Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011602983.1 FRAAL_RS07770 thiamine pyrophosphate-requiring protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000058485.1:WP_011602983.1 Length = 595 Score = 225 bits (574), Expect = 4e-63 Identities = 175/574 (30%), Positives = 265/574 (46%), Gaps = 40/574 (6%) Query: 16 VEILFGYPG----GALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGKVGVCIGTS 71 VE +FGYPG G L + A + I RHE+ AA AA GYA+ SGKVGVC TS Sbjct: 18 VEHVFGYPGDGINGLLAAWGRAENRPRFIQ--ARHEEMAAFAAVGYAKFSGKVGVCAATS 75 Query: 72 GPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVKHNFQIQKT 131 GPGA +L+ G+ A D P+VA+ GQ +G QE+D L LF + Q+ Sbjct: 76 GPGAIHLLNGLYDAKLDHVPVVAIVGQTNRSAMGGSYQQEVDLLSLFKDVASEYVQVVNV 135 Query: 132 C-QIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN-PTTIGH 189 Q+P + A +A R P + LP DVQEL+ H +G P Sbjct: 136 PEQLPNVLDRALRVALAER-APTCVILPADVQELDYSPPTHAFKMVPSSLGVRWPAVSPD 194 Query: 190 PRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGCISENHP 249 ++ A +L+ + K+ ILAG G GA EL+++ + L V L+GK + ++ P Sbjct: 195 DAGVRAAAELLNAGKKVAILAGQGA--RGARAELIEVADRLGAGVAKALLGKDVLPDDLP 252 Query: 250 LALGMVGMHGTKPANYCLSESDVLISIGCRFS-DRITGDIKSFATNAKIIHIDIDPAEIG 308 G +G+ GT+P+ + + D L++IG F + D+ A+ + IDID IG Sbjct: 253 FVTGAIGLLGTRPSYELMRDCDTLLTIGSSFPYSQFLPDLH----QARAVQIDIDARYIG 308 Query: 309 KNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSSIPVMD 368 ++ +VGDA L+ ++ LD ++ +E ++ N+++W E V +++ + Sbjct: 309 MRYPYEINLVGDAAATLRALLPLLDRKEDRSWRETVER-NVARWWETVE--REAHV---- 361 Query: 369 YDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFLSSGGLG 428 + PI P ++ E A + D N I+ D G W A + + SG L Sbjct: 362 -EGRPINPMRLFWEASARLPD-----NAILAADSGSAANWYARDLRLRGDMRGSLSGTLA 415 Query: 429 TMGFGFPSAIGAKVAKPDSKVICITGDGGFMMN-CQELGTIAEY-----NIPVVICIFDN 482 TMG G P IGAK A D VI GDG MN EL TIA Y + V+ + N Sbjct: 416 TMGPGVPYGIGAKFAHSDRPVIVFEGDGAMQMNGLAELLTIARYWHEWADPRFVVAVLHN 475 Query: 483 RTLGMVYQWQNLFYGKRQCSVNFGGAPD--FIKLAESYGIKARRIESPNEINEALKEAIN 540 L V G + + + P+ + A + G+ ++ P ++ A A+ Sbjct: 476 NDLNQVTWEMRAMQGAPKFTES-QTLPEVSYADFARAVGLHGVAVDEPGQLGPAWDRALA 534 Query: 541 CDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQ 574 D P +LD DP+ +PP DA + Sbjct: 535 ADRPTVLDVRTDPN--FPPIPPHTTFEQAKDAAE 566 Lambda K H 0.319 0.137 0.405 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: 755 Number of extensions: 41 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: 599 Length of database: 595 Length adjustment: 37 Effective length of query: 562 Effective length of database: 558 Effective search space: 313596 Effective search space used: 313596 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 (21.7 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