Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_073038672.1 BUB04_RS09005 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_900129305.1:WP_073038672.1 Length = 442 Score = 398 bits (1022), Expect = e-115 Identities = 204/433 (47%), Positives = 288/433 (66%), Gaps = 3/433 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAA-- 58 M+ V +GL+G GTVG G VL +NA I RLG + ++ + DL E R + P A Sbjct: 1 MESVRVGLIGWGTVGCGVIRVLEENASVIRARLGFPLELARVADLDLETPRPV-PVAREK 59 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 ++ E++ + +VVEL GG A+ +L+A+E GKH+VTANK LLA +GNE+F A Sbjct: 60 LTQNAREILEDPGIQIVVELIGGLEPARSFILEALERGKHVVTANKALLAHHGNELFEHA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 E+ + FEA+VAGGIP++K+LREGLA N++ +I GI+NGT N+IL+ M E+G AFAD Sbjct: 120 ERHGGSIGFEASVAGGIPLLKSLREGLAGNKVDTIFGILNGTGNYILTRMTEEGLAFADA 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L+EAQ GYAEADPT D++G D HK+ I A+AFGTP+ F Y+EGI ++D D+++A Sbjct: 180 LREAQEKGYAEADPTLDVDGIDTAHKLAIAGAMAFGTPIRFDQVYVEGIRQIDPLDVQFA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 E GY++KLL + R +E+RVHPTLIP S +LA+V G NAV ++ + VG + YG Sbjct: 240 TEFGYQLKLLAIGRHVNGQLEMRVHPTLIPSSHVLASVRGAYNAVHLHGNAVGSIMLYGL 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAG +PT SAVVADI+DIAR + + +RVP L+F P Q I PM+++T+ YY R Sbjct: 300 GAGMMPTGSAVVADIMDIARDLASGVVNRVPPLSFLPENTQDIPIRPMEDVTTKYYFRFS 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEAL 418 A D PG L +I+ +L + +SI A+IQKG + IV+LTH E+ ++ ++ AI+ L Sbjct: 360 AVDRPGVLSKISGILGENAISIAAVIQKGREVEGAVPIVMLTHEAQERAVRKSLEAIDRL 419 Query: 419 DCVEKPITMIRME 431 D V P +IR+E Sbjct: 420 DIVRGPTRIIRIE 432 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: 493 Number of extensions: 20 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: 442 Length adjustment: 32 Effective length of query: 403 Effective length of database: 410 Effective search space: 165230 Effective search space used: 165230 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