Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_035241318.1 Q366_RS17135 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000745975.1:WP_035241318.1 Length = 437 Score = 362 bits (930), Expect = e-104 Identities = 188/432 (43%), Positives = 271/432 (62%), Gaps = 1/432 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAF 59 MK ++IGLLG G VG G A +L+ E + R+G + + + DL R + Sbjct: 1 MKTIHIGLLGFGVVGAGVAKLLKGKKELLESRIGACLNLKTIADLDITTDRGVDLTGTQL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 D ++ D++++VEL GG +AK + K +EN KH+VTANK LLA +GNE+ LA Sbjct: 61 TTDAASVINDPDINIIVELIGGETVAKNFIFKTLENKKHVVTANKALLAGFGNELVSLAG 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 K V + FEA+ G +P+IK+LRE L AN I + GI+NGT N+ILS+M GS FAD L Sbjct: 121 KNQVDLAFEASCGGCMPVIKSLRESLVANDIHVMCGILNGTCNYILSKMTRDGSGFADAL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 K+AQ LG+AEA+P+ D++G D HK+ I++ALA G +N ++EGI + DI +A Sbjct: 181 KKAQELGFAEAEPSLDVDGYDTAHKLAILNALAHGMKINLDDIHVEGIRNIGPADIGFAR 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 E GY IKLL + +K +E RVHPT+IP S L++VD MNA+ ++AD G T+ YG G Sbjct: 241 EFGYTIKLLAIGKKHENHVEARVHPTMIPCSNPLSHVDHSMNAIAIDADATGRTMLYGHG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG +PTASAV++DI DIAR + + T RVP L + +Q ILPM ++++ YYLR +A Sbjct: 301 AGMMPTASAVLSDIADIARNIISGTRRRVPTLGYPEENIQKIPILPMAQLSTRYYLRFEA 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALD 419 +D PG L I+ +L + ++SI+++ QKG IV+LTH E +++A+ I D Sbjct: 361 QDHPGVLSTISGILGENDISIKSVHQKGRNTNGQVPIVMLTHLARESRVQTALTRIVQTD 420 Query: 420 CVEKPITMIRME 431 CV +IR+E Sbjct: 421 CVVGQPVIIRIE 432 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: 22 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: 437 Length adjustment: 32 Effective length of query: 403 Effective length of database: 405 Effective search space: 163215 Effective search space used: 163215 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