Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Dsui_0530 Dsui_0530 ABC-type Fe3+-siderophore transport system, permease component
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__PS:Dsui_0530 Length = 326 Score = 178 bits (451), Expect = 2e-49 Identities = 118/323 (36%), Positives = 174/323 (53%), Gaps = 15/323 (4%) Query: 17 ALIIIFWLSLFCYSAIPVSGADATRALLPG--------HTPTLPEALVQNLRLPRSLVAV 68 ALI+I L L ++ V+ A + ++ PG A+V NLRLPR+L A Sbjct: 7 ALIVIALLVLLAGVSLVVALAVGSISIPPGAVLQGLLGDAEAPGYAVVHNLRLPRALAAF 66 Query: 69 LIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACG 128 G LA+AG L+Q L NP+A P +LGI+ GA + + L ++ + ++ +A G Sbjct: 67 ACGGLLAVAGCLMQVLLRNPLADPYVLGISGGAGVGALVAILLG---LSAFGINGLAFSG 123 Query: 129 GGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHA-YGIFYWLAG 187 + LV G + + +L+L G+ ++A C L + L LA +H +G+ YWL G Sbjct: 124 ALAATFLVFGLAHG-DGSWTQTRLLLTGVIVAAGCGALVALMLSLAPEHKLHGMLYWLMG 182 Query: 188 GVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVL 247 +S A D L + A+ + L A +LNLL +TA LGV + RLR ++ ++ Sbjct: 183 DLSQAT--DARPPLLALAAALLLALPFARELNLLARGLATAQALGVAVVRLRRLVYVVAS 240 Query: 248 LLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFP 307 L V+ AG + F+GL+VPHL R G DQR +LP S L G L+ LAD LAR +A P Sbjct: 241 LATATAVTTAGSIGFVGLVVPHLVRLAVGNDQRLLLPASALAGGALLALADTLARTVAAP 300 Query: 308 GDLPAGAVLALIGSPCFVWLVRR 330 LP G + ALIG P F++L+ R Sbjct: 301 QQLPVGVLTALIGVPVFLFLLTR 323 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: 311 Number of extensions: 14 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: 326 Length adjustment: 28 Effective length of query: 304 Effective length of database: 298 Effective search space: 90592 Effective search space used: 90592 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 Apr 09 2024. 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