Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_058932573.1 AU252_RS22320 acetolactate synthase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_001484605.1:WP_058932573.1 Length = 539 Score = 219 bits (557), Expect = 3e-61 Identities = 167/534 (31%), Positives = 236/534 (44%), Gaps = 28/534 (5%) Query: 39 TGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAHV 98 T ++ LE GV ++G+PG + L V D L S + V+ RHE GAG A + Sbjct: 6 TAGHLIVAQLERAGVKRVYGVPGESFLDVLDGLHGSS-IETVVTRHEGGAGFMALAEGRL 64 Query: 99 TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMP 158 T GV M T GPGA N + A D+ P++ G + G ++FQE DI+ Sbjct: 65 TDLPGVAMVTRGPGAANAFIAIHTAHQDATPMILFVGLIPVADRGRESFQEFDINAWFGS 124 Query: 159 ITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSW--PPRMELPG 216 K + RV+ +A A SGRPG V++ +P+DVL P ++ P Sbjct: 125 TAKKVVTLDDAASAARVVDDAIFTALSGRPGPVVIGLPEDVLVHAIESGTVEPRKVSRPA 184 Query: 217 YKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276 P + + + +A A KP++ VGG E+ E L A G+PVV A Sbjct: 185 ------PAAPDLAQLEARLAGASKPLIVVGGEGWTQESGEALARWAARHGVPVVADFRAY 238 Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALG-TRFDDRVTGKLDSFAPEAKVIHA 335 A P G G + A A L+ +DL++ LG R D G V++A Sbjct: 239 DAVPHRSDAYAGFLGYGRSDANAARLEAADLIVFLGCVRGDVLSDGYTRGLDAHTVVVNA 298 Query: 336 DIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLS 395 D D +G D I DV A T L + +A W+A R Y Sbjct: 299 DADL--LGHFGRMDQHITADVTAFSTVLAGLES-----AVRPVAGWFA---DARADYLKF 348 Query: 396 YGPQSDGSLSPEY--VIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLG 453 Q DG + V+E L + DAV G G H +W A+++R+ S L + G Sbjct: 349 SSAQPDGGAGVDLGVVMEILSQEMADDAVLTFGAGNHALWPARYLRHNSANS-LAAPRNG 407 Query: 454 TMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMV 513 MG IPAA+ A +A PG +V ++ GDGCF M QE+AT G V +++NG + Sbjct: 408 AMGMGIPAAVAASLAYPGRQVISVAGDGCFMMNGQEIATAMGHGAKFIVLVVDNGIFATI 467 Query: 514 RQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQA 567 R+ Q Y R S T + PDF LA + G G R E+ ED +A Sbjct: 468 REHQEAHYPGRPSGTHMTN-----PDFAALARSYGGYGERIEKAEDFAGAFRRA 516 Lambda K H 0.319 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: 933 Number of extensions: 57 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: 618 Length of database: 539 Length adjustment: 36 Effective length of query: 582 Effective length of database: 503 Effective search space: 292746 Effective search space used: 292746 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