Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_029909042.1 P166_RS0104165 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000711315.1:WP_029909042.1 Length = 438 Score = 422 bits (1085), Expect = e-122 Identities = 225/436 (51%), Positives = 309/436 (70%), Gaps = 8/436 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRIS----AMCDLSEEKARQICPS 56 MK V +GLLGLGTVGGG +L+ EI RRLG ++ + A+ DL+ +AR + + Sbjct: 1 MKEVRLGLLGLGTVGGGTVNILQTTQTEIQRRLGGKVSVKVEQIAVRDLN--RARPVDTT 58 Query: 57 AA-FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIF 115 DP +V +VD+VVEL GGT +AK + +AI+N KHIVTANK L+AE+GNE+F Sbjct: 59 GIDLTTDPLAVVNNPNVDIVVELMGGTTLAKTCLEQAIQNKKHIVTANKALIAEHGNELF 118 Query: 116 PLAEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAF 175 AE Q V++ +E+AVAGGIPIIKALREGLAAN+I+ +AGIINGT N+IL+EM++ G+ F Sbjct: 119 KTAEAQGVMIAYESAVAGGIPIIKALREGLAANQIEWLAGIINGTGNYILTEMKKPGADF 178 Query: 176 ADVLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDI 235 + VLK+AQ LGYAEADPTFD+EG DA HK+TIM+++AFG + F Y EGISK+ DI Sbjct: 179 SQVLKKAQELGYAEADPTFDVEGIDAAHKLTIMASIAFGIELQFDKVYTEGISKVTGDDI 238 Query: 236 KYAEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLY 295 ++A++LGY+IK LG+ + G LRVHPTL+ +S L+ANV+GVMNAV V + VG+TLY Sbjct: 239 QFAQKLGYQIKHLGIAARADNGFSLRVHPTLVKDSVLIANVNGVMNAVMVAGNHVGQTLY 298 Query: 296 YGAGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYL 355 YG GAGA PTASAVVADIID+ R + RVP L F Q+ + ++ +D+I S+YYL Sbjct: 299 YGPGAGAGPTASAVVADIIDVIRALRQPQEDRVPGLGFALDQLTSAPVVAIDDIKSAYYL 358 Query: 356 RVQAKDEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAIAA 414 R AKD G L ++++++AQ +SIE L Q+ D + A IV++T+ E I AI+A Sbjct: 359 RFYAKDHAGVLAKVSSIMAQSQISIELLHQEPCADNEDDATIVMITNKVQESTINQAISA 418 Query: 415 IEALDCVEKPITMIRM 430 +E+++ ++ I IR+ Sbjct: 419 LESMEEIDGDIMRIRV 434 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: 448 Number of extensions: 9 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: 438 Length adjustment: 32 Effective length of query: 403 Effective length of database: 406 Effective search space: 163618 Effective search space used: 163618 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