Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate GFF2549 PGA1_c25900 putative iron ABC transport system, permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Phaeo:GFF2549 Length = 343 Score = 184 bits (468), Expect = 2e-51 Identities = 127/327 (38%), Positives = 176/327 (53%), Gaps = 9/327 (2%) Query: 9 LLWGLPVAALIIIFWLSLFCYS--AIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLV 66 LLW AAL+ + LS S A S A+ L +V+N+RLPR + Sbjct: 19 LLW--LAAALLTLCLLSAAALSLGARATSWAEIWGGLTAYDPNNADHIVVRNMRLPRLIG 76 Query: 67 AVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTS-ALSPTPIAGYSLSFIA 125 A L GA+L ++G L+Q +T NP+A P LLGIN GAAL + L L T A + ++A Sbjct: 77 AGLAGAALGMSGALIQAMTRNPLADPGLLGINGGAALGVVLCILVLGVTDPAEFI--WVA 134 Query: 126 ACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWL 185 GG + +LV GGG + R LILAG A+SA + LTR LL++ +W+ Sbjct: 135 LGGGLAASVLVFLLGGGSQANPLR--LILAGAAVSALFLALTRALLLVSRQTLDVYRFWV 192 Query: 186 AGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINML 245 GG + LLP ++ + ++ LN L L + TA LGV RL Sbjct: 193 LGGFDGILPATLQSLLPFLILGALLAIIAGFGLNALMLGEDTAKGLGVRTGLTRLTAGAA 252 Query: 246 VLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALA 305 ++LL GA V++AGP+AF GL+VPH+AR+ AG L S + GA L++ AD+L R Sbjct: 253 IVLLCGATVAMAGPIAFAGLIVPHMARWAAGPAIGWSLAFSAVFGALLLIAADLLGRLAL 312 Query: 306 FPGDLPAGAVLALIGSPCFVWLVRRRG 332 F G++ AG + ALIG P +WLVRR G Sbjct: 313 FGGNMQAGVMTALIGGPVLIWLVRRNG 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: 382 Number of extensions: 26 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: 343 Length adjustment: 28 Effective length of query: 304 Effective length of database: 315 Effective search space: 95760 Effective search space used: 95760 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