Align ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1646 Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
Query= uniprot:A0A166QFS3 (424 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1646 Length = 450 Score = 791 bits (2042), Expect = 0.0 Identities = 389/424 (91%), Positives = 407/424 (95%) Query: 1 MKQLRSLLPAALLTLCAGLPSLSSAADLTISCGAVGAELQLCKEAVQAWSKQTGNNVEVV 60 MKQL+S+LPAALL LC G PSL +AA LTISCGAVGAELQLCKEAV+AWSKQTGN+VEVV Sbjct: 27 MKQLKSILPAALLGLCVGFPSLCTAASLTISCGAVGAELQLCKEAVEAWSKQTGNSVEVV 86 Query: 61 STPNSATERLSFYQQILSAQSSDIDIIQIDMVWPGMLAKHLLDLREVLPANATQGYFQAQ 120 STPNSATERLSFYQQILSAQSSDIDIIQIDMVWPGMLAKHL+DLREVLPANATQGYFQAQ Sbjct: 87 STPNSATERLSFYQQILSAQSSDIDIIQIDMVWPGMLAKHLMDLREVLPANATQGYFQAQ 146 Query: 121 VDNATVNGRLVTMPWFTDSGLLYYRKDLLEKYNQQVPRTWEEMTATARNIQQAERTAGNP 180 VDNATVNGRLVTMPWFTDSGLLYYRKDLLEKYN+ VP+TWEEMT TAR +QQAER AGN Sbjct: 147 VDNATVNGRLVTMPWFTDSGLLYYRKDLLEKYNKPVPQTWEEMTTTARAVQQAERAAGNA 206 Query: 181 NAWGYIFQGRAYEGLTCNALEWISSQPEGGLVNSRGDIVVNSQASRTALTLAKSWVGDIS 240 NAWGY+FQGRAYEGLTCNALEWISSQP+GGLVN +GDIVVNSQASR ALTLAKSWVGDIS Sbjct: 207 NAWGYVFQGRAYEGLTCNALEWISSQPQGGLVNQQGDIVVNSQASRAALTLAKSWVGDIS 266 Query: 241 PRGVLNYTEEEGRGVFQSGNALFMRNWPYVWALVQGQDSAVKDKVGVAPLPRGGETGTHA 300 PRGVLNYTEEEGRGVFQSGNALFMRNWPYVWALVQ QDS VKDKVGVAPLPRGGETGTHA Sbjct: 267 PRGVLNYTEEEGRGVFQSGNALFMRNWPYVWALVQSQDSVVKDKVGVAPLPRGGETGTHA 326 Query: 301 STLGGWGLAVSRYSAHPKLAAELVSYLTSAQEQKHRALIGAYNPVIESLYQDPELLAAMP 360 STLGGWGLAVSRYSA+PKLAAELVSYL+SAQ+QKHRAL+GAYNPVIESLYQDPELLAAMP Sbjct: 327 STLGGWGLAVSRYSANPKLAAELVSYLSSAQQQKHRALVGAYNPVIESLYQDPELLAAMP 386 Query: 361 YYAQLHSILNDGVMRPASITADRYPRVSNAFFDRVHGVLAGELPVDQALAELESELTRIK 420 YY+QL SILNDGVMRPASITADRYPRVSNAFFD+VHGVLA E PVDQALAELESELTRIK Sbjct: 387 YYSQLRSILNDGVMRPASITADRYPRVSNAFFDQVHGVLADERPVDQALAELESELTRIK 446 Query: 421 RRNW 424 RRNW Sbjct: 447 RRNW 450 Lambda K H 0.316 0.131 0.392 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: 670 Number of extensions: 10 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: 424 Length of database: 450 Length adjustment: 32 Effective length of query: 392 Effective length of database: 418 Effective search space: 163856 Effective search space used: 163856 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 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