Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_019867196.1 METMI_RS0115420 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000384075.1:WP_019867196.1 Length = 436 Score = 483 bits (1244), Expect = e-141 Identities = 249/436 (57%), Positives = 320/436 (73%), Gaps = 4/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAF- 59 MKP+ +G+LGLGTVGGG +L+ NA EI+RR GREI I+ K R IC + Sbjct: 1 MKPIKVGVLGLGTVGGGTVNILKRNAAEIARRAGREIVITRASARDLHKPR-ICDTQDIQ 59 Query: 60 -VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 DPFE++ D+D++VE GG GI K+ +L AI NGKHIVTANK L+A +GNEIF A Sbjct: 60 VTNDPFEIINDPDIDIIVETIGGAGIVKDMILTAIANGKHIVTANKSLIATHGNEIFAKA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 ++ VIV FEAAVAGGIPIIKA+REGL+ N+I+ +AGIINGT NFIL+EMR+KG F DV Sbjct: 120 SEKGVIVAFEAAVAGGIPIIKAIREGLSGNQIQWVAGIINGTGNFILTEMRDKGRDFGDV 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L EAQ LGYAEADP+FD+EG DA HK+TI++++AFG P+ F + EGI+++ D++YA Sbjct: 180 LAEAQFLGYAEADPSFDVEGIDAAHKLTILASIAFGIPLQFEKVFTEGITQITRTDVEYA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 E+LGYRIK LG+ RKT +GIELRVHPTLIPE RL+ANV+GVMNAV V D VG TLYYGA Sbjct: 240 EQLGYRIKHLGIARKTPEGIELRVHPTLIPERRLIANVNGVMNAVLVKGDAVGATLYYGA 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGA PT S+VVAD+ID+ R + +D +RVPHLAFQ + +LP + I +SYYLR+ Sbjct: 300 GAGAEPTGSSVVADVIDVVRALTSDPENRVPHLAFQADALADIPVLPSECIKTSYYLRLN 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKGVI-DQTTAEIVILTHSTVEKHIKSAIAAIEA 417 A+D+PG L + +LA N+SIEA+IQK +T I++LT T+E+ + +AIA IEA Sbjct: 360 AEDKPGVLADVTKILADHNISIEAMIQKEPSKGETAVPIIMLTQITLEQEMNAAIAGIEA 419 Query: 418 LDCVEKPITMIRMESL 433 L V + IRME+L Sbjct: 420 LPAVSGKVNRIRMETL 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: 10 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