Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_004511435.1 GMET_RS08185 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000012925.1:WP_004511435.1 Length = 436 Score = 385 bits (989), Expect = e-111 Identities = 199/432 (46%), Positives = 279/432 (64%), Gaps = 1/432 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQIC-PSAAF 59 M + +GLLGLGT+G G A +L NA+ I+ ++G I + + DL R I P+ Sbjct: 1 MNEIKVGLLGLGTIGTGVAKLLMTNADLIAAKVGARITLKKIADLDITTDRGIALPADIL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 + E++ ++ VV+EL GG AK VLKAIENGKH+VTANK LLA +G EI+P A Sbjct: 61 TTNADEVLTDPEISVVIELIGGYEPAKRFVLKAIENGKHVVTANKALLALHGEEIYPAAA 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 ++ V V FEAAV GGIP+I A+R +AAN ++ GI+NGT N+IL+ M ++G FADVL Sbjct: 121 RKGVEVLFEAAVGGGIPVISAIRGNMAANNFSTVFGILNGTCNYILTRMTKEGVDFADVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 K+AQ LGYAEADPTFDIEG D HK+ ++ +L FGT + FS + EGIS L S DIK+A Sbjct: 181 KKAQELGYAEADPTFDIEGVDTAHKLALLVSLCFGTRVTFSDIHTEGISSLSSVDIKFAR 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 + GY+IKLL + ++ G +E RVHPT+IP + LA+VDG NA+R D +G ++YG G Sbjct: 241 DFGYKIKLLAIGKRDGDRVEARVHPTMIPVNNPLADVDGAFNAIRFTGDFIGPVMFYGRG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG PTASAVV DII+++R + A R L + V + PM EI S YY+R A Sbjct: 301 AGMDPTASAVVGDIIEVSRNIVAGIGRRCAPLGYCDEAVATLPLKPMGEIESKYYIRFSA 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALD 419 D PG L +I+ +L + ++SIE+++Q G + IVI+TH E +++A+ I+ D Sbjct: 361 VDRPGVLARISGILGKYDISIESMVQSGRMAGEEVPIVIMTHEARESDVRTALDEIDTFD 420 Query: 420 CVEKPITMIRME 431 + + +IR+E Sbjct: 421 IITQKSQVIRIE 432 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: 455 Number of extensions: 14 Number of successful extensions: 1 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