Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_038211760.1 Q392_RS20755 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000745855.1:WP_038211760.1 Length = 575 Score = 299 bits (766), Expect = 2e-85 Identities = 206/561 (36%), Positives = 287/561 (51%), Gaps = 46/561 (8%) Query: 11 MHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKV 70 ++ G+++ L+ G DT FTL GGHL S Y R+ G+R++DTRHEQ A FAA +++ Sbjct: 4 LNGGQILIDVLRRFGTDTAFTLHGGHLDSAYQAARDAGLRVVDTRHEQAAGFAASAYARS 63 Query: 71 TRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPF--- 127 T GVA +TAG GITN +S +A A + P++V+GG AP LQ++D +P Sbjct: 64 TGRIGVALVTAGGGITNVVSPVANALADCVPMLVIGGAAP--------LQDLDALPVNGG 115 Query: 128 ------VAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGR 181 + V ++A LV QA++ A + G +V+ P+D F + + Sbjct: 116 VDQMAVMRSVTKWAVQVPHINRLADLVGQAIRKATTGRPGPVYVEIPIDVMFGLIA---- 171 Query: 182 PGALTEL-PAG----PTPAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEER 236 P + L PAG P P DA+ R LL AQRPVI+AG + A L E Sbjct: 172 PKEVRHLDPAGAPTRPAPTADAVARIVALLRRAQRPVILAGGGTLYADCAAELRAFAERS 231 Query: 237 HIPVLMNGMARGVVPADHRL------AFSRARSKALGEADVALIVGVPMDFRLGFGG--- 287 IPVL N +RGV+P DH L + AR + L D+ L++G F + GG Sbjct: 232 GIPVLTNAKSRGVLPTDHALWGRGYATLAPARGQDL-VPDLLLVLGAR--FGIYTGGRRK 288 Query: 288 VFGSTTQLIVADRVEPA-----REHPRPVAAGLYGDLTATLSALAGSGGTDHQGWIEELA 342 F IV +EP RE VAA L A L+A + D W L Sbjct: 289 SFLPDEATIVQVDIEPGEMGRIREPDLSVAADCGETLRALLAATEVAPLPDTTAWAHRLC 348 Query: 343 TAETMARDLEKAELVDDRIPLHPMRVYAELAALLERDALVVIDAGDFGSYAGRMIDSYLP 402 ++ D P+HP R+ A +AA L RDA+V +D G+ S+ S P Sbjct: 349 AVGAASKRNFAQVAAADCGPVHPYRLAAAVAAALPRDAVVCLDGGESHSWIDLTAHSDAP 408 Query: 403 GCWLDSGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSV 462 G WL G GC+G G A+ A++A P R+VVL GDG+ GF+ E+DTLVRH + VV V Sbjct: 409 GRWLGHGYVGCMGEGLPLAVGAQVANPGRRVVLFTGDGSIGFNFAEFDTLVRHELPVVVV 468 Query: 463 IGNNGIWGLEKHPMEALYGYS--VVAELRPGTRYDEVVRALGGHGELVSVPAELRPALER 520 + N+ +WG+ H + +YG +V++L TRY++ G H E V A+L AL R Sbjct: 469 VNNDQMWGMSAHGQDLMYGEGRRMVSDL-GRTRYEQAAAGFGCHAEFVEDVAQLDAALAR 527 Query: 521 AFASGLPAVVNVLTDPSVAYP 541 A AS PA VNV+TDP V +P Sbjct: 528 ALASNRPACVNVMTDPGVMHP 548 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: 848 Number of extensions: 53 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: 575 Length adjustment: 36 Effective length of query: 511 Effective length of database: 539 Effective search space: 275429 Effective search space used: 275429 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