Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 113 bits (283), Expect = 4e-30 Identities = 77/229 (33%), Positives = 124/229 (54%), Gaps = 8/229 (3%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60 +T + + T + G L+ VSLS+ G++ +IG +G GKSTL+ + L P +G V Sbjct: 2 ITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVI 61 Query: 61 L-GDN--PINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNA 117 + GD+ + + R L RR+ ++ QH G TV + V++ L L GR +AE A Sbjct: 62 VDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFP----LKLAGRPAAEVKA 117 Query: 118 RVNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDL 177 R + + ++ A + +LSGGQ+QR +A LA N V+L DE T+ LD + Sbjct: 118 RTAELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQI 177 Query: 178 MRLMGEL-RTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225 + L+ L R G T+V + H+++ R CD++ V+ G V+ +G EEV Sbjct: 178 LDLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEV 226 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: 175 Number of extensions: 9 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: 332 Length adjustment: 26 Effective length of query: 229 Effective length of database: 306 Effective search space: 70074 Effective search space used: 70074 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