Align Lmo2664 protein (characterized, see rationale)
to candidate RR42_RS09405 RR42_RS09405 butanediol dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Cup4G11:RR42_RS09405 Length = 357 Score = 171 bits (433), Expect = 3e-47 Identities = 116/362 (32%), Positives = 184/362 (50%), Gaps = 28/362 (7%) Query: 1 MRAAVLYENNVIKAEQI---DEATCGKDQVRVEVKAVGICGSDIHK-------MQTRWKY 50 M+AAV + ++ E++ D+ G V++ V GICGSD+H+ + + Sbjct: 1 MKAAVWRGRHDVRVEEVRVPDKPAEG--WVKIRVHWCGICGSDLHEYVAGPVFIPVDHPH 58 Query: 51 PLPA-----VMGHEFAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNY 105 PL ++GHEF+G I E+G+ VT +G+RV + C +C YC G + +C++ Sbjct: 59 PLTGLKGQCILGHEFSGEIAELGAGVTGFKVGERVTADACQHCGKCYYCTHGLYNICESL 118 Query: 106 RMVGSHFHGGFAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIV 164 G +G FAE V + A+ + + + E GA+IEPLAV +H V +G TV+V Sbjct: 119 AFTGLMNNGAFAEYVNVPAELLYKLPENFPTEAGALIEPLAVGLHAVKKAGNIVGQTVVV 178 Query: 165 FGIGTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTN 224 G GTIG+ + C AG IIA+++S + A E G I+PK D +V A T Sbjct: 179 VGAGTIGLCTIMCAKAAGAGRIIALEMSSARKKKALEVGANVVIDPKECDAIAQVKALTG 238 Query: 225 GLGADIALECAGSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGF 284 G GAD++ EC G+K T + + V +K GK +GI E + N F T K Sbjct: 239 GYGADVSFECIGNKATAKLAIDVIRKAGKCVMVGI------FEEPSAFNFFEIVSTEKEI 292 Query: 285 WNSYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEE-TKEAFDMILSREHDYNKVMI 343 S + E+ I F+ GRI ++PLI+ R L + + F+ +++ + K+++ Sbjct: 293 IGSLAY---NGEFADVIRFIADGRIDVQPLITGRISLADIVSQGFEELVNNKDGNVKIIV 349 Query: 344 LP 345 P Sbjct: 350 QP 351 Lambda K H 0.321 0.139 0.417 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: 343 Number of extensions: 18 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: 350 Length of database: 357 Length adjustment: 29 Effective length of query: 321 Effective length of database: 328 Effective search space: 105288 Effective search space used: 105288 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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