Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate BPHYT_RS04855 BPHYT_RS04855 iron ABC transporter
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS04855 Length = 350 Score = 164 bits (414), Expect = 4e-45 Identities = 111/339 (32%), Positives = 176/339 (51%), Gaps = 20/339 (5%) Query: 5 KHPVLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPT-----LPEALVQNL 59 K +W L +A + + ++ ++ ++ AL+P H P L +V+ L Sbjct: 18 KRAAAIW-LALAGIALAVLMASLALGSVTLAPMRVLAALMPSHAPASGSSDLAAEIVRTL 76 Query: 60 RLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGY 119 RLPR++ GA LALAG LLQ L NP+A P +LG++ GAA + AL + ++ A + Sbjct: 77 RLPRAVAGFACGALLALAGALLQVLLRNPLAEPYVLGVSGGAA-SFALIAMIAGC--AWW 133 Query: 120 SLSFIAACGGGVSWLLVMTAG------GGFRHTHDRNKLILAGIALSAFCMGLTRITLLL 173 + A G VS LLV+ G + T R L+L G ++A L + L L Sbjct: 134 IVDASAFAGAFVSILLVLGLARRELWRGEPQDTSPR--LLLTGAVIAAGWGALITLLLNL 191 Query: 174 AEDHAY-GIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLG 232 A D+ G+ +WL G ++ W L +V + ++ A +LN+L D+ A LG Sbjct: 192 APDNRLRGMLFWLTGDLNGGAMP--WTALAALVIVLVAIVPAAPRLNVLLRGDAAAQALG 249 Query: 233 VNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGAT 292 V + LRL + ++ L A V+ AG + F+GL+VPH+ R G DQR +LP + L G Sbjct: 250 VAVMPLRLRVYLVASLAAAAAVTTAGTIGFVGLVVPHMLRLAFGNDQRMLLPAAALGGGV 309 Query: 293 LMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRRR 331 ++ AD++AR + P LP G + ++IG P F+W++ R Sbjct: 310 AVMGADLIARTVIAPAQLPVGVITSIIGVPVFLWMLLHR 348 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: 352 Number of extensions: 27 Number of successful extensions: 2 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: 350 Length adjustment: 28 Effective length of query: 304 Effective length of database: 322 Effective search space: 97888 Effective search space used: 97888 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