Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Pf6N2E2_1634 ABC-type Fe3+-siderophore transport system, permease component
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1634 Length = 321 Score = 172 bits (436), Expect = 1e-47 Identities = 120/336 (35%), Positives = 182/336 (54%), Gaps = 29/336 (8%) Query: 7 PVLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLV 66 PV L L AL + L++ A + +A +AL+ +++++ RLPR LV Sbjct: 2 PVWLGLLMAIALTSLLHLAV---GAKDIPWQEAWQALVAYAPGNPDQSVIRGSRLPRLLV 58 Query: 67 AVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSP------TPIAGYS 120 A+L+GASL LAG ++Q + NP+A P +LGINSGAAL + + P P+ ++ Sbjct: 59 AMLVGASLGLAGAIMQAVGDNPLADPGILGINSGAALFVVFGLLVLPGNDMSMIPLFAFA 118 Query: 121 LSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYG 180 + +A+ G +++ AG G H+ +L L+G ++A +T I LLL + Sbjct: 119 GALVASVG------VLLLAGRG----HNPIRLTLSGAMIAALFSAITSILLLLDQQGLDS 168 Query: 181 IFYWLAGGV-----SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNL 235 + WL G + S W VW P V+ + + L+ LN L A +GVNL Sbjct: 169 LRRWLTGSIGVTGGSMQAW--VW---PYVLLGMCLCLVNVRALNAHRLGPQAAAGMGVNL 223 Query: 236 TRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLML 295 ++R++ V+LL G V++AGP+ F+GL+VPH AR G D R +L + LLGA L++ Sbjct: 224 LKMRVLGLASVVLLSGGAVALAGPIGFVGLVVPHAARLLFGDDYRRLLLAAPLLGALLLI 283 Query: 296 LADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 LAD+ AR + P +L G V ALIG P FV LV R+ Sbjct: 284 LADIAARTVVRPFELNTGIVTALIGGPIFVVLVLRK 319 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: 313 Number of extensions: 16 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: 321 Length adjustment: 28 Effective length of query: 304 Effective length of database: 293 Effective search space: 89072 Effective search space used: 89072 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: 48 (23.1 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