Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 137 bits (345), Expect = 5e-37 Identities = 84/214 (39%), Positives = 122/214 (57%), Gaps = 9/214 (4%) Query: 29 GELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVND------VPPAQRGIAMVFQ 82 GE + VGPSG GK+TLLRMIAGL K G++ + D P R I V Q Sbjct: 28 GEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQ 87 Query: 83 SYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQRQRV 142 + L+P ++ N+ AL + A AA EK+ L DRLP LSGGQ+QRV Sbjct: 88 HFGLFPKLSALGNIMAALDHLPSQERRPRAL--AALEKVNLHGLTDRLPSQLSGGQKQRV 145 Query: 143 AIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVEAMTLA 202 A+ R++ R+P+V L DEP S +D R LE+A+LK + ++ VTHD EA+ LA Sbjct: 146 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAEL-NIPVIMVTHDLNEALLLA 204 Query: 203 TRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIG 236 +++++ G + Q G+P +++ +P NE VA+ +G Sbjct: 205 DSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 Lambda K H 0.316 0.135 0.379 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: 254 Number of extensions: 12 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: 373 Length of database: 370 Length adjustment: 30 Effective length of query: 343 Effective length of database: 340 Effective search space: 116620 Effective search space used: 116620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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