Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 6936573 Sama_0761 iron-compound ABC transporter, permease protein (RefSeq)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__SB2B:6936573 Length = 347 Score = 153 bits (387), Expect = 5e-42 Identities = 112/344 (32%), Positives = 173/344 (50%), Gaps = 19/344 (5%) Query: 1 MTAIKHPVLLWG---LPVAALIIIFWLS---LFCYSAIPVSGADATRALLP---GHTPT- 50 MTA+K + G L V ALI+ LS + A+ +S +A L G PT Sbjct: 1 MTALKAMLTPLGRRELMVLALILACLLSPVLASIFGAVDISFREAMSVYLHSLIGERPTD 60 Query: 51 ---LPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMAL 107 L ++ LRLPR L+A + GA LAL+G LQ +T NP+A P L GI++GA+L + Sbjct: 61 VAYLDSRILLELRLPRILLAFVCGAGLALSGWALQLVTRNPLADPYLFGISAGASLGAIV 120 Query: 108 TSALSPTP--IAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMG 165 +L T + L A G S L+V+T G F +++L+G+A S Sbjct: 121 VLSLGITHGVLLAIGLPLGAFIGASASVLVVLTLSG-FGLQSQVERMLLSGVATSFLFGA 179 Query: 166 LTRITLLLAEDHAYG-IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLS 224 L + L + + +W G + A W +W V V +LL+ QL L+ Sbjct: 180 LGSLLLYFSSPQVTASVIFWSLGSFARAAWDLLWLPWLVFGGFVAFLLLVRRQLFALSAG 239 Query: 225 DSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLP 284 D TAH LGV++ +LR++ ++ L+ V+ G + F+GL++PH+AR F L Sbjct: 240 DETAHALGVSVAKLRIISLLMCSLMTAVLVASCGGIGFVGLMIPHIARLL--FPGSQSLL 297 Query: 285 VSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLV 328 + +LG M+ DV+ R+L P +LP G + A++GS F+ L+ Sbjct: 298 IVAMLGGLFMVWVDVMTRSLLPPQELPVGVITAVVGSVFFLMLL 341 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: 326 Number of extensions: 18 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: 347 Length adjustment: 28 Effective length of query: 304 Effective length of database: 319 Effective search space: 96976 Effective search space used: 96976 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