Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate SMa0958 SMa0958 acetolactate synthase catalytic subunit
Query= curated2:O08353 (599 letters) >FitnessBrowser__Smeli:SMa0958 Length = 570 Score = 247 bits (631), Expect = 8e-70 Identities = 178/566 (31%), Positives = 278/566 (49%), Gaps = 34/566 (6%) Query: 4 AEAMIKALEAEKVEILFGY--PGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARAS 61 A+ + L VE +FG P +L A + + R E ADGYAR S Sbjct: 11 AQRIANILRRHGVEFIFGQSLPSAVIL----AAEAIGIRQIAYRQENMGGAMADGYARVS 66 Query: 62 GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121 GKVGV +GP AT LV +A A S P+VAL V +AFQ++D + LF Sbjct: 67 GKVGVVAAQNGPAATLLVPPLAEALKASVPIVALVQDVERDQTDRNAFQDLDQIALFQSC 126 Query: 122 VKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIG 181 K ++ +I + +AF A +GR GP + LP D+ E K P + K +G Sbjct: 127 TKWVRRVTVPERIDDYVDAAFTAAASGRAGPAALLLPADLLRAEA---KSPAVVRSKQLG 183 Query: 182 YNPTTIGHPRQ--IKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239 + P P + + LIA+A PII+AGGGV GA EL L + +PV TT M Sbjct: 184 HWPLDRVRPSDDALAEVASLIAAAHAPIIIAGGGVHCGGATHELAALQQEACLPVFTTNM 243 Query: 240 GKGCISENHPLALG----MVGMHGTKPANYCLSE-SDVLISIGCRFSDRITGDIKSFATN 294 GKG + E HPL+ G +VG +Y L E +D++I IG R + T + ++ Sbjct: 244 GKGAVDEYHPLSAGVLGSLVGPRSLGRYSYGLVEDADLVILIGTRTNQNGTDTWRQIPSS 303 Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAK---LILKEVIKQLDYIINKDSKENNDKENISQ 351 A+++HID+DP EIG+N + +VGDA+ L+ + ++D ++ + D+ + + Sbjct: 304 ARVVHIDVDPVEIGRNYEA-IRLVGDARESLAALRAALTRVDL-----TRRHGDRARLEE 357 Query: 352 WIENV-NSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMA 410 I + V+ PI+P++++ EL + + + + D + MW+ Sbjct: 358 CIAQYWKGFELDRHDVVTSRSRPIRPERVMAELQDL-----LTGDVTVVADASYSSMWVL 412 Query: 411 HYFKTQ-TPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIA 469 + + + F++ GL +G+G P AIGAKVA+P VI + GDGGF + EL T+ Sbjct: 413 GQLRARASGMRFITPRGLAGLGWGVPLAIGAKVARPGKPVIAVVGDGGFAHSWAELETMV 472 Query: 470 EYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPN 529 +PV I + +N LG + + +G + +F D KLAE+ G A R+E P Sbjct: 473 RMKLPVTIVVLNNGILGFQRDAETVKFGTYTTACHFAEV-DHAKLAEACGCPAVRVEDPG 531 Query: 530 EINEALKEAINCDEPYLLDFAIDPSS 555 E+ L ++ P L++ DP++ Sbjct: 532 ELAFHLHRGMD-QGPLLIEVMTDPAA 556 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: 716 Number of extensions: 27 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: 570 Length adjustment: 37 Effective length of query: 562 Effective length of database: 533 Effective search space: 299546 Effective search space used: 299546 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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