Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Ga0059261_1674 Ga0059261_1674 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
Query= BRENDA::P9WG41 (618 letters) >FitnessBrowser__Korea:Ga0059261_1674 Length = 555 Score = 219 bits (557), Expect = 3e-61 Identities = 176/570 (30%), Positives = 266/570 (46%), Gaps = 41/570 (7%) Query: 29 RPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKK-----LRHVLVR 83 + ++V+ + TG A++ L GVD FG+PG + D LFD + +R V R Sbjct: 8 KAENVSATRGTGGDALVAGLHRWGVDTFFGVPGVQL----DELFDGLQRGGGDIRVVHSR 63 Query: 84 HEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIG 143 HEQGA + A GYA VTG+ GVC GPG N L+ A + V+ +T V LI Sbjct: 64 HEQGAAYMALGYAMVTGKPGVCAVVPGPGLLNAGAALSTAYACNARVLCLTSTVNSALID 123 Query: 144 T--DAFQEA-DISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVL 200 A E D G+ +TK + +IP +L EAF +GRP V ++IP D+L Sbjct: 124 RRYGALHEINDQDGLLRSLTKWSARATHASEIPGLLDEAFRQLLTGRPRPVALEIPPDIL 183 Query: 201 QGQCTFSWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRE 260 F++P LP N + +AA LIA AR P++ VG G EA ++R Sbjct: 184 AQTGFFTYPDA--LPSLA-NPLADPAAIEQAATLIAGARNPMIVVGSGA--QEAGREVRA 238 Query: 261 LAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDD-RV 319 LAEL P+V+ M RG + +P AA+ D++I +G+R R Sbjct: 239 LAELIQAPIVSRHMGRGVVRSD--DDYALPA----AAALPHWPDVDVVIGIGSRLTQLRE 292 Query: 320 TGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMA 379 G KV+H D+D +EI + V IV D +L+ L ++ A Sbjct: 293 WG----MGGGLKVVHIDLDQSEINRIAPPAVGIVADAAEATAKLVDALAEKNLSPAPRTA 348 Query: 380 DWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIR 439 ++ A R+ PQ ++ + D VFV + Q + + Sbjct: 349 EFAAIRAAFREEVATEIQPQVG-------YLDVIRAAMAEDDVFVDEMTQVGYASRYALP 401 Query: 440 YEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIP 499 PR+++NS GT+G+ A+GA++ V +++GDG F T ELAT + IP Sbjct: 402 VYTPRTYVNSSYQGTLGYGFATALGAQVGAGKRRVISVNGDGGFMYTMPELATAVLHRIP 461 Query: 500 VKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREED 559 + + N+GN G VR+ Q A +Y +A++ H PDFV LA + G GL+ E E Sbjct: 462 LIAIVFNDGNFGNVRRIQ----ANKYGGRLIASNLHN-PDFVALAHSFGVAGLKAEGPEG 516 Query: 560 VVDVINQARAINDCPVVIDFIVGADAQVWP 589 + + AR + + PV+I+ + +A P Sbjct: 517 LATALETARGL-EGPVLIEVPMNLEATPSP 545 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: 905 Number of extensions: 57 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: 555 Length adjustment: 37 Effective length of query: 581 Effective length of database: 518 Effective search space: 300958 Effective search space used: 300958 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 09 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