Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_011841410.1 RSPH17029_RS10360 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >NCBI__GCF_000015985.1:WP_011841410.1 Length = 428 Score = 399 bits (1025), Expect = e-116 Identities = 213/427 (49%), Positives = 287/427 (67%), Gaps = 2/427 (0%) Query: 1 MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60 M PLR+ +AGLGTVG GV+++I +A+LIA RAGRP+ I AV ARDR+K+R D++ + Sbjct: 1 MAAPLRLGIAGLGTVGIGVVKIIQRHADLIAARAGRPVIITAVCARDRSKNRDADLSGYA 60 Query: 61 WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120 W D LA+ DV VE++GGS+G A A A LAAGK +VTANKA++AHHG LA++ Sbjct: 61 WETDAVALAQRADIDVFVEVMGGSEGAARASTEAALAAGKDVVTANKALLAHHGQALAEM 120 Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180 AE + ++FEAAVAGG+PVIK L EG A NQ+ RV G++NGTCN+IL++ME G + Sbjct: 121 AEAAGLAIRFEAAVAGGIPVIKALTEGLAGNQMRRVMGVMNGTCNYILTRMETAGLPYDH 180 Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240 V EA+ G+ EADP+ D+ G+DA HKLS+LA+IAFGT+ +F DV + GI + DI Sbjct: 181 VFEEARQLGYLEADPNLDVGGIDAGHKLSLLAAIAFGTRVSFDDVQLEGIGQISIDDIRH 240 Query: 241 AAALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQG 300 A LG+RI+LLG+A +SG GL QR+ P LVP PL + G TN VV EG+ VG+++ +G Sbjct: 241 AGDLGFRIKLLGVAQVSGRGLEQRMTPCLVPADSPLGQLQGGTNMVVLEGDAVGQIVLRG 300 Query: 301 AGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKV 360 GAG+GPTASAV+ D+ID+AR P + PATSL E V YLR T+ DK Sbjct: 301 PGAGEGPTASAVMGDVIDLARGLRLPTFGRPATSL-VEAVPAKVAAPAPWYLRMTLLDKP 359 Query: 361 GVLAEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAG 420 G LA+IA A+ +AG+SI+ + Q G G V IVTH+ I+ A+ + + L G Sbjct: 360 GALAKIATALGEAGISIDRMRQYG-HEGGHAPVLIVTHKASRDDISHAISRFGATGVLVG 418 Query: 421 EPMWMHI 427 EP+ + I Sbjct: 419 EPVAIRI 425 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: 482 Number of extensions: 16 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: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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