Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_093393243.1 BM091_RS02585 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_900114975.1:WP_093393243.1 Length = 439 Score = 398 bits (1023), Expect = e-115 Identities = 205/434 (47%), Positives = 283/434 (65%), Gaps = 3/434 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQIC-PSAAF 59 M+ +N+G+LG GTVG G +L+ + EEI +RLGRE+ + + D+ E+ R + P Sbjct: 1 MEQLNVGILGWGTVGCGVIEILQSHREEIKKRLGRELVLKKVADIDLERPRPVSLPREIL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 +D ++ D+D+VVEL GG A+ ++KA+E GKH+VTANK LLA +GNE+F A Sbjct: 61 TRDAKAVIEDPDIDIVVELIGGIEPARSFIMKALERGKHVVTANKALLAHHGNELFDFAR 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 K I+ +EA+VAGGIP IK+LREGLAAN I ++ GI+NGT+NFIL+ MRE G F + L Sbjct: 121 KHQRIIAYEASVAGGIPFIKSLREGLAANNIDTVFGILNGTANFILTRMRESGLTFQEAL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 KEAQ+ GYAEADP DIEG D HK+ I +A+AF + F + Y+EGIS +D DI++ E Sbjct: 181 KEAQSRGYAEADPRLDIEGIDTAHKLAITAAIAFNMSIVFDSIYVEGISGIDPLDIQFGE 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 E GY +KLL + R G+ELRVHPT IP +LA V G NAV V+ D VG + YG G Sbjct: 241 EFGYVLKLLAIARLGEGGVELRVHPTFIPSGHVLAGVRGAYNAVHVHGDAVGHVMLYGLG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG +PT SAVVAD++D+AR + R+P A ++ + PMDE+ + YY R A Sbjct: 301 AGMMPTGSAVVADLMDLARDIAQGIHCRLP--ALGSYELNPIPVKPMDEVVTCYYFRFSA 358 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALD 419 D+PG L +I+ +L + N+SI A+IQKG IV++TH VE ++ AI I+ LD Sbjct: 359 VDQPGVLSKISGILGRNNISISAVIQKGRHIGGAVPIVMVTHEAVESSVRRAIEEIDRLD 418 Query: 420 CVEKPITMIRMESL 433 V +IR+E+L Sbjct: 419 VVRAKTQLIRIENL 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: 464 Number of extensions: 24 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: 439 Length adjustment: 32 Effective length of query: 403 Effective length of database: 407 Effective search space: 164021 Effective search space used: 164021 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