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 H281DRAFT_03240 H281DRAFT_03240 pyruvate dehydrogenase (quinone)
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Burk376:H281DRAFT_03240 Length = 611 Score = 191 bits (484), Expect = 9e-53 Identities = 184/577 (31%), Positives = 277/577 (48%), Gaps = 63/577 (10%) Query: 6 WVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG---------------VEHLLCRHEQGA 50 +++ L+A GV +FGYPG I V+ AL +E + RHE+ A Sbjct: 8 FIIERLQAWGVRRIFGYPGDGINGVFGALNRAQTEAKKHRKTTGQPEPIEFIQVRHEEMA 67 Query: 51 AMAAIGYARATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQ 110 A A +A+ TG+ GVCIATSGPGA++L+TGL DA +D +PV+AITGQ + +G Q Sbjct: 68 AFMASAHAKFTGELGVCIATSGPGASHLVTGLYDARMDHMPVLAITGQQARSALGGHYQQ 127 Query: 111 EVDVLGLSLACTKHSFLVQSL--EELPRIMAEAFDVACSGRPGPVLVDIPKDIQ-LASGD 167 EVD++ L +F+ Q+ ++ ++ A A S R LV +P D+Q L Sbjct: 128 EVDLVSL-FKDVAGAFVQQATVPAQVRHLVDRAIRTALSERKVTALV-LPNDLQDLPYEP 185 Query: 168 LEPWFTTVENEVTF------PHAE-VEQARQMLAKAQKPMLYVG-GGVGMAQAVPALREF 219 T+ + V + P AE ++QA +L +K + VG G + V A+ E Sbjct: 186 PARKHGTLHSGVGYRAPRLVPQAEDLQQAADVLNAGKKVAILVGAGALHATDEVIAVAEK 245 Query: 220 LAATKMPATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG 279 L A A L G A+ D P+ G +G+ GTK + + ECD L+ +G+ F Sbjct: 246 LGAGVAKA---LLGKAALPDDLPWVTGSIGLLGTKPSYDLMTECDTLLMIGSGF------ 296 Query: 280 KLNTFAPH---ASVIHMDIDPAEMNKLR-QAHVALQGD----LNALLPALQQPLNQYDWQ 331 F P A + +D+ A+M LR V L GD L ALLP L+ ++ +W+ Sbjct: 297 PYAEFLPKEGAARGVQIDL-KADMLSLRYPMEVNLVGDSVETLRALLPLLEHKQDR-EWR 354 Query: 332 Q----HCAQLRDEHSWRYDHPG-DAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHI 386 + A R PG DA+ + +LS R P++ +VT+D G W A+ + Sbjct: 355 KTIEGWTADWWKTLDKRAHEPGKDAVNPQRTVWELSPRVPSNAIVTSDSGSCANWYARDL 414 Query: 387 AHTRPENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMM-NVQELGTVKRKQ 445 R S GL +MG +P A+ A+ A P V+ + GDG+ M N+ EL TV + Sbjct: 415 KVQRGMMCSLSGGLASMGAAVPYAIAAKFAYPERPVIALVGDGAMQMSNMAELITVSKYW 474 Query: 446 L----PLKI-VLLDNQRLGMVRQWQQLFFQERYSETTLTDNPD--FLMLASAFGIHGQHI 498 P I ++L+NQ L V W+Q + D P + A G+ G ++ Sbjct: 475 KGWADPRWICMVLNNQDLNQV-TWEQRVMEGDPKFEASQDIPSVPYHKFAELIGLKGIYV 533 Query: 499 TRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVP 535 +Q+ AA DT L +D P ++ V D N+ PL P Sbjct: 534 DDAEQMGAAWDTALAADRPVVIEVKAD--PNIAPLPP 568 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: 778 Number of extensions: 34 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: 611 Length adjustment: 36 Effective length of query: 512 Effective length of database: 575 Effective search space: 294400 Effective search space used: 294400 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