Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_012973715.1 AZL_RS05775 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000010725.1:WP_012973715.1 Length = 434 Score = 445 bits (1145), Expect = e-129 Identities = 233/424 (54%), Positives = 296/424 (69%) Query: 4 PLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDWVD 63 PL++A+AGLGTVGAGV++L+D A LI RR GR IE+VAVSAR + KDRGVD++ W D Sbjct: 8 PLKIAVAGLGTVGAGVLKLLDTQASLIERRCGRRIEVVAVSARSKGKDRGVDLSAVQWFD 67 Query: 64 DMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVAEK 123 D +A AD+VVELIGGS+GPA + GK +VTANKA++A HG +A+ AE Sbjct: 68 DPVAMAAQSGADLVVELIGGSEGPARDTVATAIETGKHVVTANKALLAVHGTGIARKAEA 127 Query: 124 SDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEVLA 183 + FEAAVAGG+P+IKGLREG AAN + ++GILNGTCN+IL++M GRDF +VLA Sbjct: 128 GGLTVAFEAAVAGGIPIIKGLREGLAANGVSEIHGILNGTCNYILTEMRTTGRDFADVLA 187 Query: 184 EAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEAAA 243 +AQA G+AEADPSFD+DG+DAAHKL+ILAS+AFGT F V I GIR + A D A Sbjct: 188 DAQALGYAEADPSFDVDGIDAAHKLAILASVAFGTAVDFASVFIEGIRQVSAVDFDYADQ 247 Query: 244 LGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGAGA 303 LG+RI+LLGIA + G+ QRVHP +VP + P+A V G NAVVA+ +F R+LF G GA Sbjct: 248 LGFRIKLLGIARRTDAGIEQRVHPCMVPKTAPIASVDGVFNAVVAQADFADRVLFVGRGA 307 Query: 304 GDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKVGVL 363 G GPTASAVVADLIDIAR P + +PA L A +P RRG Y+R V D+ GV+ Sbjct: 308 GAGPTASAVVADLIDIARGRSTPTFGVPAGLLGASTPSPMEARRGAYYVRLMVKDRPGVI 367 Query: 364 AEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAGEPM 423 A+IAAAMRD GVS+E +QRG D V V + TH+ E S+ +AL + S ++ P Sbjct: 368 ADIAAAMRDQGVSMEQFLQRGRSPDEGVPVVLTTHDTDEASMRRALATIAASDTVLEPPR 427 Query: 424 WMHI 427 + I Sbjct: 428 MIRI 431 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: 530 Number of extensions: 12 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: 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 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