Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_012674970.1 SULAZ_RS02015 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000021545.1:WP_012674970.1 Length = 441 Score = 347 bits (889), Expect = e-100 Identities = 192/440 (43%), Positives = 277/440 (62%), Gaps = 11/440 (2%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKA-RQICPSAAF 59 MK VN+ ++G G VG G +L E + ++ G EI + + + K Sbjct: 1 MKQVNVAIVGYGVVGNGVGKILDTQKELLKQKSGVEINLKKVYTRNWNKTFPHPIEEERR 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 K+ E++ +++D+VVEL GG +++A++ GKHIVTANK LLAE G ++F AE Sbjct: 61 AKNLDEILNDENIDIVVELTGGIDFPYNLIIQALDKGKHIVTANKALLAEKGKDVFTKAE 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 ++N+ + FEAAVAGGIPIIKALREGL AN IK I GI+NGT+N+IL+ M ++G +F+ L Sbjct: 121 EKNLRIGFEAAVAGGIPIIKALREGLVANEIKKIYGILNGTTNYILTSMYKEGKSFSQAL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 KEAQ GYAEADPT DI G DA HKI+I+S+L+FG + FS Y+EGI K+D+ DI Sbjct: 181 KEAQEKGYAEADPTLDINGTDAAHKISILSSLSFGGFVEFSQVYVEGIEKIDTLDIDLGR 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 ELGY +KLL + + +E+RVHPT +P L+ VDGV NAV V D VGET++YG G Sbjct: 241 ELGYTLKLLAIAKSHNDEVEIRVHPTFLPSDNPLSKVDGVFNAVMVEGDNVGETMFYGRG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG+ PTASAVV+DI+ IA+ ++ + + + + + + + + + YY+R Sbjct: 301 AGSFPTASAVVSDIVSIAKSIQLNIGKEI-EITSMNWKHKDLNLTKVKDFYTRYYIRFTV 359 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQK-------GVIDQTTAEIVILTHSTVEKHIKSAI 412 D G L +IA++ A+ N+SI A+IQK +I++ +VILTH+ E +I+ AI Sbjct: 360 PDITGILAKIASVFAKYNISIAAVIQKEKVLKLQKMINEKVVPLVILTHTASENNIQQAI 419 Query: 413 AAI-EALDCVEKPITMIRME 431 I E +E P T+IR+E Sbjct: 420 KEIVENHYSIEDP-TIIRVE 438 Lambda K H 0.318 0.135 0.369 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: 461 Number of extensions: 25 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: 435 Length of database: 441 Length adjustment: 32 Effective length of query: 403 Effective length of database: 409 Effective search space: 164827 Effective search space used: 164827 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 (21.7 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