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_106718644.1 CU100_RS19210 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_003010935.1:WP_106718644.1 Length = 550 Score = 251 bits (640), Expect = 7e-71 Identities = 164/537 (30%), Positives = 264/537 (49%), Gaps = 22/537 (4%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62 G + +V AL A V +F PG + + V DALYD G+ +CR E GAAM A + + TG Sbjct: 4 GGELIVEALAANQVERLFCVPGESYLAVLDALYDTGIGVTVCRAEGGAAMMAEAWGKLTG 63 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122 K G+C T GPGATN G+ A DS P++ GQV +AFQEV+ Sbjct: 64 KPGICFVTRGPGATNASPGIHIARQDSTPLILFIGQVQRDAREREAFQEVEYRRFFANTA 123 Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDI---QLASGDLEPWFTTVENEV 179 K + +P + AF VA SGRPGPV++ +P+D+ ++ + + W E Sbjct: 124 KWVAEIDDARRIPEFVTRAFSVATSGRPGPVVLALPEDMLTDKVEAVAAQGWQPV---ET 180 Query: 180 TFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239 A +E+ +L A KP + +GG AV ++ F +P C+ + + Sbjct: 181 GPSPACIEKLADLLQGATKPFMILGGSRWSEHAVRSITRFAEKWHLPVGCSFRRQMLFDH 240 Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG---KLNTFAPHASVIHMDID 296 +P Y G +G+ A V+E D+L+ VG RF + + +++ P ++IH+ D Sbjct: 241 LHPNYAGDVGIGINPALATRVKEADVLLLVGGRFGEMPSSGYTLIDSPYPKQTLIHVYPD 300 Query: 297 PAEMNKLRQAHVALQGDLNALLPALQQ--PLNQYDWQQHCAQLRDEH-SWR---YDHPGD 350 E+ ++ + +A+ + A++ P + +W + + +W PG+ Sbjct: 301 ADELGRVYRPSLAINSAPDTFAEAVEHLAPPSHINWPGEAETAHESYLAWSTPPKTGPGE 360 Query: 351 AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSG--LGTMGFGLP 408 P ++ L P D ++T G + W H H R F T + G+MG+GLP Sbjct: 361 VAMGP-IMSYLESVLPEDAIMTNGAGNYATWL--HRFH-RFRRFGTQAAPTSGSMGYGLP 416 Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468 AAV A+ P V+C +GDG F+MN Q+ T + LP+ +++++N G +R Q+ Sbjct: 417 AAVAAKQLNPERMVICFAGDGCFLMNGQDFATAVKYGLPIIVLVINNNIYGTIRMHQERE 476 Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 + R S T LT NPDF MLA A+G HG+ + ++ E A + S P ++ + +D Sbjct: 477 YPGRVSATDLT-NPDFAMLARAYGGHGETVAATEEFEGAWQRAVESGKPAIIEIQLD 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: 769 Number of extensions: 37 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: 550 Length adjustment: 36 Effective length of query: 512 Effective length of database: 514 Effective search space: 263168 Effective search space used: 263168 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