Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate PfGW456L13_80 ABC transporter (iron.B12.siderophore.hemin) , permease component
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_80 Length = 336 Score = 188 bits (477), Expect = 2e-52 Identities = 118/331 (35%), Positives = 179/331 (54%), Gaps = 20/331 (6%) Query: 3 IALVIFITLALAGCALLSLHMGVIPVP----WRALL--------TDWQAGHEHYYVLMEY 50 + L+ L L C ++SL G VP WR LL TDW G EH L+ Sbjct: 8 LMLIALGALLLVSC-VVSLGFGPARVPLDVVWRILLHKLFGFGVTDWNPGQEHIVWLI-- 64 Query: 51 RLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLP-VM 109 R+PR+LL VGA LA+ G ++Q + RNPLA P +LGV A+L +V +L + + ++ Sbjct: 65 RVPRMLLGALVGAGLALIGAVLQAVTRNPLADPHLLGVTSGATLGAVIVVLHVGEIVGLL 124 Query: 110 VLPLLAFAGGMAGLILLKMLAKTHQPM---KLALTGVALSACWASLTDYLMLSRPQDVNN 166 LP+ AF G + ++++ M+A H + +L L GVA+S ++ + L+ ++ Sbjct: 125 TLPIAAFIGALLSMLVVLMIASRHGRLDSDRLLLCGVAVSFVMMAIANLLLFMGDHRASS 184 Query: 167 ALL-WLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTR 225 A++ W+ G L W + + ++ L L L R L+ L G+ A TLG++ R Sbjct: 185 AVMFWMLGGLGLARWELLAVPTASVLFGLILLLGMARPLNALMAGEQTAVTLGLNARTVR 244 Query: 226 FWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADL 285 L+A MT V+ G I F+GL+VPH+ R + G HRRLLPV L G++ LV D+ Sbjct: 245 LRVFLIASLMTGVLVSISGSIGFVGLMVPHIARRLVGAEHRRLLPVCVLLGSVFLVWVDV 304 Query: 286 LARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 AR + P +LP+GV TA IG +F+ L+ R Sbjct: 305 AARTMIAPEDLPIGVATAAIGGLFFIGLMRR 335 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: 308 Number of extensions: 15 Number of successful extensions: 4 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: 318 Length of database: 336 Length adjustment: 28 Effective length of query: 290 Effective length of database: 308 Effective search space: 89320 Effective search space used: 89320 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