Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate SM_b20661 SM_b20661 sugar uptake ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Smeli:SM_b20661 Length = 355 Score = 354 bits (908), Expect = e-102 Identities = 188/347 (54%), Positives = 240/347 (69%), Gaps = 14/347 (4%) Query: 19 PTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRD 78 P +K N++I+D EF + VGPSGCGK+T LRM+AGLE+IT G + IG++ VN +PPKDRD Sbjct: 17 PVIKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAGEIRIGNQVVNRLPPKDRD 76 Query: 79 IAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSG 138 IAMVFQNYALYPHMTV NMAF L L PK+EID+RV AA+IL ++ LLDR P+ LSG Sbjct: 77 IAMVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAAEILGLSKLLDRYPRQLSG 136 Query: 139 GQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTE 198 GQRQRVA+GRAIVR+PQVFL DEPLSNLDAKLRV MRAEI++LHQRL+TT +YVTHDQ E Sbjct: 137 GQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKELHQRLKTTTVYVTHDQIE 196 Query: 199 AMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFR 258 AMTM D+IVVM DG+++Q P +Y P N+FVAGFIGSPAMN ++G + + + Sbjct: 197 AMTMADKIVVMHDGIVEQIGAPLELYDNPANLFVAGFIGSPAMNMLKGRLDPADPSVFLT 256 Query: 259 APSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPDSVLQMQVEVVEHM 318 A + LP R A+ A G+ +V G+RPE +M P+ L ++ V+E Sbjct: 257 ADGTA--LPVAR----PAAAAQGRDLVYGLRPE-------YMALDPNG-LPAEIAVIEPT 302 Query: 319 GSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAET 365 G E L +G + + R G ++ LAID +H+FDA T Sbjct: 303 GYETQLIARLGGHDVTCVFRERVNAKPGETIHLAIDAAHVHLFDAGT 349 Lambda K H 0.321 0.138 0.395 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: 409 Number of extensions: 18 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: 384 Length of database: 355 Length adjustment: 30 Effective length of query: 354 Effective length of database: 325 Effective search space: 115050 Effective search space used: 115050 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