Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF2648 PGA1_c26880 putative iron transport system permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Phaeo:GFF2648 Length = 359 Score = 183 bits (464), Expect = 6e-51 Identities = 99/279 (35%), Positives = 156/279 (55%), Gaps = 2/279 (0%) Query: 54 ALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSP 113 A+V ++R PR+L+A+++GA LA+ G LQ +T NP+A P LLGI++G A A+ + L Sbjct: 82 AIVWDIRFPRALLAMMVGAGLAMVGASLQAVTRNPLADPHLLGISAGGAFG-AILALLHT 140 Query: 114 TPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLL 173 G + A G + ++ A F ++L+L G+A+S M + + L Sbjct: 141 GLFLGLLTVPLLAFAGALGATALVLAVSRFAEATTADRLVLVGVAVSFVVMAGANVLIFL 200 Query: 174 AEDHA-YGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLG 232 + A + + +W+ GG+ A+W + L V+V + A N + + D TA TLG Sbjct: 201 GDPRATHTVVFWMLGGLGLAQWSHLIYPLVVLVLCGGWLWTKAGDFNAMTVGDETATTLG 260 Query: 233 VNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGAT 292 + + R RL+ + L+ G V+ +G + F+GL+VPH+AR G D R VLP S L+G Sbjct: 261 IPVARFRLITFTIGALITGVMVAFSGMIGFVGLIVPHIARLIVGGDHRRVLPASALIGGL 320 Query: 293 LMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 ++ AD+LAR L P D+P G V L+G F+WL+RRR Sbjct: 321 FLVAADILARTLMAPEDMPIGLVTGLVGGVFFIWLLRRR 359 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: 411 Number of extensions: 29 Number of successful extensions: 3 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: 359 Length adjustment: 29 Effective length of query: 303 Effective length of database: 330 Effective search space: 99990 Effective search space used: 99990 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