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 WP_010529935.1 ON01_RS05120 pyruvate oxidase
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000224785.1:WP_010529935.1 Length = 570 Score = 234 bits (598), Expect = 5e-66 Identities = 160/538 (29%), Positives = 276/538 (51%), Gaps = 24/538 (4%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYA 58 M ++ V+ L+ +N ++GYPG ++ + +++ G ++ + RHE+ AA++A A Sbjct: 1 MQASEGVIEILKDWNINHIYGYPGDSVNNLVESIRKAGEAIQFIQVRHEEVAALSASAEA 60 Query: 59 RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118 + TG GVC++ GPGA +L+ G+ DA DS P+V ITGQ+S +GTD FQEV + L Sbjct: 61 KITGDVGVCLSIGGPGAIHLLNGMYDAKKDSAPMVVITGQISHDLLGTDNFQEVTLERLF 120 Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE 178 + V S +L ++ +AF A + + G ++ +P D+ L + EP +T+ + Sbjct: 121 DDVAIFNRRVTSGNQLQPLLKQAFREAYN-QKGVAVLSVPDDVFLETIKQEPLRSTIVPD 179 Query: 179 VTFPHAE--VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGA 236 V + ++ A + +A+KP++ G G A L F P +L+G G Sbjct: 180 VNMTPGKKNIDNAISNIQQAKKPVILAGKGA--LDARDELVAFADKIAAPVVVSLRGKGV 237 Query: 237 VEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAP-HASVIHMDI 295 + ++ LG LG GTK A A+ E DLLI G F R F P HAS I +DI Sbjct: 238 LPDEHRLNLGNLGQIGTKPAYEAMAETDLLILAGTSFPYR------EFLPNHASSIQIDI 291 Query: 296 DPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQ--HCAQLRDEHSWRY-----DHP 348 +P ++ K +V L G + LP L + L + +Q Q ++ W++ + Sbjct: 292 NPDKLGKWYPVNVGLAGTVKETLPHLSEQLEDQENRQFLEACQENMKNWWKHIDRLVNAD 351 Query: 349 GDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLP 408 + + ++ L D D +++ DVG W + + T + F+ SS L TMG GLP Sbjct: 352 NEQLLGAHVINGLHDFIDDDAILSVDVGNITTWTTRFLRLTN-QQFVISSWLATMGCGLP 410 Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468 A+ A++ P++ VV I GDG F M + + T + QLP+ +++L+N+++GM++ Q+ Sbjct: 411 GAIAAKLTAPDEQVVAICGDGGFSMVMHDFMTAVKYQLPITVIVLNNEKIGMIKYEQEEM 470 Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526 Y ET L ++ A+ G G + + ++ +AL + S+ P ++ I++ Sbjct: 471 GNIPY-ETDLQPF-NYANFANISGGKGFKVKNEKELSSALQSAKESNVPVIVDAEIED 526 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: 651 Number of extensions: 29 Number of successful extensions: 6 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: 570 Length adjustment: 36 Effective length of query: 512 Effective length of database: 534 Effective search space: 273408 Effective search space used: 273408 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 Jul 26 2024. The underlying query database was built on Jul 25 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