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 YP_004142286.1 Mesci_3112 thiamine pyrophosphate TPP-binding domain-containing protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000185905.1:YP_004142286.1 Length = 549 Score = 256 bits (653), Expect = 2e-72 Identities = 167/543 (30%), Positives = 265/543 (48%), Gaps = 34/543 (6%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62 G Q +V AL A G + ++ PG + + V DAL+D + ++CR E GAAM A + R TG Sbjct: 4 GGQLIVDALEANGTDRIYCVPGESYLAVLDALHDSAIRTIVCRQEGGAAMMADCHGRLTG 63 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122 K G+C T GPGATN G+ A+ DSIPV+ GQV+ +AFQEVD Sbjct: 64 KPGICFVTRGPGATNASAGIHIAMQDSIPVILFIGQVAGHAKEREAFQEVDYKRFFGDIA 123 Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVTFP 182 K + +P + AF VA SGRPGPV++ +P+D+ + VE V P Sbjct: 124 KWVVEIDDASRIPEFVTRAFAVATSGRPGPVVISLPEDMLT---------SVVEAPVALP 174 Query: 183 H---------AEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKG 233 H AE++ ++LAK+++P + +GG A+AV +R A +P C+ + Sbjct: 175 HTPVETRAGEAELDALEKLLAKSKRPFVILGGTRWDAEAVAQMRTIAEAWSLPVGCSFRR 234 Query: 234 LGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGK---LNTFAPHASV 290 + +P Y G +G+ A+++ DL++ +G R + + L + P ++ Sbjct: 235 QMLFDHLHPNYAGDVGIGINPKLATAIKQADLVLLIGGRMGEMPSSDYTLLKSPYPAQTL 294 Query: 291 IHMDIDPAEMNKLRQAHVALQGDLNALLPAL--QQPLNQYDWQQHCAQLRDEH-SWR--- 344 +H+ D E+ ++ + +A+ +A + A ++P + W +L + W Sbjct: 295 VHVHADSGELGRVYRPALAINASPSAFVDAFAKRKPASAPVWAAETPKLHAAYLDWSTPP 354 Query: 345 YDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSG--LGT 402 PG P ++ L P D ++T G + W H H R F T G+ Sbjct: 355 ESGPGPVQMGP-IMNYLEKMLPDDAILTNGAGNYATWV--HRFH-RFRRFATQGAPTSGS 410 Query: 403 MGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVR 462 MG+G PAAV A+ P TVV +GDG F+MN QE T + LP+ +V+++N G +R Sbjct: 411 MGYGTPAAVAAKELFPERTVVAFAGDGCFLMNGQEFATAVQYDLPIVVVVVNNGIYGTIR 470 Query: 463 QWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHV 522 Q+ + R T L NPDF LA A+G HG+ + + A + S P ++ + Sbjct: 471 MHQEREYPGRVVATDL-KNPDFAALARAYGGHGETVEKTADFAPAFERARASGKPAIVEI 529 Query: 523 SID 525 +D Sbjct: 530 RLD 532 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: 706 Number of extensions: 38 Number of successful extensions: 5 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: 549 Length adjustment: 36 Effective length of query: 512 Effective length of database: 513 Effective search space: 262656 Effective search space used: 262656 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