Align putative hydrolase, required for lysine catabolism (characterized)
to candidate SMc04383 SMc04383 hypothetical protein
Query= reanno::Smeli:SMc04383 (466 letters) >FitnessBrowser__Smeli:SMc04383 Length = 466 Score = 917 bits (2369), Expect = 0.0 Identities = 466/466 (100%), Positives = 466/466 (100%) Query: 1 MKENSFVSADDIRSAFSAAMSLMYREEVPAYGTLMELVARVNGETLSADATLKGRLEATD 60 MKENSFVSADDIRSAFSAAMSLMYREEVPAYGTLMELVARVNGETLSADATLKGRLEATD Sbjct: 1 MKENSFVSADDIRSAFSAAMSLMYREEVPAYGTLMELVARVNGETLSADATLKGRLEATD 60 Query: 61 SLERISEERHGAIRLGTPAELSMMRRVFAVMGMYPVGYYDLSTAGVPVHSTAFRPVGDAA 120 SLERISEERHGAIRLGTPAELSMMRRVFAVMGMYPVGYYDLSTAGVPVHSTAFRPVGDAA Sbjct: 61 SLERISEERHGAIRLGTPAELSMMRRVFAVMGMYPVGYYDLSTAGVPVHSTAFRPVGDAA 120 Query: 121 LKHNPFRVFTSLLRLDLISDEALRAEAEAILKERRIFTSGAVELTEKAERDGGLDKADAE 180 LKHNPFRVFTSLLRLDLISDEALRAEAEAILKERRIFTSGAVELTEKAERDGGLDKADAE Sbjct: 121 LKHNPFRVFTSLLRLDLISDEALRAEAEAILKERRIFTSGAVELTEKAERDGGLDKADAE 180 Query: 181 RFVAEVLETFRWHDEANVSAGMYERLHDAHRLIADVVSFKGPHINHLTPRTLDIDRVQAL 240 RFVAEVLETFRWHDEANVSAGMYERLHDAHRLIADVVSFKGPHINHLTPRTLDIDRVQAL Sbjct: 181 RFVAEVLETFRWHDEANVSAGMYERLHDAHRLIADVVSFKGPHINHLTPRTLDIDRVQAL 240 Query: 241 MPEYGIAPKAVVEGPPTRKCPVLLRQTSFKALEEPVSFRDSDGSWKTGSHTARFGEIEQR 300 MPEYGIAPKAVVEGPPTRKCPVLLRQTSFKALEEPVSFRDSDGSWKTGSHTARFGEIEQR Sbjct: 241 MPEYGIAPKAVVEGPPTRKCPVLLRQTSFKALEEPVSFRDSDGSWKTGSHTARFGEIEQR 300 Query: 301 GIALTPKGRGLYDRLLDESRKIVRPAADGSNAREYEAALAQVFEAFPDSWAELREAGLGY 360 GIALTPKGRGLYDRLLDESRKIVRPAADGSNAREYEAALAQVFEAFPDSWAELREAGLGY Sbjct: 301 GIALTPKGRGLYDRLLDESRKIVRPAADGSNAREYEAALAQVFEAFPDSWAELREAGLGY 360 Query: 361 FSYSLTDKGRRTKLPGRRDLNSLIADGLVQFDPIVYEDFLPVSAAGIFQSNLGDGAQQEF 420 FSYSLTDKGRRTKLPGRRDLNSLIADGLVQFDPIVYEDFLPVSAAGIFQSNLGDGAQQEF Sbjct: 361 FSYSLTDKGRRTKLPGRRDLNSLIADGLVQFDPIVYEDFLPVSAAGIFQSNLGDGAQQEF 420 Query: 421 EASPNQKRFETDLGVAVLNEFDHYAGIEQASIEGCLKALTAAMAAE 466 EASPNQKRFETDLGVAVLNEFDHYAGIEQASIEGCLKALTAAMAAE Sbjct: 421 EASPNQKRFETDLGVAVLNEFDHYAGIEQASIEGCLKALTAAMAAE 466 Lambda K H 0.318 0.134 0.383 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: 890 Number of extensions: 17 Number of successful extensions: 1 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: 466 Length of database: 466 Length adjustment: 33 Effective length of query: 433 Effective length of database: 433 Effective search space: 187489 Effective search space used: 187489 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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