Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_020173663.1 A3OQ_RS0101920 ubiquinone-dependent pyruvate dehydrogenase
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000385335.1:WP_020173663.1 Length = 576 Score = 228 bits (580), Expect = 7e-64 Identities = 170/553 (30%), Positives = 268/553 (48%), Gaps = 36/553 (6%) Query: 29 DALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATGKV 88 + L GV I+G G ++ DA+ +G ++ + VRHE+ AA A A TG + Sbjct: 10 EVLAAAGVQRIYGIVGDSLNGFTDAIR---RQGKIQWLHVRHEEVAAFAASAEAHLTGSL 66 Query: 89 GVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGITLPIVKH 148 VC G+ GPG +L+ G+ VP++ I +P IG+ FQET + + Sbjct: 67 AVCAGSCGPGNLHLINGLFDCHRSRVPVLAIAAHIPSAEIGSGYFQETHPENLFKECSHY 126 Query: 149 SWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEP-GSVIPGGFHQ 207 ++ P+ + +V A + A G+ G +I IP DV + PV S+IP Sbjct: 127 CELISSPSQMPRVVEIA-IREAVGKRGAAVIVIPGDVALHEAVEAPVPTFASLIPS---- 181 Query: 208 PEP---PLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTLMGK 264 EP P +A + A +L+ A R L G G A AH L L E+ + P+ L GK Sbjct: 182 -EPVVVPKEADLKALANLLNGAGRVTLLCGSGC--AGAHSQLLALGEKLKAPMVHALKGK 238 Query: 265 GAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFAPR--ARVVH 322 + ++ VGM G+ G + FA+ +CD L+ +G F R F P+ A++ Sbjct: 239 EYVEWDNPYDVGMTGLIGFSSGYFAMNDCDALLMLGTDFPYR------QFYPQGTAKIAQ 292 Query: 323 FEIDPAEIGKNRKADVAVLGDLGLSLARMVEI---SLQRTAEPRTAAWLERINTWKDRYP 379 +I P ++GK D+ ++G++G +L ++ + +R + ++ D Sbjct: 293 IDIRPEQLGKRAPIDLGLVGEVGATLDALLPLLTEKKERKHLDQAIGHYKKAREGLDELA 352 Query: 380 LTIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHL-RNGPRGWISSAGLGT 437 + P + ++PQ+V A+ D A DAI T DVG +WAA++L NG R I S G+ Sbjct: 353 KGV-PGKRLVHPQQVAKAISDFASVDAIFTCDVGLPTVWAARYLAMNGARRLIGSFWHGS 411 Query: 438 MGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGMVR 497 M M A+GAQ P+RQV+ ++GD M + + +LA GLPVK+V+ NN G V Sbjct: 412 MANAMAQAIGAQATFPNRQVISLSGDGGFAMLMGDFLSLAQLGLPVKIVVFNNGTLGFVE 471 Query: 498 QWQES--FYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQSPTPTM 555 Q+S F D + P+F A+A + G+ G++I D + + AAL P + Sbjct: 472 LEQKSTGFIDFGTGFKN-----PNFAAMAEAAGIKGIRIEDAGEVEPGIKAALAHNGPVL 526 Query: 556 IDVHVRRGENCYP 568 +D V R E P Sbjct: 527 VDAVVNRQELAIP 539 Lambda K H 0.320 0.136 0.414 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: 894 Number of extensions: 46 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: 617 Length of database: 576 Length adjustment: 37 Effective length of query: 580 Effective length of database: 539 Effective search space: 312620 Effective search space used: 312620 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