Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_050464048.1 AKL27_RS16985 thiamine pyrophosphate-binding protein
Query= curated2:P37251 (574 letters) >NCBI__GCF_001189915.1:WP_050464048.1 Length = 604 Score = 249 bits (637), Expect = 2e-70 Identities = 173/560 (30%), Positives = 276/560 (49%), Gaps = 46/560 (8%) Query: 33 VEMIFGYPGGAVLPIYDKLYNS-GLVHILPRHEQGAIHAAEGYARVSGKPGVVIATSGPG 91 ++ +F GG + + L N+ GL HEQ AAEGYAR++GKP +V+ T+GPG Sbjct: 17 LKQVFSVTGGGAMFLNQALGNNDGLQCTFMHHEQACAMAAEGYARIAGKPAIVMVTTGPG 76 Query: 92 ATNLVTGLADAMIDSLPLVVFTGQVATS---------VIGSDAFQEADILGITMPVTKHS 142 A N G+ A DS+P++V +GQV + QE + + + K++ Sbjct: 77 AINAFNGVYGAYTDSIPMIVISGQVKRETCLSFHELPALRQLGDQEGPTIAMASAICKYA 136 Query: 143 YQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQPTTE- 201 +RQP DL RI+ EAF A TGRPGPV +DIP D+ S E+++P + Sbjct: 137 EIIRQPADLERILPEAFRQAVTGRPGPVWLDIPLDIQ------SAVEELHIPDVEIAARD 190 Query: 202 -----PNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVA----HTL 252 Q + ++ ++SA +P+ILAG GV A + L +AE+ IPVA H L Sbjct: 191 VVADAAMVAQYQDIMRRLASANRPLILAGTGVRLADAGKALLQFAERTGIPVATAWTHDL 250 Query: 253 LGLGGFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTG-NLKHFARNAKI 311 + +DHPLF G G GT N L D ++ +G+R + R T N FA+NA + Sbjct: 251 IA-----SDHPLFAGRPGTIGTRAGNFCLQNADFVLVLGSRLNIRQTSYNWDSFAKNAWV 305 Query: 312 AHIDIDPAEIGK-IMKTQIPVVGDSKIVLQELIKQ--DGKQSDSSEWKKQLAEWKEEYPL 368 A +DIDPAE+ K +K P+V D + + L Q D S W + +EY + Sbjct: 306 AQVDIDPAELAKPTIKVDQPIVADVRHFIAGLSAQLEHAALPDYSAWARWCRNIGDEYAV 365 Query: 369 ----WYVDNEEEGFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSG 424 +V N P +++ + + + + I A + Q + + ++ Sbjct: 366 VKEHRHVANAP--LNPYLVVDRVFRNMRDDDIAACGNASACILPFQIGSLKAGQRLFSNS 423 Query: 425 GLGTMGFGLPAAIGA--QLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNA 482 G +MG+ LPAA+GA +A V+ GDG QM +QEL ++ L V VV++NN Sbjct: 424 GSASMGYDLPAALGAATAVASHGGRVICFAGDGSLQMNIQELQTLKSAGLNVIVVVINNG 483 Query: 483 CLGMVRQWQEIFYEERYSESKFASQ--PDFVKLSEAYGIKGIRISSEAEAKEKLEEALTS 540 + Q E F+ + + + PD+ ++ AYGI+ I E + ++L++ L S Sbjct: 484 GYVSIWQTHENFFGKVIGATPASGVDFPDYAAVARAYGIRSATIRGEQDL-DQLDQLLAS 542 Query: 541 REPVVIDVRVASEEKVFPMV 560 P+++D+ V + ++ P + Sbjct: 543 DGPLLLDIVVDARQEFTPRI 562 Lambda K H 0.317 0.135 0.391 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: 817 Number of extensions: 50 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: 574 Length of database: 604 Length adjustment: 37 Effective length of query: 537 Effective length of database: 567 Effective search space: 304479 Effective search space used: 304479 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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