Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate BPHYT_RS19345 BPHYT_RS19345 thiamine pyrophosphate protein
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__BFirm:BPHYT_RS19345 Length = 572 Score = 238 bits (607), Expect = 5e-67 Identities = 167/543 (30%), Positives = 262/543 (48%), Gaps = 30/543 (5%) Query: 5 SGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHT-VGGIDHVLVRHEQAAVHMADGLAR 63 +GA +VV +L+ GV++VF PG + L + D+LH I ++ RHE AA +MA+ + + Sbjct: 17 TGARLVVDALLTHGVERVFCVPGESFLAVLDSLHDETERIQTIVCRHEAAAANMAEAVGK 76 Query: 64 ATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGISR 123 TG GV LVT GPGAT+A G+ TAY DS P+++L GQ A + +AFQE D + Sbjct: 77 LTGRPGVALVTRGPGATHASIGVHTAYQDSTPMILLIGQCAREHLDREAFQEIDYRRMFG 136 Query: 124 PVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESVSMR 183 + K + + IP+ L AF A SGRPGPVV+ LP+D+L+ A P + Sbjct: 137 QMAKWVAQIDDPKRIPEYLSHAFHTATSGRPGPVVLSLPEDVLSDACAAVAGAP-AYQRV 195 Query: 184 SYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCSLMG 243 + +P+ QI++ L A++P+V GG T + VE LPV + Sbjct: 196 AASPSA----AQIEKLRVLLEGAQRPMVIAGGSGWTPAACADFRRFVENWQLPVGLAFRF 251 Query: 244 LGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNN---LAKYCPNATV 300 H G +G+ + +ADV+ A+G R + TTN L T+ Sbjct: 252 QDTLDNEHPNYAGDVGLGINPALAQRIRDADVLLAIGPRLGEATTNGYTLLDIPKTKQTL 311 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDW-------WQQ 353 +H+ + + AD+PIV ++ + EL +PL E W Q Sbjct: 312 IHVHQGAEELGRVYAADLPIVSGMPELAAMLAEL-------EPLSEQLAWSGAASEAHQA 364 Query: 354 IEQWRARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRR 413 WR + + D ++ VI+ L DA +T+ G + + ++ + R Sbjct: 365 YLDWRKPRQIPGD-----VQMGEVIQQLRAHLPDDAILTNGAGNYATWLHRHFSYRHYRS 419 Query: 414 WINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNL 473 + + G MG+G+PAA+ K P VV + GDG M QEL+TA+QY+L VL + + Sbjct: 420 QL-APTSGAMGYGVPAAIAAKSMYPHRAVVALAGDGCFMMAAQELATAMQYDLHVLFIVV 478 Query: 474 NNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALE 533 NN + G ++ Q+ Y GR + + + PDF A ++G G + + L ++E Sbjct: 479 NNGHFGTIRMHQERHYPGRVHGTGLTN-PDFAAFARSFGAHGETVERTEDFLPALKRSIE 537 Query: 534 QVR 536 R Sbjct: 538 AKR 540 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: 808 Number of extensions: 43 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: 574 Length of database: 572 Length adjustment: 36 Effective length of query: 538 Effective length of database: 536 Effective search space: 288368 Effective search space used: 288368 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 09 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