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_011426123.1 RHE_RS14715 thiamine pyrophosphate protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000092045.1:WP_011426123.1 Length = 552 Score = 241 bits (615), Expect = 5e-68 Identities = 165/536 (30%), Positives = 264/536 (49%), Gaps = 20/536 (3%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62 G + +V AL+A GV + PG + + V DAL D ++ L+CR E GAAM A + R TG Sbjct: 5 GGELIVEALKANGVKRLSCVPGESFLAVLDALRDSDIDVLVCRQEGGAAMMADCWGRLTG 64 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122 + G+C+ T GPGATN GL + DSIP++ GQV +AFQEV+ Sbjct: 65 EPGICMVTRGPGATNASAGLHISRQDSIPMILFIGQVQREAREREAFQEVEFRRAFTEFA 124 Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDI--QLASGDLEPWFTTVENEVT 180 K + +P + AF +A SGRPGPV++ +P+D+ +T+VE Sbjct: 125 KWVGEIDDAARIPEFVTRAFAIATSGRPGPVVLTLPEDMLRDEVEAPRAKRYTSVEAHP- 183 Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240 ++V+ L KA++PM+ +GG A AV F ++P C+ + + Sbjct: 184 -GRSQVDDFYIRLLKAERPMVILGGTRWDADAVADFAGFAERFRLPVGCSFRRQMLFDHL 242 Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGK---LNTFAPHASVIHMDIDP 297 +P Y G +G+ ++E DLLI +G R + + ++ P S++H+ DP Sbjct: 243 HPCYAGDVGIGINPVLAKEIKESDLLILLGGRMSEMPSSSYTLIDIPYPQQSLVHVYPDP 302 Query: 298 AEMNKLRQAHVAL---QGDLNALLPALQQPLNQYDWQQHCAQLRDEH-SWR---YDHPGD 350 +E+ ++ + +A+ D A L L+ P + W + ++ + SW PG Sbjct: 303 SELGRVYRPDLAICAAPSDFVAALADLEAPAEPH-WTERTQRMHQAYLSWSKPPATGPG- 360 Query: 351 AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHT-RPENFITSSGLGTMGFGLPA 409 A++ L++ L + + T G + W H H R N + G+MG+GLPA Sbjct: 361 AVHMGPLMEWLEANTGPETIFTNGAGNYATWL--HRFHRFRRFNTQAAPTSGSMGYGLPA 418 Query: 410 AVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFF 469 AV A+ P V+C +GDG F+M+ QE T R LP+ ++++N G +R Q+ + Sbjct: 419 AVAAKRLFPEREVICFAGDGCFLMHGQEFATAIRYGLPIIAIVVNNGMYGTIRMHQEREY 478 Query: 470 QERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 R S T LT NPDF LA A+G HG+ + ++ A + P ++ V +D Sbjct: 479 PGRVSSTDLT-NPDFAALARAYGGHGETVESTEEFAPAFERARIGGKPAIIEVKLD 533 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: 728 Number of extensions: 33 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 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