Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate 3608652 Dshi_2045 thiamine pyrophosphate protein central region (RefSeq)
Query= curated2:Q9RQ65 (574 letters) >FitnessBrowser__Dino:3608652 Length = 592 Score = 178 bits (452), Expect = 5e-49 Identities = 145/571 (25%), Positives = 258/571 (45%), Gaps = 38/571 (6%) Query: 4 LSGSEMIIQSLIDQGIKYIFGYPGGAVLDIYDSLKSTKKIKHILVRHEQGATHMADGYAR 63 ++ E I+ L G+ + FG G A++ I D L I HE A MADG+ R Sbjct: 3 MTTEEAFIKVLQRHGVDHAFGIIGSAMMPISD-LFPEAGITFWDCAHEGSAGMMADGFTR 61 Query: 64 ATGKIGVVLVTSGPGATNSITGIATAYMDSIPIVVISGQVSSSLIGYDAFQECDMIGISR 123 A+G++ +++ +GPG TN +T + TAY + P+++++ Q ++ IG FQE + + Sbjct: 62 ASGRMSMMIAQNGPGITNFVTAVKTAYWNHTPLLLVTPQAANKTIGQGGFQEVAQMKLFE 121 Query: 124 PIVKHSFLVKKTEDIPITFKKAFWLASSGRPGPIVIDLPKDILNSYNKKPYIWPIEVNIR 183 +V + V+ + + A + GP I++P+D W ++I Sbjct: 122 DMVAYQEEVRDPSRMAEVLTRVISKAKT-LSGPAQINIPRD----------FWTQVIDIE 170 Query: 184 SYNPI----TKGHSRQIKKAIDILKLSKQPVIYAGGGVI-SANCHNELKELAEKLNIPVT 238 PI + G + +A +L +K PVI G GV+ S K LAE+L+ PV Sbjct: 171 IPEPIEFERSPGGEASVARAAALLSEAKNPVILNGAGVVLSEGGIAASKALAERLDAPVC 230 Query: 239 TSLMALGAFPGNHPQNLQMLGMHGTYEANMAMHYADVILAIGVRFDDRTT---NNVKKYC 295 AFPG HP LG +G+ A + ADV+LA+G R + +T ++ + Sbjct: 231 VGYQHNDAFPGGHPLFAGPLGYNGSKAAMELISEADVVLALGTRLNPFSTLPGYGMEYWP 290 Query: 296 PNATIIHIDIDPTSISKTITAHIPIVGNAKNVLQQILVFI--------NSNMFVKEFYCL 347 +A II +DI+ I T + IVG+A V + IL + + Sbjct: 291 ADAKIIQVDINSDRIGLTKKISVGIVGDAAKVARGILGQLAEDAGDAGRQERRDRIAQVK 350 Query: 348 KKWWIKIQSWKNK--------NSLNFDTNSDNIKPQSVIKTIWKLTKGKAFITSDVGQHQ 399 +W ++ + ++ N+ D + P+ + I A I+SD+G + Sbjct: 351 SRWAQQLSAMDHEEDDPGTTWNARARAAKPDWMSPRMAWRAITAALPRDAIISSDIGNNC 410 Query: 400 MFAALYYSFQKPRRWINSGGLGTMGFGLPAALGVKLAFPNETVICVTGDGSIQMNIQELS 459 Y F PR+++ G G G+GLPA +G K+A P+ V+ GDG+ + + EL+ Sbjct: 411 AIGNAYPDFDAPRKYLAPGLFGPCGYGLPAIVGAKIAQPDTPVVGFAGDGAFGIAVNELT 470 Query: 460 TAMQYELP-ILILNLNNKSLGMVKQWQDIIYSGRHSHSYMKSLPNFIKLAESYGHSGISI 518 + + P I + N G K+ + + + + ++ +A + G G+ + Sbjct: 471 AIGRGDWPAITQVVFRNYQWGAEKRNSTLWFDDNFVGTELDEEVSYAGIARACGLDGVVV 530 Query: 519 NTPKELEKKLQLALE-KLQNGHLVFVDIKID 548 T +EL L A++ ++ G +++ ++ Sbjct: 531 RTMQELTDTLATAIKAQMTEGKTTLIEVLLN 561 Lambda K H 0.319 0.136 0.403 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: 44 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 574 Length of database: 592 Length adjustment: 36 Effective length of query: 538 Effective length of database: 556 Effective search space: 299128 Effective search space used: 299128 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