Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate GFF559 PS417_02845 ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__WCS417:GFF559 Length = 336 Score = 181 bits (459), Expect = 2e-50 Identities = 116/321 (36%), Positives = 174/321 (54%), Gaps = 20/321 (6%) Query: 13 LAGCALLSLHMGVIPVP----WRALL--------TDWQAGHEHYYVLMEYRLPRLLLALF 60 L C +LSL G VP WR +L +W AG EH L+ R+PR+LL Sbjct: 18 LVSC-VLSLGFGPARVPVEVVWRIVLYKAFGVGEVNWPAGQEHIVWLI--RVPRMLLGAL 74 Query: 61 VGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS-LPVMVLPLLAFAGG 119 VGA LA+ G ++Q + RNPLA P +LGV A+L +V +L + + ++ LPL AF G Sbjct: 75 VGAGLALIGAVLQAVTRNPLADPHLLGVTSGATLGAVIVVLHVGEVIGLLTLPLAAFIGA 134 Query: 120 MAGLILLKMLAKTHQPM---KLALTGVALSACWASLTDYLMLSRPQDVNNALL-WLTGSL 175 + ++++ +A + + +L L GVA+S + + L+ +A++ W+ G L Sbjct: 135 LLSMLVVLAVASRNGRLESDRLLLCGVAVSFVMMAAANLLLFMGDHRAASAVMFWMLGGL 194 Query: 176 WGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAM 235 W + + ++L L L L R L+ L G+ A TLG++ + R L+A M Sbjct: 195 GLARWELLAVPTATVLLGLGLLLGMARPLNALMAGEQTAVTLGLNARNVRLKVFLVASLM 254 Query: 236 TSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLE 295 T V+ G I F+GL+VPH+ R + G HRRLLPV L G+L LV D+ AR + P + Sbjct: 255 TGVLVSISGSIGFVGLMVPHIARRLVGAEHRRLLPVCVLLGSLFLVWVDVAARTLIAPED 314 Query: 296 LPVGVLTAIIGAPWFVWLLVR 316 LP+GV TA IG +F+ L+ R Sbjct: 315 LPIGVATAAIGGLFFIGLMRR 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: 290 Number of extensions: 11 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: 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