Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BWI76_RS22470 BWI76_RS22470 transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Koxy:BWI76_RS22470 Length = 331 Score = 202 bits (515), Expect = 7e-57 Identities = 130/316 (41%), Positives = 190/316 (60%), Gaps = 11/316 (3%) Query: 9 ITLALAGCALLSLHMGVIPVPWRALLTDWQAGHEHYY-VLMEYRLPRLLLALFVGAALAV 67 +TL L LL+ +G + +P +LL AG E + + RLPR+LLAL VGAALA+ Sbjct: 12 MTLLLIVLTLLATTLGAMRLPLTSLLP---AGDEILRNIWLTIRLPRVLLALLVGAALAL 68 Query: 68 AGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVL---PLLA-FAGGMAGL 123 +G ++QG+ RNPLA P +LG++ A+LA L+L SLP +V P+LA F G A + Sbjct: 69 SGCVMQGLFRNPLADPGLLGISGGAALAVACWLVLPLSLPALVALYAPMLAAFIGSTAVM 128 Query: 124 ILLKMLAKTHQPM--KLALTGVALSACWASLTDYLM-LSRPQDVNNALLWLTGSLWGRDW 180 +++ +L++ +L L G+A++A +L L +S + LW GSL +W Sbjct: 129 VVIFILSQAGDASLSRLLLVGIAINALCGALVGVLAWISNDTQLRQLSLWGMGSLGQAEW 188 Query: 181 SFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGV 240 S + +A LMI + + L+LL LGD A LGV+V + LL + + ++ V Sbjct: 189 STLLVAATLMIPASLVVWAMASRLNLLQLGDEEAHYLGVNVRALQRLLLLCSALLVASAV 248 Query: 241 AACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGV 300 A G I FIGLVVPH+MR G HR L+P S L GA+LL++AD LAR + P E+PVG+ Sbjct: 249 AISGIIGFIGLVVPHLMRMWLGPDHRGLVPGSLLCGAILLLLADTLARTVAAPAEMPVGL 308 Query: 301 LTAIIGAPWFVWLLVR 316 LT+++GAPWF+WL+ R Sbjct: 309 LTSVLGAPWFLWLIFR 324 Lambda K H 0.330 0.142 0.447 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: 335 Number of extensions: 13 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: 318 Length of database: 331 Length adjustment: 28 Effective length of query: 290 Effective length of database: 303 Effective search space: 87870 Effective search space used: 87870 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 (21.8 bits) S2: 48 (23.1 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