Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate H281DRAFT_00137 H281DRAFT_00137 iron complex transport system permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_00137 Length = 352 Score = 159 bits (402), Expect = 1e-43 Identities = 118/346 (34%), Positives = 181/346 (52%), Gaps = 27/346 (7%) Query: 1 MTAIKHPVLLWGLPVAALIIIFWLSLFCYSAIPVSGADATRALLPGH-------TPTLPE 53 MTA + + L +AAL ++ ++ ++ ++ A AL P H + L Sbjct: 15 MTAKRAAAIWLVLALAALAVL--MASLALGSVSLAPARVIEALSPLHAGASDANSADLAG 72 Query: 54 ALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSP 113 +V+ LRLPR+L GA LALAG LLQ L NP+A P +LG++ GAA AL + ++ Sbjct: 73 EIVRTLRLPRALAGFACGALLALAGALLQVLLRNPLAEPYVLGVSGGAA-TFALVAMIAG 131 Query: 114 TPIAGYSLSFIAACGGGVSWLLVMTAG------GGFRHTHDRNKLILAGIALSAFCMGLT 167 A + + A G VS LLV+ G + T R L+L G ++A L Sbjct: 132 C--AWWLVDASAFAGAFVSILLVLGLARRELWRGEPQDTSPR--LLLTGAVIAAGWGALI 187 Query: 168 RITLLLAEDHAY-GIFYWLAGGVSHAR--WQDVWQLLPVVVTAVPVVLLLANQLNLLNLS 224 + L LA D+ G+ +WL G ++ W + L+ V++ VPV A +LN+L Sbjct: 188 TLLLNLAPDNRLRGMLFWLTGDLNGNALPWTALVALVVVLIAIVPV----APRLNVLLRG 243 Query: 225 DSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLP 284 D+ A LGV + LRL + + L A V+ AG + F+GL+VPH+ R G DQR +LP Sbjct: 244 DAAAQALGVAVMPLRLRVYLAASLAAAAAVTTAGTIGFVGLVVPHMLRLAFGNDQRMLLP 303 Query: 285 VSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 + L G ++ AD++AR + P LP G + ++IG P F+W++ R Sbjct: 304 AAALGGGVAVMGADLIARLVIAPAQLPVGVITSIIGVPVFLWMLLR 349 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: 24 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: 352 Length adjustment: 29 Effective length of query: 303 Effective length of database: 323 Effective search space: 97869 Effective search space used: 97869 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