Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 167 bits (422), Expect = 6e-46 Identities = 90/221 (40%), Positives = 134/221 (60%), Gaps = 2/221 (0%) Query: 21 EMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPPKD 80 E + GEF+ ++GPSG GKTT LRMIAGL +P G I G ++ D ++GI P++ Sbjct: 20 EADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQN 79 Query: 81 RDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLNRKPREL 140 R I V Q + L+P ++ NI L +P QE R E + L L +R P +L Sbjct: 80 RHIGFVPQHFGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVNLHGLTDRLPSQL 137 Query: 141 SGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQ 200 SGGQ+QRVAL RA+ R+P+V L+DEP S +D + R R+ EL +L+ +L + I VTHD Sbjct: 138 SGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDL 197 Query: 201 VEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIG 241 EA+ + D + ++++G + Q G+P +V+ +P N VA +G Sbjct: 198 NEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 Lambda K H 0.323 0.142 0.406 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: 277 Number of extensions: 11 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: 372 Length of database: 370 Length adjustment: 30 Effective length of query: 342 Effective length of database: 340 Effective search space: 116280 Effective search space used: 116280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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