Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_028486580.1 B076_RS0106360 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000483485.1:WP_028486580.1 Length = 436 Score = 417 bits (1071), Expect = e-121 Identities = 219/437 (50%), Positives = 305/437 (69%), Gaps = 6/437 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGR--EIRISAMCDLSEEKARQICPSAA 58 MK V +GL+G GTVGGG +L++ EI RR+G+ EI I AM DL ++ R + Sbjct: 1 MKTVKVGLIGFGTVGGGTVDILKNTLPEIQRRIGQTVEITIIAMRDL--QRTRPVDTGDI 58 Query: 59 FVKDPF-ELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPL 117 + D ++V DV++VVEL GGT +AK + AI NGKH+VTANK L+AE+GNE+F L Sbjct: 59 PLTDQASDVVNHPDVEIVVELMGGTSVAKSLLETAIRNGKHVVTANKALIAEHGNELFAL 118 Query: 118 AEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFAD 177 AEK V++ +EAAVAGGIPIIKALREGLA NRI+ +AGIINGT N+IL+EM++ + F Sbjct: 119 AEKHQVMIAYEAAVAGGIPIIKALREGLAGNRIEWLAGIINGTGNYILTEMKQPNADFYQ 178 Query: 178 VLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKY 237 VLK AQ LGYAEA+PTFD+EG DA HK+TI++++AFG + F Y EGIS++ + DI+Y Sbjct: 179 VLKTAQELGYAEANPTFDVEGIDAAHKLTILASIAFGIELQFDKVYTEGISRVTADDIRY 238 Query: 238 AEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYG 297 AE++GY +K LG+ +T G LRVHPTLIP++ L+ANV+GVMNAV + VG T+YYG Sbjct: 239 AEQMGYAVKHLGIASRTATGFSLRVHPTLIPDNVLIANVNGVMNAVMAYGNHVGPTMYYG 298 Query: 298 AGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRV 357 GAGA PTASAVVADIID+ R T RVP L F+ Q++ Q ++ +DEI ++YY+R Sbjct: 299 PGAGAGPTASAVVADIIDVIRWKHQPTEDRVPALGFKADQMKNQPVVDIDEIETAYYIRC 358 Query: 358 QAKDEPGTLGQIAALLAQENVSIEALIQK-GVIDQTTAEIVILTHSTVEKHIKSAIAAIE 416 A D G L +I +LA +S+E ++Q+ + A +V++T++ E + A+ ++ Sbjct: 359 FALDHAGVLAKITTILADYEISVEHMLQEPSTNNSKDATLVMVTNTVKENKLNQALQTLQ 418 Query: 417 ALDCVEKPITMIRMESL 433 ALD ++ I IR+++L Sbjct: 419 ALDEIDGEIMRIRVDAL 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: 467 Number of extensions: 10 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 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