Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_012172011.1 AZC_RS17935 glyoxylate carboligase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000010525.1:WP_012172011.1 Length = 591 Score = 337 bits (865), Expect = 7e-97 Identities = 202/561 (36%), Positives = 290/561 (51%), Gaps = 20/561 (3%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 + + A +R LE+ G+ FG+PG A+ P Y L +RHVL RH +GA H A G Sbjct: 1 MAHMRAVDAAVRVLEKEGISCAFGVPGAAINPFYSALKARGSIRHVLARHVEGASHMAEG 60 Query: 95 YAH-VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153 Y V G +GVC+ TSGP T+++T L A DSIP++ ITGQ R + + FQ DI Sbjct: 61 YTRAVAGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLYKEDFQAVDIE 120 Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213 I P+TK VR +P V +AFH+ SGRPG VL+D+P DV + F Sbjct: 121 SIAKPVTKWAVTVREPALVPMVFQQAFHVMRSGRPGPVLIDLPIDVQMAEIEFDEDTYAP 180 Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273 LP YKP Q +A ++A A +P++ GGG+I +A++ L E AELTG+PV+ TL Sbjct: 181 LPVYKPAAT--RAQAEKAIAMLAKADRPLIVSGGGIINADASDLLVEFAELTGVPVIPTL 238 Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 M G PD H GM G+ + A + SD + +G R+ +R TG ++ + Sbjct: 239 MGWGTIPDDHPLMAGMCGLQTSHRYGNATMLASDFVFGIGNRWANRHTGSVEVYTKGRTF 298 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADW--WAYLNGVRK 390 IH DI+P +IG+ D IV D A + I + + G ++ DW WA RK Sbjct: 299 IHVDIEPTQIGRVFGPDFGIVSDAGAALKLFIEVAKEWKAAG--KLPDWSAWAKECFGRK 356 Query: 391 TYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSG 450 L + L P+ V E++ E G D +V +G Q+ AQF+ PR W+N G Sbjct: 357 ETMLRKSHYDNVPLKPQRVYEEMNEAFGRDVTYVTTIGLSQIAGAQFLHVHHPRHWINCG 416 Query: 451 GLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNL 510 G +G+ +PAA+G + A P ++ A+ GD FQ +ELA A +P ++NN L Sbjct: 417 QAGPLGWTLPAALGVRAADPDRKIVALSGDYDFQFLIEELAVGAQHKLPYLHVVVNNSYL 476 Query: 511 GMVRQWQSLFYAERYSQTDLATHSHRIP-------DFVKLAEALGCVGLRCEREEDVVDV 563 G++RQ Q F E + LA + D V +AE LGC +R + D Sbjct: 477 GLIRQAQRGF--EMDFEVSLAFENINSEEAGAYGVDHVAVAEGLGCKAIRVRTPNEFKDA 534 Query: 564 INQARAI---NDCPVVIDFIV 581 +QA A+ + PVVI+FI+ Sbjct: 535 FSQAEALMEEHQVPVVIEFIL 555 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: 945 Number of extensions: 60 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: 618 Length of database: 591 Length adjustment: 37 Effective length of query: 581 Effective length of database: 554 Effective search space: 321874 Effective search space used: 321874 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