Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_003554655.1 RLEG_RS30735 pyruvate oxidase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000023185.1:WP_003554655.1 Length = 600 Score = 217 bits (552), Expect = 1e-60 Identities = 180/579 (31%), Positives = 270/579 (46%), Gaps = 35/579 (6%) Query: 41 AQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSK-KLRHVLVRHEQGAGHAASGYAHVT 99 A +I +L E V VIFG+PG + V + L + ++R + VRHE+ A AS YA T Sbjct: 5 ADILIDTLIEWDVKVIFGLPGDGINGVMEALRKRQDQIRFIQVRHEESAAFMASAYAKFT 64 Query: 100 GRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMPI 159 G +GVC+ATSGPG TNL+T L DA++D +PV+AITG LI T Q+ D++ + + Sbjct: 65 GNLGVCLATSGPGGTNLLTGLYDAKLDQMPVLAITGTQYHDLIETFTQQDVDLTRVFDNV 124 Query: 160 TKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDV--LQGQCTFSWPPRMELPGY 217 +N V + V + A A S R G + I DV + G+ + P + Sbjct: 125 ALYNAHVSDASHMENVASLACRSALS-RRGVAHLSIANDVQEMDGKSR----SKRNRPKH 179 Query: 218 KPNTKPHSRQVRE------AAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVT 271 PN H RQV E AA+++ ARK + G GV+ A E+LRE+A+L PV Sbjct: 180 VPNRYFHGRQVPEEIELDRAARILNDARKVAILAGRGVV--GAAEELREIADLLAAPVAK 237 Query: 272 TLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSF-APE- 329 L+ + A D G G+ GT + +++ D ++ +G+ F ++ + PE Sbjct: 238 ALLGKTALADDDPLTTGGIGILGTAPSQEIMEQCDAVLIVGSSFP-----YIEYYPRPEA 292 Query: 330 AKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVR 389 A+ + D DP IG D +VGD + + L L +E A A R Sbjct: 293 ARGVQIDSDPQRIGLRFPVDAGLVGDARETLRLLRPRLTRKTDRSFLEKAQ-TAMSEWRR 351 Query: 390 KTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNS 449 K + + L P+ V+ G D V VA GQ+ AA+ I + S Sbjct: 352 KMETME--TERSAPLKPQAVVRAFGRRIAADGVLVADSGQNTELAARHIDLRTTNQFAVS 409 Query: 450 GGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGN 509 G L +M +P A+ A A P ++A+ GDG F M E +T +P+K+ +I NG Sbjct: 410 GALASMASGLPYAIAAGAADPKRPIYAVIGDGGFGMQLGEFSTAVRMALPLKLLVICNGM 469 Query: 510 LGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARA 569 L + Q +F +LA DF K AEA+G G R + + + +A + Sbjct: 470 LNQIAWEQMMFLGNPQFACELAP-----IDFAKAAEAMGGRGFTIRRFDQIEPTLTEAFS 524 Query: 570 INDCPVVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRP 608 + PVVI +V Q PM+ D ++ R P Sbjct: 525 VAG-PVVIQAMVD---QYEPMMPPKMPKDYAKSFRQALP 559 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: 884 Number of extensions: 44 Number of successful extensions: 8 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: 600 Length adjustment: 37 Effective length of query: 581 Effective length of database: 563 Effective search space: 327103 Effective search space used: 327103 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