Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_077278754.1 B1C78_RS08605 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_002000365.1:WP_077278754.1 Length = 436 Score = 469 bits (1207), Expect = e-137 Identities = 243/435 (55%), Positives = 311/435 (71%), Gaps = 2/435 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAF 59 MKPV +GLLGLGTVG G VL N +EI+RR GR I + A ++ R Sbjct: 1 MKPVKVGLLGLGTVGCGTINVLTRNGDEIARRAGRGIEVVAASARDIQRPRDCRLEGIRL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 DPF++V +V +VVEL GGT A+E L AI GKH+VTANK L+A +GNEIF A+ Sbjct: 61 TTDPFDVVNDPEVGIVVELIGGTSPARELALAAIAQGKHVVTANKALIALHGNEIFAEAQ 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 K+ V+V FEAAVAGGIPIIKA+REGLA NRI +AGIINGT NFIL+EMR+KG F DVL Sbjct: 121 KRGVMVAFEAAVAGGIPIIKAIREGLAGNRILWLAGIINGTGNFILTEMRDKGREFDDVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 EAQ LGYAEADPTFD+EG DA HK+TI++++AFG P+ F Y EGI+++ D+ YA Sbjct: 181 AEAQRLGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKVYTEGITRVTREDVAYAA 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 ELGYRIK LGV R+T +GIELRVHPTLIP RL+ANVDGVMNAV V D VG TLYYGAG Sbjct: 241 ELGYRIKHLGVARQTDQGIELRVHPTLIPHRRLIANVDGVMNAVLVKGDAVGPTLYYGAG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AGA PTASAVVAD++D+ R + +D +RVPHLAFQ + +LPM+++ +++YLR++ Sbjct: 301 AGADPTASAVVADLVDVVRALTSDPENRVPHLAFQADALSDTPVLPMEDVQTAFYLRLRV 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTT-AEIVILTHSTVEKHIKSAIAAIEAL 418 +D+PG L I + E +S+EA++Q+ +Q + A +++LTH E ++ AI AI L Sbjct: 361 QDKPGVLADITRIFGDERISLEAVLQREPDEQASEASVILLTHKVREGNMNRAIEAIRQL 420 Query: 419 DCVEKPITMIRMESL 433 D V P+ IRME+L Sbjct: 421 DTVIAPVVRIRMETL 435 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: 519 Number of extensions: 16 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: 436 Length adjustment: 32 Effective length of query: 403 Effective length of database: 404 Effective search space: 162812 Effective search space used: 162812 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