Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate SMc01511 SMc01511 hemin transport system permease transmembrane protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Smeli:SMc01511 Length = 366 Score = 181 bits (458), Expect = 3e-50 Identities = 102/287 (35%), Positives = 166/287 (57%), Gaps = 15/287 (5%) Query: 55 LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114 ++ ++RLPR+++ +L+GASLA++G ++Q L NP+A P L+G++SGA+L L L Sbjct: 77 IILDIRLPRAVLGMLVGASLAVSGVVMQGLFRNPLADPGLVGVSSGASLGAVLLIVLGDV 136 Query: 115 PIAG-------YSLSFIAACGGGVSWLL---VMTAGGGFRHTHDRNKLILAGIALSAFCM 164 Y+L F A GG + LL + T GG ++LAGIAL A Sbjct: 137 AFGPLFAVFGFYALPFGAFLGGLATTLLLYRIATRGGQTSVA----TMLLAGIALGALAG 192 Query: 165 GLTRITLLLAEDHAY-GIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNL 223 +T + + +A+D + +W G ++ A W + P+++ ++ VV LA LN + L Sbjct: 193 AVTGVLVFIADDKQLRDLTFWGLGSLAGANWTKIAAAGPIILVSLAVVPFLARGLNAITL 252 Query: 224 SDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVL 283 ++ A+ +GV + RL+ + V GA V+V+G + F+G++VPHL R G D R +L Sbjct: 253 GEAAAYHMGVPVQRLKNIAVFSVAGATGASVAVSGGIGFVGIVVPHLLRLVIGPDHRYLL 312 Query: 284 PVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 P S LLG TL++ AD+LAR + P +LP G + A +G+P F+W++ R Sbjct: 313 PASALLGGTLLIFADMLARTIVSPAELPIGIITAFVGAPFFLWVLLR 359 Score = 23.9 bits (50), Expect = 0.007 Identities = 13/42 (30%), Positives = 21/42 (50%) Query: 151 KLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGVSHA 192 + ++A +A+ A +T IT A+ IF WL+G A Sbjct: 28 RCLIAVLAVLAAATFMTSITTGAADASLSSIFRWLSGETDQA 69 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: 329 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 332 Length of database: 366 Length adjustment: 29 Effective length of query: 303 Effective length of database: 337 Effective search space: 102111 Effective search space used: 102111 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