Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Echvi_3111 Echvi_3111 ABC-type Fe3+-siderophore transport system, permease component
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Cola:Echvi_3111 Length = 357 Score = 168 bits (425), Expect = 2e-46 Identities = 97/280 (34%), Positives = 156/280 (55%), Gaps = 9/280 (3%) Query: 54 ALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSP 113 A++ +R PR ++ VL+G SLA+AG LQ L NP+ P+++G++SG+AL + S Sbjct: 67 AVLWAIRFPRVVLGVLVGGSLAVAGACLQGLFRNPLVEPAIIGVSSGSALFAVIVIVFSS 126 Query: 114 T-------PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGL 166 + ++L A GG ++ L T D + LILAG+A++A L Sbjct: 127 SIGWQLQSVFGAFALPLAAFTGGLLNTFLAYRLASKAGKT-DISILILAGVAINALSAAL 185 Query: 167 TRITLLLAEDHAYGIF-YWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSD 225 + + +DHA F +W G + A W V+ + + + V+L LN L + + Sbjct: 186 IGLVIYYGDDHAIRNFTFWSLGSLGGASWSKVYIVGVFIFLSTVVMLSFPRSLNALAVGE 245 Query: 226 STAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPV 285 + A+ +G+N+ R++ ++ L VGA VSV G + F+GL+VPHL R G D R +LP+ Sbjct: 246 AEAYHMGINVQRVKHLLLFFSALAVGAGVSVTGAIGFVGLVVPHLVRMLLGADHRILLPM 305 Query: 286 SMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFV 325 + L GA LML+ADV++R + P +L G + ALIG+P F+ Sbjct: 306 AFLFGAILMLVADVVSRLVVAPAELSIGIITALIGAPFFI 345 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: 275 Number of extensions: 15 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: 357 Length adjustment: 29 Effective length of query: 303 Effective length of database: 328 Effective search space: 99384 Effective search space used: 99384 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