Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_019556226.1 F612_RS0102770 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000381085.1:WP_019556226.1 Length = 436 Score = 424 bits (1091), Expect = e-123 Identities = 227/436 (52%), Positives = 303/436 (69%), Gaps = 4/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGR--EIRISAMCDLSEEKARQICPSAA 58 MK V IGLLGLGTVGGG ++ + EI RRLG+ EI I AM DL+ ++ Sbjct: 1 MKTVKIGLLGLGTVGGGTVDIINNTMPEIQRRLGQNIEIVIIAMRDLNRSRSADTT-GIQ 59 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 P E+V DV++VVEL GGTG+AKE + AI+NGKH+VTANK L+AE+GN +F LA Sbjct: 60 LTDIPAEVVNHPDVEIVVELMGGTGLAKELIETAIQNGKHVVTANKALIAEHGNGLFALA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 +K NVIV +EAAV GGIP+IKALREGLAAN+I+ +AGIINGT N+IL+EM+E G+ FA V Sbjct: 120 KKHNVIVNYEAAVTGGIPVIKALREGLAANKIEWLAGIINGTGNYILTEMKEPGADFAKV 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L+ AQ LGYAEADPTFD+EG DA HK+TI++++AFG + F Y EGISK+ + DI++A Sbjct: 180 LQVAQELGYAEADPTFDVEGIDAAHKLTILASIAFGIKLQFDKVYTEGISKVSADDIRFA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 E+LGY IK LG+ + G LRVHP L+P + L+ANV GVMNAV D VG T+YYGA Sbjct: 240 EQLGYEIKHLGMASRLENGYSLRVHPALVPNTVLMANVSGVMNAVMAYGDHVGATMYYGA 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGA PTAS+VVADIID+ R + A +VP L F Q+Q+ ++ ++EI + YY+R Sbjct: 300 GAGAGPTASSVVADIIDVIRWKDQPLADQVPSLGFALDQLQSAPVVSVEEIETCYYIRCF 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKGVIDQ-TTAEIVILTHSTVEKHIKSAIAAIEA 417 KD G L +I +LA N++IE L Q+ + + A +V++T+ E + A++A+ Sbjct: 360 VKDNAGVLVKITTILADSNINIEHLYQEPSTQKPSDATLVMITNKVKESKLNLALSALSQ 419 Query: 418 LDCVEKPITMIRMESL 433 L V+ I IR+E+L Sbjct: 420 LKEVDGEIMRIRIETL 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: 449 Number of extensions: 11 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: 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