Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate 3607140 Dshi_0562 transport system permease protein (RefSeq)
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Dino:3607140 Length = 348 Score = 179 bits (454), Expect = 9e-50 Identities = 119/334 (35%), Positives = 183/334 (54%), Gaps = 32/334 (9%) Query: 10 TLALAGCALLSLH------MGVIPVP----WR--------ALLT-DWQAGHEHYYVLMEY 50 +L +AG A+L L +G + VP W LLT DW G ++ E Sbjct: 18 SLTVAGVAVLLLSISVAVSLGAVAVPLGTVWGIMADRILPGLLTPDWTTGQAA--IVWEI 75 Query: 51 RLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS-LPVM 109 RLPR LLA VGA LA+ G +Q + RNPLA P +LG++ A+ ++ ALL L ++ Sbjct: 76 RLPRALLAAMVGAGLALVGASLQSVTRNPLADPHLLGISSGAAFGAILALLHTGLFLGLL 135 Query: 110 VLPLLAFAGGMAGLILLKMLAKTHQPM---KLALTGVALSACWASLTDYLM-LSRPQDVN 165 +PLLAFAG +A +L+ + Q +L L GVA+S S + L+ + P+ + Sbjct: 136 TVPLLAFAGALAATLLVLGVTSFAQATGADRLVLAGVAVSFIVMSCANILIFIGDPRATH 195 Query: 166 NALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRD---LDLLALGDARATTLGVSVP 222 + W+ G L W ++ P +IL + L F + L+ + +GD A+TLG+ + Sbjct: 196 TVVFWMLGGLGLAQWD--QLLFPAVIL-VGCGLWFLANASRLNAMTIGDETASTLGIPIA 252 Query: 223 HTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVV 282 R ++ +T VA G I F+GL++PH++R + GG + R+LP SAL GA+ LV Sbjct: 253 RFRLSVFVVGALLTGCMVAFSGIIGFVGLMIPHIVRMLVGGDYARVLPASALVGAIFLVW 312 Query: 283 ADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 AD+ AR + P ++P+G++T +IG +FVWLL R Sbjct: 313 ADIAARTVMAPEDIPIGIVTGLIGGAFFVWLLRR 346 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: 339 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: 348 Length adjustment: 28 Effective length of query: 290 Effective length of database: 320 Effective search space: 92800 Effective search space used: 92800 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