Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_092994380.1 BLP65_RS06305 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_900102855.1:WP_092994380.1 Length = 436 Score = 466 bits (1200), Expect = e-136 Identities = 245/436 (56%), Positives = 312/436 (71%), Gaps = 4/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSA--A 58 M+PV +GLLGLGTVGGG +L++NAEEI RR GR I + C K R IC + + Sbjct: 1 MEPVKVGLLGLGTVGGGTINLLQENAEEIMRRAGRGIEVIHACARDLNKPR-ICDTEGIS 59 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 DP E+V DVDV++EL GG G+A++ +L+AIENGKHIVTANK L+A++GNEIF A Sbjct: 60 LSTDPNEVVDNPDVDVILELIGGEGMARDVMLRAIENGKHIVTANKALIAKHGNEIFAAA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 E + VIV FEAAVAGGIPIIK LREGLAANRI+ +AGIINGT NFIL+EMR++ FADV Sbjct: 120 EARGVIVAFEAAVAGGIPIIKGLREGLAANRIEWLAGIINGTGNFILTEMRDEDRDFADV 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L EAQ LGYAEADPTFD+EG DA HK+ IM+++AFG P+ F Y EGI+ + D+ +A Sbjct: 180 LAEAQRLGYAEADPTFDVEGIDAAHKLAIMASIAFGMPLKFDRVYTEGITHVTRDDVTFA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 EELGYRIK LG+ R+T GIELRVHPTLIPE +L+ANVDGVMNAV V +MVG TLYYGA Sbjct: 240 EELGYRIKHLGIARRTWNGIELRVHPTLIPERQLIANVDGVMNAVVVKGNMVGPTLYYGA 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGA PTASAVVAD+ID+ R + RVPHL P + ++IL MDE+ ++YYLR+Q Sbjct: 300 GAGAEPTASAVVADLIDVVRALSCAPESRVPHLGVHPHALADESILAMDEVETAYYLRMQ 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQK-GVIDQTTAEIVILTHSTVEKHIKSAIAAIEA 417 D PG L + A +SIEA++QK ++ I++LT + E+ + A+ + Sbjct: 360 VVDRPGVLADLTRTFADLEISIEAVVQKEPPPGESLVTIILLTRTVQERQMVKAMEMLGK 419 Query: 418 LDCVEKPITMIRMESL 433 +D + +T IR+E L Sbjct: 420 MDAIFGDVTRIRLEYL 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: 507 Number of extensions: 12 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