Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate AZOBR_RS07835 AZOBR_RS07835 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >FitnessBrowser__azobra:AZOBR_RS07835 Length = 435 Score = 457 bits (1177), Expect = e-133 Identities = 236/426 (55%), Positives = 304/426 (71%) Query: 2 TEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDW 61 T PL++A+AGLGTVGAGV++L++ A+LI +R GR IE+VAVSAR R KDRGVD+++ +W Sbjct: 7 TGPLKIAVAGLGTVGAGVLKLLERQADLIEQRCGRRIEVVAVSARSRGKDRGVDLSKAEW 66 Query: 62 VDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVA 121 DD LA HP DVVVELIGGS+G A L G+ +VTANKA++AHHG LA A Sbjct: 67 YDDPVALAAHPGVDVVVELIGGSEGAAKETVELALERGRHVVTANKALLAHHGTALAAKA 126 Query: 122 EKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEV 181 E + + FEAAVAGG+P+IKGLREG AAN++ V+GILNGTCN+IL++M GRDF +V Sbjct: 127 EAAGLAIGFEAAVAGGIPIIKGLREGLAANRVSEVHGILNGTCNYILTEMRTTGRDFADV 186 Query: 182 LAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEA 241 LA+AQ G+AEADPSFDIDGVDAAHKL+IL S+AFGT F V + GIRH+ A D A Sbjct: 187 LADAQKLGYAEADPSFDIDGVDAAHKLAILTSVAFGTPVDFKSVHVEGIRHVSAVDFDYA 246 Query: 242 AALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGA 301 ALGYRI+LLGIA + +G+ QRVHP +VP + P+A V G NAV+A+G+FV R+LF G Sbjct: 247 DALGYRIKLLGIARRTDHGIEQRVHPCMVPKAAPIAAVDGVFNAVIAQGDFVDRVLFVGR 306 Query: 302 GAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKVG 361 GAG+GPTASAVVADLIDIAR P + +PA L+ +P RRG Y+R V D+ G Sbjct: 307 GAGEGPTASAVVADLIDIARGRSTPTFGVPAAQLSEAQPSPMEARRGSYYVRLMVVDRPG 366 Query: 362 VLAEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAGE 421 V+A++AAAMRD VS+E +QRG +V V + TH+ E ++ +AL + S+ Sbjct: 367 VIADVAAAMRDQNVSMEQFLQRGRAPGEAVPVVLTTHDTEEAAMQRALATIADKESVVEP 426 Query: 422 PMWMHI 427 P + I Sbjct: 427 PRMIRI 432 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: 544 Number of extensions: 13 Number of successful extensions: 1 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: 435 Length adjustment: 32 Effective length of query: 398 Effective length of database: 403 Effective search space: 160394 Effective search space used: 160394 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 Apr 09 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