Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_011969935.1 SMED_RS21560 glyoxylate carboligase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000017145.1:WP_011969935.1 Length = 594 Score = 328 bits (841), Expect = 4e-94 Identities = 196/561 (34%), Positives = 291/561 (51%), Gaps = 18/561 (3%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 + ++ A + LE+ G+D FG+PG A+ P Y L +RH+L RH +GA H A G Sbjct: 1 MAKMRAVDAAVFVLEKEGIDCAFGVPGAAINPFYSALRARGSIRHILARHVEGASHMAEG 60 Query: 95 YAHVT-GRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153 Y G +GVC+ TSGP T+++T L A DSIP++ ITGQ R + + FQ DI+ Sbjct: 61 YTRAKHGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLDKEDFQAVDIA 120 Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213 I P+TK V +P V +AFH+ SGRPG VL+D+P DV + F Sbjct: 121 KIAAPVTKWAVTVMEPALVPFVFQKAFHLMRSGRPGPVLIDLPVDVQLAEIEFDPETYEP 180 Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273 L YKP Q +A ++ AA +P++ GGG+I +A++ L E AE+TG+PVV TL Sbjct: 181 LTPYKPAAT--RAQAEKALAMLNAAERPLIVAGGGIINADASDLLTEFAEITGVPVVPTL 238 Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 M G PD H GM G+ + A L SD + +G R+ +R TG + ++ K Sbjct: 239 MGWGVIPDDHPLMAGMCGLQTSHRYGNATLLASDFVFGIGNRWANRHTGNVPTYTEGRKF 298 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392 IH DI+P +IG+ D IV D A + + + G + WA RK Sbjct: 299 IHVDIEPTQIGRVFAPDFGIVSDAGAALKLFLDVATEWKTAGKLRDWSGWAGECRERKRT 358 Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452 L L P+ V E++ + G D +V+ +G Q+ AQF+ KPR+W+N G Sbjct: 359 MLRKTHFDQTPLKPQRVYEEMNKAFGRDTCYVSTIGLSQIAGAQFLHVYKPRNWINCGQA 418 Query: 453 GTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGM 512 G +G+ +PAA+G + A P + A+ GD FQ +ELA A +P ++NN LG+ Sbjct: 419 GPLGWTLPAALGVRAADPNRPIVALSGDYDFQFLIEELAVGAQHKLPYLHVVVNNSYLGL 478 Query: 513 VRQWQ---------SLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDV 563 +RQ Q SL + ++ D A + + D V +AE LGC +R + D Sbjct: 479 IRQAQRGFNMDFEVSLAFENINAEGD-AEKGYGV-DHVAVAEGLGCKAIRVRSPNEFADA 536 Query: 564 INQARAI---NDCPVVIDFIV 581 ++A+A+ + PVVI+FI+ Sbjct: 537 FDRAQALMEEHQVPVVIEFIL 557 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: 981 Number of extensions: 53 Number of successful extensions: 5 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: 594 Length adjustment: 37 Effective length of query: 581 Effective length of database: 557 Effective search space: 323617 Effective search space used: 323617 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 Jul 25 2024. The underlying query database was built on Jul 25 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