Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate Pf1N1B4_2867 Hemin ABC transporter, permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2867 Length = 345 Score = 167 bits (422), Expect = 5e-46 Identities = 123/341 (36%), Positives = 175/341 (51%), Gaps = 17/341 (4%) Query: 4 IKHPVLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPG-HTPTLPEALVQ----- 57 +K L GL + L+ I WLSL + + D RA L P P+ L Q Sbjct: 5 VKPRALFIGLSLLCLLAI-WLSL-ALGPVSLPLFDTLRASLRLIGLPIAPDGLEQAELIL 62 Query: 58 -NLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALS---- 112 +RLPR+L+ + +G LAL+G +Q L NP+A P L+G++SGAAL A+ Sbjct: 63 GQIRLPRTLLGLAVGGVLALSGVAMQGLFRNPLADPGLVGVSSGAALGAAIAIVGGSVFG 122 Query: 113 --PTPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRIT 170 P Y LS A GG LV G T+ ++LAGIAL+A + Sbjct: 123 GLPESFGPYLLSLCAFLGGLGVTALVYRLGRRNGQTNVAT-MLLAGIALTALAGSAVGLF 181 Query: 171 LLLAEDHAYG-IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAH 229 LA+D + +W G ++ A + +W LL V + A LN L L +S A Sbjct: 182 TYLADDATLRTLTFWNLGSLNGASYSRLWPLLLVSTGVALWLPRRAKALNALLLGESEAG 241 Query: 230 TLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLL 289 LG+++ L+ + L VGA V+ AG + F+GL+VPHL R AG D R +LP S+L Sbjct: 242 HLGIDVEGLKRELVFCTALGVGAAVAAAGMIGFVGLVVPHLVRLLAGPDHRVLLPASVLA 301 Query: 290 GATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 GA+L+L AD++AR P +LP G V A IG+P F++L+ R Sbjct: 302 GASLLLFADLVARLALAPAELPIGIVTAFIGAPFFLYLLLR 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: 343 Number of extensions: 24 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: 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