Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 379 bits (973), Expect = e-110 Identities = 208/378 (55%), Positives = 265/378 (70%), Gaps = 16/378 (4%) Query: 1 MASVQLRNVTKAWGD-VVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGD 59 MAS+ LR V KA+G+ V +D++L+I + EF VF+GPSGCGKSTLLRMIAGLE +T GD Sbjct: 1 MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 LFIGETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAE 119 L IG MND+P A+RGV MVFQSYAL+PH+SV ENM+FGLKLA K+ ++++V + A Sbjct: 61 LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120 Query: 120 VLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRL 179 +LQL LLERKPKALSGGQRQRVAIGR +V EP VFL DEPLSNLDA LR Q RIEI+RL Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HKRLGR-TMIYVTHDQVEAMTLADKIVVLDAGR-------VAQVGKPLELYHYPADRFVA 231 HK+ + +++YVTHDQ+EAMTLADKIV+L AG+ +AQ+G PLELYH P RFVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240 Query: 232 GFIGSPKMNFLPVKVTATAIEQVQVELPNRQQ-IWLPVESRGVQVGANMSLGIRPEHLL- 289 GFIGSP+MNFLP +V + + V + L + Q+ + +PV G+Q ++LG+RPEHL Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300 Query: 290 --PSDIA--DVTLEGEVQVVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGL 345 PS +A D L V +VEQLG + +H+ P LV + + G ++ + Sbjct: 301 VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPG-GAALVAKAPGNTRLAPGERASLRV 359 Query: 346 PPERCHLFREDGSACRRL 363 P CHLF EDG A L Sbjct: 360 PRAACHLFTEDGFAAASL 377 Lambda K H 0.321 0.138 0.396 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: 401 Number of extensions: 14 Number of successful extensions: 7 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: 369 Length of database: 384 Length adjustment: 30 Effective length of query: 339 Effective length of database: 354 Effective search space: 120006 Effective search space used: 120006 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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