Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_011425931.1 RHE_RS13725 iron ABC transporter permease
Query= SwissProt::P15030 (332 letters) >NCBI__GCF_000092045.1:WP_011425931.1 Length = 334 Score = 167 bits (424), Expect = 3e-46 Identities = 113/321 (35%), Positives = 162/321 (50%), Gaps = 9/321 (2%) Query: 12 GLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIG 71 GL V A ++ L L A +S A R LL L L+ LRLPRSL A G Sbjct: 11 GLIVVAAMLAAMLGLLV-GAKTLSVETAIRVLL-APDGKLESVLIWTLRLPRSLAAAAGG 68 Query: 72 ASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGG-- 129 A LA++G +LQTLT NP+A P + G+ +G+ + P Y FI GG Sbjct: 69 AGLAVSGYVLQTLTRNPLADPGITGVTAGSVAPIVCCFVFVPWLSPAY-YPFIGLAGGLA 127 Query: 130 GVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGGV 189 S ++ GG R +L L G+++S F +T LLL + + +WLAGG Sbjct: 128 AASVTFWVSRGGQGRPL----QLALGGVSVSLFLGAITTYVLLLTGPQSASLLFWLAGGF 183 Query: 190 SHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLL 249 W + +LP + V LLL + + LSD A +G+ L + +I +L ++ Sbjct: 184 QGRTWSHLLYMLPWTIAGVVGALLLRRVIGMFMLSDHAAAGMGLQLGLWKPLILILAVIP 243 Query: 250 VGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGD 309 V +AGPVAF+GL PH+AR + +S LGA ++ +ADV AR++A P + Sbjct: 244 VAGVAPIAGPVAFVGLAAPHIARLLKPRGTGWEIGLSAALGALIVTVADVFARSIAIPRE 303 Query: 310 LPAGAVLALIGSPCFVWLVRR 330 LP G V AL G P F++LV+R Sbjct: 304 LPVGIVTALFGGPIFIYLVQR 324 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: 341 Number of extensions: 18 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 Apr 09 2024. 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