Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_057507247.1 ABB28_RS03270 heme ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >NCBI__GCF_001431535.1:WP_057507247.1 Length = 254 Score = 171 bits (433), Expect = 1e-47 Identities = 95/238 (39%), Positives = 136/238 (57%), Gaps = 4/238 (1%) Query: 17 VLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPINMLSSRQLAR 76 +L DV L+ G +TAL+GPNG GKSTLL L P SG V L P++ L + LAR Sbjct: 20 ILADVELAFAPGTVTALVGPNGAGKSTLLGVACGDLQPDSGEVLLAGTPLSALRAGALAR 79 Query: 77 RLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHLAVRRL 136 + +++PQ H +V+E+V+ GR P AED RV A++ + L R + Sbjct: 80 QRAVMPQEHAVRFAFSVEEVVAMGRLPHPPA----PAEDARRVEAALDAAELQALRQREV 135 Query: 137 TELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQGKTVVAVLH 196 +LSGG+ R A VLAQ+TP++ LDEPT LD+ HQ +R + L QG V+ VLH Sbjct: 136 QQLSGGESARTTFARVLAQDTPLLFLDEPTAALDLRHQERTLRSVRTLADQGACVIVVLH 195 Query: 197 DLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIHPEPVSGRPMCLM 254 DLN A+ + D++V++ G V A GTP EV+T LR V+ + + P P+ ++ Sbjct: 196 DLNLAAGHADRIVLLERGRVAADGTPREVLTEDTLRRVYQQDVLVLQHPRRPVPLVVV 253 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: 171 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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 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