Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate YP_427497.1 Rru_A2410 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000013085.1:YP_427497.1 Length = 430 Score = 449 bits (1154), Expect = e-130 Identities = 234/427 (54%), Positives = 305/427 (71%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M +PL+VA+AGLGTVGAGV++L+ + +L+A RAGRP+ + AVSAR R +DRGVD++ + Sbjct: 1 MNDPLKVAVAGLGTVGAGVVKLLADHKDLLAARAGRPVVVSAVSARSRTRDRGVDLSSYA 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W DD L R KADVVVELIGGSDGPA A+ L G+ +VTANKA++AHHGL LA Sbjct: 61 WFDDPVALVREAKADVVVELIGGSDGPAKAVCETALDLGRPVVTANKALLAHHGLALAAR 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE + + FEAAVAGG+P+IK LREG AAN+ID ++GILNGTCN+IL+ M GRDF + Sbjct: 121 AEATGAGLWFEAAVAGGIPIIKALREGLAANRIDALHGILNGTCNYILTTMRESGRDFAD 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 VLAEAQA G+AEADP FDIDG+DAAHKL++LAS+AF G V+I GIRH+ + DI Sbjct: 181 VLAEAQALGYAEADPGFDIDGIDAAHKLALLASLAFHVPVDLGGVSIQGIRHISSLDIRF 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 A LGYRI+LL +A + G+ QRV P +VPL PLAHV G NAVV EG+FVGR +FQG Sbjct: 241 ADELGYRIKLLAMARRTAEGVEQRVAPVMVPLDAPLAHVEGVNNAVVTEGDFVGRSVFQG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 GAG GPTASAVVADLID+AR P + +P+++L+ P A + GR Y+R V D+ Sbjct: 301 RGAGAGPTASAVVADLIDLARGHKVPVFGVPSSALSVLPRAEPEDHVGRYYVRLMVVDRP 360 Query: 361 GVLAEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAG 420 GV AE+AAA+RD VS+ES++QR +V V + H+ E ++ +AL ++ ++ Sbjct: 361 GVFAEVAAALRDEQVSMESVLQRARDPGETVPVVMTLHDTGEAAMTRALARIGAIDAMVE 420 Query: 421 EPMWMHI 427 P + I Sbjct: 421 PPRVIRI 427 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: 502 Number of extensions: 16 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: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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