Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 3610459 Dshi_3840 thiamine pyrophosphate protein TPP binding domain protein (RefSeq)
Query= BRENDA::P9WG41 (618 letters) >FitnessBrowser__Dino:3610459 Length = 546 Score = 253 bits (647), Expect = 1e-71 Identities = 168/512 (32%), Positives = 257/512 (50%), Gaps = 20/512 (3%) Query: 39 TGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAHV 98 +GAQA++ SL GVD ++G+PG + L DS+ + VL RHEQ A A + + Sbjct: 6 SGAQALVESLFSAGVDTVYGVPGEETTALMAALHDSE-MAFVLCRHEQAAAFMAGVHGRL 64 Query: 99 TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMP 158 TGR C+AT GPGATNLVT +ADA +D +P++AITGQ G G +G ++ Q D+ + P Sbjct: 65 TGRPAACLATLGPGATNLVTGVADATLDFVPMIAITGQGGCGRLGRESHQIIDLEALFAP 124 Query: 159 ITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYK 218 +TK + + D +P +AEA +A + +PGAV + +P+DV Q P +P Sbjct: 125 VTKQSRTLLEADAVPGAVAEAVRLARAEKPGAVHLCLPEDVADAQTALRDVP---VPQVL 181 Query: 219 PNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARGA 278 P + P + +A L+ A +P+L G GVIR AT +LR AE TGI VVT+ MA G Sbjct: 182 P-SPPAPEAIAQALTLLTRAERPILLAGAGVIRAGATAELRAFAEATGIAVVTSFMAGGV 240 Query: 279 FPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEA-KVIHADI 337 P H L G + + +DL++++G FD D A V+H Sbjct: 241 LPPEHELTLFTVGQPEGDYVDLSFEAADLIVSVG--FDPVEYPAADLSRDGAIPVLHLGA 298 Query: 338 DPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLN-GVRKTYPLSY 396 PA H + G V A + E +A L +M +A + G+RK + +Y Sbjct: 299 GPAPADAGWH----VAGQVVAGLPETLAALAEALEARRWDMPPAFAGVQAGMRKAFARAY 354 Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456 S+G ++P+ + ++ + ++GVG H++W A+ + +P + GL MG Sbjct: 355 STSSEGPVAPQDICAEITRQLRAEDTVLSGVGLHKLWIARHVLPRRPGQVIIPNGLAGMG 414 Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516 A+P A+ A V AI GDG M Q++ T A G+ + V + +G G++ Sbjct: 415 LALPGAVAAARLQQAGRVLAICGDGDVMMNVQDMETAARLGLDLTVMVWEDGGYGLID-- 472 Query: 517 QSLFYAERYSQTDLATHSHRIPDFVKLAEALG 548 A + D +T PD+ +LA A G Sbjct: 473 -----AHQQKAGDDSTFGFGTPDWGRLARAFG 499 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: 953 Number of extensions: 41 Number of successful extensions: 4 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: 546 Length adjustment: 36 Effective length of query: 582 Effective length of database: 510 Effective search space: 296820 Effective search space used: 296820 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