Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_011939064.1 GURA_RS11050 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000016745.1:WP_011939064.1 Length = 436 Score = 366 bits (940), Expect = e-106 Identities = 187/432 (43%), Positives = 273/432 (63%), Gaps = 1/432 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPS-AAF 59 MK + IGLLG GT+G G +L N+ + +LG + + + DL R + Sbjct: 1 MKEIKIGLLGFGTIGAGVVKLLTKNSALLEEKLGARLSLKKIADLDITTDRGVSVEPGVL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 + E++ ++ +V+EL GG A+ VLKAI NGKHI+TANK LLA +G EI+ A Sbjct: 61 TTNVDEVLCDPEISIVIELIGGYEPARSFVLKAIANGKHIITANKALLAVHGEEIYAAAA 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 ++ V + FEAAV GGIP++ A++ +A N ++ GI+NGT N+ILS+M + G FA+VL Sbjct: 121 QKGVEILFEAAVGGGIPVLSAIKGNMAGNNFSTVLGILNGTCNYILSKMTQDGVDFAEVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 + AQ LGYAEADPTFD+EG D HK+ ++ +L FGT ++ EGIS + + DI +A Sbjct: 181 QTAQELGYAEADPTFDVEGIDTAHKLCLLLSLCFGTRVDLKDISTEGISSISAVDINFAR 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 + GY+IKLL + ++ G+ IE RVHPT+IP + LA+V+GV NA+R+ D VG ++YG G Sbjct: 241 DFGYKIKLLAIGKRDGERIEARVHPTMIPVNYPLADVNGVFNAIRLTGDFVGPVMFYGRG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG PTASAV+ D++DIAR + A + R L + +V+ TI PM EI S YY+R A Sbjct: 301 AGMEPTASAVIGDVVDIARNMLAGISRRSAPLGYLDDRVKKLTIKPMGEIVSKYYIRFNA 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALD 419 D PG L +I+ L N+SIE+++Q T IVI+TH E ++ A+A I+A D Sbjct: 361 VDRPGVLAKISGALGASNISIESMMQTARSASETVPIVIMTHEAREMDVRKALAEIDAFD 420 Query: 420 CVEKPITMIRME 431 +++ +IR+E Sbjct: 421 FIKEKSNLIRIE 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: 444 Number of extensions: 12 Number of successful extensions: 1 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: 436 Length adjustment: 32 Effective length of query: 403 Effective length of database: 404 Effective search space: 162812 Effective search space used: 162812 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