Align Lmo2664 protein (characterized, see rationale)
to candidate PP_0552 PP_0552 2,3-butanediol dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Putida:PP_0552 Length = 362 Score = 175 bits (443), Expect = 2e-48 Identities = 116/360 (32%), Positives = 181/360 (50%), Gaps = 24/360 (6%) Query: 1 MRAAVLYENNVIKAEQID-EATCGKDQVRVEVKAVGICGSDIHK-------MQTRWKYPL 52 MRAAV + + I+ EQ+ A V+++V GICGSD+H+ + +PL Sbjct: 9 MRAAVWHGRHDIRVEQVPLPADPAPGWVQIKVDWCGICGSDLHEYVAGPVFIPVEAPHPL 68 Query: 53 PAV-----MGHEFAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRM 107 + +GHEF G I ++G V A+GD VA + C C YC G + +C+ Sbjct: 69 TGIQGQCILGHEFCGHIAKLGEGVEGYAVGDPVAADACQHCGTCYYCTHGLYNICERLAF 128 Query: 108 VGSHFHGGFAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFG 166 G +G FAE V + A+ + + E GA+IEPLAV MH V LG TV+V G Sbjct: 129 TGLMNNGAFAELVNVPANLLYRLPQGFPAEAGALIEPLAVGMHAVKKAGSLLGQTVVVVG 188 Query: 167 IGTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGL 226 GTIG+ + C AG +IA+++S + A A+E G ++P D + A T GL Sbjct: 189 AGTIGLCTIMCAKAAGAAQVIALEMSSARKAKAKEAGANVVLDPSQCDALAEIRALTAGL 248 Query: 227 GADIALECAGSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWN 286 GAD++ EC G+K T + + +K GK +GI E + N F T K Sbjct: 249 GADVSFECIGNKHTAKLAIDTIRKAGKCVLVGI------FEEPSEFNFFELVSTEKQVLG 302 Query: 287 SYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKE-AFDMILSREHDYNKVMILP 345 + + E+ I F+ GR+ ++PL++ R LE+ E F+ +++ + + K+++ P Sbjct: 303 ALAY---NGEFADVIAFIADGRLDIRPLVTGRIGLEQIVELGFEELVNNKEENVKIIVSP 359 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: 334 Number of extensions: 15 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: 362 Length adjustment: 29 Effective length of query: 321 Effective length of database: 333 Effective search space: 106893 Effective search space used: 106893 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