Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate AO356_28845 AO356_28845 ferrichrome ABC transporter
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28845 Length = 251 Score = 124 bits (311), Expect = 2e-33 Identities = 80/243 (32%), Positives = 130/243 (53%), Gaps = 11/243 (4%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLS-LPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTV 59 +T+R ENL YG V++ V+ + G++ A++GPN GKSTL + L+ Sbjct: 2 VTIRLENLGARYGQRTVIHGVTTAAFVGGQVVAVVGPNAAGKSTLFKRMAGLID------ 55 Query: 60 FLGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARV 119 G + + S++ + +S +PQ +TV E V R W + ++ RV Sbjct: 56 --GPGQVILEGSKKGPQGISYMPQGLNASARLTVYESVLLARKQLTPGWV-VHDDELKRV 112 Query: 120 NVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMR 179 + + I L+ R L ELSGGQ+Q +A L + ++L+DEPT+ LD++ QV ++ Sbjct: 113 DDILAALGITELSFRNLGELSGGQQQLVSIAQTLVREPEILLMDEPTSALDMHRQVQVLN 172 Query: 180 LMGELRTQGKTVVAV-LHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVE 238 M L + + +V + +HDLNQA R+ DQ++V+A+ G EV+T +LR V+ VE Sbjct: 173 FMRALARKRQVIVFIAIHDLNQALRFADQVLVIADNTAQGSGPSAEVITESMLRQVYKVE 232 Query: 239 AEI 241 A I Sbjct: 233 ARI 235 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: 154 Number of extensions: 7 Number of successful extensions: 4 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: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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: 46 (22.3 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