Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate 200281 SO1100 extracellular solute-binding protein, family 7 (NCBI ptt file)
Query= uniprot:Q48AL6 (362 letters) >FitnessBrowser__MR1:200281 Length = 370 Score = 292 bits (748), Expect = 9e-84 Identities = 137/321 (42%), Positives = 210/321 (65%), Gaps = 3/321 (0%) Query: 36 WKLAETWGPNFPIFGDATKNMAKMVKEMSNGRLTIRIDSSNKHKSALGIFDFVKSGQYQM 95 W+LA +W NFP G A + A +V +MS+G+L I + + + A +FD V G+ QM Sbjct: 46 WRLATSWPKNFPGLGMAPERFATLVNDMSHGQLRITVHGAGELMPAFAVFDGVSQGKIQM 105 Query: 96 GHSASYYWKGKNFNTMFFTTVPFGMIASEQHAWFYYGGGMELMKKVYDQYGIMSFPGGNT 155 H+ASYYWKGK + FF+++PFGM A E + W +YGG M L ++VY +GI+ GGNT Sbjct: 106 AHAASYYWKGKTPASQFFSSIPFGMTAQEMNGWLHYGG-MALWEEVYRPFGIIPLAGGNT 164 Query: 156 GNQMGGWFKKEINSVEDLKGLKMRIPGFAGEVLAKLGAKPTNIPSGELYTALERNTIDAL 215 G QMGGWF K IN++ D KGLK+R+PG GEVL ++GA P N+ EL++AL+ ++DA Sbjct: 165 GMQMGGWFNKPINTIADFKGLKIRMPGLGGEVLKRVGAVPVNMAGRELFSALQTGSLDAA 224 Query: 216 EWVGPSLDLRMGFHKIAP-YYYTGWHEPGTELQFMVNQKAYNSLPKDLQKILTVAMKAAA 274 EWVGP DL G HK+A YYY GWHEPG+ ++F++N+ A+ SLP+DLQ ++ A +A Sbjct: 225 EWVGPVNDLAFGLHKVAKYYYYPGWHEPGSNMEFLINKAAFESLPEDLQTVVKTAARAIN 284 Query: 275 YDMYSQSMHASGVNLASLKKDYPNVQMRSFPKPVMEAIVQANDELLEEFAAKDPMTAEIL 334 DM + ++ L +L K+ V++R+FP V+ + + + +++ E A +DPM ++ Sbjct: 285 QDMLDEYTTSNVTALETLVKE-EGVELRAFPPAVLTELERISHQVIGEQAEQDPMMGKVY 343 Query: 335 KSLNDYKHQIRAWTNLSDRAY 355 ++ + Y+ +R + +S+ AY Sbjct: 344 RAYHAYEQGVREYHKISEDAY 364 Lambda K H 0.318 0.133 0.402 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: 417 Number of extensions: 14 Number of successful extensions: 5 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: 362 Length of database: 370 Length adjustment: 30 Effective length of query: 332 Effective length of database: 340 Effective search space: 112880 Effective search space used: 112880 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 (21.7 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