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_057506889.1 ABB28_RS01265 pyruvate oxidase
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_001431535.1:WP_057506889.1 Length = 572 Score = 197 bits (501), Expect = 9e-55 Identities = 160/540 (29%), Positives = 246/540 (45%), Gaps = 22/540 (4%) Query: 4 AQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGK 63 A VV L+ GV +G G + V A++ ++ + RHE+ AA AA + +G+ Sbjct: 6 ADIVVETLQQAGVRRCYGIVGDTLNHVTTAIHGSDIDWVHVRHEEVAAFAAGADSLISGQ 65 Query: 64 TGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACTK 123 C + GPG+ + I G+ + + P+V I QV +G + QEVD + +C+ Sbjct: 66 LTACAGSCGPGSLHFINGVFENNRNKAPMVLIASQVVTSELGMEFPQEVDFKAVYSSCSV 125 Query: 124 HSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVTFPH 183 V S E+ R++ A A S R G +V +P DI +P F + Sbjct: 126 FCEQVYSAEQARRVVTLACQAAIS-RRGVAVVILPSDISEQVVKHDPPFAVHYTQPVLRP 184 Query: 184 AEVEQAR--QMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADY 241 + E R ++L + ++ +Y G G A A L E + P T + VE D Sbjct: 185 GDDELLRIAELLGQGKRIGIYAGAGCQGAHA--PLLELARRLQAPIAHTSRAKDFVEPDN 242 Query: 242 PYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEMN 301 P+ +GM G+ G ++ AV ECD L+ +GA F G+ + A++I +D D + + Sbjct: 243 PFNMGMTGIFGIESGFHAVMECDTLLLLGADF---AWGQY--YPDKATIIQVDHDGSHLG 297 Query: 302 KLRQAHVALQGD----LNALLPALQQPLNQYDWQQHCAQLRDE---HSWRYDHPGDA-IY 353 + + + GD L ALLP L P D+ C R++ + PG+ + Sbjct: 298 RRHPVTLGVVGDIGPTLEALLPML-PPREDTDFLDECIGHREKALAKRAEEEAPGEGELI 356 Query: 354 APLLLKQLSDRKPA-DCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVG 412 P L L D+ A D + T D G +W +HI +TS GTM +P A+G Sbjct: 357 HPQYLTALLDQHAADDALFTADCGSPMVWVLRHIRVNGRRRTLTSLLHGTMANAMPQALG 416 Query: 413 AQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQER 472 Q A P VV + GDG M + +L T ++ LP+KIV+ +N L V Q++ + Sbjct: 417 LQKAFPGRQVVALCGDGGLSMLMGDLLTAVQENLPIKIVVYNNGSLNFVELEQKV--EGL 474 Query: 473 YSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWP 532 T NPDF LA G HG+ +TR + A+ +L GP LL V E V P Sbjct: 475 LDYYTELKNPDFGKLAEVIGFHGRTVTRSQDLALAVQDLLAQPGPALLDVHTAPTELVMP 534 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: 715 Number of extensions: 38 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: 572 Length adjustment: 36 Effective length of query: 512 Effective length of database: 536 Effective search space: 274432 Effective search space used: 274432 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 10 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