Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_013841990.1 DESRU_RS10020 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000215085.1:WP_013841990.1 Length = 536 Score = 239 bits (609), Expect = 3e-67 Identities = 171/527 (32%), Positives = 255/527 (48%), Gaps = 30/527 (5%) Query: 39 TGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAHV 98 T AQ ++ L GV +FG+ G + + D L K+ VRHE+ A AS YA + Sbjct: 4 TVAQVMVDQLVNWGVKQVFGVVGDGIFHLLDALAHQPKIHFYAVRHEETAALMASAYAKL 63 Query: 99 TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMP 158 TG+V VC ATSGPG +L+ LADAQ D +PVVAITGQV R +GT Q D + P Sbjct: 64 TGQVAVCTATSGPGLVHLLNGLADAQKDGVPVVAITGQVARKDMGTRKKQYIDQQTLVQP 123 Query: 159 ITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYK 218 + ++ L+ +++ AF A S R A L +P DV C P P Sbjct: 124 LVSYSTLLVDPQATVKLMDRAFRSALSKRMAAHLC-VPLDVFPLPCLEEIRP--PEPYLF 180 Query: 219 PNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARGA 278 T+ + + V+EAAK+ A+KPV+ G G +A + LRELAE G V+ TL G Sbjct: 181 TETRSNLQVVKEAAKIFDQAQKPVILAGAGA--RKAVQPLRELAEKWGAGVIHTLGGMGV 238 Query: 279 FPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHADID 338 FP H LG G G+ +A A L+++D+ +G + D VI D + Sbjct: 239 FPGDHPLALGGLGHAGSSSAEAILKQADVCFRVGVNWWPE-----DYIPQNITVIELDHE 293 Query: 339 PAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSYGP 398 PA IG + AD + G + ++ E+ + ++ E DW L+ + L Sbjct: 294 PANIGGSSPADYGLAGKAENLLPEITSFIQ------PAERKDWSKILHKGHLDWHLQVQR 347 Query: 399 QSDGS---LSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTM 455 +++G + P +++ LGE+ +AV G H +W + ++ R L SG TM Sbjct: 348 EANGKDPRVPPAKIVQSLGEVVAAEAVICLDTGDHTIWFGRNFIPQEQRILL-SGKWRTM 406 Query: 456 GFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQ 515 GF +PAA+ AKIA P +V A+ GDG M + T +PV + ++NNG G++ + Sbjct: 407 GFGLPAALAAKIAEPNRQVTALVGDGGMGMLLADFTTAVKYNLPVMIVVVNNG--GLIEE 464 Query: 516 WQSLFYAERYSQTDLATHSHRI--PDFVKLAEALGCVGLRCEREEDV 560 R +L H + PDF A+A G G E +++ Sbjct: 465 ------KNRMMVGNLIPHGVYLHNPDFAAFAKACGGEGFTVENADEL 505 Lambda K H 0.319 0.136 0.414 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: 798 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: 618 Length of database: 536 Length adjustment: 36 Effective length of query: 582 Effective length of database: 500 Effective search space: 291000 Effective search space used: 291000 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