Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_012101484.1 CKL_RS05440 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000016505.1:WP_012101484.1 Length = 433 Score = 359 bits (921), Expect = e-103 Identities = 188/430 (43%), Positives = 285/430 (66%), Gaps = 4/430 (0%) Query: 1 MEAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQL 60 M+ +++ L+GLG VG+GV I+++++ ++M + G V+V KILV++ +KKRDV+V + Sbjct: 1 MKKVKIALMGLGNVGTGVWMILDSNKKEIMKRSGYDVEVAKILVRNKDKKRDVEVPEEII 60 Query: 61 TTNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAAS 120 TT+ +DIL+D I +VIEVMGGIE + Y+LK + KH+VTANK L+A G EL A Sbjct: 61 TTDFNDILEDDSIKIVIEVMGGIEPAKEYMLKCMDRNKHIVTANKMLIATEGDELFEKAH 120 Query: 121 ANGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVL 180 G YEASVAGGIPI++ + + L +++I + GIVNGTTNYIL+KM ++ L Sbjct: 121 DKGVVFNYEASVAGGIPIIKGIEESLTANKIEEFYGIVNGTTNYILSKMQLERLNFDVAL 180 Query: 181 KEAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGK 240 K+AQ++GYAEADP SD+EG DA K+AIL++L F K+D+++V EGIT+I D++Y K Sbjct: 181 KQAQDMGYAEADPTSDIEGFDAQYKLAILSSLAFGTKVDVNNVYREGITKIESIDMKYAK 240 Query: 241 QLGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPG 300 + +KL+ IA K+E+ VQPT++ HPLA+V D +NA+++ G AVG+ MFYG G Sbjct: 241 KFDMVIKLLAIAKESNGKLELKVQPTMIPKEHPLANVYDSFNAIFIKGNAVGDLMFYGRG 300 Query: 301 AGSLPTATAVVSDLVGVMK-NMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEV 359 AGSLPT +AVV D+V +++ N+ + A + ++++ E +SKF++R+ V D+ Sbjct: 301 AGSLPTGSAVVGDIVAILRSNVDVANYSHIAQNDLWHREIQNISESHSKFYIRITVIDQP 360 Query: 360 GVFANITSIFSEHSVSFEKILQMPLKEN--GLAEIVLVTHQASLQDYEDILVKLRDLNAV 417 GV IT+I +++VS ++Q +EN G IVL TH+ S D + +L +L V Sbjct: 361 GVLGEITTILGKYNVSLRSVIQKG-EENSKGQVTIVLFTHKTSEADVSSAIEELMNLKPV 419 Query: 418 HEIKSSYRVE 427 I + R+E Sbjct: 420 ITIDNVIRIE 429 Lambda K H 0.316 0.134 0.368 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: 451 Number of extensions: 22 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: 432 Length of database: 433 Length adjustment: 32 Effective length of query: 400 Effective length of database: 401 Effective search space: 160400 Effective search space used: 160400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Jul 25 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