Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 7026137 Shewana3_3279 transport system permease protein (RefSeq)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__ANA3:7026137 Length = 381 Score = 154 bits (388), Expect = 4e-42 Identities = 104/307 (33%), Positives = 163/307 (53%), Gaps = 29/307 (9%) Query: 50 TLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAAL-AMALT 108 ++ E +V LRLPR ++A + GA L+LAG++LQT+T NP+A P L GI+SGA+ A+ + Sbjct: 75 SMTERIVMELRLPRIILAFVAGAGLSLAGSVLQTVTRNPLADPYLFGISSGASFGAVVML 134 Query: 109 SALSPTPIAG----------------------YSLSFIAACGGGVSWLLVMT-AGGGFRH 145 + + + + G +SL F A G +S L+V+ AG G + Sbjct: 135 TLFTGSGLFGNAGTIANSGIFSGSGTFAGLLWFSLPFGAFIGASLSVLIVLALAGLGLKS 194 Query: 146 THDRNKLILAGIALSAFCMGLTRITLLLAEDHA-YGIFYWLAGGVSHARWQDVWQLLPVV 204 +R ++L+G+A S LT + L A A + +W G + A W + VV Sbjct: 195 QVER--MLLSGVATSFMFSALTSLLLYFASPQATASVLFWSLGSFAKASWSLLVLPSLVV 252 Query: 205 VTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIG 264 + + ++L Q+ L D TAHTLGVN+ +LRL + +L L+ V+ G + F+G Sbjct: 253 LLSFFIILGWKRQIMALQAGDETAHTLGVNVPKLRLNMLLLCSLITAILVATCGGIGFVG 312 Query: 265 LLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCF 324 L++PH R F R + ++ L+G M+ DVLAR L +LP G + A IGS F Sbjct: 313 LMIPHTVRLL--FPGRQPILLTALVGGLFMVWIDVLARCLLGNQELPVGIITAAIGSFFF 370 Query: 325 VWLVRRR 331 + ++RRR Sbjct: 371 LLILRRR 377 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: 346 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 332 Length of database: 381 Length adjustment: 29 Effective length of query: 303 Effective length of database: 352 Effective search space: 106656 Effective search space used: 106656 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