Align Lmo2664 protein (characterized, see rationale)
to candidate BPHYT_RS23440 BPHYT_RS23440 alcohol dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__BFirm:BPHYT_RS23440 Length = 348 Score = 148 bits (374), Expect = 2e-40 Identities = 107/350 (30%), Positives = 175/350 (50%), Gaps = 29/350 (8%) Query: 1 MRAAVLYENNVIKAEQIDEATCGKDQVRVEVKAVGICGSDIHKM----QTRWKYPLPAVM 56 M AAVL+E +I+ +++D G +VRV V+A GICGSD+ + P V+ Sbjct: 1 MLAAVLHEPKLIRIDEVDPPEPGPGEVRVRVRAGGICGSDLSYYFKGKSGDFAVREPFVL 60 Query: 57 GHEFAGVITEIGSEVT---NVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGS--- 110 GHE AG I +G VT +A G RVA P C C +C G C N R +GS Sbjct: 61 GHEVAGEIDSLGEGVTAERRLAPGQRVAVNPGLACGTCRFCVGGMPNHCLNMRFMGSAST 120 Query: 111 --HFHGGFAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGI 167 H G F + +V+ A + + D +DF + +M EPLAV++H V +G +V++ G Sbjct: 121 FPHTQGMFRQYIVVAARQCVPVPDGVDFAQASMAEPLAVALHAVKQAGSLVGASVLLVGC 180 Query: 168 GTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLG 227 G IG +++ AG ++A+D+SD+ L AR+ G T+N + ++ ++ G Sbjct: 181 GPIGCILLSVARRAGAHRVVALDLSDRALQVARQLGADQTVNAAERAVIDQ-WSVQRGT- 238 Query: 228 ADIALECAGSKITQEQCLLVTKKKG---KVGFLGIAYADVLLHEEAFENIFRRELTLKGF 284 D+ +E +GS + L + G +VG L + V A + +EL +G Sbjct: 239 FDVVIEASGSPAGLDTALHAARAGGTVIQVGNLPAGQSPV-----AANLVMSKELRYQGS 293 Query: 285 WNSYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSR 334 + S E+ + + + G++ L+PL++H + + E AF++ L R Sbjct: 294 FRFTS------EYAIAADEIASGKVDLRPLMTHAFAMSEANRAFEVALDR 337 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: 249 Number of extensions: 12 Number of successful extensions: 5 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: 348 Length adjustment: 29 Effective length of query: 321 Effective length of database: 319 Effective search space: 102399 Effective search space used: 102399 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