Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__Phaeo:GFF776 Length = 363 Score = 331 bits (848), Expect = 2e-95 Identities = 180/357 (50%), Positives = 241/357 (67%), Gaps = 5/357 (1%) Query: 1 MASVQLQNVTKAWGE-VVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGD 59 MA+++L NV K +G V V +DINLDI +GE +VFVGPSGCGKSTLLRMIAGLE I+ G Sbjct: 1 MANLKLTNVAKTYGGGVEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGGT 60 Query: 60 LFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAE 119 L I MND PPA+RG+ MVFQSYALYPH++V +NM+F LK+A K+ I+ +++ A+ Sbjct: 61 LEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAAK 120 Query: 120 VLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRL 179 +LQL LDR PKALSGGQRQRVAIGR++V +P V+L DEPLSNLDAALRV RIEI++L Sbjct: 121 ILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 HKRL-GRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238 + + TMIYVTHDQVEAMTLA +IVVL +AQVG PL+LY P + FVA FIGSP Sbjct: 181 KEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSPA 240 Query: 239 MNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADV 298 MN +P V AT + + + + ++V + + D G +++G+RPE L+ Sbjct: 241 MNLIPGTVVATG---PRTTVRLTSGEEVVAEIPTTDADQGLAVNVGVRPEDLVEEGTGGA 297 Query: 299 ILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 355 +++ V +VE LG T ++I + L+ + + G++ + P R HLF Sbjct: 298 LIDSRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYADPARLHLF 354 Lambda K H 0.320 0.137 0.393 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: 374 Number of extensions: 13 Number of successful extensions: 3 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: 371 Length of database: 363 Length adjustment: 30 Effective length of query: 341 Effective length of database: 333 Effective search space: 113553 Effective search space used: 113553 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