Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013819452.1 METME_RS14270 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000214665.1:WP_013819452.1 Length = 436 Score = 494 bits (1273), Expect = e-144 Identities = 257/436 (58%), Positives = 327/436 (75%), Gaps = 4/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSA--A 58 MKPV +G+LGLGTVGGG VL+ NAEEI+RR GREI +S ++IC + + Sbjct: 1 MKPVKVGVLGLGTVGGGTVNVLKRNAEEIARRAGREILVSR-ASARHLTQQRICDTQGMS 59 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 DPFE+V D+DVVVEL GG +AK+ VL AI NGKH+VTANK L+A +GNEIF A Sbjct: 60 LTVDPFEIVNDPDIDVVVELIGGYDLAKQLVLTAIANGKHVVTANKALIALHGNEIFAAA 119 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 K+ V+V FEAAVAGGIPIIKA+REGL+ NRIK +AGIINGT NFIL+EMR+KG FADV Sbjct: 120 SKKGVMVMFEAAVAGGIPIIKAIREGLSGNRIKWLAGIINGTGNFILTEMRDKGRDFADV 179 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L EAQALGYAEADPTFD+EG DAGHK+TI++++AFG P+ F + EGI+++ D++YA Sbjct: 180 LAEAQALGYAEADPTFDVEGIDAGHKLTILASIAFGIPLRFDKVFTEGITQITRADVEYA 239 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 EELGYRIK LGV R T +G+ELRVHPTLIP+ RL+ANVDGVMNAV V D VG TLYYGA Sbjct: 240 EELGYRIKHLGVARNTEQGVELRVHPTLIPKRRLIANVDGVMNAVLVCGDAVGPTLYYGA 299 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGA PTASAVVAD++D+ R + +D +RVPHLAFQ + +L D+I ++YYLR+ Sbjct: 300 GAGAEPTASAVVADLVDVVRAMTSDPENRVPHLAFQANAIVDTPVLSADDIKTAYYLRLT 359 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQK-GVIDQTTAEIVILTHSTVEKHIKSAIAAIEA 417 A+D+PG L ++ +LA +SIEALIQK + +++ I++LT T+EK + +AIA IE Sbjct: 360 AEDKPGVLADVSRILAAHQISIEALIQKEPLAGESSVPIIMLTQQTLEKEMNAAIAEIET 419 Query: 418 LDCVEKPITMIRMESL 433 L V + IR+E+L Sbjct: 420 LATVTGKVARIRLETL 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: 512 Number of extensions: 13 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: 436 Length adjustment: 32 Effective length of query: 403 Effective length of database: 404 Effective search space: 162812 Effective search space used: 162812 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