Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate YP_004142767.1 Mesci_3597 glyoxylate carboligase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000185905.1:YP_004142767.1 Length = 593 Score = 324 bits (831), Expect = 6e-93 Identities = 197/597 (32%), Positives = 301/597 (50%), Gaps = 29/597 (4%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 + ++ A + LE+ G+ FG+PG A+ P Y L +RHVL RH +GA H A G Sbjct: 1 MARMRAVDAAVLVLEKEGISCAFGVPGAAINPFYSALKARGTIRHVLARHVEGASHMAEG 60 Query: 95 YAHV-TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153 + G +G+C+ TSGP T+++T L A DSIP++ ITGQ R + + FQ DIS Sbjct: 61 FTRAKAGNIGLCIGTSGPAGTDMITGLYSAAADSIPILCITGQAPRARLNKEDFQAVDIS 120 Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213 I P+ K V +P L +AFH+ S RPG VL+D+P DV + F Sbjct: 121 AIAAPVAKWAVTVMEPYLVPMALQKAFHLMRSSRPGPVLIDLPVDVQLAEIEFDIDAYEP 180 Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273 L +KP Q +A ++ AA KP++ GGG+I +A++ L E AE++G+PVV TL Sbjct: 181 LTPFKPAMT--RAQAEKALTMLNAAEKPLIVAGGGIINADASDLLIEFAEISGVPVVPTL 238 Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 M GA PD HR GM G+ + A + +D + +G R+ +R TG +D + K Sbjct: 239 MGWGAIPDDHRLMAGMCGLQTSHRYGNATMLEADFVFGIGNRWANRHTGSVDVYTKGKKF 298 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392 IH DI+P +IG+ D+ +V D A + L+ + G + WA RK Sbjct: 299 IHVDIEPTQIGRVFAPDLGVVSDAGAALKMLLDVATEWKTAGRLRDWSGWARECQARKKT 358 Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452 L P+ V E++ + G D +V +G Q+ AQF+ KPR+W+N G Sbjct: 359 MKRKTHFDQVPLKPQRVYEEMNKAFGRDVTYVTTIGLSQIAGAQFLHVYKPRNWINCGQA 418 Query: 453 GTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGM 512 G +G+ +PAA+G + A P + A+ GD FQ +ELA A +P ++NN LG+ Sbjct: 419 GPLGWTLPAALGVRAADPDRTIVALSGDYDFQFMIEELAVGAQHKLPYLHVVVNNAYLGL 478 Query: 513 VRQWQSLFYAERYSQTDLATHSHRIP---------DFVKLAEALGCVGLRCEREEDVVDV 563 +RQ Q F + + DLA + D V +AEA+GC +R + E+ Sbjct: 479 IRQAQRGFSMD--FEVDLAFENINRAGDPEAGYGVDHVAVAEAMGCKAVRVRKPEEFAGA 536 Query: 564 INQARAI---NDCPVVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRPLFDDITEGH 617 +A+ + + PVV++FI+ ++ GT D+I F+++ E H Sbjct: 537 FKEAQRLMKEHRIPVVLEFILERVTN----ISMGTEIDKITE-------FEELAESH 582 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: 951 Number of extensions: 52 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: 593 Length adjustment: 37 Effective length of query: 581 Effective length of database: 556 Effective search space: 323036 Effective search space used: 323036 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