Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate CCNA_01250 CCNA_01250 FecCD-family transporter protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Caulo:CCNA_01250 Length = 346 Score = 132 bits (332), Expect = 1e-35 Identities = 98/294 (33%), Positives = 144/294 (48%), Gaps = 12/294 (4%) Query: 41 RALLPGHTPTLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGIN-- 98 +ALL +P P ++ +R PR VA L+GA+L +AG LQ L NP+A P +LG++ Sbjct: 54 QALLLPASP--PGEVLWTIRAPRVTVAALVGAALGMAGATLQGLLRNPLADPGVLGVSAV 111 Query: 99 SGAALAMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIA 158 SG A+A+++ L+ P A + A G V+ V+ FR + LIL G+A Sbjct: 112 SGLGAALAISAGLAVLPGA---IELSALAGALVAGGTVVVVAARFR---EPEALILFGVA 165 Query: 159 LSAFCMGLTRITLLLAEDHAYG--IFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLAN 216 LSA LT + L+ I WL G V + D + L + + L Sbjct: 166 LSALGGALTALVFNLSPSPVATAEILAWLMGSVENRDLMDALRALVPMAIGALLCLRAGA 225 Query: 217 QLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAG 276 L +L L + A + + RLR+ LL GA V+ +G + F+GL PHL R Sbjct: 226 GLRMLTLGEDAARMSALPMARLRIYAVAGSALLTGAAVAASGVIGFVGLAAPHLVRALVR 285 Query: 277 FDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 D + +L + L GA L++LAD+ AR + +L G V AL G+P F L R Sbjct: 286 DDPKRILWPAALAGALLVVLADLAARMIPTEQELKLGVVTALFGAPVFALLAWR 339 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: 343 Number of extensions: 20 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: 346 Length adjustment: 28 Effective length of query: 304 Effective length of database: 318 Effective search space: 96672 Effective search space used: 96672 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