Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_010959942.1 MCA_RS02965 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000008325.1:WP_010959942.1 Length = 436 Score = 483 bits (1244), Expect = e-141 Identities = 244/436 (55%), Positives = 327/436 (75%), Gaps = 4/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSA--A 58 M PV IG+LGLGTVGGG VLR NA+EI+RR GREI++ ++R IC + A Sbjct: 1 MNPVKIGILGLGTVGGGTVNVLRRNADEITRRAGREIQVCRASTRDLTRSR-ICDTTGIA 59 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 DP+E+V+ D+ +VVE GG A++ V+KA+ NGKH+VTANK L+A +GNEIF A Sbjct: 60 LTDDPYEIVSDPDIQIVVETIGGETPARDLVMKALANGKHVVTANKMLIALHGNEIFAAA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 ++ ++V FEAAVAGGIPIIK +REGLA N+++ +AGIINGTSNFIL+EM EKG FADV Sbjct: 120 RERGLMVAFEAAVAGGIPIIKTIREGLAGNKVEWLAGIINGTSNFILTEMWEKGRDFADV 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L+EAQ LGYAEADPTFDIEG DA HK+TI++++AFG P+ F Y+EGI+ + + D+KYA Sbjct: 180 LQEAQRLGYAEADPTFDIEGVDAAHKLTILASIAFGIPLQFGKVYIEGITGITAADVKYA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 E LGYRIKLLG+ R+T KGIELRVHPTLIP RL+ANV+GVMNAV + D VG TL+YGA Sbjct: 240 EALGYRIKLLGIARRTPKGIELRVHPTLIPARRLIANVNGVMNAVLIKGDAVGPTLHYGA 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGA PTASAVVADI+D+ R + +D +RVPHLAFQPA + ILP++ I ++YYLR+ Sbjct: 300 GAGAEPTASAVVADIVDVVRTLTSDPENRVPHLAFQPAAISEIPILPIEAIETAYYLRLS 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAIAAIEA 417 A+D+PG L + +LA ++SIEA++QK + + ++ +++LT E+ + +A+ IEA Sbjct: 360 AEDKPGVLADVTRILAAHHISIEAVLQKEMPEGESHLPVIMLTQKVTERELNAAVREIEA 419 Query: 418 LDCVEKPITMIRMESL 433 L ++ + IR+E+L Sbjct: 420 LPTIKGAVKRIRLETL 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: 529 Number of extensions: 11 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 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