Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_090443019.1 BLS63_RS09060 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_900100495.1:WP_090443019.1 Length = 434 Score = 499 bits (1284), Expect = e-146 Identities = 252/434 (58%), Positives = 324/434 (74%), Gaps = 2/434 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60 MKPV +G+ GLGTVGGG VL+ NAEEI+RR GR+I ++ + S+ I Sbjct: 1 MKPVKVGICGLGTVGGGTFNVLKRNAEEIARRAGRDIEVAQIALRSQNPQCDIT-GTPIT 59 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 +D FELV ++D+V+EL GG +A++ VLKAI+NGKH+VTANK L+A +GNEIF A + Sbjct: 60 QDVFELVCNPEIDIVIELIGGYTLARDLVLKAIDNGKHVVTANKALIAVHGNEIFAKARE 119 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 + VIV FEAAVAGGIP+IKA+REGLAANRI +AGIINGT NFILSEMREKG AFADVL+ Sbjct: 120 KGVIVAFEAAVAGGIPVIKAIREGLAANRINWLAGIINGTGNFILSEMREKGRAFADVLQ 179 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 EAQALGYAEADPTFD+EG DA HK+TI++++AFG P+ F Y EGI++L + D+ YAE Sbjct: 180 EAQALGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKAYTEGITQLTTADVNYAEA 239 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 LGYRIK LGV R+T GIELRVHPTLIP RL+ANV+GVMNAV VN D G TLYYGAGA Sbjct: 240 LGYRIKHLGVARRTDAGIELRVHPTLIPADRLIANVNGVMNAVMVNGDAAGSTLYYGAGA 299 Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360 G PTAS+V+AD++D+ R + D +RVPHLAFQP + ILP+ S+YYLR+QAK Sbjct: 300 GMEPTASSVIADLVDVVRALTTDPTNRVPHLAFQPDALSDHPILPIGACESAYYLRIQAK 359 Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQT-TAEIVILTHSTVEKHIKSAIAAIEALD 419 D PG L Q+A++L++ ++IE+++QK V + ++++TH +E I AI+A+EALD Sbjct: 360 DHPGVLAQVASILSERGINIESIMQKEVEEHDGLVPMILVTHRVLEARINEAISALEALD 419 Query: 420 CVEKPITMIRMESL 433 V + IR+E L Sbjct: 420 DVVGSVVRIRVEQL 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: 530 Number of extensions: 14 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: 434 Length adjustment: 32 Effective length of query: 403 Effective length of database: 402 Effective search space: 162006 Effective search space used: 162006 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