Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_028314263.1 G491_RS0108280 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000429905.1:WP_028314263.1 Length = 442 Score = 365 bits (938), Expect = e-105 Identities = 181/429 (42%), Positives = 276/429 (64%), Gaps = 1/429 (0%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAFVKD 62 +++GLLG G VG G A +L N + I+ R+G EI+++ D++ + + + D Sbjct: 9 ISVGLLGCGVVGAGVAKLLAQNGDLIASRIGMEIKLAKAADINPDAVADLNLADGVYTND 68 Query: 63 PFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEKQN 122 +++ + ++VEL GG GIAK+ VL A+ GK +VTANK L+A Y +EI EK Sbjct: 69 AMDVINDPTIPIIVELIGGQGIAKDFVLAALNKGKTVVTANKALIAAYRDEIAEACEKSG 128 Query: 123 VIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLKEA 182 FEA+V G +P+IK+LRE L +N++ SI GI+NGT N+IL+++ ++G F L +A Sbjct: 129 ADFLFEASVGGCMPVIKSLRESLVSNKVDSIFGILNGTCNYILTQITQEGMPFDQALAQA 188 Query: 183 QALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEELG 242 Q LG+AEADPT D+EG D HK+ + ALAFGT +N+ Y++GI+++ DI A E G Sbjct: 189 QELGFAEADPTLDVEGMDTVHKLALSVALAFGTRVNYKEIYVDGITRITPLDITIAAEFG 248 Query: 243 YRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGAGA 302 Y +KLL + + G +E RVHPT+IP LL++V MNAV++ D VGE + YGAGAG Sbjct: 249 YSVKLLAIAKNHGDFVEARVHPTMIPHDNLLSSVGRNMNAVKIVGDAVGEMVLYGAGAGM 308 Query: 303 LPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAKDE 362 +PTASAVV DI+D AR ++ R+P ++QPA ++ ++PMDE+ S YY+R A D Sbjct: 309 MPTASAVVGDIVDAARNIQLGCHPRIPAFSYQPAAIRELPLMPMDELVSRYYVRFSALDR 368 Query: 363 PGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALDCVE 422 PG L +++ +LA+ ++SI ++ QKG + IV+LTH E +I+ A+ + +LD + Sbjct: 369 PGVLSKVSGVLAKYSISIASVHQKGRHTEGPVPIVMLTHEAKEANIRKALEEVGSLDVIA 428 Query: 423 KPITMIRME 431 + +IR+E Sbjct: 429 EAPMLIRIE 437 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: 444 Number of extensions: 17 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