Align Lmo2664 protein (characterized, see rationale)
to candidate WP_041099430.1 SUTH_RS11655 Zn-dependent alcohol dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >NCBI__GCF_000828635.1:WP_041099430.1 Length = 368 Score = 139 bits (349), Expect = 2e-37 Identities = 103/342 (30%), Positives = 156/342 (45%), Gaps = 30/342 (8%) Query: 11 VIKAEQIDEATCGKDQVRVEVKAVGICGSDIHKMQTRWKYPLPAVMGHEFAGVITEIGSE 70 V++ +D G +V +++ A G+C SD+ P P V+GHE AG I +G Sbjct: 18 VVETVSVDAPQRG--EVMIKLAACGVCHSDLSVTTGTLPLPPPVVLGHEGAGSIVAVGEG 75 Query: 71 VTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGSHFHGG--------------- 115 V++ A+GD V + C +C YC+ G LCD G G Sbjct: 76 VSSFALGDHVVSSFVSMCGKCRYCQTGRPQLCDQAAKAGFTLPDGTTRFKDAAGKPLNIF 135 Query: 116 -----FAENVVMKADNVISI-GDLDFEEGAMIEPLAVSMHG--VLGIQPRLGDTVIVFGI 167 AE + DNVI I + ++ A+I ++ G V + G +VFG Sbjct: 136 SGCGVMAEYATLHVDNVIKIDAAVPLDKAALIGCGVMTGVGAAVNTAKVEPGSATVVFGC 195 Query: 168 GTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLG 227 G +G+ +Q +AG + I+AVD SD KL A++FG +T+NPKNE+ + G Sbjct: 196 GGVGLNAIQGCAIAGARIIVAVDTSDAKLEMAKQFGATHTVNPKNEENIVKALKKLTEGG 255 Query: 228 ADIALECAGSKITQEQCLLVTKKKGKVGFLGIA-YADVLLHEEAFENIFRRELTLKGFWN 286 AD A EC G Q +K G +G+A D A + E TLKG + Sbjct: 256 ADYAFECVGFGEIAAQAYGCLRKGGTAVVVGVAGPKDTTTIRTA--TLTFEEKTLKGSY- 312 Query: 287 SYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKEAF 328 + + P +++ I + GR+KL LI+ Y +EE +AF Sbjct: 313 -FGSARPQQDFPRLIGLYRSGRLKLDELITRTYSVEEAPQAF 353 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: 299 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: 368 Length adjustment: 29 Effective length of query: 321 Effective length of database: 339 Effective search space: 108819 Effective search space used: 108819 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 Apr 09 2024. 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