Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 202769 SO3674 hemin ABC transporter, permease protein (NCBI ptt file)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__MR1:202769 Length = 338 Score = 164 bits (415), Expect = 3e-45 Identities = 105/278 (37%), Positives = 157/278 (56%), Gaps = 5/278 (1%) Query: 53 EALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALS 112 + +V N+RLPR+L+A+ +GA LA G ++Q L NP+A P ++G++SGAAL A+ L Sbjct: 56 QLVVSNVRLPRTLLALTVGAILAQCGAVMQGLFRNPLADPGIIGVSSGAALGAAICIVLF 115 Query: 113 PTPIAGYSLSFIA-ACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITL 171 P + +S A CG + ++ A G + L+L+G+A++A + Sbjct: 116 PD-VGSLMISLGAFLCGLATTLIVYRLASNGLGTSVVL--LLLSGVAIAALAGAGIGVLT 172 Query: 172 LLAEDHAY-GIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHT 230 LA D A + W G ++ A+WQ V L V+V A LN L L ++ A Sbjct: 173 YLANDMALRDLTLWQMGSIAGAQWQYVGLCLLVLVLLSWRFQRDAMALNALLLGEAEARH 232 Query: 231 LGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLG 290 LG+N+ RL+L + +L L VG V+ G + FIGL+VPHL R G D + +LP+S LLG Sbjct: 233 LGINVDRLKLRLILLCALGVGVSVAATGIIGFIGLVVPHLVRMILGPDHKRLLPMSALLG 292 Query: 291 ATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLV 328 A L+ LAD+ AR P +LP V ALIG+P F++L+ Sbjct: 293 AALLALADIGARTFLPPAELPVSLVTALIGAPFFIFLL 330 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: 282 Number of extensions: 14 Number of successful extensions: 2 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: 338 Length adjustment: 28 Effective length of query: 304 Effective length of database: 310 Effective search space: 94240 Effective search space used: 94240 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