Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 125 bits (314), Expect = 1e-33 Identities = 78/224 (34%), Positives = 124/224 (55%), Gaps = 7/224 (3%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 +R + + +SYG+ +VL D+ L + G+ A +GP+GCGK+TLL + Q G V +G Sbjct: 19 VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122 I+ L + + R + ++ Q + +TV+ V++G L AE RV+ A Sbjct: 79 GRDISGLPAHK--RDVGMVFQSYALWPHMTVRRNVAFG----LEERRVPRAEIERRVDAA 132 Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDL-MRLM 181 ++ + HLA RR ++LSGGQ+QR LA + V+LLDEP + LD +V + L+ Sbjct: 133 LDLVGLKHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELL 192 Query: 182 GELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225 R G T + V HD +A+ CD++ VM +G V GTP+E+ Sbjct: 193 SLQRKLGLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQEL 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: 229 Number of extensions: 8 Number of successful extensions: 3 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: 371 Length adjustment: 27 Effective length of query: 228 Effective length of database: 344 Effective search space: 78432 Effective search space used: 78432 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