Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_013402814.1 CALHY_RS04485 ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >NCBI__GCF_000166355.1:WP_013402814.1 Length = 410 Score = 144 bits (363), Expect = 3e-39 Identities = 79/245 (32%), Positives = 133/245 (54%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60 M+L ENL Y V D L GK+ +GPNG GKSTL+ + L+ G + Sbjct: 1 MSLFVENLKCGYSYPIVEVDGRLKFEEGKVYGFVGPNGSGKSTLIKALAGLVKIFEGRIC 60 Query: 61 LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120 G+ I+ LS + A+ +S +PQH + TV ++V GR P+ + E Sbjct: 61 FGEVQISKLSDIERAKLISYMPQHIFSSFPFTVLDVVMMGRFPYEKSRFFATYESKKIAE 120 Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180 + Q ++ + + ++SGG+RQR A VLAQ++ V+L DEP + LDI+HQ ++R+ Sbjct: 121 EKIEQVDLSSKKLSSILKISGGERQRTSFARVLAQSSKVLLFDEPNSSLDISHQEKILRI 180 Query: 181 MGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAE 240 + GK V+ +H+L A++ CD +++M +G ++ G P+EV+ ++ V+ V+A Sbjct: 181 AKQEALDGKIVIMAIHNLKIAAKVCDSVIMMKDGKIVDIGRPDEVLNQQNIKKVYDVDAV 240 Query: 241 IHPEP 245 ++ P Sbjct: 241 VYKNP 245 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: 193 Number of extensions: 4 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: 410 Length adjustment: 28 Effective length of query: 227 Effective length of database: 382 Effective search space: 86714 Effective search space used: 86714 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 24 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