Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_012991647.1 THAL_RS03030 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000025605.1:WP_012991647.1 Length = 434 Score = 347 bits (891), Expect = e-100 Identities = 191/436 (43%), Positives = 273/436 (62%), Gaps = 16/436 (3%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAFVKD 62 V +G++G GTVG G A +L N I ++ G +I ++ + D+ E+ R P Sbjct: 3 VRVGIVGCGTVGTGTAELLLKNGHLIRKKTGLDIVLTKVADVDWERPRSFEVPHHLRTTH 62 Query: 63 PFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEKQN 122 E++ ++ D+VVEL GG G AK+ +L+A+E GKH+VTANK LLAE G EIF A+++ Sbjct: 63 YTEVI--EESDIVVELVGGKGFAKQVILEALEKGKHVVTANKHLLAEDGKEIFLKAQEKG 120 Query: 123 VIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLKEA 182 + + FEA+V GGIPI+KALREGL+ANRI +I GI+NGT+N+IL+ M E+ F + L EA Sbjct: 121 LWIGFEASVGGGIPIVKALREGLSANRILNIYGILNGTTNYILTRMLEEDMTFDEALAEA 180 Query: 183 QALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEELG 242 + +GYAEADP+ DI+G D+ HKITI++ +AFG F + ++EGI ++D D++ +ELG Sbjct: 181 KRMGYAEADPSLDIDGWDSAHKITILATVAFGKFFPFGSVHVEGIRQVDLLDVELGKELG 240 Query: 243 YRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGAGA 302 Y +KLL + ++ +ELRVHPT IP LA V V NAV V D VG+T++YG GAG+ Sbjct: 241 YTLKLLAICKRVDSEVELRVHPTFIPSEEQLAKVSDVFNAVMVEGDFVGKTMFYGRGAGS 300 Query: 303 LPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAKDE 362 PTASAVVADIIDIAR + A P + + + S YYLR+ D Sbjct: 301 HPTASAVVADIIDIARNIAGGIR------ALHPFYWEEEELHISSNFYSRYYLRLDVPDR 354 Query: 363 PGTLGQIAALLAQENVSIEALIQK-------GVIDQTTAEIVILTHSTVEKHIKSAIAAI 415 PG L ++A +L +SI +++QK G Q+ +V+LTH EK ++ AI I Sbjct: 355 PGVLAKVAQVLGDNGISIASVLQKEKVCRMAGREGQSVIPLVLLTHKAYEKQMRKAIEEI 414 Query: 416 EALDCVEKPITMIRME 431 + L VE +IR+E Sbjct: 415 KNLPMVEGHPVLIRVE 430 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: 489 Number of extensions: 17 Number of successful extensions: 3 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: 434 Length adjustment: 32 Effective length of query: 403 Effective length of database: 402 Effective search space: 162006 Effective search space used: 162006 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