Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate HSERO_RS11350 HSERO_RS11350 pyruvate dehydrogenase
Query= curated2:Q7U5G1 (617 letters) >FitnessBrowser__HerbieS:HSERO_RS11350 Length = 564 Score = 197 bits (500), Expect = 1e-54 Identities = 167/564 (29%), Positives = 256/564 (45%), Gaps = 36/564 (6%) Query: 18 PQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHA 77 P T+ A L+D L GV IFG G A+ P+ DA+ + W+ VRHE+ A Sbjct: 2 PATV--ADILIDTLYEIGVRQIFGVVGDALNPLTDAIRRDKRIEWIG---VRHEEGAALA 56 Query: 78 ADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETD 137 A A+ TG++ VC GT+GPGA +LV G+ A+ D P++ I+G VP GTD QE Sbjct: 57 AAGQAKLTGRLAVCCGTTGPGANHLVAGLYEARKDHAPVLAISGGVPAAHRGTDYLQENS 116 Query: 138 IFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDV-GQEQFNYVPVE 196 + + +S ++ P ++ QA A + R G ++IP DV G + VP Sbjct: 117 PELLFRDVAAYSQIITSPDQAPAVFHQAIAQAYAQR-GVAHLNIPADVIGAKTSGSVP-- 173 Query: 197 PGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256 S+ P P A + AA DLI A ++ G G A D + LA + Q P Sbjct: 174 --SLHTLRERTPLSPPAADIQAAADLINAAGSVAIFAGNGCRGAI--DEVLALASKLQAP 229 Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFAP 316 V T GK + +G +G+ G A A+ ++++ +G+ + F P Sbjct: 230 VMHTFRGKDLASYDHPHWIGGVGLIGGAPGTDALHAAEVMLMLGSDY------PYSEFLP 283 Query: 317 -RARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWK 375 +++V+ + +G+ + + G S+A V+ L+R A+L++ N + Sbjct: 284 TKSKVIQIDERGFVLGRRAPVTLGITG----SVAPAVQQLLERVEGKTDGAFLQQANAHR 339 Query: 376 DRYPLTIPPA------EGAIYPQEVLLAVRDLA-PDAIVTTDVGQHQMWAAQHLR-NGPR 427 +R+ + A I PQ V A+ DLA DA D G +W +R G + Sbjct: 340 ERWNAKLDSAAEIKRHHKKIKPQSVARAISDLADDDAAFVVDTGVVTLWCGNWIRQRGGQ 399 Query: 428 GWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVI 487 ++S +G + A G Q +RQVV GD M + E T + LPVKVV+ Sbjct: 400 RILASFNNAAVGTSLGQANGIQALDRERQVVVAVGDGGFTMLLGEFMTSVEHRLPVKVVV 459 Query: 488 VNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAA 547 NN G+V E + S+ N PDF A AR+ G G + E L L Sbjct: 460 FNNREWGLVHLEMEEAGMPAFEGSEFPN--PDFAAFARACGGQGFSVRTPEELEGGLQQL 517 Query: 548 LQSPTPTMIDVHVRRGENCYPMVP 571 L +P P ++DV + E P++P Sbjct: 518 LAAPGPAVLDVFIDPDE--LPVMP 539 Lambda K H 0.320 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: 915 Number of extensions: 51 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: 617 Length of database: 564 Length adjustment: 37 Effective length of query: 580 Effective length of database: 527 Effective search space: 305660 Effective search space used: 305660 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 09 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