Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 200217 SO1034 iron-compound ABC transporter, permease protein (NCBI ptt file)
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__MR1:200217 Length = 380 Score = 154 bits (390), Expect = 3e-42 Identities = 107/311 (34%), Positives = 160/311 (51%), Gaps = 33/311 (10%) Query: 48 TPTLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMAL 107 T + + +V LRLPR L+A + GA L+LAG++LQT+T NP+A P L GI+SGA+ + Sbjct: 72 TAAMTDRIVMELRLPRILLAFVAGAGLSLAGSVLQTVTRNPLADPYLFGISSGASFGAVV 131 Query: 108 TSAL--------------------SPTPIAG---YSLSFIAACGGGVSWLLVMTAGG-GF 143 L +AG +SL F A G +S L+V+ G G Sbjct: 132 MLTLFSGSGFFANAGVIANSGIFSGAEILAGLQWFSLPFGAFIGASLSVLIVLALSGLGL 191 Query: 144 RHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHA-YGIFYWLAGGVSHARWQDVWQLLP 202 +R ++L+G+A S LT + L A A + +W G + A W + +LP Sbjct: 192 NSQVER--MLLSGVATSFMFGALTSLLLYFASPQATASVLFWSLGSFAKASWSLL--ILP 247 Query: 203 VVVTAVPVVLLLA--NQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPV 260 +V V ++L Q+ L D TAHTLGVN+ +LRL + +L L+ V+ G + Sbjct: 248 TIVVLVSFFIILGWKRQIMALQAGDETAHTLGVNVPKLRLNMLLLCSLITAILVATCGGI 307 Query: 261 AFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIG 320 F+GL++PH R F R + ++ L+G M+ DVLAR L +LP G + A IG Sbjct: 308 GFVGLMIPHTVRLL--FPGRQPILLTALVGGLFMVWIDVLARCLLGNQELPVGIITASIG 365 Query: 321 SPCFVWLVRRR 331 S F+ ++RRR Sbjct: 366 SFFFLLILRRR 376 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: 345 Number of extensions: 19 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: 380 Length adjustment: 29 Effective length of query: 303 Effective length of database: 351 Effective search space: 106353 Effective search space used: 106353 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