Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_028989924.1 G579_RS0109025 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000423825.1:WP_028989924.1 Length = 439 Score = 490 bits (1262), Expect = e-143 Identities = 255/438 (58%), Positives = 327/438 (74%), Gaps = 8/438 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICP-SAAF 59 M+PV IG++GLGTVG G VLR NA EI RR+GR +R++ + + + + P A Sbjct: 1 MEPVRIGIIGLGTVGRGTLDVLRRNALEIERRVGRPVRVAQVAVRNPARLAGVSPVDFAV 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 DPF LV ++DVVVEL GG A+E VL AI +GKH+VTANK LLA +GNEIF A+ Sbjct: 61 TGDPFALVNSPELDVVVELIGGIEPARELVLTAIRSGKHVVTANKALLALHGNEIFEAAQ 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 +Q V+V FEAAVAGGIPIIKALREGLA NRI+ + GIINGT N+IL++MRE+G +FA+ L Sbjct: 121 QQGVVVAFEAAVAGGIPIIKALREGLAGNRIEWLCGIINGTCNYILTQMREQGWSFAEAL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 +EAQALGYAEADPTFDIEG D+ HK+TI+ A+AFG P++F++ +EGI+ L D+ YAE Sbjct: 181 REAQALGYAEADPTFDIEGIDSAHKLTILGAIAFGIPLDFASVPVEGINGLHGMDVTYAE 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 ELGYRIKLLG+ R+ +G+ELRVHPTL+P LLA+V+G NAV V D VG+TLYYG G Sbjct: 241 ELGYRIKLLGLARRVEQGVELRVHPTLVPARHLLASVEGAFNAVLVKGDAVGQTLYYGRG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AGA PTASAVVAD++D+AR + AD ++RVPHLAFQP Q+ ILPM E+ S+YYLR+QA Sbjct: 301 AGAEPTASAVVADLVDVARTLTADPSNRVPHLAFQPEQLAELPILPMAEVQSAYYLRLQA 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQK----GVIDQTTAEIVILTHSTVEKHIKSAIAAI 415 DEPG L Q+ +LA E +SIEALIQK G +D +V+LTH+T E + AIAAI Sbjct: 361 LDEPGVLAQVTRILADEGISIEALIQKEAPAGAVD---VPVVLLTHATREGRLNRAIAAI 417 Query: 416 EALDCVEKPITMIRMESL 433 E L + +P+ +R+E+L Sbjct: 418 ENLPVITQPVVRLRLENL 435 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: 515 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