Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate SMa2211 SMa2211 thiamine pyrophosphate protein
Query= curated2:Q02137 (575 letters) >FitnessBrowser__Smeli:SMa2211 Length = 566 Score = 218 bits (555), Expect = 5e-61 Identities = 168/550 (30%), Positives = 267/550 (48%), Gaps = 33/550 (6%) Query: 12 GSQLVLQTLKELGVEIIFGYPGGAMLPLYDAIHN-FEGIQHILARHEQGATHEAEGYAKS 70 G++++ L G EI++ PG + L D++ I+ + RHE GA AE Y K Sbjct: 4 GAEILADELAVNGAEIVYHVPGESFLTALDSLTTRHPRIRSVSCRHENGAAQMAEAYGKL 63 Query: 71 SGKVGVVVVTSGPGATNAVTGIADAYLDSVPLLVFTGQVGPLSIGKDAFQEADTVGITAP 130 +GK G+ T PGATNAV G+ A+ DS P+++ GQV + ++AF D + AP Sbjct: 64 TGKPGIAFATRSPGATNAVNGVHTAFQDSSPMILIVGQVKRSILEREAFMSYDFRTMFAP 123 Query: 131 ITKYNYQIRETADIPRIVTEAYYLARTGRPGPVEIDLPKDVSTLEVTEINDPSLNLPHYH 190 + K+ QI + A IP V A+ A +GR GPV + +P+DV LE PS Sbjct: 124 MAKWVGQIDDPARIPEFVQRAWATALSGRRGPVVLVVPEDV--LEEKCDVAPSARPAVAS 181 Query: 191 ESEKATDEQLQELLTELSVSKKPVIIAGG-GINYSGSVDIFRAFVEKYQIPVVSTLLGLG 249 + +E L + L+ + KP+++ GG G + + D+ R F +PVV+T Sbjct: 182 HAGAPREEDLDRIFAMLAAAAKPLVVVGGSGWSETAREDVQR-FATNLGLPVVTTFRRRD 240 Query: 250 TLPISHELQLGMAGMHGSYAANMALVEADYIINLGSRFDD------------RVVSNPAK 297 + +G G+ + + EAD+I+ L D + S P Sbjct: 241 IIDHRLHCYVGEIGIGSNPTLLAHIREADFILMLNDALSDVNTIGAGYMEGFTLFSIPRP 300 Query: 298 VAKNAVVAHIDIDAAELGKIVKTDIPILSDLKAALSRLLQLNKV-RTDFNDWIKTV--TK 354 + V H+ D +L ++ + D+ + +D A L + R + DW T+ T Sbjct: 301 RQR---VVHVMPDHGDLNRVFQVDLALAADNDATARALAGRSATPRAEHADWTSTLRATL 357 Query: 355 NKEKAPFTYEPQNHDIRPQETIKLIGEYTQGDAIIVTDVGQHQMWVAQYYPYKNARQLIT 414 KE P +P I + + E DAI+ VG + W +Y+P+ +L T Sbjct: 358 MKECEP---QPCPGAIDLPGVMGWLRERLPEDAIVTNGVGAYATWSQRYFPH---YRLHT 411 Query: 415 SGG--MGTMGFGIPAAIGAKLAQPNKNVIVFVGDGGFQMTNQELALLNGYGIAIKVVLIN 472 G G+MG+ +PAAI AK+A P++ V+ FVGDG FQM+++ELA YG+ I +VL N Sbjct: 412 QLGPISGSMGYSLPAAISAKIAHPDRVVVEFVGDGCFQMSSEELATAVQYGVNIIIVLFN 471 Query: 473 NHSLGMVRQWQESFYEERRSQSVFDVEPNFQLLAEAYGIKHVKLDNPKTLADDL-KIITE 531 N G +R +E+ E R + + P+F LLA+AYG ++ K A + + Sbjct: 472 NGLYGTIRIHEETRLEGRVNGTDL-TNPDFLLLAKAYGAHGERVTCTKEFAPAFERCLAA 530 Query: 532 DEPMLIEVLI 541 +P LIE+++ Sbjct: 531 GKPALIELVV 540 Lambda K H 0.316 0.135 0.385 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: 661 Number of extensions: 25 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: 575 Length of database: 566 Length adjustment: 36 Effective length of query: 539 Effective length of database: 530 Effective search space: 285670 Effective search space used: 285670 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: 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