Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate N515DRAFT_1567 N515DRAFT_1567 pyruvate dehydrogenase (quinone)
Query= BRENDA::P9WG41 (618 letters) >FitnessBrowser__Dyella79:N515DRAFT_1567 Length = 594 Score = 216 bits (549), Expect = 3e-60 Identities = 168/556 (30%), Positives = 260/556 (46%), Gaps = 43/556 (7%) Query: 44 VIRSLEELGVDVIFGIPGGAVLPVYDPLFDS-KKLRHVLVRHEQGAGHAASGYAHVTGRV 102 ++ L + G+ +FG PG + + + + ++ +V VRHE+ A A G+A TGR+ Sbjct: 8 ILERLSDWGIQRVFGYPGDGINGLMGAMGRAAERFDYVRVRHEEMAAFMACGHAKFTGRI 67 Query: 103 GVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMPITKH 162 GVC+ATSGPGA +L+ L DA++D +PV+AI GQ R +G+D QE D+ + + + Sbjct: 68 GVCLATSGPGAIHLLNGLYDARLDHMPVLAIVGQQARAALGSDYQQEVDLQALFKDVANY 127 Query: 163 NFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYK---- 218 V + + VL A IA + R V++ +P D LQ PPR Y Sbjct: 128 AQTVTTPAQVRHVLDRAIRIAQAERAVTVVI-VPHD-LQLMPAVPSPPRKHGNVYSGVGL 185 Query: 219 --PNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276 P+ +P + ++ AA +I A+ + + VG G + +A+ ++R+LAE V L+ + Sbjct: 186 ALPHPQPTAMELERAASVINASERVAILVGAGAL--DASTEVRQLAERLDAGVAKALLGK 243 Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAP---EAKVI 333 PD G G+ G+ + + D L+ +GT F F P +A+ + Sbjct: 244 TVLPDDLPYVTGPIGLLGSKPSWRLMNGCDTLLMIGTTF------PYSEFLPPDGQARAV 297 Query: 334 HADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG-----TIEMADWWAYLNGV 388 DI P + A+V +VGD I L+ +L +++ WW L G Sbjct: 298 QIDIAPRNMSLRYPAEVNLVGDAAQTIRRLLPLLSEKRNADWRERIEVDVRKWWRLLEG- 356 Query: 389 RKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLN 448 R P S ++P+ V +L + A+ G H W A+ ++ + Sbjct: 357 RAMAPAS-------PINPQRVFWELSDCLPDRAIVCGDCGSHTGWFARDVKLREGMLASL 409 Query: 449 SGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMT-NQELATCAV-----EGIPVKV 502 SGGL TMG +P A+ AK+A P V AI GDG QM N EL T V Sbjct: 410 SGGLATMGGGVPYAIAAKMAWPDRPVLAIVGDGAMQMNGNAELVTVKQYWRRWSDPRFVV 469 Query: 503 ALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVD 562 +++N +L V Q + + D A P + + AE LG GLR +R E + D Sbjct: 470 LVVSNRDLNQVTWEQRALAGD--PKFDAAQDVEPFP-YARYAELLGFRGLRVDRPEQITD 526 Query: 563 VINQARAINDCPVVID 578 QA A DCPVVI+ Sbjct: 527 AWRQAFAA-DCPVVIE 541 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: 897 Number of extensions: 44 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: 594 Length adjustment: 37 Effective length of query: 581 Effective length of database: 557 Effective search space: 323617 Effective search space used: 323617 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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