Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_043879985.1 AZC_RS03690 ubiquinone-dependent pyruvate dehydrogenase
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000010525.1:WP_043879985.1 Length = 575 Score = 215 bits (547), Expect = 5e-60 Identities = 168/549 (30%), Positives = 262/549 (47%), Gaps = 20/549 (3%) Query: 22 AEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARATG 81 A+++ LA GVE VWG G ++ D L + + + VRHE+ A AA A+ TG Sbjct: 7 ADVMARTLAAAGVERVWGVVGDSLNGFTDALRTIPQVQWMHVRHEEVAAFAAGAEAQLTG 66 Query: 82 KVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPIV 141 K+ V + GPG + + G+ + P++ I ++P+ IG FQE + + Sbjct: 67 KLAVCAGSCGPGNLHLINGLFDCHRTRTPVLAIAAHIPSAEIGSGYFQETHPEQLFKECS 126 Query: 142 KHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNPV 201 + V + ++ A A + G V+ IP DV+ A E P + P Sbjct: 127 HYCEFVSSPSQMPRIMEIAMRTAIQ-KQGVAVIVIPGDVALQAA--EGPTEPRWTAIAPP 183 Query: 202 NKGHS-GQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260 + ++ K +AL+ GA R I GGG A DE+ LAA P+ +TL G Sbjct: 184 TVVPADSELEKLMALVDGARRITILAGGGC--EGAHDEVVALAAALKAPMVHTLRGKPFV 241 Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320 + VGM G G AM D+L+ +G F R F K+ IDI Sbjct: 242 EYDNPYDVGMTGFIGFPSGYHAMLEADLLLMVGTDFPYR------QFYPTDAKVAQIDIR 295 Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE-QWRSVDCLKY 379 P ++ +R ++D+ +VG+VK L L+ ++K + + LAK E + R +D L Sbjct: 296 PENLGRRTRLDLGLVGDVKATLATLLPRLKP---RTDGDFLAKVQEHYKTSRRDLDALAV 352 Query: 380 DR-SSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMG 438 ++ I PQY+ + I E+ DA DVG+ +WAA++ + RR I S G+M Sbjct: 353 GNPGTKPIHPQYLAKVIDEVAAQDALFSVDVGETTVWAARYIAMNGKRRLIGSLIHGSMA 412 Query: 439 VGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQW 498 +P A+G + A P ++VV+++G+G M + ++ + Q PVKI NNG LG V Sbjct: 413 NAMPQALGAQAAHPGRQVVSLSGDGGFAMLMGDILSLRQLQLPVKIVIFNNGLLGFVD-- 470 Query: 499 QEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQ 558 E++ + PDF +A A G +G+RVE +DV+ AL++AF D +D Sbjct: 471 MEMKAAGFLNVGTDLQNPDFAAMANAIGILGIRVEDPADVKGALQKAF-AHDGPAVVDVV 529 Query: 559 TDPTENVWP 567 TD E V P Sbjct: 530 TDKMELVMP 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: 742 Number of extensions: 37 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: 575 Length adjustment: 36 Effective length of query: 549 Effective length of database: 539 Effective search space: 295911 Effective search space used: 295911 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