF +A+IL P A S YY R V D GV+ L Sbjct: 306 PTGSAVLADIMALSKTDTPDNTGFCNAPIKKAEILSPELATSEYYFRFTVQDKAGVMAAL 365 Query: 375 AGAMADHSISIAQAIQKGQ-HPQGVPLVFMTHAAKASAIQGAIAQVQAAGLLLAPPVCYR 433 + +A+++ISIAQA+QKG + +P+VF TH A + A+ ++ + V R Sbjct: 366 SKCLAEYNISIAQAVQKGNPSEKDIPVVFTTHQASTKDVNAALKEIDNMPFITRQTVSLR 425 Query: 434 VLQ 436 +L+ Sbjct: 426 ILK 428 Lambda K H 0.319 0.137 0.394 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: 524 Number of extensions: 20 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: 436 Length of database: 429 Length adjustment: 32 Effective length of query: 404 Effective length of database: 397 Effective search space: 160388 Effective search space used: 160388 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 (21.7 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