Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate HSERO_RS10460 HSERO_RS10460 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >FitnessBrowser__HerbieS:HSERO_RS10460 Length = 436 Score = 506 bits (1303), Expect = e-148 Identities = 260/435 (59%), Positives = 331/435 (76%), Gaps = 2/435 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAA-F 59 MK + +GLLG+GTVG G VL+ N EEI+RR GR I I+ + DL+ E+A ++ Sbjct: 1 MKSIKVGLLGIGTVGSGTFNVLKRNQEEIARRAGRGIEITMVADLNTERATELTNGEVKV 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 V D +V+ D+D+V+EL GG GIAK+ VLKAI NGKH+VTANK L+A +GNEIF A+ Sbjct: 61 VNDANLVVSNPDIDIVIELIGGYGIAKDLVLKAIANGKHVVTANKALIATHGNEIFKAAQ 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 ++ V+V FEAAVAGGIPIIKALREGL ANRI+ IAGIINGT+NFILSEMR+KG F VL Sbjct: 121 EKGVMVAFEAAVAGGIPIIKALREGLTANRIQWIAGIINGTTNFILSEMRDKGLDFDVVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 KEAQ LGYAEADPTFDIEG DA HK+TIM+++AFG P+ F ++EGI+KL + DI YAE Sbjct: 181 KEAQRLGYAEADPTFDIEGVDAAHKLTIMASIAFGIPVQFDKAHVEGITKLQASDITYAE 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 +LGYRIKLLG+TR+T KGIELRVHPTLIP +RL+ANV+G MNAV V D VGETLYYG G Sbjct: 241 QLGYRIKLLGITRQTAKGIELRVHPTLIPAARLIANVEGAMNAVVVRGDAVGETLYYGKG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG+ PTASAV+AD++DI RL AD HRVP+LAFQP + +LPM E+++SYYLR++ Sbjct: 301 AGSEPTASAVIADLVDITRLATADPEHRVPYLAFQPNAMADTPVLPMSEVSTSYYLRMRV 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAIAAIEAL 418 D+ G L + +LA +SI+A++QK + + +I++LTH T EK+I++AIA IEAL Sbjct: 361 ADQAGVLADVTRILADSTISIDAMLQKEPAEGEQQTDIIMLTHQTQEKNIEAAIAKIEAL 420 Query: 419 DCVEKPITMIRMESL 433 V +T IR+E L Sbjct: 421 TTVMGTVTKIRLEEL 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: 497 Number of extensions: 6 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 09 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