Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 325 bits (833), Expect = 1e-93 Identities = 188/363 (51%), Positives = 227/363 (62%), Gaps = 16/363 (4%) Query: 1 MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 M ++ L V K +GDV V K ++L+I DGEFVVFVGPSGCGKSTLLRMI GLE + G + Sbjct: 1 MGAITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAM 60 Query: 61 FIGETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEV 120 I + D PPA+RG+ MVFQSYALYPH+SV ENM F LK AGA + ++V A V Sbjct: 61 LIDGVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAV 120 Query: 121 LQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLH 180 L+L L+R+PK LSGGQRQRVAIGR++V P FL DEPLSNLDAALRV+MR EI++LH Sbjct: 121 LKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLH 180 Query: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 + L TMIYVTHDQVEAMTLAD+IVVL+ G++AQVG P ELY PA+ FVA FIGSPKMN Sbjct: 181 QSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMN 240 Query: 241 FLPVKVTATAIEQVQVELPNRQQIWLPVESRGVQVGAN--MSLGIRPEHLLPSDIADVTL 298 +P A L GV G + LGIRPEH+ P Sbjct: 241 VMPCTTDAGRYR-------------LSAGRGGVFSGDRPAVQLGIRPEHITPGAPGTGAC 287 Query: 299 EGEVQVVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGS 358 +G V VVE LG +T + + + V D L G + P+R F DG Sbjct: 288 DGRVDVVEYLGADTLLVLDCGPEGRVTVRVIGDTDLT-PGDAVGLSFNPDRLSFFDTDGL 346 Query: 359 ACR 361 A R Sbjct: 347 AIR 349 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: 337 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: 369 Length of database: 349 Length adjustment: 29 Effective length of query: 340 Effective length of database: 320 Effective search space: 108800 Effective search space used: 108800 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: 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