Align Lmo2664 protein (characterized, see rationale)
to candidate GFF1391 Psest_1428 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__psRCH2:GFF1391 Length = 362 Score = 168 bits (425), Expect = 2e-46 Identities = 119/360 (33%), Positives = 175/360 (48%), Gaps = 24/360 (6%) Query: 1 MRAAVLYENNVIKAEQIDEATCGKDQ-VRVEVKAVGICGSDIHK-------MQTRWKYPL 52 M AAV + I+ EQ+ + V++ V GICGSD+H+ + +PL Sbjct: 7 MTAAVWHGRKDIRLEQVPLPGAPQPGWVQIRVHWCGICGSDLHEYLAGPVFIPVDAPHPL 66 Query: 53 PAV-----MGHEFAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRM 107 + +GHEF G I IG V A GD+VA + C +C +CK G + LC+ Sbjct: 67 TGIKGQCILGHEFCGEIVAIGEGVEGYAPGDKVAADACQHCGQCRFCKTGQYNLCEQLAF 126 Query: 108 VGSHFHGGFAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFG 166 G +G FAE V + A+ + + + E GA+IEPLAV MH V LG+TV+V G Sbjct: 127 TGLMNNGAFAEFVNVPAELLYRLPEGFPLEAGALIEPLAVGMHAVKKAGSLLGETVVVVG 186 Query: 167 IGTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGL 226 GTIG+ + C AG +IA+++S + A A E G + I+P D + A T G Sbjct: 187 AGTIGLCTIMCAKAAGAGQVIALEMSAARKAKALEVGANWVIDPSECDAIAEIKALTGGY 246 Query: 227 GADIALECAGSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWN 286 GA ++ EC G K T + + V +K G+ +GI E + N F T K Sbjct: 247 GAGVSFECIGHKATAKLAIDVIRKAGRCVMVGI------FEEPSEFNFFEIVATEKQVIG 300 Query: 287 SYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSREHDYN-KVMILP 345 S + + G E+ I + GRI + PLI+ R L+ E L+ D N K+++ P Sbjct: 301 SLA--YAG-EFADVIALIDDGRIDVTPLITGRIGLDNILEQGFEELANHKDRNVKIIVSP 357 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: 360 Number of extensions: 21 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