Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate YP_001312783.1 Smed_4042 thiamine pyrophosphate binding domain-containing protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000017145.1:YP_001312783.1 Length = 605 Score = 218 bits (556), Expect = 4e-61 Identities = 170/569 (29%), Positives = 261/569 (45%), Gaps = 34/569 (5%) Query: 2 NGAEAMIKALEAEKVEILFGYPGGALLPFYDALHH-SDLIHLLT-RHEQAAAHAADGYAR 59 N ++ +I+ L KVE++FG PG + +AL D I ++ RHEQ+AA A YA+ Sbjct: 3 NASDILIETLIEWKVEVVFGLPGDGINGIMEALRRRQDRIRFVSVRHEQSAAFMACAYAK 62 Query: 60 ASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFM 119 +G++GVC+ TSGPG TNL+TG+ A D P++A+TG LI + Q++D +F Sbjct: 63 FTGRLGVCLATSGPGGTNLLTGLYDAKLDQMPVLAITGMQYHDLIETFSQQDVDLTRVFE 122 Query: 120 PIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKL 179 + +N Q+ + + A A + R G H+ + DVQE + S+ Sbjct: 123 NVAVYNAQVNDAAHMENLANLACRSALSKR-GVAHLSIANDVQERMAGGGR----SRRNR 177 Query: 180 IGYNPTTIGHPR------QIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIP 233 G+ P+ R I +A L+ + ++ ILAG G L A L + +LL P Sbjct: 178 EGHMPSRFFEGRLVPREDDILRAADLLNAGRKVAILAGRGAL--EAKGLLRETADLLGAP 235 Query: 234 VCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFAT 293 V L+GK + ++ P G +G+ GT P+ + + D L+ +G F I K A Sbjct: 236 VAKALLGKAVLPDDDPFTTGGIGILGTVPSQEIMQQCDTLLIVGSTF-PYIEYYPKPHAA 294 Query: 294 NAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWI 353 I ID DP IG V+V +VG A L+ ++N+ + D+ + Q Sbjct: 295 TG--IQIDHDPQRIGLRYPVEVGLVGAAGETLR--------MLNERLQRKADRTFLEQAQ 344 Query: 354 ENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYF 413 E + ++ + P+KPQ V I N I+ TD GQN A + Sbjct: 345 EKTRNWRRELRAMEGDRSSPLKPQAAVGAF-----GRRIAANGIVVTDSGQNTELAARHV 399 Query: 414 KTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNI 473 F SG L +M G P AI A +A P + + GDGGF M E T Y I Sbjct: 400 DLGADHMFAVSGALASMASGLPYAIAAGIAMPARPIYAVVGDGGFAMQLGEFATAVRYEI 459 Query: 474 PVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINE 533 P+ + + N L + Q +F G Q + DF AE+ G + I S +EI+ Sbjct: 460 PLKLLVIRNDMLNQIAWEQMMFLGNPQFACELPPI-DFAAAAEAMGGRGFTIRSFDEIDG 518 Query: 534 ALKEAINCDEPYLLDFAIDPSSALSMVPP 562 L +A + P ++ +D L +PP Sbjct: 519 VLDQAFAAEGPVVIQALVDRYEPL--MPP 545 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: 778 Number of extensions: 36 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: 599 Length of database: 605 Length adjustment: 37 Effective length of query: 562 Effective length of database: 568 Effective search space: 319216 Effective search space used: 319216 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