Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate RR42_RS02175 RR42_RS02175 acetolactate synthase
Query= BRENDA::P9WG39 (547 letters) >FitnessBrowser__Cup4G11:RR42_RS02175 Length = 541 Score = 253 bits (646), Expect = 1e-71 Identities = 177/539 (32%), Positives = 259/539 (48%), Gaps = 26/539 (4%) Query: 8 AQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGW 67 A++ +A L +G+ +FTLSG H+ ++D C E I LI TRHE A+ W Sbjct: 2 AKSHRGADALAGTLAKAGVRRIFTLSGNHIMPVFDACLEAEIALIHTRHEAATVHMADAW 61 Query: 68 SKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPF 127 S++T G+A +T GPG N +SA+ AQ +++PLV+L G AP + G G+ QE+ Sbjct: 62 SRITGEVGMAMVTGGPGHANAVSALYTAQMSEAPLVLLSGHAPNSQRGFGAFQEMRQAEM 121 Query: 128 VAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGRPGALTE 187 APV + + + SA+ + A++ A S G + P D + + G P ++ Sbjct: 122 AAPVTKASWASASADTVAADIALAMRIAQSGRPGPVHLSLPTDALENAVTRAGEPASIAA 181 Query: 188 LPAGPTPAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMAR 247 P L+ A+RP+I+AG + L IPV+ R Sbjct: 182 PQEAPAFDARTASEVLAALAAAKRPLILAGPAWLTASGRSRTAELEARTGIPVVGMESPR 241 Query: 248 GVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFG--GVFGSTTQLIVADRVEPAR 305 G D L A + L +AD L++G +DF L FG F + + D + Sbjct: 242 G--NNDPSLG---AFGQMLAQADCILLLGKRLDFTLKFGRPPAFAADCNFLQIDADDAEL 296 Query: 306 EHPRPVAAGL--------YGDLTATLSALAGSGGTDHQGWIEELATAETMARDLEKAELV 357 E R A G A L A A +G H W+E++ A + K Sbjct: 297 ERSRRAAGARVLLARRADVGSAIAQLLACA-TGREQHCAWLEDVKAAIRYRPEAWKT--A 353 Query: 358 DDRIPLHPMRVYAELAALLER--DALVVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCLG 415 R LHP +V + L +LE +A++V D G+FG +A + + + +GP G +G Sbjct: 354 SSRGALHPAQVCSPLQPILESHPEAVLVSDGGEFGQWAQACLQA---PHRVINGPAGAIG 410 Query: 416 SGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWGLEKHP 475 S ALAA+LA+P V+ + GDG GF E+DT VR+ + V+V+GN+ W E Sbjct: 411 SALPMALAARLAKPDAPVIAMMGDGTTGFHIAEFDTAVRYGLPFVAVVGNDARWNAEYQI 470 Query: 476 MEALYGYS--VVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNV 532 YG V EL P TRYD+V A GG+GE V P +L PA++RA ASG PA VNV Sbjct: 471 QLNSYGKDRLVGCELLP-TRYDQVCAAFGGYGEFVQAPEQLLPAVQRAIASGRPACVNV 528 Lambda K H 0.319 0.135 0.405 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: 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: 547 Length of database: 541 Length adjustment: 35 Effective length of query: 512 Effective length of database: 506 Effective search space: 259072 Effective search space used: 259072 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: 52 (24.6 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