Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_046009583.1 OLEAN_RS13040 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000967895.1:WP_046009583.1 Length = 432 Score = 462 bits (1189), Expect = e-135 Identities = 237/434 (54%), Positives = 316/434 (72%), Gaps = 4/434 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60 MK V +G+ GLGTVG G VL NA+EI+RR GREI I + + A + Sbjct: 1 MKAVKVGICGLGTVGSGTFNVLTGNAQEITRRAGREIIIQQVGSRRDNPAADTS-NTDVT 59 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 +D F++ ++D+VVEL GG +AK+ VL AIENGKH+VTANK L+AE+G EIF AE Sbjct: 60 RDIFDVATNPEIDIVVELIGGYDVAKKLVLLAIENGKHVVTANKALIAEHGTEIFAAAEA 119 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 + V V +EA +AGGIPI+KALREGLA N+I +AGIINGT NFIL+EMR+KG FADVLK Sbjct: 120 KGVSVMYEAGIAGGIPIVKALREGLAGNKINWLAGIINGTGNFILTEMRDKGRDFADVLK 179 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 EAQ LGYAEADPTFD+EG DA HK+TI+S++A+G P+ F C+ EGI + D++YAEE Sbjct: 180 EAQELGYAEADPTFDVEGIDAAHKLTILSSIAYGIPLQFENCFCEGIGGITPEDVQYAEE 239 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 LGYRIK LGV+ +T +GI+LRVHPTLIPE R +A +DGV+NA+ VN D VG+TL+ G GA Sbjct: 240 LGYRIKHLGVSSRTARGIDLRVHPTLIPEKRSIAKIDGVLNAIMVNGDAVGDTLFSGPGA 299 Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360 GA PTASAVVADIID+ARL++A + RV HL ++ QV +LP+++I ++YYLR+ A Sbjct: 300 GAGPTASAVVADIIDLARLIDAPASSRVHHLGYK--QVDDTKVLPIEDIETAYYLRIPAL 357 Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAIAAIEALD 419 D+ G L IA +L++ ++IEALIQK + + ++++LTH EK + AI+AI+AL+ Sbjct: 358 DKTGVLANIATILSERGINIEALIQKEQAEGEEIVQVILLTHIIQEKIMNDAISAIQALE 417 Query: 420 CVEKPITMIRMESL 433 + +T IR+E L Sbjct: 418 GTQGDVTRIRVEYL 431 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: 522 Number of extensions: 23 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: 432 Length adjustment: 32 Effective length of query: 403 Effective length of database: 400 Effective search space: 161200 Effective search space used: 161200 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