Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013721123.1 ALIDE2_RS00115 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000204645.1:WP_013721123.1 Length = 461 Score = 316 bits (810), Expect = 8e-91 Identities = 170/385 (44%), Positives = 240/385 (62%), Gaps = 11/385 (2%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI---CPSAAFV 60 + +G++G+GTVG G VLR N I+ R GR I I A+ + +A + P + Sbjct: 24 LRVGMIGMGTVGAGVWRVLRRNQALIAARAGRPIDIVAVAARTPARAAAVLEGAPGVRLL 83 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 DP L VDVV+EL GG+G A+ VL A+ +GKH+VTANK LLAE+G E+ +A + Sbjct: 84 ADPMRLATDPGVDVVLELAGGSGAARGWVLAALAHGKHVVTANKALLAEHGEELATVAAR 143 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 + +EAAVAGG+P++KALREGLAANRI ++AG++NGTSN+IL+ M+ G A L Sbjct: 144 HGRTLAYEAAVAGGVPVVKALREGLAANRIHALAGVLNGTSNYILTRMQAGGLDLAAALA 203 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 EAQALGYAEADP D++G DA HK+ +++A AFG P+ A ++EG+ L D+ A + Sbjct: 204 EAQALGYAEADPALDVDGTDAAHKLALLAANAFGMPVRLDAVHVEGLRGLRQGDVAAAAQ 263 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 LGY ++LL + R+ +G+ELRVHP L+PE LA + G N + V D GE Y GAGA Sbjct: 264 LGYAVRLLAIARRGAEGVELRVHPALVPERHALARLSGAANGLLVQGDAAGEAFYGGAGA 323 Query: 301 GALPTASAVVADIIDIARL-VEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 G PTASAV+AD++D+ARL A VP L + LPM ++ + ++LR+ Sbjct: 324 GGEPTASAVLADLVDLARLPAGAHARAGVPTLGVHSRAAEQPAPLPMAQVRTRHFLRLL- 382 Query: 360 KDEPGTL---GQIAALLAQENVSIE 381 PG + LLA+ +S++ Sbjct: 383 ---PGPALNEAEALRLLARAGLSVQ 404 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: 453 Number of extensions: 9 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: 461 Length adjustment: 33 Effective length of query: 402 Effective length of database: 428 Effective search space: 172056 Effective search space used: 172056 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