Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate CA265_RS08170 CA265_RS08170 homoserine dehydrogenase
Query= BRENDA::P19582 (433 letters) >FitnessBrowser__Pedo557:CA265_RS08170 Length = 414 Score = 202 bits (513), Expect = 2e-56 Identities = 132/428 (30%), Positives = 224/428 (52%), Gaps = 23/428 (5%) Query: 2 KAIRVGLLGLGTVGSGVVKIIQDHQDKLMHQVGCPVTIKKVLVKDLEKKREVDLPKEVLT 61 K +++GL G G VG G++ IIQ L I K+ +KD KKR ++ K++ T Sbjct: 3 KNLKIGLFGFGVVGQGLLDIIQSQNLNL--------EIIKIAIKDPRKKRTLN--KDLFT 52 Query: 62 TEVYDVIDDPDVDVVIEVIGGVEQTKQYLVDALRSKKHVVTANKDLMAVYGSELLAEAKE 121 T+ +++++ +++ ++E+I + + + AL++ K+VV+ANK ++A + EL+ +E Sbjct: 53 TDRNEILNNTEINTIVELINDADAAYEIVTTALKNGKNVVSANKKMIATHLKELVDLQQE 112 Query: 122 NGCDIYFEASVAGGIPILRTLEEGLSSDRITKMMGIVNGTTNFILTKMIKEKSPYEEVLK 181 G + +E +V G IPI+R LEE ++ + GI NG++N+IL+K+ E Y+ LK Sbjct: 113 LGTSLLYEGAVCGSIPIIRNLEEYYDNELFHALSGIFNGSSNYILSKIFNENQSYDSALK 172 Query: 182 EAQDLGFAEADPTSDVEGLDAARKMAILARLGFSMNVDLEDVKVKGISQITDEDISFSKR 241 EAQDLGFAE DP DV G D K+AI + + V+ + + GI +++ DI +++ Sbjct: 173 EAQDLGFAETDPILDVGGYDPKYKLAIATAHAYGLFVNPDAILNIGIQNLSNHDIKYARE 232 Query: 242 LGYTMKLIGIAQRDGSK-IEVSVQPTLLPDHHPLSAVHNEFNAVYVYGEAVGETMFYGPG 300 + +KL+ A++ +K I V P L+ L V NE+NAV V + FYG G Sbjct: 233 KNFKIKLVPTARKVNTKDIVTYVLPKLVAKDDFLYNVENEYNAVAVQAAFADKQFFYGKG 292 Query: 301 AGSMPTATSVVSDLVAVMKNMRLGVTGNSFVGPQYEKNMKSPSDIYAQQFLRIHVKD--- 357 AG PT +V+SD+ A+ + R + E +K DI + +LR +D Sbjct: 293 AGGHPTGAAVLSDIAALRYDYRY-----EYKKYHSENGVKHTEDILLEIYLRYADEDLIT 347 Query: 358 --EVGSFSKITSVFSERGVSFEKILQLPIKGHDELAEIVIVTHHTSEADFSDILQNLNDL 415 E + S+ + S + V L+ IK D L + + +T + + L++ Sbjct: 348 LLEFDNISERYAASSYKYVVGTVKLESLIKNRDLLLDESVFVAYTGRQIYKQ--EQLSEN 405 Query: 416 EVVQEVKS 423 QE+ S Sbjct: 406 VFAQELAS 413 Lambda K H 0.316 0.135 0.372 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: 379 Number of extensions: 16 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: 433 Length of database: 414 Length adjustment: 32 Effective length of query: 401 Effective length of database: 382 Effective search space: 153182 Effective search space used: 153182 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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