Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate WP_011386084.1 AMB_RS18865 homoserine dehydrogenase
Query= uniprot:A0A1L6J6Q3 (430 letters) >NCBI__GCF_000009985.1:WP_011386084.1 Length = 428 Score = 399 bits (1025), Expect = e-116 Identities = 213/415 (51%), Positives = 280/415 (67%), Gaps = 2/415 (0%) Query: 4 PLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDWVD 63 PL++A+AGLGTVG G ++L+ +A L+A RAGRP+ +V +A + D +D F Sbjct: 5 PLKIAIAGLGTVGGGTVQLLHDHAPLLAARAGRPLALVGAAALAKPADLPLDGVPF--FT 62 Query: 64 DMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVAEK 123 D ++A+ DV+VELIGG+ G AL + R L GK +VTANKAMIAHHG+ELA++AE Sbjct: 63 DARDMAKTCDYDVLVELIGGAKGIALDVVRTALERGKSVVTANKAMIAHHGIELARIAEA 122 Query: 124 SDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEVLA 183 + FEA+V GG+PVIK LREG A N++ +V GILNGTCN+IL+ M GRDF +VLA Sbjct: 123 KGGNIGFEASVGGGIPVIKSLREGLAGNRVTKVMGILNGTCNYILTTMRDSGRDFSDVLA 182 Query: 184 EAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEAAA 243 EAQA G+AEADPSFDIDG D AHKL+ILAS+AF V+ GIR++ A DI A Sbjct: 183 EAQALGYAEADPSFDIDGTDTAHKLAILASLAFAMPLDIDAVSCEGIRNVSALDIRYADE 242 Query: 244 LGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGAGA 303 LGYRI+LLG+A LS G+ RV+P +VPLS PLAHV GP NA+V EG+FVGR + +G GA Sbjct: 243 LGYRIKLLGVASLSDQGVETRVYPAMVPLSFPLAHVSGPFNAIVTEGDFVGRTVLEGRGA 302 Query: 304 GDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKVGVL 363 G PTASAVVADL+D+A GP + + +L A P AP+G R Y+R V D+ GV Sbjct: 303 GARPTASAVVADLMDLATGRVGPTFGIAVDALKALPAAPSGTHRSAYYIRLMVRDEPGVF 362 Query: 364 AEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSL 418 A++A ++ VS+E +IQRG V V + HE E S+ A++ +R S+ Sbjct: 363 ADVAGILKAHKVSMEQIIQRGRSPSEVVPVVMTVHETDEASMLGAVKAIRALGSV 417 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: 504 Number of extensions: 21 Number of successful extensions: 2 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: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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