Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate SM_b21106 SM_b21106 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Smeli:SM_b21106 Length = 365 Score = 310 bits (793), Expect = 5e-89 Identities = 170/330 (51%), Positives = 219/330 (66%), Gaps = 14/330 (4%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA VT K Y GA E V +LE+ D EF+ LVGPSGCGKSTTLRM+AGLE V+ G Sbjct: 1 MAPVTLKKLVKRY-GALE-VVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 AI IG + V + PR R+I+MVFQ+YALYPHMTV ENMGF+LKIAG+ +EI RV EAA Sbjct: 59 AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 A L L LER+P LSGGQRQRVAMGRAIVR P VFL DEPLSNLDAKLR Q RT+I Sbjct: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L ++ T +YVTHDQ EA+T+ DRI +++DG+++QVG P +++ RPA FVAGFIGSP Sbjct: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238 Query: 241 MNLGTFSVKDGD-ATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDL- 298 MN+ + DG A + A + L P + + + ++T G RP+ ++ P G Sbjct: 239 MNMEEAVLTDGKLAFASGATLPLPPRFRSLV--REGQKVTFGLRPD--DVYPSGHGLHAG 294 Query: 299 ------SIPIKLDFVEELGSDSFLYGKLVG 322 I + + E LG+++ ++ + G Sbjct: 295 DADAVHEIELPVTITEPLGNETLVFTQFNG 324 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: 402 Number of extensions: 18 Number of successful extensions: 1 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: 365 Length adjustment: 30 Effective length of query: 346 Effective length of database: 335 Effective search space: 115910 Effective search space used: 115910 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