Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_106717976.1 CU100_RS14805 thiamine pyrophosphate-requiring protein
Query= BRENDA::P00893 (574 letters) >NCBI__GCF_003010935.1:WP_106717976.1 Length = 555 Score = 201 bits (512), Expect = 5e-56 Identities = 170/559 (30%), Positives = 255/559 (45%), Gaps = 40/559 (7%) Query: 2 EMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGL 61 + +SGA++V L +G+KQ+ G+P + D A I V+ R + AV++A+G Sbjct: 10 QTMSGAQIVASILKLEGIKQIIGFPNSELFDACAARD----IPPVIARTPRVAVNIAEGY 65 Query: 62 AR--ATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMV 119 AR A GE+ VV V GPGA +A GIA A+ D P++ L GY E Sbjct: 66 ARTVADGELAVVTVQYGPGAESAFGGIAQAFNDRTPILFLP-------TGYPRGSEAVTP 118 Query: 120 GIS-----RPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDIL----NPAN 170 R V K S E +P+++ A +GRP PV+++LP D+L +P N Sbjct: 119 NFHASRNFRHVTKWSETAGCVEHLPKLMHSAISRVRNGRPAPVLLELPVDLLAERLDPTN 178 Query: 171 KLPYVWPESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETV 230 + V R G G+I ++TL+AAK PVV G G + A ++L E Sbjct: 179 E--------VYQRPRRSAPQGDAGEIAELVKTLLAAKNPVVLAGQGVLAAFATKELVEFA 230 Query: 231 EALNLPVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNN 290 E L +PV+ + G FP H ALG G + M ADV+ A+G + Sbjct: 231 ELLRIPVMTTPNGKSGFPENHPLALGAAGRARPTTVDHFMDKADVVLALGTSL--TRSYY 288 Query: 291 LAKYCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLD--EIR 348 + + +LH+ +D + K +V DAR L QM L Q H +D ++ Sbjct: 289 ILPIPKDKVLLHVTVDEGDLGKDYPIAQGVVSDARSALRQMNAYLKQHK-HVLVDRADVM 347 Query: 349 DWWQQIEQ-WRARQCLKYDTHSEKIKPQAVI-ETLWRLTKGDAYVTSDVGQHQMFAALYY 406 D + I +R R SE I P V+ E + + ++ VT D G + + +Y Sbjct: 348 DEIRSIRSVFRERWMPLLTADSEPISPYRVVWEIMQVVDPSNSVVTHDAGNPRDQFSPFY 407 Query: 407 PFDKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYEL 466 PR +I G +G GL ALG K+A P+ TVV + G+ + M + TA++ L Sbjct: 408 EAVIPRSYIGWGKTTQLGSGLGFALGAKLARPKATVVNLMGESAFGMVGIDFETAIRCHL 467 Query: 467 PVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELES 526 P+L V L N LG I S ++ + M + +AEA G G +S P L Sbjct: 468 PILTVVLRNNVLGGYAASMP-IASRKYGANLMSGA--YAPIAEALGGYGECVSLPKNLRP 524 Query: 527 KLSEALEQVRNNRLVFVDV 545 L LE+V + ++V Sbjct: 525 ALLRGLERVGKGQAALIEV 543 Lambda K H 0.319 0.135 0.403 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: 745 Number of extensions: 40 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: 574 Length of database: 555 Length adjustment: 36 Effective length of query: 538 Effective length of database: 519 Effective search space: 279222 Effective search space used: 279222 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