Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate SMa1745 SMa1745 ABC transporter permease, Fe3+-siderophore transport system
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Smeli:SMa1745 Length = 366 Score = 191 bits (484), Expect = 3e-53 Identities = 118/322 (36%), Positives = 175/322 (54%), Gaps = 3/322 (0%) Query: 10 LWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVL 69 LW + AL+I+ + V G D A + G + A V LR+PR+++A+L Sbjct: 43 LWLAALFALVIVLLAASVTVGTRNV-GWDDVAAAMGGAQNNIDRASVA-LRIPRTVLALL 100 Query: 70 IGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGG 129 G +L LAG ++Q +T NP+A P +LG+N GA+LA+ + A Y+ ++A G Sbjct: 101 AGGALGLAGAIMQGVTRNPLADPGILGVNMGASLAVVVGVAWFGMSSL-YAYIWVAILGA 159 Query: 130 GVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGV 189 G + + V G R K+ LAG A S + +L D A GI W GGV Sbjct: 160 GCAAIFVYAIGSLGRGGATPLKMALAGAATSVAFASMVIAVVLPRGDIAGGIHSWQIGGV 219 Query: 190 SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLL 249 A ++ + +LP ++ + LL A +LN L L D A LG ++ R V ++ +LL Sbjct: 220 GGATYERILPVLPFLLVGFVISLLSARKLNSLALGDELATGLGESVATARAVASLGAILL 279 Query: 250 VGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGD 309 GA ++ GP+ F+GL+VPHL R G D R +LP S L GA L+L ADVL R +A P + Sbjct: 280 CGATTAICGPIGFLGLVVPHLCRLLVGVDHRWLLPFSTLAGACLLLAADVLGRIVARPAE 339 Query: 310 LPAGAVLALIGSPCFVWLVRRR 331 + G V A+IG+P F+W+VRR+ Sbjct: 340 IDVGIVTAMIGAPFFIWIVRRQ 361 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: 358 Number of extensions: 24 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: 332 Length of database: 366 Length adjustment: 29 Effective length of query: 303 Effective length of database: 337 Effective search space: 102111 Effective search space used: 102111 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