Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_011158054.1 TX73_RS12760 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000195775.1:WP_011158054.1 Length = 441 Score = 374 bits (961), Expect = e-108 Identities = 202/438 (46%), Positives = 274/438 (62%), Gaps = 11/438 (2%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M PLRV +AGLGTVGA V+R+I+ ++ R GRP+ +VAV+AR +AK RG+D++ Sbjct: 1 MVAPLRVGIAGLGTVGAEVVRVIERQERTLSARCGRPVRVVAVTARSKAKKRGLDLSGIK 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W +A P+ D VELIGG+ PA A LAAGK +VTANKA+IA HGL+LA + Sbjct: 61 WAKSPLAIATDPEVDCFVELIGGAGDPAGPAIEAALAAGKAVVTANKALIAKHGLKLASL 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AEK + + +EAAV +PVIK LREG A IDR+YGILNGTCN+IL++ME EG F + Sbjct: 121 AEKHNAALNYEAAVGAAIPVIKTLREGLAGTDIDRIYGILNGTCNYILTRMEQEGLSFDD 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 LA+AQ G+AEADP+FDIDG D A KL+ILAS+AFGT+ + V + GIR + D+ Sbjct: 181 CLADAQRLGYAEADPTFDIDGHDTAQKLAILASLAFGTKVSESSVYVEGIRSITPEDLRA 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 A LGYR++LLG+A + G+ QRVHP +VP + +A V+G TNAV +G+ + + G Sbjct: 241 ADDLGYRVKLLGVAVRTAKGIEQRVHPTMVPKTSSIAQVMGVTNAVSIDGDGIPPITLVG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 AGAG TASAVVAD+ D+AR P+ P L A AP G YLR D Sbjct: 301 AGAGAAATASAVVADIADVARGIRAVPFGRPVAGLKATAKAPMQRHEGGYYLRLLARDHA 360 Query: 361 GVLAEIAAAMRDAGVSIESLIQR---------GAMADGS--VLVAIVTHEVPERSIAQAL 409 G A IA + + +SIES++QR G A S V V ++T+ E ++ +AL Sbjct: 361 GTAATIAKRLAEQDISIESIVQRHPHRSLDANGKAAKSSIPVPVILITYATAEDAVRRAL 420 Query: 410 EKLRGSPSLAGEPMWMHI 427 + ++ ++G P + I Sbjct: 421 QAVQRDKVISGRPQVIRI 438 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: 456 Number of extensions: 21 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: 441 Length adjustment: 32 Effective length of query: 398 Effective length of database: 409 Effective search space: 162782 Effective search space used: 162782 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