Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BWI76_RS02700 BWI76_RS02700 D-serine/D-alanine/glycine transporter
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Koxy:BWI76_RS02700 Length = 467 Score = 870 bits (2249), Expect = 0.0 Identities = 435/467 (93%), Positives = 450/467 (96%) Query: 1 MVDQVKVVADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 60 MVDQVKVVAD+QAP EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY Sbjct: 1 MVDQVKVVADEQAPTEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 60 Query: 61 MIIGFMLFFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVV 120 MIIGFMLFFVMRAMGELLLSNLEYKSFSDFA+DLLGPWAGYFTGWTYWFCWVVTGMADVV Sbjct: 61 MIIGFMLFFVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGMADVV 120 Query: 121 AITAYAQFWFPDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGL 180 AITAYAQFWFP LSDWVASLAVI+LLL LNLATVKMFGEMEFWFAMIKIVAIV+LIVVGL Sbjct: 121 AITAYAQFWFPGLSDWVASLAVILLLLGLNLATVKMFGEMEFWFAMIKIVAIVALIVVGL 180 Query: 181 VMVAMHFQSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKD 240 VMV MHFQSPTGVEASFAHLWNDGGWFPKG+SGFFAGFQIAVFAFVGIELVGTTAAETKD Sbjct: 181 VMVMMHFQSPTGVEASFAHLWNDGGWFPKGISGFFAGFQIAVFAFVGIELVGTTAAETKD 240 Query: 241 PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVIN 300 PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVP KSPFVELFVLVGLPAAAS+IN Sbjct: 241 PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVPSKSPFVELFVLVGLPAAASLIN 300 Query: 301 FVVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVV 360 FVVLTSAASSANSGVFSTSRMLFGLAQ+G APK FAKLSKRAVPAKGLTFSC+CLLGGVV Sbjct: 301 FVVLTSAASSANSGVFSTSRMLFGLAQDGQAPKMFAKLSKRAVPAKGLTFSCMCLLGGVV 360 Query: 361 MLYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCW 420 ML VNPSVI AFTMITTVSAILFMFVWTIILCSYLVYRK+RP LHE+S YKMPLGKLMCW Sbjct: 361 MLMVNPSVIAAFTMITTVSAILFMFVWTIILCSYLVYRKKRPQLHEQSKYKMPLGKLMCW 420 Query: 421 VCMAFFVFVVVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467 VCMAFF FV+VLLTLE DTR+AL+VTPLWF+ LG GWLF GKKR A+ Sbjct: 421 VCMAFFAFVLVLLTLEADTREALMVTPLWFVLLGAGWLFAGKKRLAK 467 Lambda K H 0.329 0.141 0.440 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: 911 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: 470 Length of database: 467 Length adjustment: 33 Effective length of query: 437 Effective length of database: 434 Effective search space: 189658 Effective search space used: 189658 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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