Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate PfGW456L13_3769 Hemin ABC transporter, permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3769 Length = 345 Score = 180 bits (456), Expect = 5e-50 Identities = 129/346 (37%), Positives = 184/346 (53%), Gaps = 20/346 (5%) Query: 1 MTAIKHPVLLWGLPVAALIIIFWLSLFCYSAIPVS---------GADATRALLPGHTPTL 51 MTAI P + L+++FWLSL + PVS G L G Sbjct: 1 MTAIFRPRPTLIFLLLLLVLVFWLSL---ALGPVSLPLGDTLLGGMRLLGLPLDGGDTQQ 57 Query: 52 PEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALT--- 108 E ++ +RLPRSL+ + +G+ LAL+G +Q L NP+A P L+G++ GAAL AL Sbjct: 58 AELILGQIRLPRSLLGIAVGSVLALSGVAMQGLFRNPLADPGLVGVSGGAALGAALAIVG 117 Query: 109 -SALSPTP--IAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMG 165 S L P I Y LS A GG + +V G T D ++LAG+A++A Sbjct: 118 GSLLGGLPPVIEPYLLSVCAFAGGLIVTAVVYRFGRRNGQT-DVATMLLAGVAMTAMAGA 176 Query: 166 LTRITLLLAEDHAYG-IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLS 224 + LA+D + +W G ++ A + +W LL V + + A LN L L Sbjct: 177 GVGLFTYLADDATLRTLTFWNLGSLNGASYPRLWPLLIVTLGVALWLPRRAAALNALLLG 236 Query: 225 DSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLP 284 +S A LG ++ R++L + + L VGA V+ AG + FIGL+VPHL R G D R +LP Sbjct: 237 ESEARHLGFDIERIKLELVLCTALGVGAAVAAAGLIGFIGLVVPHLMRLLVGPDHRVLLP 296 Query: 285 VSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 S+L GA+L+LLAD+ AR L P +LP G V ALIG+P F++L+ R Sbjct: 297 ASLLAGASLLLLADLAARLLLAPAELPIGIVTALIGAPFFLYLLVR 342 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: 370 Number of extensions: 27 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: 345 Length adjustment: 28 Effective length of query: 304 Effective length of database: 317 Effective search space: 96368 Effective search space used: 96368 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