Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_029001697.1 H537_RS0135675 glyoxylate carboligase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000430725.1:WP_029001697.1 Length = 598 Score = 331 bits (848), Expect = 6e-95 Identities = 194/563 (34%), Positives = 289/563 (51%), Gaps = 20/563 (3%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 + ++ A A + +E+ GV FG+PG A+ P+Y L + + HVL RH + A H A G Sbjct: 1 MAKMKAAMAAVLVMEKEGVSQAFGVPGAAINPLYAALRERGGISHVLARHVEAASHMAEG 60 Query: 95 YAHV-TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153 Y G +GVC+ TSGP T+++T L A DSIP++ ITGQ R + + FQ DI Sbjct: 61 YTRARAGNIGVCIGTSGPAGTDMITGLYSAGADSIPILCITGQAPRARLYKEDFQAVDIE 120 Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213 I P+TK VR +PR +AFH+ SGRPG VL+D+P DV + F Sbjct: 121 SIAKPVTKWAVTVREPAQVPRAFQQAFHLMRSGRPGPVLIDLPFDVQMAEIEFDIDTYEP 180 Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273 LP YKP +Q+ +A ++ A+ KP++ GGG+I +A+ L ELAE G+PV+ TL Sbjct: 181 LPVYKPAAS--RKQIDKALDMLLASEKPLIVAGGGIINADASNLLVELAETLGVPVIPTL 238 Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 M G+ PD H GM G+ + A + SD ++ +G R+ +R TG +D + Sbjct: 239 MGWGSIPDDHPLMAGMVGLQTSHRYGNATMLASDFVLGIGNRWANRHTGSVDVYTKGRTF 298 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392 +H DI+P +IG+ D IV D KA + + + GT++ D WA+ RK Sbjct: 299 VHVDIEPTQIGRVFMPDFGIVSDAKAALELFVQAAKERKAAGTLKSYDDWAFRCAERKRL 358 Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452 + P V E++ + D ++V+ +G Q+ AQF+ PR W+N G Sbjct: 359 MHRKSHYEQTPIKPMRVYEEMNAVFPRDTIYVSTIGLSQIAGAQFLHVYGPRQWINCGQA 418 Query: 453 GTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGM 512 G +G+ IPAA+G A P V + GD FQ +ELA A +P L+NN LG+ Sbjct: 419 GPLGWTIPAALGVVAADPTRTVVGLSGDYDFQFLIEELAVGAQFRLPYVQVLVNNSYLGL 478 Query: 513 VRQWQSLFYAERYSQTDLATHSHRIP-----------DFVKLAEALGCVGLRCEREEDVV 561 +RQ Q F + Q L+ + +P D V + E LGC LR E + Sbjct: 479 IRQAQRGFDMDYCVQ--LSFENQNMPEEAGELRGYGVDHVTVVEGLGCKALRVTDPEKIG 536 Query: 562 DVINQARAI---NDCPVVIDFIV 581 + + QA A+ + PVV++ I+ Sbjct: 537 ETLKQAHAMALEHRVPVVVECIL 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: 956 Number of extensions: 59 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: 598 Length adjustment: 37 Effective length of query: 581 Effective length of database: 561 Effective search space: 325941 Effective search space used: 325941 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