Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_086508980.1 BZY95_RS05570 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_002151265.1:WP_086508980.1 Length = 438 Score = 459 bits (1181), Expect = e-134 Identities = 239/445 (53%), Positives = 313/445 (70%), Gaps = 19/445 (4%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAM--------CDLSEEKARQ 52 MKPV +G+ GLGTVGGG VL NA+EI+RR GR I I + CDL+ K Sbjct: 1 MKPVRVGICGLGTVGGGTFNVLTRNADEIARRAGRPIVIEQVALRSTNPECDLTGIKT-- 58 Query: 53 ICPSAAFVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGN 112 D FE+ D+DV+VE+ GG + +E VL AI NGKH+VTANK L+A +GN Sbjct: 59 -------TNDVFEVARNPDIDVLVEVLGGYDVPRELVLTAIANGKHVVTANKALIAVHGN 111 Query: 113 EIFPLAEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKG 172 EIF A +Q VIV FEAAVAGGIP+IK+LREGL ANRI+ +AGIINGT N+IL+ MR +G Sbjct: 112 EIFQAAHEQGVIVAFEAAVAGGIPVIKSLREGLGANRIEWVAGIINGTGNYILTHMRSEG 171 Query: 173 SAFADVLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDS 232 AF DVL EAQALGYAEADPTFD+EG DA HK+TI++++A+G P+ F Y EGIS++ Sbjct: 172 RAFEDVLAEAQALGYAEADPTFDVEGIDAAHKLTILASIAYGVPLQFEKAYTEGISRVTF 231 Query: 233 RDIKYAEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGE 292 D++ A+ LGY IK LG++++T G+ELRVHPTLIP+ RLLANV GV NA+ + D VG Sbjct: 232 DDVEQADNLGYVIKHLGISKRTEHGLELRVHPTLIPKERLLANVHGVKNAIAIMGDAVGP 291 Query: 293 TLYYGAGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPA--QVQAQTILPMDEIT 350 TLYYGAGAG+ PTASAVVAD++D+AR + D +RVP+LAF ILPM++I Sbjct: 292 TLYYGAGAGSEPTASAVVADLLDVARDIATDHHYRVPYLAFSGIGDDDGGMPILPMEDIV 351 Query: 351 SSYYLRVQAKDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKS 410 ++YYLR+ A D PG L ++A +L+++ +SIEAL+QK + I++LTH EKH+ Sbjct: 352 TAYYLRLLAVDRPGVLARVATILSEQGISIEALVQKEATEGELVPIILLTHRCREKHMNE 411 Query: 411 AIAAIEALDCVEKPITMIRMESLHD 435 AI IE++ + P+T IR+ESL + Sbjct: 412 AIRQIESMADIAGPVTRIRVESLDE 436 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: 499 Number of extensions: 21 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: 438 Length adjustment: 32 Effective length of query: 403 Effective length of database: 406 Effective search space: 163618 Effective search space used: 163618 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 Jul 25 2024. The underlying query database was built on Jul 25 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