Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_011382725.1 AMB_RS01410 cobalt ABC transporter
Query= CharProtDB::CH_088321 (255 letters) >NCBI__GCF_000009985.1:WP_011382725.1 Length = 264 Score = 99.0 bits (245), Expect = 9e-26 Identities = 80/234 (34%), Positives = 117/234 (50%), Gaps = 14/234 (5%) Query: 1 MTLRTENLTVSY-GTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTV 59 M L LT Y G L+ + L + G+ A++GPNG GK+TLL + L P +GTV Sbjct: 1 MILEAAGLTYRYPGGVAALSGLDLGVERGRRLAVLGPNGAGKTTLLLHLNGTLKPSAGTV 60 Query: 60 FLGDNPINMLSSRQLA--RRLSLLPQHHLTPE----GITVQELVSYGRNPWLSLWGRLSA 113 LG + + RR+ L+ Q P+ TV E VS+G L+L G A Sbjct: 61 RLGGEIMGYSRAALTGWRRRVGLVLQE---PDDQLFAATVAEDVSFGP---LNL-GLSEA 113 Query: 114 EDNARVNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINH 173 E RV A++ I+ LA R LS GQ++R +A LA V+LLDEP LD Sbjct: 114 ETRRRVEAALDALGISDLAGRATHMLSFGQKKRVAIAGALAMEPEVLLLDEPLAGLDHQG 173 Query: 174 QVDLMRLMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMT 227 L+ + L G T+V H+++ A + D++ + +G V+AQG EV++ Sbjct: 174 GKRLLAALDALARAGTTLVFTTHEVDLAHGFADRVALFRDGRVIAQGEAAEVLS 227 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: 146 Number of extensions: 6 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: 264 Length adjustment: 24 Effective length of query: 231 Effective length of database: 240 Effective search space: 55440 Effective search space used: 55440 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 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