Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_013091211.1 BC1002_RS16900 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000092885.1:WP_013091211.1 Length = 586 Score = 325 bits (833), Expect = 3e-93 Identities = 204/564 (36%), Positives = 293/564 (51%), Gaps = 29/564 (5%) Query: 5 TAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAA 64 T A + G L+A+ LK GIDT+FTL GGH+ IYDGC +EGIR+ID RHEQ AA AA Sbjct: 24 TRDAGVVSGGHLVAKALKNEGIDTIFTLCGGHIIDIYDGCVDEGIRIIDVRHEQVAAHAA 83 Query: 65 EGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDH 124 +G+++ T G TAGPG TN ++ +A A +++SP++ +GG+ + MGSLQ++ H Sbjct: 84 DGYARQTGKLGCVVTTAGPGCTNAVTGIATAFRSESPILHIGGQGALTQHKMGSLQDLPH 143 Query: 125 VPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMD----HAFSMSSDNG 180 V +AP+ +FAA+ S E ++ A + + G A+++ P D + + Sbjct: 144 VDIMAPITKFAASVSSTERVADMISMAARECFNGAPGPAYLEIPRDVLDREVDATRAIVP 203 Query: 181 RPGALTELPAGPTPAGDA--LDRAAGLLSTAQRPVIMAGTNVWW--GHAEA-ALLRLVEE 235 RPG A GD +++ A +L A+RP I+ G VW GH +A ALLR +E Sbjct: 204 RPG---HYRASTKSIGDPRDIEKLADILVDAERPAILYGQQVWTARGHDQAIALLRGIE- 259 Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFGGVFGSTTQL 295 IP NG +RG++P F R RS+A ADV ++VG P DFR+G+G L Sbjct: 260 --IPGYFNGASRGLLPPGDPHHFDRTRSQAFANADVLIVVGTPFDFRMGYGRRISKELTL 317 Query: 296 IVADRVEPAREHPRPVAAGLYGD----LTATLSALAGSGGTD----HQGWIEELATAETM 347 + D R + GL GD L A L A +G D + W+ +L AE Sbjct: 318 VQIDMDYRTVGKNRDIDLGLVGDPGAILAAVLQAASGRIKDDKRQARRKWMAQLRDAEAT 377 Query: 348 ARDLEKAELVDDRIPLHPMRVYAELAALLERDALVVIDAGDFGSYAGRMIDSYLPGCWLD 407 A + + P+HP RV EL L D + + D GD + + + + PG W+D Sbjct: 378 ATEKLLPLFRSNSTPIHPYRVAYELNEFLSDDTVYIGDGGDVVTISAQAVRPRRPGQWMD 437 Query: 408 SGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNG 467 G G LG G G+ALAAKLA P ++V+ GDG+FG + + +T R ++VIGNN Sbjct: 438 PGALGSLGVGTGFALAAKLAHPHKEVLCYYGDGSFGMTAFDMETANRFGAPYLAVIGNNS 497 Query: 468 IWGLEKHPMEALYG--YSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERA---- 521 ++ A YG V L + + LGG+GE V PA++ AL+RA Sbjct: 498 AMNQIRYGQLAKYGEERGNVGNLLGDVPFSKFAEMLGGYGEEVRDPAQIASALQRAREAI 557 Query: 522 FASGLPAVVNVLTDPSVAYPRRSN 545 +G AVVN+ DP P N Sbjct: 558 HRTGRSAVVNIWVDPREYAPGTKN 581 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: 817 Number of extensions: 35 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: 586 Length adjustment: 36 Effective length of query: 511 Effective length of database: 550 Effective search space: 281050 Effective search space used: 281050 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 10 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