Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >MicrobesOnline__882:208681 Length = 349 Score = 290 bits (743), Expect = 3e-83 Identities = 168/368 (45%), Positives = 226/368 (61%), Gaps = 25/368 (6%) Query: 1 MAGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI 60 M+ + L V + +G+V AV ++S EV+ G+ ++LLGPSGCGK+TTLR+IAGLE + G+I Sbjct: 1 MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120 IG + V + +PP R +AMVFQSYAL+PH+TV DNI F L +RKVP E +R+ Sbjct: 61 LIGGRDVTN------LPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRL 114 Query: 121 REVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRA 180 E+LGL +LL RKP ELSGGQ+QRVALGRA+V + V LMDEPLSNLDAKLR MR Sbjct: 115 DRAVEILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRR 174 Query: 181 ELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 E++ LQ+ LG+T +YVTHDQ EAM+M DRI +M G + Q +P E+Y +PA F FI Sbjct: 175 EIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFI 234 Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300 G+PPMN + +DG G ++ + G + + GIRPE Sbjct: 235 GTPPMNLVRLQGNDDGIRVAGSRSGRV----------TCHAGADCMLGIRPE-------- 276 Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360 +R+ + RAVVE VE LGS ++ RVG + G E+ + + + Sbjct: 277 HIRIVDDGW-RAVVESVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHV 335 Query: 361 HIFDKTTG 368 HIFD TG Sbjct: 336 HIFDAATG 343 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: 369 Number of extensions: 14 Number of successful extensions: 4 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: 349 Length adjustment: 29 Effective length of query: 343 Effective length of database: 320 Effective search space: 109760 Effective search space used: 109760 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