Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 235 bits (600), Expect = 1e-66 Identities = 134/331 (40%), Positives = 204/331 (61%), Gaps = 17/331 (5%) Query: 4 VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63 +++ V K+F +V AV ++SL + GE LLG SG GK+T LRM+AG E P+ G+IY+ Sbjct: 21 LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLD 80 Query: 64 DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123 + + D +PP +R I M+FQSYAL+PHMTV NIAF LK K+ + +I QRV+E+ Sbjct: 81 GQDITD------LPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEM 134 Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183 +L+ + + RKP +LSGGQRQRVAL R++ ++P++ L+DEP+ LD KLR +M+ E+ Sbjct: 135 LKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVV 194 Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243 ++ ++GVT + VTHDQ EAMTM RIA+M+ G + QVGSP ++Y+ P + +A FIG+ Sbjct: 195 EILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT- 253 Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGE---LGYVGREVIFGIRPEDLYDAMFA 300 +N D + ED D + LP F ++G + V +RPE + Sbjct: 254 -VNLFDCEIIEDE-ADHAILKSPTLPQPF-LIGHGVTTSLEDKHVWLAVRPE---KTLIT 307 Query: 301 QVRVPGE-NLVRAVVEIVENLGSERIVHLRV 330 + + GE N R V + LG + ++++ Sbjct: 308 REQPEGEYNWARGKVHDIAYLGGLSVYYIKL 338 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: 352 Number of extensions: 20 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: 378 Length adjustment: 30 Effective length of query: 342 Effective length of database: 348 Effective search space: 119016 Effective search space used: 119016 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: 50 (23.9 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