Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_086509530.1 BZY95_RS08595 ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >NCBI__GCF_002151265.1:WP_086509530.1 Length = 269 Score = 233 bits (595), Expect = 2e-66 Identities = 119/249 (47%), Positives = 167/249 (67%), Gaps = 6/249 (2%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 L T +L++ YG ++++++LSLPTG++TA++GPNGCGKSTLL +RL P G V L Sbjct: 6 LATRDLSLGYGRITIIDELALSLPTGQVTAIVGPNGCGKSTLLAGLARLHAPSHGAVLLD 65 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNP---WLSLWGRLSAEDNARV 119 I L +R+LARRL+LLPQ PEG+TV ELV +GR P WL W SAED V Sbjct: 66 GQDIQQLPARELARRLALLPQEASAPEGLTVAELVRFGRQPHQGWLRQW---SAEDQQVV 122 Query: 120 NVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMR 179 + A+ ++ LA R L LSGGQRQRA++AM + Q TP++LLDEPT+ LD+ HQ+++ Sbjct: 123 HEALAAADVDELADRPLDTLSGGQRQRAWIAMTITQQTPLLLLDEPTSALDLGHQIEVFE 182 Query: 180 LMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEA 239 L+ L G+TVV VLHDL A RY D LV + +G ++A G P EV+T L+R ++ ++ Sbjct: 183 LVRRLAAHGRTVVMVLHDLASACRYADHLVALRHGQLVAAGPPGEVVTTELVRQLYDIDC 242 Query: 240 EIHPEPVSG 248 + P+P +G Sbjct: 243 TLIPDPATG 251 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: 181 Number of extensions: 6 Number of successful extensions: 1 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: 269 Length adjustment: 25 Effective length of query: 230 Effective length of database: 244 Effective search space: 56120 Effective search space used: 56120 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 Apr 09 2024. 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