Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_011735216.1 PPRO_RS06410 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000015045.1:WP_011735216.1 Length = 438 Score = 357 bits (916), Expect = e-103 Identities = 188/435 (43%), Positives = 274/435 (62%), Gaps = 5/435 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCD--LSEEKARQICPSAA 58 M + +GL+G G +G G +L +NAE I ++G I + + D ++ ++ + PS Sbjct: 1 MNDIKVGLIGFGNIGAGVVKLLTNNAEVIRGKVGAGIVLKRIADRDITTDRGVAVDPSC- 59 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 D ++ ++ VV+EL GG AK VL+AIE GKHIVTANK LLA +G +IF A Sbjct: 60 MTTDVNDIFDDPEISVVIELVGGYEPAKSFVLRAIEKGKHIVTANKALLALHGQDIFAAA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 ++NV VQFEAAV GGIP++ A++ +AAN S+ GI+NGT N+IL+ M ++G+ FAD+ Sbjct: 120 ARKNVEVQFEAAVGGGIPVLTAIKGNMAANNFGSVFGIMNGTCNYILTRMTQEGADFADM 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L AQ LGYAE DPTFDIEG D HK+ I+ +L FGT ++F+A + EGIS++ D+K+A Sbjct: 180 LTAAQELGYAEPDPTFDIEGVDTAHKLAILVSLCFGTRIDFNAIHTEGISRISGLDVKFA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 + GYRIKLL + + + +E RVHPT+IP +A+V+GV NA+R+ D VG ++YG Sbjct: 240 RDFGYRIKLLAIGKLSDGKVEARVHPTMIPLHNPMADVNGVFNAIRLTGDFVGAVMFYGR 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAG PTASA+V D+I ++R + A R+ L QV+ + PM +I S Y LR Sbjct: 300 GAGQDPTASAIVGDLIGLSRSMLAGAGRRMAPLGLMDEQVRDLPVKPMADIVSKYMLRFS 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKG--VIDQTTAEIVILTHSTVEKHIKSAIAAIE 416 +D PG LG I L + +SI +++Q D IVI+TH VE +++A+ I+ Sbjct: 360 TRDIPGVLGTITGALGKHGISISSMVQTAHEANDNAPVPIVIMTHEAVEGSVQAALEEID 419 Query: 417 ALDCVEKPITMIRME 431 LD V + + IR+E Sbjct: 420 RLDFVCEKTSFIRIE 434 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: 14 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: 438 Length adjustment: 32 Effective length of query: 403 Effective length of database: 406 Effective search space: 163618 Effective search space used: 163618 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