Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Echvi_4679 Echvi_4679 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Cola:Echvi_4679 Length = 337 Score = 149 bits (375), Expect = 1e-40 Identities = 80/229 (34%), Positives = 134/229 (58%), Gaps = 5/229 (2%) Query: 3 LRTENLTVSYGTDK----VLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGT 58 L +N+ + Y K V + L GK+T L+GPNG GKSTL+ L P +G Sbjct: 8 LEGKNVAIGYRKGKYPLKVSEHLDFQLSAGKLTCLLGPNGVGKSTLIKTLMGQLPPLAGD 67 Query: 59 VFLGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNAR 118 + P++ RQLA+++S++ +T +TVQ+LV+ GR P+ + G+LS+ED Sbjct: 68 ITFAGIPLHQQHPRQLAQKISVVLTDRITAGNLTVQQLVALGRTPFTNWLGKLSSEDQHI 127 Query: 119 VNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLM 178 + A+ T+ +L + ++E+S GQ Q+ +A LAQ+ +++LDEPT +LD+ ++ + M Sbjct: 128 IKEALQATKTLYLKDQLISEISDGQLQKVMIARALAQDGQLIILDEPTAHLDLINRYETM 187 Query: 179 RLMGEL-RTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVM 226 L+ E+ + QGK+++ V HDL A D L +M G + GTPE+++ Sbjct: 188 HLLREITKRQGKSILVVTHDLEIAVETADHLWIMQCGEPLTTGTPEDLI 236 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: 217 Number of extensions: 13 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: 337 Length adjustment: 26 Effective length of query: 229 Effective length of database: 311 Effective search space: 71219 Effective search space used: 71219 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: 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