Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 283 bits (724), Expect = 5e-81 Identities = 153/310 (49%), Positives = 208/310 (67%), Gaps = 16/310 (5%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80 V +L+I DGEF+VLVGPSGCGKST +RM+AGLE ++ G + IG +AP+ R+I+ Sbjct: 19 VHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDLMIGGTRANSLAPQQRNIS 78 Query: 81 MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 MVFQ+YALYPH++V EN+ F +I +S R++ AA L L +L+R P+ALSGGQ Sbjct: 79 MVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKMLNLGGYLDRLPRALSGGQ 138 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 RQRVAMGRA+VR P +FL DEPLSNLDAKLRVQ RT+I AL ++L T +YVTHDQ EA+ Sbjct: 139 RQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALHQRLKNTVIYVTHDQIEAM 198 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLG---TFSVKDGDA---- 253 TM DRI V+ G ++Q+G P ELYD PAN+FVA F+GSP+MN S G Sbjct: 199 TMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMNFAEGVIASRAQGQGLALN 258 Query: 254 TSGHARIKLSPETLAAMTPEDNGRITIGFRPEALE-IIPEGESTDLSIPIKLDFVEELGS 312 +G I L +A+ ++T+G RPE +E + P ++T ++++ VE G+ Sbjct: 259 LTGGGEIVLEGAPASAVV---GAKVTLGVRPEHIETMTPTPDAT-----MEVEVVEPTGA 310 Query: 313 DSFLYGKLVG 322 ++ LYGK+ G Sbjct: 311 ETHLYGKIGG 320 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: 371 Number of extensions: 14 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: 360 Length adjustment: 30 Effective length of query: 346 Effective length of database: 330 Effective search space: 114180 Effective search space used: 114180 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