Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 14726 b0590 iron-enterobactin transporter subunit (NCBI)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Keio:14726 Length = 334 Score = 177 bits (449), Expect = 3e-49 Identities = 108/277 (38%), Positives = 160/277 (57%), Gaps = 2/277 (0%) Query: 55 LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114 +V + RLPR+L +L G +L LAG L+QTLT NP+A P LLG+N+GA+ A+ L +AL Sbjct: 55 IVLDARLPRTLAGLLAGGALGLAGALMQTLTRNPLADPGLLGVNAGASFAIVLGAALFGY 114 Query: 115 PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLA 174 A L+ +A G V+ L+V G +L LAG+AL+A GLT LL Sbjct: 115 SSAQEQLA-MAFAGALVASLIVAFTGSQGGGQLSPVRLTLAGVALAAVLEGLTSGIALLN 173 Query: 175 EDHAYGIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVN 234 D + +W AG + + +L V+ A LLL+ LN L+L TA LG Sbjct: 174 PDVYDQLRFWQAGSLDIRNLHTLKVVLIPVLIAGATALLLSRALNSLSLGSDTATALGSR 233 Query: 235 LTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLM 294 + R +L+ + + +L G+ ++ GP+AFIGL++PH+AR+ G D R LPV++L L+ Sbjct: 234 VARTQLIGLLAITVLCGSATAIVGPIAFIGLMMPHMARWLVGADHRWSLPVTLLATPALL 293 Query: 295 LLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 L AD++ R + PG+L V A IG+P ++LVRR+ Sbjct: 294 LFADIIGRVIV-PGELRVSVVSAFIGAPVLIFLVRRK 329 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: 327 Number of extensions: 13 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: 334 Length adjustment: 28 Effective length of query: 304 Effective length of database: 306 Effective search space: 93024 Effective search space used: 93024 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