Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_013402813.1 CALHY_RS04480 iron ABC transporter permease
Query= SwissProt::P15030 (332 letters) >NCBI__GCF_000166355.1:WP_013402813.1 Length = 336 Score = 167 bits (422), Expect = 4e-46 Identities = 95/280 (33%), Positives = 158/280 (56%), Gaps = 6/280 (2%) Query: 55 LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPT 114 +V +RLPR ++A+++G SL++AG L+Q L NPMA P ++G +SGA+L + A S Sbjct: 54 IVGQIRLPRIIIAMIVGMSLSIAGALVQGLYRNPMADPGIIGTSSGASLGAIVCIAFSLN 113 Query: 115 PIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLA 174 I + L +A G + LV T N LIL GIA+S F + +L+L+ Sbjct: 114 TINIFYLPLLAFAGALLISFLVYRLSTKNNKTPITN-LILIGIAVSTFVSSIN--SLILS 170 Query: 175 EDHAYGI---FYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTL 231 + Y + +W+ G + W V + + LL A ++N+L L + + T+ Sbjct: 171 NINQYQVSEYIFWMLGSLDGRSWVHVKISFVPLCILILCSLLFAKRINILILGEEESFTI 230 Query: 232 GVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGA 291 GVN +L+ + LV L+ G VSV+GP++F+GL+VPH+ R G D R ++P S+L G Sbjct: 231 GVNPEKLKKTLLFLVSLITGIAVSVSGPISFVGLIVPHMLRLIVGSDYRRLIPASILSGG 290 Query: 292 TLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 +++ D +AR L P ++ G + +L+G P F++L+++R Sbjct: 291 IFLIMCDTIARVLFSPVEVKVGIITSLVGVPYFLYLLKKR 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: 241 Number of extensions: 8 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: 336 Length adjustment: 28 Effective length of query: 304 Effective length of database: 308 Effective search space: 93632 Effective search space used: 93632 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 24 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