Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate N515DRAFT_1560 N515DRAFT_1560 sulfate transport system permease protein
Query= CharProtDB::CH_088337 (275 letters) >FitnessBrowser__Dyella79:N515DRAFT_1560 Length = 274 Score = 78.2 bits (191), Expect = 2e-19 Identities = 48/153 (31%), Positives = 82/153 (53%), Gaps = 5/153 (3%) Query: 58 SLNMALIATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTK 117 S AL+A + L+LG AW L + +R + L+ +PF + + L + Sbjct: 59 SFGGALVAAVLDLLLGLLLAWVLVRYRFPLRRVCDALIDLPFALPTAVAGIALTALYAPN 118 Query: 118 GYLNEFLLWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDL 177 G++ + L LGV ++ +T V++ +V++ LPF+V L IE L++ + EAA L Sbjct: 119 GWVGQLLQPLGV-----QVAYTRLGVLLAMVFVGLPFVVRTLQPVIESLEREVEEAALTL 173 Query: 178 GASKLQTFIRIIIPLTMPGIIAGCLLVMLPAMG 210 GAS Q+F R+++PL P ++ G L + A+G Sbjct: 174 GASPWQSFRRVLLPLLAPTLLTGFALALARAVG 206 Lambda K H 0.333 0.148 0.456 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: 213 Number of extensions: 9 Number of successful extensions: 2 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: 275 Length of database: 274 Length adjustment: 25 Effective length of query: 250 Effective length of database: 249 Effective search space: 62250 Effective search space used: 62250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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