Align ABC transporter substrate-binding protein (characterized, see rationale)
to candidate SM_b21461 SM_b21461 sugar uptake ABC transporter substrate-binding protein precursor
Query= uniprot:A0A166QFS3 (424 letters) >FitnessBrowser__Smeli:SM_b21461 Length = 420 Score = 389 bits (999), Expect = e-113 Identities = 182/406 (44%), Positives = 272/406 (66%), Gaps = 1/406 (0%) Query: 13 LTLCAGLPSLSSAADLTISCGAVGAELQLCKEAVQAWSKQTGNNVEVVSTPNSATERLSF 72 +T+ A + + AD T+S + +LC++AVQ W+ TG+ V++ P + + + Sbjct: 11 MTVFAVASAFPAKAD-TVSMFCSATDYELCEKAVQKWTNDTGHEVKLNRMPQNLDDAIPI 69 Query: 73 YQQILSAQSSDIDIIQIDMVWPGMLAKHLLDLREVLPANATQGYFQAQVDNATVNGRLVT 132 YQQ+ +AQSSD+D++ ID++W GM HLLDL ++P N +F + D A ++G+L++ Sbjct: 70 YQQLFAAQSSDMDVLYIDVIWLGMFKDHLLDLTSLVPENEVTAHFASAADAARLDGKLLS 129 Query: 133 MPWFTDSGLLYYRKDLLEKYNQQVPRTWEEMTATARNIQQAERTAGNPNAWGYIFQGRAY 192 MP++ D+GL++YRKDLLEKY +Q P+TW+E+TATA+ IQ AER AG+P+ WGY +QGR+Y Sbjct: 130 MPFYIDTGLMFYRKDLLEKYGKQPPKTWDELTATAKEIQDAERKAGSPDIWGYSWQGRSY 189 Query: 193 EGLTCNALEWISSQPEGGLVNSRGDIVVNSQASRTALTLAKSWVGDISPRGVLNYTEEEG 252 EGLTC+ALEWI+S G +++ G++ +N+ + ALT A+ W+G ISP GVLNY EE Sbjct: 190 EGLTCDALEWIASAGGGTILSGDGEVTINNPQTEAALTRARGWIGTISPEGVLNYDEENS 249 Query: 253 RGVFQSGNALFMRNWPYVWALVQGQDSAVKDKVGVAPLPRGGETGTHASTLGGWGLAVSR 312 R +F+SGNA+F RNWPYVW Q + + KVGV+ LP G E + LG L VS+ Sbjct: 250 RALFESGNAVFHRNWPYVWGTSQAEGGKLVGKVGVSALPVGAEGQKSSGALGTAYLGVSK 309 Query: 313 YSAHPKLAAELVSYLTSAQEQKHRALIGAYNPVIESLYQDPELLAAMPYYAQLHSILNDG 372 YS P+LAAEL+ Y+ A++QK RA+ G YNP +E+LY+D ++LA +P+ + + Sbjct: 310 YSKKPELAAELLRYMVGAEDQKMRAIEGGYNPTVEALYEDADVLAKIPFLGMAKAAFEES 369 Query: 373 VMRPASITADRYPRVSNAFFDRVHGVLAGELPVDQALAELESELTR 418 V RP++ T Y RVS F+ VH +++G+ V + LA+LE L R Sbjct: 370 VARPSAATGKNYNRVSRTFYRAVHDIISGKDDVAKELADLERRLER 415 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: 430 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: 424 Length of database: 420 Length adjustment: 32 Effective length of query: 392 Effective length of database: 388 Effective search space: 152096 Effective search space used: 152096 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: 50 (23.9 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