Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 244 bits (622), Expect = 4e-69 Identities = 143/349 (40%), Positives = 208/349 (59%), Gaps = 27/349 (7%) Query: 4 VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63 +++ V K+F +V AV ++SL + GE LLG SG GK+T LRM+AG E+P+ G+IY+ Sbjct: 21 LKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLD 80 Query: 64 DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123 + + D +PP +R I M+FQSYAL+PHMTV NIAF LK K+P+ EI+QRV+E+ Sbjct: 81 GQDITD------MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEM 134 Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183 +L+ + RKP +LSGGQRQRVAL R++ ++P++ L+DEP+ LD KLR +M+ E+ Sbjct: 135 LKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVV 194 Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243 + +GVT + VTHDQ EAMTM +RIA+MN G + Q GSP ++Y+ PAN VA FIGS Sbjct: 195 DILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGS- 253 Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVG---------REVIFGIRPEDL 294 +N + + ED VD + +P F YVG +V IRPE Sbjct: 254 -VNLFEGDIVEDE-VDHVVINVANIPQPF-------YVGYGVSTSVDTTQVWVAIRPEKT 304 Query: 295 YDAMFAQVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSES 343 + + + N VE + LG + ++R+ + S + S Sbjct: 305 H--ISREQPEDARNWCAGKVEDIAYLGGISVYYIRLCNGQLIQSVMTNS 351 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: 353 Number of extensions: 15 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