Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_050777596.1 M446_RS33940 acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000019365.1:WP_050777596.1 Length = 573 Score = 243 bits (620), Expect = 2e-68 Identities = 165/551 (29%), Positives = 271/551 (49%), Gaps = 17/551 (3%) Query: 1 MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60 MP+ E D N A+ ++ G++++V AL GV+YV G PG +L I + LH +K Sbjct: 1 MPACE----DENVGASSKIKGSDLIVKALENMGVDYVIGIPGEEILEIIESLHN-SKIRF 55 Query: 61 ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120 I VRHEQAAV A + R TG+ GV L T GPG N VTG+A A L ++P+++ITG P Sbjct: 56 IPVRHEQAAVMMAATHGRLTGRPGVCLATCGPGALNLVTGVAYAQLGAMPVLIITGQKPI 115 Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180 A Q FQ DTV + RP+ K + + +++AF +A R G V +++PKDV Sbjct: 116 SAPPQSRFQLIDTVSVMRPLTKMTRQIVSAASIPTLVREAFRVATDERRGAVHLEVPKDV 175 Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQ--IRKAVALLQGAERPYIYTGGGVVLANASDE 238 + E + + + +P+++ + + I A A++ A+ P I G + Sbjct: 176 ATEDVATEMAE-VALAPSHPIDRPVAAEAAIEHAAAMILSAQSPLIMIGAAGNRPGLGEP 234 Query: 239 LRQLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDD 298 L + T P +T MG GA G S ++G + + A+ D++I+IG D Sbjct: 235 LSEFVRRTQIPFCDTQMGKGAVTGASSLYLGTAALSERDYVHAAIDRADLIISIG---HD 291 Query: 299 RVIGNPAHFTSQA--RKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKP 356 V P + A K+IHI P+S+ + D +VG++ + L ++ ++P Sbjct: 292 AVEKPPFLYEKIAGGLKVIHIGYTPASVEQVFHPDAEVVGDISSTVTALADRL-GGRLEP 350 Query: 357 KREALAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWA 416 L +E+ ++ + +S + + +V + + D F+C D G++++ Sbjct: 351 DPGMLELRQSLLERINGINDGTEEATSS-MTVRRIVHAVRTVMPEDGFVCLDNGEYKIEF 409 Query: 417 AQFYKFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCL 476 A++Y P + L TMG GLP AM + +PE+ V+ + G+G M QE+ T + Sbjct: 410 ARYYLTYAPNTLLLDNALATMGAGLPSAMMAAELYPERRVLAVCGDGGFMMNSQEMETAV 469 Query: 477 QYDTPVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTS 536 + + L+N GM+R+ Q Y ++ + PDFV A +YG G V Sbjct: 470 RLRLNLVALILDNSAYGMIRRKQREGGFAEYGTTFTN--PDFVAYANSYGATGHCVTAVR 527 Query: 537 DVEPALREAFR 547 D+ P L AF+ Sbjct: 528 DLAPTLEAAFK 538 Lambda K H 0.319 0.135 0.407 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: 726 Number of extensions: 34 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: 585 Length of database: 573 Length adjustment: 36 Effective length of query: 549 Effective length of database: 537 Effective search space: 294813 Effective search space used: 294813 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