Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_028485478.1 A377_RS0110715 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000384235.1:WP_028485478.1 Length = 439 Score = 421 bits (1082), Expect = e-122 Identities = 221/439 (50%), Positives = 307/439 (69%), Gaps = 8/439 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRI----SAMCDLSEEKARQI-CP 55 M+ + +GLLGLGTVGGG +LRD EI RRLG + I +A+ DL E+AR + Sbjct: 1 MEKIKVGLLGLGTVGGGTLTILRDTLTEIERRLGGQTTIEVTHAAVRDL--ERARGLNTD 58 Query: 56 SAAFVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIF 115 S DP + DVD+V+EL GGT +AKE + AI+ GKHIVTANK L+AE+GNE+F Sbjct: 59 SLVLTDDPKAVAGHPDVDIVIELMGGTTLAKECLEAAIKAGKHIVTANKALIAEHGNELF 118 Query: 116 PLAEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAF 175 LAE+ V++ +EAAVAGGIPIIKALREGL+ANRI+ +AGIINGT N+IL+EM + + F Sbjct: 119 ALAEQHQVMIAYEAAVAGGIPIIKALREGLSANRIEWVAGIINGTGNYILTEMNDPEADF 178 Query: 176 ADVLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDI 235 VL+ AQ LGYAEADPTFD+EG DA HK+TIM+++AFG + F Y EGIS++ + DI Sbjct: 179 YQVLRTAQELGYAEADPTFDVEGTDAAHKLTIMASIAFGIELQFDKVYTEGISEITAEDI 238 Query: 236 KYAEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLY 295 ++A++LGY++K LG+ +T G LRVHPTL+PES LL+ ++GVMNAV V + VG TLY Sbjct: 239 QFAQKLGYQVKHLGIASRTDDGFSLRVHPTLVPESVLLSQINGVMNAVMVKGNHVGPTLY 298 Query: 296 YGAGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYL 355 YG GAG PTASAVVAD+ID+ R A RVP L F + Q++ P++EI ++YYL Sbjct: 299 YGPGAGGGPTASAVVADLIDVIRWRHQPAADRVPALGFAANSLSTQSVAPVEEIETAYYL 358 Query: 356 RVQAKDEPGTLGQIAALLAQENVSIEALIQK-GVIDQTTAEIVILTHSTVEKHIKSAIAA 414 R A D G L +++ +LA+ +++IE L Q+ ++ A +V+LT+ EK + A+ + Sbjct: 359 RFFAHDNSGVLAKVSTILAEFDINIELLHQEPSAVNPNDATLVMLTNVVPEKAMNRAVKS 418 Query: 415 IEALDCVEKPITMIRMESL 433 ++A++ ++ I IR+ +L Sbjct: 419 LQAMEEIDGKIMRIRVGAL 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: 461 Number of extensions: 13 Number of successful extensions: 2 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: 439 Length adjustment: 32 Effective length of query: 403 Effective length of database: 407 Effective search space: 164021 Effective search space used: 164021 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