Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate H281DRAFT_02406 H281DRAFT_02406 acetolactate synthase-1/2/3 large subunit
Query= curated2:Q7U5G1 (617 letters) >FitnessBrowser__Burk376:H281DRAFT_02406 Length = 572 Score = 243 bits (619), Expect = 2e-68 Identities = 176/558 (31%), Positives = 266/558 (47%), Gaps = 30/558 (5%) Query: 14 DANAPQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQA 73 D A +T +GA ++DAL HGV+ +F PG + L + D+LH + ++ I+ RHE A Sbjct: 10 DTAAART-TGARLVVDALLTHGVERVFCVPGESFLAVLDSLH--DETERIQTIVCRHEAA 66 Query: 74 GTHAADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAF 133 + A+A + TG+ GV T GPGAT+ G+ TA DS PM+++ GQ R + +AF Sbjct: 67 AANMAEAIGKLTGRPGVALVTRGPGATHASIGVHTAFQDSTPMILLIGQCAREHLDREAF 126 Query: 134 QETDIFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYV 193 QE D + + K + DP + ++ AF A SGRPGPV++ +P+DV + V Sbjct: 127 QEIDYRRMFGQMAKWVAQIDDPKRIPEYLSHAFYTATSGRPGPVVLSLPEDVLSDACGAV 186 Query: 194 PVEPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERY 253 P P P A + +L+E +QRP++ GG + A L+ E + Sbjct: 187 PGAPRYQ-----RVAASPSTAQIGKLRELLESSQRPMVIAGGSGWTPAACADLQRFVENW 241 Query: 254 QLPVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTG---K 310 QLPV + D G +G+ + + DLL+A+G R + T Sbjct: 242 QLPVGLAFRFQDTLDNEHPNYAGDVGLGINPALAQRIRDADLLLALGPRLGEATTNGYTL 301 Query: 311 LDTFAPRARVVHFEIDPAEIGKNRKADVAVLG---DLGLSLARMVEISLQRT----AEPR 363 LD + +VH E+G+ AD+ ++ +L +LA + + T AE Sbjct: 302 LDIPKTKQTLVHVHQGAEELGRVYAADLPIVSGMPELATALAALEPSARTLTWAGAAEEA 361 Query: 364 TAAWLERINTWKDRYPLTIPPAEGAIYPQEVLLAVR-DLAPDAIVTTDVGQHQMWAAQHL 422 A+LE W R P IP G + EV+ +R L DAI+T G + W +H Sbjct: 362 HRAYLE----W--RKPRPIP---GDVQMGEVIQQLRAHLPDDAILTNGAGNYATWLHRHF 412 Query: 423 RNGPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLP 482 + G MG+G+PAA+ A+ P R VV +AGD +M QEL T Y L Sbjct: 413 SYRQYRSQLAPTSGAMGYGVPAAIAAKSLYPQRAVVALAGDGCFMMAAQELATAMQYDLH 472 Query: 483 VKVVIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHR 542 V ++VNN G +R QE Y R + + N PDF A ARSFG G + E Sbjct: 473 VLFIVVNNGHFGTIRMHQERHYPNRVHGTRLTN--PDFAAFARSFGAHGETVERTEDFLP 530 Query: 543 DLAAALQSPTPTMIDVHV 560 L +L++ +I++ + Sbjct: 531 ALQRSLEAKCAAVIEIRM 548 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: 965 Number of extensions: 47 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: 617 Length of database: 572 Length adjustment: 37 Effective length of query: 580 Effective length of database: 535 Effective search space: 310300 Effective search space used: 310300 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