Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate 16478 b2373 hypothetical protein (NCBI)
Query= BRENDA::P9WG39 (547 letters) >FitnessBrowser__Keio:16478 Length = 564 Score = 219 bits (559), Expect = 2e-61 Identities = 166/552 (30%), Positives = 270/552 (48%), Gaps = 22/552 (3%) Query: 1 MSTDTAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTA 60 MS MH +I LK + IDT++ + G + + + EGIR I RHEQ+A Sbjct: 1 MSDQLQMTDGMH---IIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSA 57 Query: 61 AFAAEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRA--PALRWGMGS 118 +AA +T+ PG+ + PG NG++A+A A N P++++ G + + G Sbjct: 58 GYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGD 117 Query: 119 LQEIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMD-HAFSMSS 177 +E+D + P A+ A ++ G+ + +A++ +VS G ++D P + A +M Sbjct: 118 YEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEK 177 Query: 178 DNGRPGALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEE 235 D + P P ++ A LL+ A+RP+I+ G + A+ L +E Sbjct: 178 DEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIES 237 Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFGGV-FGSTTQ 294 IP L MA+G++ H L+ + ARS AL ADV ++VG +++ L G + + TQ Sbjct: 238 AQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQ 297 Query: 295 LIVADRVEPAR-EHPRPVAAGLYGDLTAT----LSALAGSGGTDHQGWIEELATAETMAR 349 I D +EP + RP+A + GD+ ++ L+ L + T W + L + Sbjct: 298 FIQLD-IEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNA 356 Query: 350 DLEKAELVDDRIPLHPMRVYAELAALL--ERDALVVIDAGDFGSYAGRMIDSYLPGCWLD 407 +L D PL+ + + +L +D +V + + A +ID Y P LD Sbjct: 357 QKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLD 416 Query: 408 SGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNG 467 G +G +G G GYA+ A + VV ++GD AFGFSGME +T+ R+N+ V VI NNG Sbjct: 417 CGTWGVMGIGMGYAIGASVTSGS-PVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNG 475 Query: 468 IWGLEKHPMEALYGYSVVA--ELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASG 525 G+ + L G + +L RYD+++ A G G V+ ELR AL S Sbjct: 476 --GIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSR 533 Query: 526 LPAVVNVLTDPS 537 P ++NV+ DP+ Sbjct: 534 KPTIINVVIDPA 545 Lambda K H 0.319 0.135 0.405 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: 715 Number of extensions: 35 Number of successful extensions: 6 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: 547 Length of database: 564 Length adjustment: 36 Effective length of query: 511 Effective length of database: 528 Effective search space: 269808 Effective search space used: 269808 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: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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