Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_041099888.1 SUTH_RS13350 thiamine pyrophosphate-binding protein
Query= BRENDA::P00893 (574 letters) >NCBI__GCF_000828635.1:WP_041099888.1 Length = 577 Score = 231 bits (588), Expect = 8e-65 Identities = 166/555 (29%), Positives = 266/555 (47%), Gaps = 24/555 (4%) Query: 5 SGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLARA 64 +GA + VR+L G+K FG PG ++YD L++ I +LV HE A MADG++R Sbjct: 4 TGAWLAVRALEALGIKYTFGIPGVHNTELYDELNSSDLITPILVTHEGGASFMADGVSRT 63 Query: 65 TGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGISRP 124 +G+ G +++ GAT+A +GI A++D +P++V+ G + T L + D +P Sbjct: 64 SGQTGTLVIVPAAGATHAASGIGEAFLDGVPMLVICGGIRTDLDKRYQLHQMDQHAFLKP 123 Query: 125 VVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDI-LNPANKLPYVWPESVSMR 183 + K +FLV DI L KA+ +A SG PGPV V++P ++ + P P +++ Sbjct: 124 LTKATFLVTAHADIVPTLFKAWEIAHSGEPGPVFVEIPVNLQMFPGEAGDIPAPPAIARP 183 Query: 184 SYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCSLMG 243 T I+RA + L+AAK P ++VG GA A H+Q + E L PV +L G Sbjct: 184 QPTVAT-----DIRRAAEMLLAAKHPAMFVGWGARDA--HEQTRAIAEFLQAPVATTLQG 236 Query: 244 LGAFPATHRQALGM-LGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVLH 302 L F A H G G A + D + AVG RF + T + P ++H Sbjct: 237 LSVFSAAHPLHTGFSFGASAVPAARNAFADCDCLLAVGTRFAEIATGSFGVTVP-PNLIH 295 Query: 303 IDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQ----ESAHQPLDE--IRDWWQQIEQ 356 DI+P S A + + GDA VL +LE L + +A+ L + RD E+ Sbjct: 296 ADINPAVFSANYPAAVALEGDAAAVLTALLEELRRVGAGATANVELQQRIARDKAAYNEE 355 Query: 357 WRARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWIN 416 W L++D+ K+ P L DA D G H A +P +P+ I Sbjct: 356 W-----LRHDS-GGKVNPAVFFNALRAAVPDDAIAVVDDGNHTYLTAELFPVRQPKALIV 409 Query: 417 SGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNR 476 +MG+ +PAA+G K+A P V + GDG+ M E+ +A + L ++ ++ Sbjct: 410 PTDFNSMGYAVPAAIGAKLANPGREVFAIIGDGAFTMTCMEIVSATRIGLGLVFYVFHDG 469 Query: 477 YLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVR 536 L + Q Q++ ++ + + DF +A A G + + + + ++ A E Sbjct: 470 ELSQIAQAQEIPFNRKPCTAL--GAIDFSGVAIATGAEYLPVPSNDGVAAAIARARELAA 527 Query: 537 NNRLVFVDVTVDGSE 551 R V VD+ +D S+ Sbjct: 528 AGRPVIVDLIMDYSK 542 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: 759 Number of extensions: 41 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: 577 Length adjustment: 36 Effective length of query: 538 Effective length of database: 541 Effective search space: 291058 Effective search space used: 291058 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