Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_012400339.1 BPHY_RS04720 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000020045.1:WP_012400339.1 Length = 443 Score = 499 bits (1284), Expect = e-146 Identities = 266/442 (60%), Positives = 322/442 (72%), Gaps = 9/442 (2%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAA-- 58 M+P+ +GLLG GTVG G VLR N EEI+RR GR I I+ + + KA + A Sbjct: 1 MEPIKVGLLGFGTVGSGTFTVLRRNQEEINRRAGRGIEIARIAVRNSAKATAALGAEAGT 60 Query: 59 -FVKDPF-ELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFP 116 + D F +V +D+V E+ GGTGIA+E VL+AI NGKH+VTANK LLA +G EIF Sbjct: 61 VVITDDFGSVVDDPSIDIVAEMIGGTGIARELVLRAIGNGKHVVTANKALLAVHGTEIFE 120 Query: 117 LAEKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFA 176 A + V+V FEAAVAGGIPIIKALREGL ANRI+ IAGIINGT+N+ILSEMR++G FA Sbjct: 121 AARAKGVMVAFEAAVAGGIPIIKALREGLTANRIQYIAGIINGTTNYILSEMRDRGLDFA 180 Query: 177 DVLKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIK 236 LK AQ LGYAEADPTFDIEG DA HK TIMSA+AFG P+ F Y+EGISKL + DIK Sbjct: 181 TALKAAQELGYAEADPTFDIEGVDAAHKATIMSAIAFGVPVQFDKAYVEGISKLAAIDIK 240 Query: 237 YAEELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYY 296 YAEELGYRIKLLG+TR+T KGIELRVHPTLIP RLLANV+G MNAV V+ D VG TLYY Sbjct: 241 YAEELGYRIKLLGITRRTDKGIELRVHPTLIPAKRLLANVEGAMNAVVVHGDAVGTTLYY 300 Query: 297 GAGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLR 356 G GAGA PTASAVVAD++D+ RL AD HRVPHLAFQP ++ ILP+DE+TS YYLR Sbjct: 301 GKGAGAEPTASAVVADLVDVTRLHTADPEHRVPHLAFQPDRLSNTPILPIDEVTSGYYLR 360 Query: 357 VQAKDEPGTLGQIAALLAQENVSIEALIQK-----GVIDQTTAEIVILTHSTVEKHIKSA 411 ++ D G L I +LA +SI+AL+QK + +I+++TH TVEK++ +A Sbjct: 361 LRVADVTGVLADITRILADTGISIDALLQKESEHVDASKKGETDIILITHETVEKNVNAA 420 Query: 412 IAAIEALDCVEKPITMIRMESL 433 IA IEAL V +T +RME+L Sbjct: 421 IANIEALKTVVSKVTKLRMEAL 442 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: 503 Number of extensions: 19 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: 443 Length adjustment: 32 Effective length of query: 403 Effective length of database: 411 Effective search space: 165633 Effective search space used: 165633 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