Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate PP_2417 PP_2417 putative Iron ABC transporter, permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Putida:PP_2417 Length = 339 Score = 166 bits (419), Expect = 1e-45 Identities = 103/281 (36%), Positives = 149/281 (53%), Gaps = 4/281 (1%) Query: 55 LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114 +V N RL R+LVA GA LA G +LQ + NP+A P LLG+++GA+ L L Sbjct: 58 IVWNYRLTRTLVAAACGAGLATCGVILQAMLRNPLAEPYLLGLSAGASTGAVLVGLLGLG 117 Query: 115 PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTR--ITLL 172 +A S+S A G G ++ LV+ + + ++ILAGIA S LT IT Sbjct: 118 SLA-LSMSAGAFIGAGAAFALVLVLARAAGPSSNNAQVILAGIAGSQLFNALTAFLITKS 176 Query: 173 LAEDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLG 232 + A GI +WL G +S RW VW +PV V + V L L+ +A +LG Sbjct: 177 ATAEQARGILFWLLGNLSGVRWPSVWLAVPVAVFGLLVCLWHRRALDAFTFGADSAASLG 236 Query: 233 VNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGAT 292 + + R +L++ L+ VS+ G + F+GL++PH R G +LP S L GA Sbjct: 237 IPVRRTQLLLISCAALVTAVMVSIVGAIGFVGLVIPHALRLLLGPGHSRLLPASALGGAL 296 Query: 293 LMLLADVLARALAFPGDLPAGAVLALIGSPCF-VWLVRRRG 332 +++AD+L+R L +P G V ALIG+P F + LV RRG Sbjct: 297 FLIVADILSRTLITGQVIPVGVVTALIGAPVFALILVSRRG 337 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: 344 Number of extensions: 20 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: 339 Length adjustment: 28 Effective length of query: 304 Effective length of database: 311 Effective search space: 94544 Effective search space used: 94544 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