Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_026596525.1 H035_RS0111190 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000421465.1:WP_026596525.1 Length = 436 Score = 473 bits (1218), Expect = e-138 Identities = 250/436 (57%), Positives = 314/436 (72%), Gaps = 4/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAF- 59 M PV IGLLGLGTVGGG VL N EI+RR GREI+++ EK R IC + Sbjct: 1 MHPVKIGLLGLGTVGGGTVNVLARNTREITRRAGREIQVAKAFTRDPEKPR-ICGTEGID 59 Query: 60 -VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 V DP+E+V ++ +V EL GGT +AKE VL+AIE GKH+VTANK L+A +GNEIF A Sbjct: 60 LVTDPWEVVEDPEIAIVAELIGGTSLAKELVLRAIELGKHVVTANKALIALHGNEIFSRA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 +Q V+V FEAAVAGGIPIIK LREGL NRI+ +AGIINGT NFIL+ MR++G F DV Sbjct: 120 SEQGVMVAFEAAVAGGIPIIKVLREGLTGNRIEWVAGIINGTGNFILTGMRDQGRVFDDV 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L EAQALGYAEA+P FD+EG DA HK+TI++A+AFG P+ + Y EGI+++ DI+YA Sbjct: 180 LTEAQALGYAEANPAFDVEGIDAAHKLTILAAIAFGIPLQYDKVYTEGITRITPEDIRYA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 +ELGY+IK LG+ R+T GIELRVH LIP RLLANV+GVMNAV V D VG TLYYG Sbjct: 240 QELGYQIKHLGIARQTPDGIELRVHLCLIPARRLLANVEGVMNAVVVKGDAVGPTLYYGP 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGA PTASAVVAD++D+ R+ AD +RVPHLAFQP + +LP+ EI ++YYLR++ Sbjct: 300 GAGAEPTASAVVADLVDVVRVFTADPGNRVPHLAFQPDALSDLPVLPISEIETAYYLRLK 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAIAAIEA 417 D+PG L IA +LA +SIEA+IQK + Q ++ LTH EK + +A A IEA Sbjct: 360 VADQPGVLADIARILADHEISIEAVIQKEPQEGQMDLPLIFLTHKVKEKALDAAAAKIEA 419 Query: 418 LDCVEKPITMIRMESL 433 L V+ P+ IR+E+L Sbjct: 420 LPAVKAPLYRIRLETL 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: 484 Number of extensions: 14 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