Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BWI76_RS03120 BWI76_RS03120 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Koxy:BWI76_RS03120 Length = 356 Score = 296 bits (758), Expect = 6e-85 Identities = 167/354 (47%), Positives = 225/354 (63%), Gaps = 19/354 (5%) Query: 18 EPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDR 77 +P + +L+I +GEF+VLVGPSGCGKST LR+LAGLE V++G I++ D+++T ++PR+R Sbjct: 14 KPALSALSLDIREGEFVVLVGPSGCGKSTLLRLLAGLEPVSEGEIWLHDENITDMSPRER 73 Query: 78 DIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALS 137 + AM+FQNYAL+PH++V +N+ F +K+ + + RVD+ A L L L+RKP LS Sbjct: 74 NFAMIFQNYALFPHLSVRDNITFGMKVRKEEKTSWQPRVDKVAQMLQLDTLLDRKPAKLS 133 Query: 138 GGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQT 197 GGQRQRVAM RAIVRNP++FLMDEPLSNLDA+LR + R I L ++L +TVYVTHDQT Sbjct: 134 GGQRQRVAMARAIVRNPRLFLMDEPLSNLDARLRSEVRDSIMDLHQQLRTSTVYVTHDQT 193 Query: 198 EALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGH 257 EA++M DRI V+ G++QQVG P LY PAN+FVAGFIGSPAMNL + DG+ G Sbjct: 194 EAMSMADRIVVMNGGHVQQVGRPEYLYANPANLFVAGFIGSPAMNLLSLPCADGEVLLGE 253 Query: 258 ARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLY 317 R L P + R+ +G RPE I E L +P + E +G+D L+ Sbjct: 254 LRYPLPPRY------REESRVWLGIRPE--HISDRVEENHLRLPATVLQRELMGADYLLH 305 Query: 318 GKLVGEGDLGSSSED---VPESGQIVVRAAPNAAPAPGSVFHARIVEGGQHNFS 368 G L S VPE G ++ +PA +FHA QHN + Sbjct: 306 VS-TPIGTLRFSRRHRGAVPEKGDSLIL---GFSPADVHLFHAE----KQHNLA 351 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: 365 Number of extensions: 13 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: 356 Length adjustment: 30 Effective length of query: 346 Effective length of database: 326 Effective search space: 112796 Effective search space used: 112796 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