Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 351479 BT1951 Fe3+ ABC transporter, permease protein (NCBI ptt file)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Btheta:351479 Length = 326 Score = 149 bits (375), Expect = 1e-40 Identities = 104/327 (31%), Positives = 173/327 (52%), Gaps = 18/327 (5%) Query: 9 LLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAV 68 +L+ + + + +F L L A+ + D AL G+ E +V N+RL +++VA+ Sbjct: 7 ILFSILITLTVGLFLLDL-AVGAVNIPIRDVWAALTGGNCSRATEKIVLNIRLIKAIVAL 65 Query: 69 LIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSAL---SPTPIAGYSLSFIA 125 L GA+L+++G +QTL NP+A P +LGI+SGA+L +AL S IAG A Sbjct: 66 LAGAALSVSGLQMQTLFRNPLAGPYVLGISSGASLGVALVVLAGIGSSIGIAG------A 119 Query: 126 ACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIF-YW 184 A G LLV+TA G + D +++ G+ S+ + +I L+++ + F W Sbjct: 120 AWVGAAVVLLVITAVG--QRIKDIMVILILGMMFSSGVGAVVQILQYLSKEESLKAFVIW 177 Query: 185 LAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINM 244 G + + L+P V + + +L LNLL + A T+G+N+ R R ++ + Sbjct: 178 TMGALGDVTSGQLLILVPSVFAGLLLAVLTIKPLNLLLFGEEYAVTMGLNIRRSRSLLFL 237 Query: 245 LVLLLVGACVSVAGPVAFIGLLVPHLAR-FWAGFDQRNVLPVSMLLGATLMLLADVLARA 303 LL G + GP+ FIGL +PH+ R + D +LP ++L GA+++LL D++++ Sbjct: 238 STTLLAGTITAFCGPIGFIGLAMPHVTRMLFQNSDHHVLLPGTILSGASILLLCDIISKI 297 Query: 304 LAFPGDLPAGAVLALIGSPCFVWLVRR 330 LP A+ AL+G P VW+V R Sbjct: 298 FT----LPINAITALLGIPIVVWVVLR 320 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: 264 Number of extensions: 18 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: 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 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