Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Ga0059261_0623 Ga0059261_0623 ABC-type Fe3+-siderophore transport system, permease component
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Korea:Ga0059261_0623 Length = 331 Score = 168 bits (425), Expect = 2e-46 Identities = 114/278 (41%), Positives = 163/278 (58%), Gaps = 6/278 (2%) Query: 46 VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLL-MP 104 +++E R+PR+LL L VGA L +AG +QG +RNPLA P +LG ++AA+ +V AL + Sbjct: 52 IVLELRMPRMLLGLLVGAMLGLAGAALQGFLRNPLAEPSVLGASNAAAFGAVIALYFGIA 111 Query: 105 SLPVMVLPLLAFAGGMAGLILLKMLA-KTHQPMKLALTGVALSA-CWASLTDYLMLS-RP 161 L +LPLLA A M L+LL L+ ++ + L L G+A++ A ++ L LS P Sbjct: 112 ELHPALLPLLAIAAAMVALVLLFGLSGQSESALTLILAGIAIATLAGAGISLALNLSPNP 171 Query: 162 QDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSV 221 + WL GSL R V IA+P +++ L L R LD L LG+ A LG+++ Sbjct: 172 FAAMEIMNWLLGSLENRSSQHVWIALPCIVVGAALLLWDARALDALTLGEDGARALGINL 231 Query: 222 PHTRFWALLLAVAMTSTG-VAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLL 280 R W LL+ VA+ G VA G I FIGL+VPH++R T +L SA+ GALLL Sbjct: 232 RAVR-WRLLVGVAIGVGGAVAVSGSIGFIGLIVPHIIRPFTDRSPSAILWPSAIGGALLL 290 Query: 281 VVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 ++DL R+I EL +GV+TA +G P F+ L+R R Sbjct: 291 TLSDLGVRMIPATNELKLGVVTAFLGIPVFLVHLLRER 328 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: 272 Number of extensions: 14 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: 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