Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 8500756 DvMF_1497 transport system permease protein (RefSeq)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Miya:8500756 Length = 387 Score = 158 bits (399), Expect = 2e-43 Identities = 121/358 (33%), Positives = 173/358 (48%), Gaps = 42/358 (11%) Query: 8 VLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRAL----LPGH-------TPTLPEALV 56 +LL L AA +++ L + ++ D RAL LPG TP LV Sbjct: 28 ILLAALCWAATVVLACL----FGPFHIAVGDVLRALAELALPGGLADGAGATPDATHMLV 83 Query: 57 -QNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTP 115 +RL R +A+L G LA+AGT+ Q + NP+A P LG++ GAA +L L P Sbjct: 84 VTRIRLARVCLALLAGGGLAVAGTVFQGVLRNPLADPFTLGVSGGAAFGASLALTLGIGP 143 Query: 116 IAGY--------------SLSFIAACGG-----GVSWLLVMTAGGGFRHTHDRNKLILAG 156 +A + +L +AA G G LL AGGGFR R ++LAG Sbjct: 144 LAAWLTMHLPAFAALSPQALLPLAALAGALASLGAVLLLGGAAGGGFR----RETVVLAG 199 Query: 157 IALSAFCMGLTRITLLLAEDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLAN 216 + +S L + L E+ I +W+ G + W LLP + + +VL Sbjct: 200 VVVSTVLSALVSLVKALDEESVSSIVFWIMGSLQGRGWAHAAVLLPWLALGLLLVLPRFR 259 Query: 217 QLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAG 276 +L++L L D A LG++ R+RL + + L+ CV+V+G + F+GL+VPHLAR G Sbjct: 260 ELDILALGDVQARQLGMDTARVRLQLLVGASLITAGCVAVSGVIGFVGLVVPHLARMRLG 319 Query: 277 FDQRNVLPVSMLLGATLMLLADVLARALAFPG--DLPAGAVLALIGSPCFVWLVRRRG 332 +L G L+ ADVLAR L PG +LP G V AL+G P F L+ R G Sbjct: 320 AAHGPLLAAGWFGGGVLLAWADVLARTL-LPGGAELPVGVVTALLGGPFFCLLLVRGG 376 Lambda K H 0.327 0.140 0.436 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: 444 Number of extensions: 29 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: 332 Length of database: 387 Length adjustment: 29 Effective length of query: 303 Effective length of database: 358 Effective search space: 108474 Effective search space used: 108474 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 (21.7 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