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_012331547.1 M446_RS07735 thiamine pyrophosphate protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000019365.1:WP_012331547.1 Length = 559 Score = 266 bits (680), Expect = 2e-75 Identities = 170/537 (31%), Positives = 267/537 (49%), Gaps = 19/537 (3%) Query: 2 NGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARAT 61 +G + +V L GV F PG + + V DAL+D + +CR E AAM A + T Sbjct: 9 SGGRILVDQLLVHGVRDAFCVPGESYLAVLDALHDAAIRLTVCRQEGSAAMMAEAAGKLT 68 Query: 62 GKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLAC 121 G+ G+C T GPGA N GL A DS P++ GQV +AFQE+D + Sbjct: 69 GEPGICFVTRGPGAMNAAPGLHVARQDSTPLILFVGQVERGAREREAFQEIDYRAVFGTV 128 Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLAS---GDLEPWFTTVENE 178 K V+ LP +++ AF VA +GRPGPV+V +P+D+ A+ D P+ T + Sbjct: 129 AKWVTEVEDPARLPELISRAFHVATAGRPGPVVVALPEDVLTATAAVADAPPYAPTETHP 188 Query: 179 VTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVE 238 A++ +++L +A++P+ +GG AV L F ++P C+ + G Sbjct: 189 AL---AQMVALQRLLGEAERPLALLGGSRWSEAAVRRLARFAGLFRLPVACSFRRQGLFP 245 Query: 239 ADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDD---RVTGKLNTFAPHASVIHMDI 295 AD+P Y G LG+ ++E DLL+ VG R + + L+ P ++H+ Sbjct: 246 ADHPSYAGDLGLGANPRLLARIREADLLLLVGGRLGEIPSQGYSLLDIPGPRQRLVHVHP 305 Query: 296 DPAEMNKLRQAHVALQGDLNALLPALQ--QPLNQYDW-----QQHCAQLRDEHSWRYDHP 348 DP E+ ++ + H+A+ A A++ QP + W + H + L R P Sbjct: 306 DPEELGRVYRPHLAVNATPAAFAAAIETVQPPARLPWAEGTDEAHASYLAWSDPARVATP 365 Query: 349 GDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLP 408 G+ + ++ L + PAD ++ G W + + + + G+MG+G+P Sbjct: 366 GE-LQMGGVMAHLREVLPADAILCNGAGNFATWVHRFWPFRAFDGQLAPTS-GSMGYGVP 423 Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468 AAV A+ RP TVV +SGDG F+MN Q+ T + LP+ ++L+DN G +R Q+ Sbjct: 424 AAVAAKRLRPERTVVAVSGDGDFLMNGQDFATAVQYGLPILVILVDNGMYGTIRMHQERE 483 Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 + R S T+L NPDF A+AFG +G+ +TR + AL S P +LH ID Sbjct: 484 YPGRVSGTSLR-NPDFAAYATAFGGYGERVTRTEDFPEALARARASGLPAILHCPID 539 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: 792 Number of extensions: 44 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: 559 Length adjustment: 36 Effective length of query: 512 Effective length of database: 523 Effective search space: 267776 Effective search space used: 267776 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