Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 300 bits (769), Expect = 3e-86 Identities = 177/362 (48%), Positives = 233/362 (64%), Gaps = 13/362 (3%) Query: 1 MADLKLTGVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 MA L L V+K Y G+VKV+ I+++I GE IV VGPSGCGKSTLLRM+AGLE I+GG Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119 + I VVN + PA+R IAMVFQ+YALYPHM+V +NM++ LKI ++EI+ V+ AA Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 L+L L+R P+ALSGGQRQRVA+GR+IVR+P V+LFDEPLSNLDA LRV RLE+ +L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239 + +T +YVTHDQVEAMTLA R++VL GG + Q+G+PLE+Y +P + FVA FIGSP Sbjct: 181 HRRL-RTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 240 MNLLPGKIIGTG---AQTTVEMTDGGR----AVSDYPSDDSLMGAAVNVGVRPEDMVEAA 292 MNL+P G AQ VE G + + P L A+ +G+RPE +E Sbjct: 240 MNLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERAL-LGLRPEH-IEPC 297 Query: 293 PGGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVH 352 + + E +V + EALG + Y G P + +L G +TA +H Sbjct: 298 AAHEAIAEIEVRLVEALGADSYAY--GTLGGQPVVVRLDSNMPVSSGDRLPITAAAEHLH 355 Query: 353 VF 354 F Sbjct: 356 FF 357 Lambda K H 0.316 0.135 0.379 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: 408 Number of extensions: 20 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: 373 Length of database: 367 Length adjustment: 30 Effective length of query: 343 Effective length of database: 337 Effective search space: 115591 Effective search space used: 115591 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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