Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 141 bits (356), Expect = 2e-38 Identities = 83/228 (36%), Positives = 128/228 (56%), Gaps = 10/228 (4%) Query: 29 GEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGR------DVTTVEPADRDLAMVFQ 82 GEF+ VGPSG GK+TLLR +AGL +G I G R + P +R + V Q Sbjct: 28 GEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQ 87 Query: 83 SYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQRQRV 142 + L+P ++ N+ + + R+ R A + L DR P QLSGGQ+QRV Sbjct: 88 HFGLFPKLSALGNIMAAL--DHLPSQERRPRALAALEKVNLHGLTDRLPSQLSGGQKQRV 145 Query: 143 AIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAMTMAD 202 A+ RA+ + P V L DEP S +D + R ++ +EL L +L +I VTHD EA+ +AD Sbjct: 146 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNEALLLAD 205 Query: 203 KIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDVGLQD 250 ++++++G + Q G+P D++ +P + VA +G N+F++ V QD Sbjct: 206 SMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG--LRNIFNAHVVAQD 251 Lambda K H 0.320 0.139 0.396 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: 261 Number of extensions: 13 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: 338 Length of database: 370 Length adjustment: 29 Effective length of query: 309 Effective length of database: 341 Effective search space: 105369 Effective search space used: 105369 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 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