Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_011812942.1 HHAL_RS00660 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000015585.1:WP_011812942.1 Length = 436 Score = 442 bits (1136), Expect = e-128 Identities = 229/437 (52%), Positives = 303/437 (69%), Gaps = 6/437 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAF 59 MKPVN+G+LGLGTVG G +L NA+ I+RR GREIR++ E+ R Sbjct: 1 MKPVNVGMLGLGTVGSGVVNILERNADVINRRAGREIRVTHASARHPERPRSCRLEGIRL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 DPFE+V +V+++ EL GG A+E VL+A++NGKH++TANK L+A +GNEIF A Sbjct: 61 TTDPFEVVDDPEVEIIAELIGGHEPARELVLRALDNGKHVITANKALIASHGNEIFARAR 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V V FEAAVAGGIPIIKA+RE L NRI+ +AGIINGTSN+IL+EM +G F DVL Sbjct: 121 ENGVTVAFEAAVAGGIPIIKAVREALTGNRIEWLAGIINGTSNYILTEMFYEGRQFGDVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 EAQ LGYAEADP+FD++G DA HK+TI++++AFG P+ + Y+EGI + D+ +AE Sbjct: 181 AEAQRLGYAEADPSFDVDGTDAAHKLTILASIAFGIPLQYDKVYVEGIDHITREDVAFAE 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 ELG+RIK LG+ G LRVHPTL+P +LANVDGVMNAV V D VG TLYYGAG Sbjct: 241 ELGFRIKHLGMAFHEEGGYALRVHPTLLPRRHMLANVDGVMNAVMVKGDAVGPTLYYGAG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AGA PTASAVVAD+ID+ R + +RVP+LAF + + +LPM ++ ++YYLR+ A Sbjct: 301 AGAEPTASAVVADMIDVVREFNLEPENRVPYLAFHTESLSREPVLPMRDVETAYYLRLSA 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAE---IVILTHSTVEKHIKSAIAAIE 416 +DEPG L + +L +SIEA+IQK Q AE I++LTH E+H+ +AI +E Sbjct: 361 RDEPGVLADVTRVLGDFGISIEAIIQKQ--PQAGAEHVPIILLTHRIHERHMDAAIERLE 418 Query: 417 ALDCVEKPITMIRMESL 433 L+ V+ + IR+ESL Sbjct: 419 HLEQVDGRVVRIRVESL 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: 522 Number of extensions: 20 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