Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate 200216 SO1033 iron-compound ABC transporter, ATP-binding protein, putative (NCBI ptt file)
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__MR1:200216 Length = 285 Score = 161 bits (408), Expect = 1e-44 Identities = 85/251 (33%), Positives = 145/251 (57%), Gaps = 3/251 (1%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60 M L L+ + +L+ V+ +L G++ LIGPNG GKS+LL C R + P G + Sbjct: 1 MALNVSQLSWTIEGKTILSGVNFALQRGEMLGLIGPNGAGKSSLLRCLYRFIRPTQGQIS 60 Query: 61 LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120 L I+ LS + A +++++ Q +T ++LV+ G P ++ S+ D+ ++ Sbjct: 61 LFSQDISQLSPKAFACKVAVVQQDTPHYFDMTTEQLVAMGLTPHKGMFDSHSSGDSDKII 120 Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180 A+ + ++H ++ LSGG++QRA +A + Q +++LDEPT +LD+ +Q+ ++ L Sbjct: 121 KALEKVGLSHKLHQQYERLSGGEKQRALIARAIVQQPLLLILDEPTNHLDVRYQIQILEL 180 Query: 181 MGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAE 240 +R+ G +V+A +HDLN AS CD L+++ NG V A GTP EV+T + VF V A+ Sbjct: 181 ---VRSLGISVIASIHDLNLASALCDSLLLLDNGQVSAMGTPTEVLTEERIAQVFGVCAQ 237 Query: 241 IHPEPVSGRPM 251 + P P P+ Sbjct: 238 VMPHPQHANPL 248 Lambda K H 0.320 0.134 0.393 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: 182 Number of extensions: 5 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: 255 Length of database: 285 Length adjustment: 25 Effective length of query: 230 Effective length of database: 260 Effective search space: 59800 Effective search space used: 59800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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