Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000284315.1:WP_232502519.1 Length = 588 Score = 96.7 bits (239), Expect = 2e-24 Identities = 64/207 (30%), Positives = 103/207 (49%), Gaps = 3/207 (1%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDR-DI 79 V + GE L+G +G GK+TT RMLAGL T G + + +DV VA + R I Sbjct: 357 VNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVAGEDVRKVAAQARGKI 416 Query: 80 AMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGG 139 + Q ++LY +TV +N+ F G S +++ ++ L + L G Sbjct: 417 GYMAQKFSLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSLNFFELEPYKNVSSGILPLG 476 Query: 140 QRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEA 199 RQR+A+ A++ P + +DEP S +D R + I AL +GV+ + TH EA Sbjct: 477 FRQRLALSCALIHEPSILFLDEPTSGVDPNARREFWHIINAL-ATVGVSVLVTTHFMEEA 535 Query: 200 LTMGDRIAVLKDGYLQQVGAPRELYDR 226 DR+ ++ G L +G+P E+ ++ Sbjct: 536 -EYCDRLLIMAQGALLAMGSPAEIKEK 561 Score = 78.2 bits (191), Expect = 6e-19 Identities = 70/294 (23%), Positives = 128/294 (43%), Gaps = 12/294 (4%) Query: 4 VTFKDASLSYPGAKE--PTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGA 61 +T + + ++P + + K + + G L+GP G GK+T +R+L+GL G Sbjct: 11 ITVNELTKTFPSPRGIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGD 70 Query: 62 IFIGDKDVTHVAPRDRDIAMVF--QNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEA 119 I I D + AP ++ + Q + LY ++V EN+ + G +D + Sbjct: 71 IRIMGNDPSK-APLSVQGSLGYMPQKFGLYEDLSVQENLDLYANLQGVPKDRRKELYAPL 129 Query: 120 AATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIA 179 + GL+ F +R LSGG +Q++ + ++V P + L+DEP +D R + + Sbjct: 130 LSMTGLSPFQKRLAGQLSGGMKQKLGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILR 189 Query: 180 ALQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAP----RELYDRPANVFVAGF 235 L + G T++V+ + D I +L +G + G P +E+ R G Sbjct: 190 KLVSESG-ATLFVSTSYLDEAERCDEILILYNGKVLGSGPPESFRKEVAGRGYRAETTGS 248 Query: 236 IGSPAMNLGTF-SVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALE 288 + + + V D RI + +T + PE+ G+I + P E Sbjct: 249 LRTVEPQISLLPGVVDTVLEGSTVRIVMDGDT-PPIFPENLGKIILKSAPPRFE 301 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: 504 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 376 Length of database: 588 Length adjustment: 33 Effective length of query: 343 Effective length of database: 555 Effective search space: 190365 Effective search space used: 190365 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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