Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_092056780.1 BQ4888_RS09615 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_900111775.1:WP_092056780.1 Length = 436 Score = 368 bits (945), Expect = e-106 Identities = 196/433 (45%), Positives = 275/433 (63%), Gaps = 1/433 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60 M+ + IGLLG GT+G G VL+DNA+ + RLG ++ ++ + DL + R + + + Sbjct: 1 MREIKIGLLGFGTIGTGVVKVLQDNAQLLQDRLGAKLTLARIADLDIQTPRAVTVAPELL 60 Query: 61 K-DPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 D +++ +D+V+EL GG A+ VLKAI NGKH+VTANK LLA +G EIF AE Sbjct: 61 TTDADAILSDPAIDLVIELIGGYEPARSFVLKAIANGKHVVTANKALLALHGAEIFAAAE 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V V FEAAV GGIPII A+RE L ANR S+ GI+NGT N+ILS M G + VL Sbjct: 121 AKGVDVYFEAAVGGGIPIISAIRENLCANRFTSLFGILNGTCNYILSRMTNDGDDYGAVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 K+AQ LGYAEADPTFD+EG D HK+ I+ +L FGT + F + EGIS + + DI +A Sbjct: 181 KDAQELGYAEADPTFDVEGIDTAHKLAILISLCFGTRVRFKDIHTEGISNISALDIHFAS 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 + GYRIKLL + + IE RVHPT+IP++ LA+V G NAVR+ D +G + YG G Sbjct: 241 QFGYRIKLLAIGKNENGQIEARVHPTMIPDNYPLADVHGAFNAVRLVGDFLGPAMLYGRG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG TASAV+ D++ I+R + A R P L + P ++ I PMD+I S YYLR A Sbjct: 301 AGMDATASAVMGDVMAISRDMLCGVAGRTPALGYVPEAIKDLAIKPMDDIVSQYYLRFAA 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALD 419 D+PG L Q++ +L + +SI ++IQ IV++TH E +++ A+A I+AL Sbjct: 361 DDKPGVLSQVSGILGKYEISITSMIQPERQIGGGVPIVMMTHDAKEANVRKALAEIDALA 420 Query: 420 CVEKPITMIRMES 432 +++ IR+E+ Sbjct: 421 VIKEQSRFIRIEN 433 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: 434 Number of extensions: 12 Number of successful extensions: 4 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