Align ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS11210 BPHYT_RS11210 ABC transporter permease
Query= uniprot:A0A166R405 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS11210 Length = 351 Score = 496 bits (1277), Expect = e-145 Identities = 253/314 (80%), Positives = 285/314 (90%) Query: 7 AGKRSGNFYGLGTYLGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTF 66 +GK +G G YLGLAGALL M+ LFS+LSSHFL+YDTFST+ANQIPDL+V++VGMTF Sbjct: 35 SGKPAGTRLGFSNYLGLAGALLGMIVLFSLLSSHFLTYDTFSTIANQIPDLVVMSVGMTF 94 Query: 67 VLIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRI 126 VLII GIDLSVGSVLAL AS VSVA L WGW LP+A+LG+A AAL GTITG++TV WRI Sbjct: 95 VLIIAGIDLSVGSVLALGASVVSVAALKWGWGPLPSAVLGVAAAALTGTITGAVTVGWRI 154 Query: 127 PSFIVSLGVLEMARGLAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAV 186 PSFIVSLGVLE ARG+AYQMT SRTAYIGDAF +LSNPIA GISP+F+IA+ ++ IAQ V Sbjct: 155 PSFIVSLGVLEAARGMAYQMTNSRTAYIGDAFDFLSNPIALGISPAFLIAVAVMVIAQLV 214 Query: 187 LTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNA 246 LTRTVFGRYL+GIGTNEEAVRLAG+NP+PYK++VF+LMG L+G+AALFQISRLEAADPNA Sbjct: 215 LTRTVFGRYLVGIGTNEEAVRLAGVNPRPYKVIVFALMGALSGLAALFQISRLEAADPNA 274 Query: 247 GSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAV 306 G G+ELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGA EPTKR+ITGAV Sbjct: 275 GQGVELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGANEPTKRMITGAV 334 Query: 307 IVVAVVLDTYRSQR 320 IVVAVVLDTYRS+R Sbjct: 335 IVVAVVLDTYRSRR 348 Lambda K H 0.325 0.139 0.393 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: 411 Number of extensions: 7 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: 325 Length of database: 351 Length adjustment: 28 Effective length of query: 297 Effective length of database: 323 Effective search space: 95931 Effective search space used: 95931 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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