Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate CCNA_01447 CCNA_01447 homoserine dehydrogenase
Query= reanno::Korea:Ga0059261_2711 (430 letters) >FitnessBrowser__Caulo:CCNA_01447 Length = 429 Score = 360 bits (923), Expect = e-104 Identities = 194/422 (45%), Positives = 258/422 (61%), Gaps = 2/422 (0%) Query: 6 RVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDWVDDM 65 RV +AGLGTVG G+++ + AG + AVSAR +++ R VDI+ W DD Sbjct: 7 RVGVAGLGTVGGGLLQFLAERPGFAP--AGDLAVVTAVSARSKSRPRTVDISNLVWFDDP 64 Query: 66 TELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVAEKSD 125 LA P+ D+ VEL+GGSDGPA A L AGK +VTANKA+IA HG ELA +AE ++ Sbjct: 65 VALAASPEIDIFVELVGGSDGPAKAAVETALKAGKPVVTANKALIAEHGAELAALAEATN 124 Query: 126 TPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEVLAEA 185 TP+ FEAAV GGVP +K +RE + I V GILNGTCNFILS+ME GR F +VL EA Sbjct: 125 TPLLFEAAVMGGVPAVKMMREALVGDDIISVAGILNGTCNFILSEMEKTGRSFADVLREA 184 Query: 186 QAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEAAALG 245 Q G+AEADP+ D+ G DA HK+SILA++AFG P F I GI + DI A LG Sbjct: 185 QGLGYAEADPTMDVGGFDAGHKVSILAALAFGCAPNFAAAEIEGISEVDLLDIKLAKDLG 244 Query: 246 YRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGAGAGD 305 YRI+L+ A S +G+ +VHP LVPL HPLA G NA+ EG +GR+ QG GAG Sbjct: 245 YRIKLIAGAAKSEDGVAVKVHPSLVPLDHPLAQAGGALNALFIEGKRIGRIFLQGPGAGA 304 Query: 306 GPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKVGVLAE 365 GPTA+AV AD+ D+ P + PA L + G+AYLR V D+ GV+A Sbjct: 305 GPTAAAVAADIADVMTKAVRPVFQAPAGDLKPFVSIDPSKAVGKAYLRVMVQDQPGVIAA 364 Query: 366 IAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSLAGEPMWM 425 I+ + + GVSI+S +Q+ G V + +VTH PE ++ A+ ++ ++ P + Sbjct: 365 ISETLAECGVSIDSFLQKPVEGAGGVPIVLVTHATPESNLLDAISRIEKLQTVLERPRLL 424 Query: 426 HI 427 + Sbjct: 425 RV 426 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: 496 Number of extensions: 18 Number of successful extensions: 2 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: 429 Length adjustment: 32 Effective length of query: 398 Effective length of database: 397 Effective search space: 158006 Effective search space used: 158006 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 09 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