Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011800434.1 PNAP_RS05095 benzoylformate decarboxylase
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000015505.1:WP_011800434.1 Length = 529 Score = 151 bits (381), Expect = 8e-41 Identities = 164/553 (29%), Positives = 235/553 (42%), Gaps = 50/553 (9%) Query: 26 ALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARAT 85 A++D LR + TIFG PG LP++ + +++L E AD YA+AT Sbjct: 8 AVLDLLRAFNMTTIFGNPGSTELPLF-----LDFPDDFRYVLGLQESVVVGMADGYAQAT 62 Query: 86 GKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAF----QETDIFGI 141 S G + + I TA + PMV+ GQ R + D F Q T++ Sbjct: 63 HNAAFVNLHSAAGVGHAMGNIFTAHKNRTPMVITAGQQARSILPFDPFLFSGQATEL--- 119 Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVI 201 P VK S D+ +A+A+ IA GPVL+ IP D + V S Sbjct: 120 PKPYVKWSIEPARAEDVPLAIARAYYIAMQQPRGPVLVSIPADDWTRRCEPVAARRVSTE 179 Query: 202 PGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTL 261 +PEP L A + ALD A+RP VG A D + LAER+ V Sbjct: 180 T----RPEPQLLALIGDALDA---AKRPAFVVGAAVDRDRAWDDVVRLAERHNAAVWVAP 232 Query: 262 M-GKGAFDENDALSVGML-GMHGTAYANFAVTECDLLIAVGAR-FDDRVTGKLDTFAPRA 318 M G+ F E+ L G L M A A DL+ A+GA F V G A Sbjct: 233 MSGRCGFPEDHRLFAGFLPAMREKIVALLAGH--DLVFALGAAAFTYHVEGAGPHLPAGA 290 Query: 319 RVVHFEIDPAEIGKNRKADVAVLG-DLGLS--LARMVEISLQRTAEPRTAAWLERINTWK 375 +V DPA + AV G LG+ LAR V +L +P+ A R Sbjct: 291 ELVQLIEDPAIAAWAPEGTSAVGGIRLGVQDLLARPVPPALADREDPQPRALPARAE--- 347 Query: 376 DRYPLTIPPAEGAI----YPQEVLLAVRDLAPDAIVTTDVGQHQMWAAQHLRNGPRGWIS 431 P A G + + + L VRD +IV + + HL Sbjct: 348 -------PGASGELMSVAFVMQTLAEVRDA--HSIVVEEAPSSRPVMQAHLPILHSETFY 398 Query: 432 SAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNH 491 + G +G GMPAA+G +A P ++V+ + GD S + +IQ L + A LP+ +I+ N Sbjct: 399 TMCSGGLGHGMPAAVGVALAKPGKKVIGLLGDGSSMYSIQALWSAAQLKLPITFIILKNR 458 Query: 492 WQGMVRQWQESFYDERYSASDMLNGMP----DFIALARSFGVDGVKITDRELLHRDLAAA 547 ++++ +F + + L G DF+ALAR G D V + D + L L A Sbjct: 459 RYAALQEFAPTF---GFKPGETLQGTDLPELDFLALARGQGCDAVNVVDADQLADVLREA 515 Query: 548 LQSPTPTMIDVHV 560 L SP P +++V V Sbjct: 516 LNSPRPILVEVDV 528 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: 849 Number of extensions: 50 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: 617 Length of database: 529 Length adjustment: 36 Effective length of query: 581 Effective length of database: 493 Effective search space: 286433 Effective search space used: 286433 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