Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate GFF2648 PGA1_c26880 putative iron transport system permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Phaeo:GFF2648 Length = 359 Score = 185 bits (469), Expect = 2e-51 Identities = 107/287 (37%), Positives = 160/287 (55%), Gaps = 7/287 (2%) Query: 35 TDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASL 94 TDW G ++ + R PR LLA+ VGA LA+ G +Q + RNPLA P +LG++ + Sbjct: 74 TDWSKGQAA--IVWDIRFPRALLAMMVGAGLAMVGASLQAVTRNPLADPHLLGISAGGAF 131 Query: 95 ASVGALLLMPS-LPVMVLPLLAFAG--GMAGLIL-LKMLAKTHQPMKLALTGVALS-ACW 149 ++ ALL L ++ +PLLAFAG G L+L + A+ +L L GVA+S Sbjct: 132 GAILALLHTGLFLGLLTVPLLAFAGALGATALVLAVSRFAEATTADRLVLVGVAVSFVVM 191 Query: 150 ASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLAL 209 A + L P+ + + W+ G L WS + + +++L + D + + + Sbjct: 192 AGANVLIFLGDPRATHTVVFWMLGGLGLAQWSHLIYPLVVLVLCGGWLWTKAGDFNAMTV 251 Query: 210 GDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLL 269 GD ATTLG+ V R + +T VA G I F+GL+VPH+ R I GG HRR+L Sbjct: 252 GDETATTLGIPVARFRLITFTIGALITGVMVAFSGMIGFVGLIVPHIARLIVGGDHRRVL 311 Query: 270 PVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 P SAL G L LV AD+LAR + P ++P+G++T ++G +F+WLL R Sbjct: 312 PASALIGGLFLVAADILARTLMAPEDMPIGLVTGLVGGVFFIWLLRR 358 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: 342 Number of extensions: 18 Number of successful extensions: 3 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: 359 Length adjustment: 28 Effective length of query: 290 Effective length of database: 331 Effective search space: 95990 Effective search space used: 95990 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: 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