Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_018945867.1 B1A74_RS05210 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_001995255.1:WP_018945867.1 Length = 435 Score = 452 bits (1164), Expect = e-132 Identities = 240/435 (55%), Positives = 305/435 (70%), Gaps = 2/435 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAA-F 59 M PV IG+LGLGTVG G VL N +I+ R GR I + A E+ R S Sbjct: 1 MTPVKIGILGLGTVGCGTVNVLARNGTDIAGRAGRGIEVVAAAARDIERERDCDTSGIRL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 DP +V +V+VVVEL GGT A++ VL+AI+ GKH+VTANK ++A YGNEIF A Sbjct: 61 TTDPGVVVDDPEVEVVVELMGGTETARDLVLRAIDAGKHVVTANKAMIALYGNEIFERAH 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V+V FEAAVAGGIPIIKA+REGLA NRI+ +AGIINGT NFIL+EMR+KG F DVL Sbjct: 121 ARGVMVAFEAAVAGGIPIIKAIREGLAGNRIEWLAGIINGTGNFILTEMRDKGRDFEDVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 EAQ+LGYAEADPTFD+EG DA HK+ I++++AFG P+ F +EGIS + D+ +A Sbjct: 181 AEAQSLGYAEADPTFDVEGIDAAHKLAILASIAFGIPLQFDRVAVEGISGITREDVSFAA 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 ELGYRIK LG+ R+ G ELRVHPTLIPE RL+ANVDGVMNAV V D VG TLYYGAG Sbjct: 241 ELGYRIKHLGIARRMDNGYELRVHPTLIPERRLIANVDGVMNAVLVQGDAVGPTLYYGAG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AGA TASAVVAD++D+ R + D +RVPHLAFQP + +L M+++ +S+YLR++ Sbjct: 301 AGAEATASAVVADLVDVVRALTTDPENRVPHLAFQPDALSDHPVLAMEDVHTSFYLRLRT 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQT-TAEIVILTHSTVEKHIKSAIAAIEAL 418 +D PG L I +L + +SIEA++Q+ Q A I++LTH+ E + AI A+EAL Sbjct: 361 QDRPGVLADITRILGEHGISIEAILQREPDPQRGEATIIMLTHAVREGAMNEAITAVEAL 420 Query: 419 DCVEKPITMIRMESL 433 + PIT IRME+L Sbjct: 421 PHLLTPITRIRMEAL 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: 511 Number of extensions: 11 Number of successful extensions: 2 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: 435 Length adjustment: 32 Effective length of query: 403 Effective length of database: 403 Effective search space: 162409 Effective search space used: 162409 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