Align ABC transporter permease (characterized, see rationale)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= uniprot:A0A166R405 (325 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 545 bits (1405), Expect = e-160 Identities = 281/316 (88%), Positives = 302/316 (95%) Query: 9 KRSGNFYGLGTYLGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVL 68 +RSG ++GLGTYLGLAGALLAM+ LFS LSSHF SY TFSTLANQIPDLMVLAVGMTFVL Sbjct: 15 RRSGTYFGLGTYLGLAGALLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVL 74 Query: 69 IIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPS 128 IIGGIDLSVGSVLALAAS VSVAILGWGW VLP+ALLGMAVAALAG+ITG +TVAWRIPS Sbjct: 75 IIGGIDLSVGSVLALAASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPS 134 Query: 129 FIVSLGVLEMARGLAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLT 188 FIVSLGVLEMARGLAYQ T SRTAYIGDA+AW SNP+AFG+SP+FIIALL+I +AQ VLT Sbjct: 135 FIVSLGVLEMARGLAYQFTDSRTAYIGDAYAWFSNPVAFGVSPAFIIALLVIVLAQLVLT 194 Query: 189 RTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGS 248 RTVFGRYLIGIGTNEEAVRLAGI+P+PYK+LVF+LMGLLAG+AALFQISRLEAADPNAGS Sbjct: 195 RTVFGRYLIGIGTNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGS 254 Query: 249 GLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIV 308 GLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGA+EPTKRIITGAVIV Sbjct: 255 GLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIV 314 Query: 309 VAVVLDTYRSQRASRR 324 +AVVLDTYRS+RA RR Sbjct: 315 IAVVLDTYRSRRAGRR 330 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: 424 Number of extensions: 6 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: 331 Length adjustment: 28 Effective length of query: 297 Effective length of database: 303 Effective search space: 89991 Effective search space used: 89991 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 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