Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_085636118.1 MGEO_RS07590 thiamine pyrophosphate-binding protein
Query= BRENDA::P00893 (574 letters) >NCBI__GCF_002115805.1:WP_085636118.1 Length = 522 Score = 138 bits (348), Expect = 5e-37 Identities = 148/561 (26%), Positives = 229/561 (40%), Gaps = 60/561 (10%) Query: 3 MLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLA 62 M GA++V+++L GVK +F G ++ ++DA G+ RHE AAV+MA+G A Sbjct: 1 MTRGADVVMQTLAAHGVKNIFALSGNQIMPLFDA-SLDAGVRLYHTRHEAAAVYMAEGYA 59 Query: 63 RATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGIS 122 + + +GV LVT+G G NA+ + TA P+++LSG G AFQE D V ++ Sbjct: 60 QLSRGLGVALVTAGAGLGNALGPLLTARASDTPVLLLSGDSPVGRDGQGAFQEMDQVALT 119 Query: 123 RPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESVSM 182 + + K S V + ED+ L KA +A SGRPGPV V LP D+L M Sbjct: 120 QSLTKWSVRVTRAEDLSGTLHKAVHVALSGRPGPVHVSLPADVL----------LADTGM 169 Query: 183 RSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVE-ALNLPVVCSL 241 S + L AA+ P++ V G A+ A L E +E A + PV+ Sbjct: 170 ISEAIAEASADTNVAALCDWLSAARAPLI-VLGPALNATRQPDLAERLEQATDAPVIVME 228 Query: 242 MGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVL 301 G +LG L AD + +G D A ++ Sbjct: 229 SPRG----LKDPSLGAL--------TDVFAEADRVLLLGKPMDFTVQFGAAAPRAGWAIV 276 Query: 302 HIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIR-----DWWQQIEQ 356 H D D + ++ E L+ P+D R +Q Sbjct: 277 HADRDELARAQL----------------NCSERLTLRLEADPVDVARGLSYGSGSEQSSA 320 Query: 357 WRARQCLKYDTHSE------KIKPQAVIETLWRLTKG--DAYVTSDVGQHQMFAALYYPF 408 WR R SE I P + + +G D V D G+ +A Sbjct: 321 WRDRVHAACARRSEIVRQESPIDPSGLCAAVQSSLEGLPDPVVICDGGEFGQWAQA--GV 378 Query: 409 DKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPV 468 RR IN G G +G GL A+ + A P TV+ + GDG++ ++ E TA++ +LP Sbjct: 379 SASRRIIN-GVSGAIGGGLCYAMAARAADPTATVIALMGDGTVGFHLGEFETAVREDLPF 437 Query: 469 LVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKL 528 + + N++ Q Q + S + A G G ++ EL + Sbjct: 438 VAIVGNDQRWNAEHQIQLREFGADRLHGCALSEARYDEAVAALGGFGALVTKLSELPGAI 497 Query: 529 SEALEQVRNNRLVFVDVTVDG 549 A + + R ++V ++G Sbjct: 498 EAA---IGSGRPACINVLMEG 515 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: 665 Number of extensions: 33 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 574 Length of database: 522 Length adjustment: 36 Effective length of query: 538 Effective length of database: 486 Effective search space: 261468 Effective search space used: 261468 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