Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate YP_004143377.1 Mesci_4216 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000185905.1:YP_004143377.1 Length = 437 Score = 384 bits (987), Expect = e-111 Identities = 203/433 (46%), Positives = 281/433 (64%), Gaps = 6/433 (1%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M E LRV +AGLGTVGA V R++ A + R+ GR + + AVSARD +DRGVD++ Sbjct: 1 MAEALRVGIAGLGTVGASVARVLRDKAVELTRQCGRDVIVTAVSARDHKRDRGVDLSSAK 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W DD ++A+ + DV VELIGG +GPA + + L AG+ +VTANKA++A HG+ LA++ Sbjct: 61 WFDDPVKMAQTAEIDVFVELIGGDEGPARSSVKTALEAGRHVVTANKALLAKHGVALAEI 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AEK + +EAAVAGG+PVIK +RE A N + RV+GILNGTCN+IL++MEAEG F Sbjct: 121 AEKKGVLLNYEAAVAGGIPVIKTMREAMAGNSVTRVFGILNGTCNYILTRMEAEGISFDA 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 L +AQ G+AEADP+FDI+G D AHKLSIL S+AFGT+ A D+ + GI ++ ADI Sbjct: 181 CLKDAQRLGYAEADPTFDIEGHDTAHKLSILTSLAFGTRIAANDIYMEGISNITQADIRA 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 AA LGYRI+LLG+A + +G+ QRVHP +VP + +A V G TNAV E + +G LL G Sbjct: 241 AADLGYRIKLLGVAQRTESGIEQRVHPTMVPTASVIAQVHGVTNAVAIETDILGELLLSG 300 Query: 301 AGAGDGPTASAVVADLIDIART----EFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTV 356 GAG TASAV+ D+ DIA++ + GP + PA L A G ++R TV Sbjct: 301 PGAGGNATASAVIGDIADIAKSRPGFQHGPVFGRPAKELKPYKKAQMRSHAGGYFIRLTV 360 Query: 357 ADKVGVLAEIAAAMRDAGVSIESLIQRGAMADGSV--LVAIVTHEVPERSIAQALEKLRG 414 D++GV A IA M D +S+ES++Q + + V +VTHE E ++ +A++ + Sbjct: 361 HDRIGVFAAIAKRMADNDISLESIVQHAVNGEAAAQKTVILVTHETTEAAVRKAVDGITK 420 Query: 415 SPSLAGEPMWMHI 427 L +P + I Sbjct: 421 DGHLTDKPQVIRI 433 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: 476 Number of extensions: 18 Number of successful extensions: 3 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: 437 Length adjustment: 32 Effective length of query: 398 Effective length of database: 405 Effective search space: 161190 Effective search space used: 161190 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