Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate PfGW456L13_1723 Homoserine dehydrogenase (EC 1.1.1.3)
Query= uniprot:A0A1L6J6Q3 (430 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1723 Length = 434 Score = 336 bits (862), Expect = 7e-97 Identities = 194/428 (45%), Positives = 268/428 (62%), Gaps = 16/428 (3%) Query: 3 EPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARD---RAKDRGVDITRF 59 +P++V + GLGTVG G ++ NAE IARRAGR IE+ ++ R + + G+ IT Sbjct: 2 KPVKVGICGLGTVGGGTFNVLQRNAEEIARRAGRGIEVAQIAMRTPKPQFQTTGIAIT-- 59 Query: 60 DWVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQ 119 +D+ E+A +P+ D+V+EL+GG A L + GK +VTANKA+IA HG E+ Sbjct: 60 ---NDVFEVATNPEIDIVIELMGGYT-VARELVLKAIENGKHVVTANKALIAVHGNEIFA 115 Query: 120 VAEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFG 179 A + + FEAAVAGG+PVIK +REG +AN+I+ V GI+NGT NFIL++M +GR F Sbjct: 116 KAREKGVIVAFEAAVAGGIPVIKAIREGLSANRINWVAGIINGTGNFILTEMREKGRTFE 175 Query: 180 EVLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIA 239 +VLAEAQA G+AEADP+FD++G+DAAHKL+ILASIAFG F GI L AD+ Sbjct: 176 DVLAEAQALGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKAYTEGITKLTTADVN 235 Query: 240 EAAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQ 299 A ALGYRI+ LG+A + G+ RVHP L+P +A+V G NAV+ G+ G LF Sbjct: 236 YAEALGYRIKHLGVARSTAAGIELRVHPTLIPADRLIANVNGVMNAVMVNGDAAGSTLFY 295 Query: 300 GAGAGDGPTASAVVADLIDIARTEFGPP------YAMPATSLAAEPVAPTGERRGRAYLR 353 GAGAG PTAS+V+ADL+D+ R P A SL+A P+ P YLR Sbjct: 296 GAGAGMEPTASSVIADLVDVVRAMTSDPENRVPHLAFQPDSLSAHPILPIEACESAYYLR 355 Query: 354 FTVADKVGVLAEIAAAMRDAGVSIESLIQRGAMA-DGSVLVAIVTHEVPERSIAQALEKL 412 D GVLA++A+ + + G++IES++Q+ A DG V + ++TH V E+ I A+ L Sbjct: 356 IQAKDHPGVLAQVASILSERGINIESIMQKEAEEHDGLVPMILLTHRVVEQRINDAIAAL 415 Query: 413 RGSPSLAG 420 + G Sbjct: 416 EALAGVVG 423 Lambda K H 0.319 0.136 0.388 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: 458 Number of extensions: 18 Number of successful extensions: 4 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: 430 Length of database: 434 Length adjustment: 32 Effective length of query: 398 Effective length of database: 402 Effective search space: 159996 Effective search space used: 159996 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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