Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085769830.1 B1812_RS00440 molybdenum ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_002117405.1:WP_085769830.1 Length = 370 Score = 145 bits (365), Expect = 2e-39 Identities = 83/203 (40%), Positives = 112/203 (55%), Gaps = 14/203 (6%) Query: 32 TVFVGPSGCGKSTLLRLIAGLEDITSGTIRIDGE-----DATNIPPAKRGLAMVFQSYAL 86 T GPSGCGK+T++R +AGL + G RIDGE D +P KR L VFQ +L Sbjct: 32 TALFGPSGCGKTTVIRCVAGLTRVKDGYCRIDGEIWQDRDGVFLPTHKRPLGYVFQEASL 91 Query: 87 YPHMSVRKNIAFPMKMAGIPADEQKRR----IDNAAAALNLTDYLDRRPGQLSGGQRQRV 142 +PH+SVR+N+ F G P ++ K R D L L L+R P LSGG+RQRV Sbjct: 92 FPHLSVRRNLLF-----GAPKEKSKDRPQIDFDEVVDLLGLRRLLERSPTNLSGGERQRV 146 Query: 143 AIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRLATTMIYVTHDQVEAMTMAD 202 IGRA++ +P L DEPLS LD + + I +L A + Y+THD E +AD Sbjct: 147 GIGRALLTQPKLLLMDEPLSALDRKTKNEILPFIEKLRDHFAVPIFYITHDITEVERLAD 206 Query: 203 KIVVLQAGVIEQVGSPMELYRAP 225 ++V+L+ G + G EL P Sbjct: 207 QVVLLEKGHVVMAGPLAELQSNP 229 Lambda K H 0.320 0.138 0.400 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: 289 Number of extensions: 7 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: 334 Length of database: 370 Length adjustment: 29 Effective length of query: 305 Effective length of database: 341 Effective search space: 104005 Effective search space used: 104005 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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