Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate H281DRAFT_03007 H281DRAFT_03007 acetolactate synthase-1/2/3 large subunit
Query= BRENDA::P9WG39 (547 letters) >FitnessBrowser__Burk376:H281DRAFT_03007 Length = 587 Score = 327 bits (837), Expect = 1e-93 Identities = 204/564 (36%), Positives = 294/564 (52%), Gaps = 29/564 (5%) Query: 5 TAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAA 64 T A + G L+A+ LK G+DT+FTL GGH+ IYDGC +EGIR+ID RHEQ AA AA Sbjct: 25 TRNAGVVSGGHLVAKALKNEGVDTIFTLCGGHIIDIYDGCVDEGIRIIDVRHEQVAAHAA 84 Query: 65 EGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDH 124 +G+++ T G TAGPG TN ++ +A A +++SP++ +GG+ + MGSLQ++ H Sbjct: 85 DGYARQTGKLGCVVTTAGPGCTNAVTGIATAFRSESPILHIGGQGALTQHKMGSLQDLPH 144 Query: 125 VPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGRPGA 184 V +AP+ +FAA+ S E ++ A + + G A+++ P D D R A Sbjct: 145 VDIMAPITKFAASVSSTERVADMISMAARECFNGAPGPAYLEIPRD-VLDREVDLSR--A 201 Query: 185 LTELP----AGPTPAGDA--LDRAAGLLSTAQRPVIMAGTNVWW--GHAEA-ALLRLVEE 235 + P A GD +++ A +L ++RP I+ G VW GH EA ALLR ++ Sbjct: 202 VVPQPGHYRASTKSIGDPRDIEKLADILVNSERPAILYGQQVWTARGHEEAIALLRGLD- 260 Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFGGVFGSTTQL 295 IP NG +RG++P F R RS+A ADV ++VG P DFR+G+G L Sbjct: 261 --IPGYFNGASRGLLPPGDPHHFDRTRSQAFANADVLIVVGTPFDFRMGYGKRISKELTL 318 Query: 296 IVADRVEPAREHPRPVAAGLYGD----LTATLSALAGSGGTD----HQGWIEELATAETM 347 + D R + GL GD L A L A +G D + W+ +L AE Sbjct: 319 VQIDMDYRTVGKNRDIDLGLVGDPGAILAAVLQAASGRLKDDKRQARRKWMAQLQDAEAT 378 Query: 348 ARDLEKAELVDDRIPLHPMRVYAELAALLERDALVVIDAGDFGSYAGRMIDSYLPGCWLD 407 A + + P+HP RV EL L D + + D GD + + + + PG W+D Sbjct: 379 ATEKLMPLFKSNSTPIHPYRVAYELNEFLADDTVYIGDGGDVVTISAQAVRPRRPGQWMD 438 Query: 408 SGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNG 467 G G LG G G+ALAAK+A PQ++V+ GDG+FG + + +T R ++VIGNN Sbjct: 439 PGALGSLGVGTGFALAAKIAHPQKEVLCYYGDGSFGMTAFDMETANRFGAPYLAVIGNNS 498 Query: 468 IWGLEKHPMEALYG--YSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERA---- 521 ++ A YG V L + + LGGHGE V PA++ AL+RA Sbjct: 499 AMNQIRYGQLAKYGDERGNVGNLLSDVPFSKFAEMLGGHGEEVRDPAQIAGALQRAREAI 558 Query: 522 FASGLPAVVNVLTDPSVAYPRRSN 545 +G AVVN+ DP P N Sbjct: 559 HRTGRSAVVNIWVDPREYAPGTKN 582 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: 807 Number of extensions: 33 Number of successful extensions: 5 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: 587 Length adjustment: 36 Effective length of query: 511 Effective length of database: 551 Effective search space: 281561 Effective search space used: 281561 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 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