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::Q8NMV1 (376 letters) >FitnessBrowser__Smeli:SM_b20661 Length = 355 Score = 332 bits (852), Expect = 7e-96 Identities = 192/379 (50%), Positives = 241/379 (63%), Gaps = 30/379 (7%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA V F D S+ P +K N+EI DGEF++LVGPSGCGKST LRMLAGLEN+T G Sbjct: 1 MAGVDFVDVRKSFGAF--PVIKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAG 58 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 I IG++ V + P+DRDIAMVFQNYALYPHMTV +NM F+L +A + + EI+KRV AA Sbjct: 59 EIRIGNQVVNRLPPKDRDIAMVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAA 118 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 LGL++ L+R P+ LSGGQRQRVAMGRAIVR+PQVFL DEPLSNLDAKLRV R +I Sbjct: 119 EILGLSKLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKE 178 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L ++L TTVYVTHDQ EA+TM D+I V+ DG ++Q+GAP ELYD PAN+FVAGFIGSPA Sbjct: 179 LHQRLKTTTVYVTHDQIEAMTMADKIVVMHDGIVEQIGAPLELYDNPANLFVAGFIGSPA 238 Query: 241 MNLGTFSVKDGD----ATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGEST 296 MN+ + D T+ + ++ AA + + G RPE + + P G Sbjct: 239 MNMLKGRLDPADPSVFLTADGTALPVARPAAAAQGRD----LVYGLRPEYMALDPNG--- 291 Query: 297 DLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFH 356 +P ++ +E G ++ L +L G DV V R NA PG H Sbjct: 292 ---LPAEIAVIEPTGYETQLIARLGG--------HDV----TCVFRERVNA--KPGETIH 334 Query: 357 ARIVEGGQHNFSASTGKRL 375 I H F A TG+RL Sbjct: 335 LAIDAAHVHLFDAGTGRRL 353 Lambda K H 0.316 0.135 0.380 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: 392 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: 376 Length of database: 355 Length adjustment: 30 Effective length of query: 346 Effective length of database: 325 Effective search space: 112450 Effective search space used: 112450 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