Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate BPHYT_RS31615 BPHYT_RS31615 thiamine pyrophosphate protein
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__BFirm:BPHYT_RS31615 Length = 610 Score = 179 bits (454), Expect = 3e-49 Identities = 172/577 (29%), Positives = 273/577 (47%), Gaps = 64/577 (11%) Query: 6 WVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--------------VEHLLCRHEQGAA 51 +++ L A GV ++GYPG I V+ AL +E + RHE+ AA Sbjct: 8 FIIGRLHAWGVRRIYGYPGDGINGVFGALNRAQSEARNSKSGNPTQPIEFVQVRHEEMAA 67 Query: 52 MAAIGYARATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQE 111 A +A+ TG+ GVCIATSGPGA++LITGL DA +D +PV+AI GQ + +G QE Sbjct: 68 FMASAHAKFTGELGVCIATSGPGASHLITGLYDARMDHMPVLAIAGQQARAALGGHYQQE 127 Query: 112 VDVLGLSLACTKHSFLVQSL--EELPRIMAEAFDVACSGRPGPVLVDIPKDIQ-LASGDL 168 +D+ + +F+ Q+ ++ ++ A A + R L+ +P D+Q L Sbjct: 128 LDLASM-FKDVAGAFVEQASVPAQVRHLVDRAVRTALAERKVTALI-LPNDLQDLRYEAP 185 Query: 169 EPWFTTVENEVTF------PHA-EVEQARQMLAKAQKPMLYVG-GGVGMAQAVPALREFL 220 + T+ + V + P+ +++QA ++L +K + VG G + V A+ E L Sbjct: 186 DRKHGTLHSGVGYRAPRLVPYPDDLQQAAEVLNAGKKVAILVGAGALHATDEVIAIAEKL 245 Query: 221 AATKMPATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGK 280 A A L G A+ D P+ G +G+ GTK + + ECD L+ +G+ F Sbjct: 246 GAGVAKA---LLGKAALPDDLPWVTGAIGLLGTKPSYDLMMECDTLLMIGSGF------P 296 Query: 281 LNTFAPH---ASVIHMDIDPAEMNKLR-QAHVALQGD----LNALLPALQQPLNQ----- 327 + F P A + +D+ A+M LR V L GD L ALLP L+ ++ Sbjct: 297 YSEFLPKEGAARGVQIDL-KADMLSLRYPMEVNLVGDSVETLRALLPLLEDKKDRAWRGK 355 Query: 328 -YDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHI 386 W + + D+ + ++ DA+ + +LS R PAD +VT+D G W A+ + Sbjct: 356 IEGWTKDWWKTLDKRA--HEAGKDAVNPQRTVWELSKRIPADSIVTSDSGSCANWYARDL 413 Query: 387 AHTRPENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMM-NVQELGTVKRKQ 445 R S GL +MG +P A+ A+ A P V+ + GDG+ M N+ EL TV + Sbjct: 414 KVQRGMMCSLSDGLASMGAAVPYAIAAKFAFPERPVIALVGDGAMQMNNMAELITVSKYW 473 Query: 446 LPLK-----IVLLDNQRLGMVRQWQQLFFQERYSETTLTDNPD--FLMLASAFGIHGQHI 498 ++L+N L V W+Q + D P + A G+ G ++ Sbjct: 474 KDWANPRWICMVLNNSDLNQV-TWEQRAVEGDPKFEASQDIPSVPYHKFAELIGLKGIYV 532 Query: 499 TRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVP 535 +Q+ AA D L +D P ++ V D N+ PL P Sbjct: 533 DNDEQMGAAWDEALAADRPVVIEVKSD--PNIAPLPP 567 Lambda K H 0.320 0.135 0.410 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: 770 Number of extensions: 33 Number of successful extensions: 4 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: 548 Length of database: 610 Length adjustment: 36 Effective length of query: 512 Effective length of database: 574 Effective search space: 293888 Effective search space used: 293888 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