Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 238 bits (607), Expect = 2e-67 Identities = 139/320 (43%), Positives = 197/320 (61%), Gaps = 23/320 (7%) Query: 4 VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63 V L +V K FG T + ++L + G+ + LLGPSGCGKTT LR++AGLE+PS GQI+I Sbjct: 7 VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFI- 65 Query: 64 DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123 D E + RDI MVFQSYAL+PHM++ +N+ + LK+ VPR E+ RV+E Sbjct: 66 -----DGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEA 120 Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183 ++ L +R ++SGGQ+QRVAL RA++ KP+V L DEPLSNLDA LR MR +++ Sbjct: 121 LAMVDLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIR 180 Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243 +LQ+Q +T++YVTHDQ EA + D + VMN+G + Q+GSP ++Y +PA+ F+A F+G Sbjct: 181 ELQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD- 239 Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFAQVR 303 N A + DG+VD + L P F GE G V G+RPE + + Sbjct: 240 -ANLFPATFS-DGYVDIYGYHLP-RPLHFGTQGE-GMV------GVRPEAI------TLS 283 Query: 304 VPGENLVRAVVEIVENLGSE 323 GE R V+ V +G + Sbjct: 284 DRGEESQRCVIRHVAYMGPQ 303 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: 14 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: 348 Length adjustment: 29 Effective length of query: 343 Effective length of database: 319 Effective search space: 109417 Effective search space used: 109417 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