Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate RR42_RS31370 RR42_RS31370 acetolactate synthase
Query= BRENDA::P9WG39 (547 letters) >FitnessBrowser__Cup4G11:RR42_RS31370 Length = 584 Score = 320 bits (820), Expect = 9e-92 Identities = 194/561 (34%), Positives = 288/561 (51%), Gaps = 23/561 (4%) Query: 5 TAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAA 64 T A + G L+AR LK G+DT+FTL GGH+ IYDGC +EGIR+ID RHEQ AA AA Sbjct: 22 TRDAGVISGGHLVARALKNEGVDTIFTLCGGHIIDIYDGCVDEGIRIIDVRHEQVAAHAA 81 Query: 65 EGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDH 124 +G+++ T G TAGPG TN ++ +A A +++SP++ +GG+ + MGSLQ++ H Sbjct: 82 DGYARQTGKLGCVVTTAGPGCTNAVTGVATAFRSESPIIHIGGQGALSQHKMGSLQDLPH 141 Query: 125 VPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFP---MDHAFSMS-SDNG 180 V ++ + +FAAT S E ++ A + + G A+++ P +D +S + Sbjct: 142 VDMMSAITKFAATIPSTERVADMISMAARECFNGAPGPAYLEIPRDVLDREVDVSRAVIP 201 Query: 181 RPGALTELPAGPTPAGDA--LDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHI 238 RPG A GD ++R A +L A+RP I+ G VW + L++ I Sbjct: 202 RPG---HYRASTRSIGDPRDIERLADILVNAERPAILYGQQVWTARGHEEAIALLKGLDI 258 Query: 239 PVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFGGVFGSTTQLIVA 298 P NG +RG++P F R R++A ADV +IVG P DFR+G+G L+ Sbjct: 259 PGYFNGASRGLLPPGDPHHFDRTRTQAFANADVLIIVGTPFDFRMGYGKRISKELTLVQI 318 Query: 299 DRVEPAREHPRPVAAGLYGD----LTATLSALAGSGGTD----HQGWIEELATAETMARD 350 D R + GL GD L A L A +G D Q W+ +L AE +A + Sbjct: 319 DMDYRTVGKNREIDLGLVGDPGAILGAVLQAASGRIKNDKRQARQKWMGQLTEAEAVAAE 378 Query: 351 LEKAELVDDRIPLHPMRVYAELAALLERDALVVIDAGDFGSYAGRMIDSYLPGCWLDSGP 410 + P+HP RV EL L D + + D GD + + + + PG W+D G Sbjct: 379 KLMPLFRSENTPIHPYRVAYELNEFLSEDTVYIGDGGDVVTISAQAVRPRRPGQWMDPGA 438 Query: 411 FGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWG 470 G LG G G+A+AA LA P ++++ GDG+FG + + +T R V ++VIGNN Sbjct: 439 LGSLGVGTGFAIAAGLANPNKEILCYYGDGSFGMTAFDMETANRFGVPYLAVIGNNSAMN 498 Query: 471 LEKHPMEALYGYS--VVAELRPGTRYDEVVRALGGHGELVSVPAELRPALER----AFAS 524 ++ A YG + V L + + LGG+GE V P ++ AL+R + Sbjct: 499 QIRYGQLAKYGEARGNVGNLLSDVPFSKFAEMLGGYGEEVRDPGKIAGALQRGREAVQRT 558 Query: 525 GLPAVVNVLTDPSVAYPRRSN 545 G AV+N+ DP P N Sbjct: 559 GKSAVINIWVDPREYAPGTKN 579 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: 815 Number of extensions: 36 Number of successful extensions: 4 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: 584 Length adjustment: 36 Effective length of query: 511 Effective length of database: 548 Effective search space: 280028 Effective search space used: 280028 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