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_211260195.1 Q392_RS03110 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000745855.1:WP_211260195.1 Length = 563 Score = 246 bits (629), Expect = 1e-69 Identities = 174/536 (32%), Positives = 256/536 (47%), Gaps = 20/536 (3%) Query: 7 VVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYARATGKT 64 +V L AQGV+ VFG PG + + D +D + ++CR E GAA A + + TG+ Sbjct: 10 LVECLVAQGVSHVFGVPGESYLAALDGFHDHADRIRFVICRQEGGAAFMAEAHGKLTGRP 69 Query: 65 GVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACTK- 123 GVC T GPGATN G+ A DS P+V + G V + F +AFQEVD TK Sbjct: 70 GVCFVTRGPGATNASIGVHTAFQDSTPMVLLVGDVGSDFRDREAFQEVDYASFFGPSTKG 129 Query: 124 HSFLVQSLEE---LPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 + V+ ++E LP +A AF A +GRPGPV++ +P+D+ P Sbjct: 130 FAKRVERVDEAARLPEYVARAFATAMNGRPGPVVLVLPEDMLRTPVQAAPLPRVAPTPAW 189 Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240 A + + R ML AQ+P++ GGG Q+ AL+ F ++P + + Sbjct: 190 ADPAGLHELRGMLLAAQRPLVIAGGGGWTPQSAQALQRFAEQWQLPVANAFRFQDTFDNH 249 Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG---KLNTFAPHASVIHMDIDP 297 +P Y G +G+ + V+E DL+IAVG R + TG L P ++H D Sbjct: 250 HPLYAGDVGIAISPKLAARVREADLVIAVGPRLGEMTTGGYTLLEAPRPKQKLVHFHADA 309 Query: 298 AEMNKLRQAHVALQGDLNALLPALQ--QPLNQYDWQQHCAQLRDEHSWR---YDHPGDAI 352 E+N++ QA +A +NA AL+ P + W+ ++ PG I Sbjct: 310 EELNRVYQADLAFNTTMNAAACALETLAPPPELPWRAWAEAAHADYEANLVPQPLPG-PI 368 Query: 353 YAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIA-HTRPENFIT--SSGLGTMGFGLPA 409 P +++ L PAD V+T G W + H + F T + G MG+G+PA Sbjct: 369 DMPAIVRSLQAHLPADAVLTNGAGNFASWIHRFFRHHGLAKGFKTQLAPTSGAMGYGVPA 428 Query: 410 AVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFF 469 V A +A I+GDG F+MN QEL T + +VLL+N G +R Q+ + Sbjct: 429 GVAASIA-TGRVAFTIAGDGDFLMNGQELATAVQHGGRSIVVLLNNGMYGTIRMHQEREY 487 Query: 470 QERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 ER S T L NPDF LA A+G + +T Q E AL L + L+ + +D Sbjct: 488 PERVSGTALA-NPDFCALARAYGYAAERVTETAQFEPALLRALACETGTLIEIPLD 542 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: 760 Number of extensions: 40 Number of successful extensions: 8 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: 563 Length adjustment: 36 Effective length of query: 512 Effective length of database: 527 Effective search space: 269824 Effective search space used: 269824 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 25 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