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 Ga0059261_0285 Ga0059261_0285 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Korea:Ga0059261_0285 Length = 552 Score = 220 bits (561), Expect = 1e-61 Identities = 163/546 (29%), Positives = 250/546 (45%), Gaps = 36/546 (6%) Query: 2 NGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD-GGVEHLLCRHEQGAAMAAIGYARA 60 NG + +V L AQG + +F PG + + V DAL+D ++ + CR E GAA A Sbjct: 6 NGGRILVDNLVAQGCDRIFHVPGESFLAVLDALHDVPEIDLVTCRQEGGAAFMACADGTM 65 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 TGK GVC T GPGATN G+ A+ DS P++ G V + FQEVD + Sbjct: 66 TGKPGVCFVTRGPGATNASIGVHVAMQDSQPMLLFIGDVDRSMRDREGFQEVDFPAMFAP 125 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 K + ++ +P +A A++VA SGRPGPV++ +P+D+ L + V+ V+ Sbjct: 126 LAKWATRIEDARRIPEYVARAWNVATSGRPGPVVIALPEDMLLDEVE------AVDRPVS 179 Query: 181 FPHA--------EVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLK 232 P+ Q + + A++PM VGG F +P + Sbjct: 180 TPYPLMPDVNEDAAHQIVERIRAAKRPMAIVGGAGWDISTGRDFATFAERWGIPVAGAFR 239 Query: 233 GLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPH---AS 289 A+ + G LG +++ DLL+ VGAR + T P + Sbjct: 240 RQDAIANTSSAWAGNLGYGPNPKLVQRIRDADLLLVVGARLGEATTDGYTLVTPDHPGQT 299 Query: 290 VIHMDIDPAEMNKLRQAHVA------LQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSW 343 +IH+ DP E+N++ A +A + D+ + L L P + + H L W Sbjct: 300 LIHVHPDPEELNRVYHADMAVCCDVGIFADMLSSLKPLDTPFSGAA-EAHAEWL----DW 354 Query: 344 RYDHPGDAIYAPL--LLKQLSDR-KPADCVVTTDVGQHQMWAAQHIAH-TRPENFITSSG 399 P + + L + + +R P D ++ G W ++ + +P +S Sbjct: 355 STPKPREGVTLDLGQCVAAMRERLGPDDAIICNGAGNFSGWWHRYWHYGAQPTQLAPTS- 413 Query: 400 LGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLG 459 G MG+G PAAV A + + V ++GDG FMMN QEL T + L ++++DN G Sbjct: 414 -GAMGYGTPAAVAAALRLRDRLAVALAGDGDFMMNGQELATAIQHDADLLVLIIDNGAYG 472 Query: 460 MVRQWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYL 519 +R Q+ F R S TTL NPDF LA A+G + + + D+ ALD L G L Sbjct: 473 TIRMHQEREFPARLSGTTL-HNPDFAALARAYGCWAETVVKTDEFAPALDRALAQTGVRL 531 Query: 520 LHVSID 525 LH+ D Sbjct: 532 LHLKTD 537 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: 754 Number of extensions: 40 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: 552 Length adjustment: 36 Effective length of query: 512 Effective length of database: 516 Effective search space: 264192 Effective search space used: 264192 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