Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_041750370.1 BBTA_RS05905 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000015165.1:WP_041750370.1 Length = 593 Score = 266 bits (679), Expect = 2e-75 Identities = 178/592 (30%), Positives = 295/592 (49%), Gaps = 50/592 (8%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLI--HLLTRHEQAAAHAADGYA 58 MNGA A++ L V+++FG PG + Y+AL + H+L R E++A AD YA Sbjct: 1 MNGATALVSMLSGYGVDVIFGVPGDTNVALYEALRMTKGAPRHILCRDERSAVFMADCYA 60 Query: 59 RASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 R SGK GV SG GA + GVA A+ S P++ L +P +G E+ LF Sbjct: 61 RLSGKPGVAEVPSGAGALYGLPGVAEANKSSVPLILLVNDIPQPGVGRGTLTELPVQDLF 120 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELEL---DIDKHPIPS 175 PI K + ++PE+ R AF A GRPG V + LP+D+ +L + H P Sbjct: 121 KPISKRAETLAHVRKLPEVVRRAFREATGGRPGAVVLALPEDILYQDLPSEGVSLHVEPQ 180 Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235 + Y + A+ I +A+RP+I+AGGG S A E + E L IPV Sbjct: 181 CRQAPSYRSRPA--DADLDSALNAILAAERPLIVAGGGANRSAAAEAITAFAERLGIPVV 238 Query: 236 TTLMGKGCISENHPLALGMVGMHGTKP-ANYCLSESDVLISIGCRFSDRITGDIKSFATN 294 TT+ G+G I ++H L +G++G +G P A + L +D++I +GCR T + + N Sbjct: 239 TTITGQGVIRDDHKLGIGIIGDNGFHPHAVWALGRADLVIYVGCRMGSVATMNWQWPVPN 298 Query: 295 --AKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENI-SQ 351 +I+ +D++P IG +D P+VGDA+ +++ +I +K D ++ + Sbjct: 299 GETRIVQVDLEPEVIGNTYAIDFPLVGDARAVVEALI----------AKAPADHASVTAA 348 Query: 352 WIENVNSLKKS----SIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQM 407 W++ +NS + P + D++P++P+++++ L + + N + +D G Sbjct: 349 WVDEINSRRADFWDVMAPHLQSDEVPLRPERVIETLNRCL-PMPCN----VVSDAGTPTP 403 Query: 408 WMAHYFKTQTPRSFLSSGGL-GTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELG 466 + + + + P+S L G +G+ P+ IGA A P + + + GDG M+ EL Sbjct: 404 YATRFLRLRDPQSKLVIPRFYGGLGYAIPAVIGAYFAAPHLRPVGLFGDGSLGMSAGELE 463 Query: 467 TIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKR----------------QCSVNFGGAPD 510 T++ +P V+ F+N G + Q + R SV+F G D Sbjct: 464 TLSRLQVPAVLIHFNNACFGWIKALQRVVDRDRARKASEHSPAVPVNDPTFSVDF-GKYD 522 Query: 511 FIKLAESYGIKARRIESPNEINEALKEAINCDEPYLLDFAIDPSSALSMVPP 562 +LA YGI++ R+E+P ++ AL+EA +EP +D A++ S +PP Sbjct: 523 MSRLASVYGIRSFRVETPAQLEAALREAFELNEPVFIDVAVE--SIADRLPP 572 Lambda K H 0.319 0.137 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: 809 Number of extensions: 44 Number of successful extensions: 7 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: 599 Length of database: 593 Length adjustment: 37 Effective length of query: 562 Effective length of database: 556 Effective search space: 312472 Effective search space used: 312472 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 (21.7 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