Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013133979.1 ARNIT_RS00825 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000092245.1:WP_013133979.1 Length = 420 Score = 330 bits (847), Expect = 4e-95 Identities = 187/430 (43%), Positives = 266/430 (61%), Gaps = 14/430 (3%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREI--RISAMCDLSEEKARQICPSAAFVK 61 + I ++G+GTVG A +L+DN + I+ R G EI I + DLS K R + S Sbjct: 2 LKIAIIGVGTVGASVANILKDNKDIITSRAGVEIVPTIGVVNDLS--KKRDV--SIELTD 57 Query: 62 DPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEKQ 121 D + + +D++VEL GG E + +A+ GK +VTANK LLA + ++ LA Sbjct: 58 DLDKALNDDSIDIIVELMGGVERPYEIIKRALSKGKPVVTANKALLAYHRYDLEKLAG-- 115 Query: 122 NVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLKE 181 ++ ++EAAVAGGIPII ALR+GL+AN I+SI GI+NGT N++L+ M G + +LKE Sbjct: 116 DIPFEYEAAVAGGIPIINALRDGLSANNIESIRGILNGTCNYMLTRMINDGIDYESILKE 175 Query: 182 AQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEEL 241 AQ LGYAEADPTFD+ G DA HK+ I++++A+ +EGI +D+ DI +A E Sbjct: 176 AQELGYAEADPTFDVGGFDAAHKLLILASIAYDVDAKPEDILIEGIQNIDTPDIDFANEF 235 Query: 242 GYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGAG 301 Y IKLL + ++ GK IELRVHP IP++ ++A VDGVMN + V D VGET+YYG GAG Sbjct: 236 NYSIKLLAIAKRVGKQIELRVHPVFIPKTEMIAKVDGVMNGISVIGDKVGETMYYGPGAG 295 Query: 302 ALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAKD 361 TASAV+A+I+DIAR P L F+ TI+P DEI + YYLR++ +D Sbjct: 296 GNATASAVIANIVDIAR-----RGKGAPMLGFEFDYKANLTIMPKDEIETKYYLRLRIED 350 Query: 362 EPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALDCV 421 + G L ++ +L + +SIE +IQK + T A +++ TH +EK+I A+ IE Sbjct: 351 KVGVLAKVTKILGEHEISIEKMIQK-PYNTTCAHLLLSTHVCIEKNINKALKEIENSGVA 409 Query: 422 EKPITMIRME 431 MIR+E Sbjct: 410 TTKPVMIRIE 419 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: 436 Number of extensions: 19 Number of successful extensions: 4 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: 420 Length adjustment: 32 Effective length of query: 403 Effective length of database: 388 Effective search space: 156364 Effective search space used: 156364 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