Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_017596976.1 D471_RS0101440 iron ABC transporter permease
Query= SwissProt::P15030 (332 letters) >NCBI__GCF_000341125.1:WP_017596976.1 Length = 356 Score = 172 bits (437), Expect = 9e-48 Identities = 113/302 (37%), Positives = 166/302 (54%), Gaps = 12/302 (3%) Query: 34 VSGADATRALLPGHTPTLPEA---LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMA 90 ++GAD +PG+ P +PEA +V LR PR AV +GA LA+AG ++Q L NP+A Sbjct: 51 LAGADG----VPGNGP-VPEAEDFIVWRLRAPRVFQAVFVGAGLAVAGAVVQALVRNPVA 105 Query: 91 SPSLLGINSGAAL-AMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDR 149 P +LG++SGA++ A+ L + L + +L A G V+ LLV A R T + Sbjct: 106 DPHILGLSSGASVGAVLLMTTLGSAALGALALPLAAFAGALVAGLLVF-AVARTRGTLEP 164 Query: 150 NKLILAGIALSAFCMGLTRITLLLAE--DHAYGIFYWLAGGVSHARWQDVWQLLPVVVTA 207 +LIL G+A+ G+T +L + D + +WL G +S ARW V+ Sbjct: 165 LRLILVGVAIGQLLGGVTSFLVLRKQSGDAQQQVLFWLLGSLSGARWSSALVCAAAVLAL 224 Query: 208 VPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLV 267 ++ A LN+L L A +LGV+ R R + LL G V+VAG + F+GL+V Sbjct: 225 SALLTARAGSLNVLVLGSEGAASLGVDADRSRERLFAAAALLTGTTVAVAGAIGFVGLVV 284 Query: 268 PHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWL 327 P+LAR G D R VLPV L GA +++ AD+ AR + P +LP G + A++G P FV Sbjct: 285 PNLARLLVGADHRRVLPVCALSGALMLVWADLAARTVLRPTELPIGVLTAVVGVPFFVAA 344 Query: 328 VR 329 +R Sbjct: 345 LR 346 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: 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: 356 Length adjustment: 29 Effective length of query: 303 Effective length of database: 327 Effective search space: 99081 Effective search space used: 99081 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