Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_012676079.1 PERMA_RS05240 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000021565.1:WP_012676079.1 Length = 441 Score = 345 bits (886), Expect = 1e-99 Identities = 191/438 (43%), Positives = 277/438 (63%), Gaps = 8/438 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAF 59 MK ++IGL+G G VG G A +L + E +S++ G EI + + + K+ P + Sbjct: 1 MKRIDIGLVGYGVVGNGVARILEEKKELLSKKSGVEINLKKVFTRNWNKSFPYPLPESKK 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 E++ D+ +VVEL GG + + +A+E GKH+VTANK LLAE G EIF AE Sbjct: 61 AYSLDEILQDDDISIVVELTGGIDFPYKLISEAVEKGKHVVTANKALLAERGKEIFLKAE 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 ++++ + +EAAVAGGIPII+ALREGL AN I I GI+NGT+N+IL+ M ++G F L Sbjct: 121 QKDIRIGYEAAVAGGIPIIRALREGLIANDIIKIYGILNGTTNYILTSMYKQGKDFKTAL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 +EAQ LGYAEADPT DI G DA HKITI+++L++G ++FS Y+EGI + DI+ + Sbjct: 181 REAQELGYAEADPTLDINGTDAAHKITILASLSYGGFLDFSQVYVEGIESIHPLDIELGK 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 +LGY +KLL + + +E+RVHPT IPE LA VDGV NAV V D VGE+++YG G Sbjct: 241 DLGYVLKLLAIAKGHNGEVEVRVHPTFIPEDNPLAKVDGVFNAVMVEGDAVGESMFYGKG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG+LPTASAV++DI+DI++ + A+ R + + + T+ + + + YYLR Sbjct: 301 AGSLPTASAVISDIVDISKSI-AEGVGRGIEITSMNWEHKDLTLTRVPDFYTRYYLRFTV 359 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVI------DQTTAEIVILTHSTVEKHIKSAIA 413 D G L ++AA+ A+ N+SI A+IQK + + +VILTH+ E +I+ AI Sbjct: 360 PDVTGILAKVAAVFARFNISIAAVIQKEKVVSMYESKEKVVPLVILTHTASENNIQKAIK 419 Query: 414 AIEALDCVEKPITMIRME 431 IE + +IR+E Sbjct: 420 EIEQQGITVEKTVIIRVE 437 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: 466 Number of extensions: 24 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