Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_015817208.1 TERTU_RS05175 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000023025.1:WP_015817208.1 Length = 439 Score = 464 bits (1195), Expect = e-135 Identities = 240/441 (54%), Positives = 322/441 (73%), Gaps = 11/441 (2%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60 MKPVN+G+ GLGTVG G VL N ++I+ + GREI+I+ + + R+ C Sbjct: 1 MKPVNVGICGLGTVGSGTFNVLTRNNKDINAKAGREIKIT---HIGARRTREDCDLTGVT 57 Query: 61 --KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 D F +V +VD++VEL GGT +AK+ VL+A+ NGKH+VTANK L+AEYGNE+F A Sbjct: 58 VSNDIFAVVNDPNVDILVELIGGTTVAKDLVLQAVRNGKHVVTANKALIAEYGNELFAEA 117 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 NV + +EAAVAGGIPII++LREGLAAN+++ +AGIINGT NFIL+EMR+KG F DV Sbjct: 118 VSNNVTISYEAAVAGGIPIIRSLREGLAANKVEWLAGIINGTGNFILTEMRDKGRQFDDV 177 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 LKEAQALGYAEADPTFD+EG DA HK+ I++++AFG P+ F + EGIS++ D+ YA Sbjct: 178 LKEAQALGYAEADPTFDVEGIDAAHKLVILASIAFGMPLQFDKVFTEGISQIRPEDVAYA 237 Query: 239 EELGYRIKLLGVTRK-TGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYG 297 +ELGYRIK LG+TR+ GKGIELRVHPT+IP+SRLLANV+GVMNAV V D VG TLYYG Sbjct: 238 DELGYRIKHLGITRRLPGKGIELRVHPTMIPQSRLLANVNGVMNAVVVKGDAVGPTLYYG 297 Query: 298 AGAGALPTASAVVADIIDIARLVE----ADTAHRVPHLAFQPAQVQAQTILPMDEITSSY 353 AGAGA PTASAV++DI+ ++R+V ++ A VPHL + + TILP++EI S+Y Sbjct: 298 AGAGAEPTASAVISDIVHVSRMVNSSYVSEDATAVPHLGYGEDHLHDYTILPIEEIESAY 357 Query: 354 YLRVQAKDEPGTLGQIAALLAQENVSIEALIQKGVID-QTTAEIVILTHSTVEKHIKSAI 412 YLR+ A D+PG L ++ + ++ +SIEALIQK + Q +++LT+ T+EK + AI Sbjct: 358 YLRLSALDQPGVLSRVTQIFSEAGISIEALIQKEPKEGQEHVSVILLTNRTIEKQVNKAI 417 Query: 413 AAIEALDCVEKPITMIRMESL 433 IE+L ++ + IR+ESL Sbjct: 418 EQIESLSPIQGNVVRIRVESL 438 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: 515 Number of extensions: 12 Number of successful extensions: 5 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: 439 Length adjustment: 32 Effective length of query: 403 Effective length of database: 407 Effective search space: 164021 Effective search space used: 164021 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