Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013536949.1 THEAM_RS00980 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000185805.1:WP_013536949.1 Length = 431 Score = 379 bits (973), Expect = e-109 Identities = 204/437 (46%), Positives = 286/437 (65%), Gaps = 10/437 (2%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAF 59 M +G++G GTVGGG +L +N E I R+GR + I+ + D E+A + P Sbjct: 1 MDSFKVGIVGCGTVGGGVVKLLLENGELIRERIGRPVEIAFVADPQRERALALGVPKEKV 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 D E + + D D VVEL GGTGIAK V +A++ G+H+VTANK LLA+YG E+F LA+ Sbjct: 61 FPDGIEAL-KADCDAVVELIGGTGIAKRVVEEALKKGRHVVTANKALLADYGEELFRLAK 119 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V ++FEA+V GGIP+IKALREGLA NRI++I GIINGT+NFIL++M ++G +F + L Sbjct: 120 ENGVSLKFEASVGGGIPVIKALREGLAGNRIEAIYGIINGTANFILTQMSQRGISFEEAL 179 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA- 238 KEAQ LGYAEADPT D++G DA HKI I++ LA+ + ++ GI ++ DI+ A Sbjct: 180 KEAQELGYAEADPTLDVDGYDAAHKIAILATLAYCRFVKTEQVFVRGIREITPLDIEIAR 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 EE GY +KLL +T+ IE+RVHPT+IPE+ +LA+V+GV NA V D VGETL+YG Sbjct: 240 EEFGYGVKLLAITKLVNGEIEVRVHPTMIPENHILASVNGVFNACFVEGDFVGETLFYGK 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAG PTASAVV+DI+D+A + VP F+ ++ + +E TSS+YLR Sbjct: 300 GAGREPTASAVVSDIVDLA----LGNTYAVPECLFKGENLR---VREPEEFTSSFYLRFT 352 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEAL 418 A D PG L +IA++L + N+SI+ +QK + +V+ TH +K I AI I+AL Sbjct: 353 ALDRPGVLAKIASILGKHNISIKMALQKSIEFDGGVPVVMTTHPAPKKAISLAIKEIDAL 412 Query: 419 DCVEKPITMIRMESLHD 435 D + KP + +E L + Sbjct: 413 DVIVKPTFVCMIEELEE 429 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: 479 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: 431 Length adjustment: 32 Effective length of query: 403 Effective length of database: 399 Effective search space: 160797 Effective search space used: 160797 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