Align ABC transporter permease (characterized, see rationale)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0A166R405 (325 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910 Length = 325 Score = 601 bits (1549), Expect = e-177 Identities = 316/325 (97%), Positives = 321/325 (98%) Query: 1 MNTASLAGKRSGNFYGLGTYLGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVL 60 MNTAS AGKRSGNFYGLGTYLGLAGALLAM+ LFSVLSSHFLSYDTFSTLANQIPDLMVL Sbjct: 1 MNTASYAGKRSGNFYGLGTYLGLAGALLAMIVLFSVLSSHFLSYDTFSTLANQIPDLMVL 60 Query: 61 AVGMTFVLIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSI 120 AVGMTFVLIIGGIDLSVGSVLALAAS VSVAILGWGW VLPAALLGMAVAALAGTITGSI Sbjct: 61 AVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSI 120 Query: 121 TVAWRIPSFIVSLGVLEMARGLAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLII 180 TVAWRIPSFIVSLGVLEMARG+AYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLII Sbjct: 121 TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLII 180 Query: 181 FIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLE 240 F+AQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYK+LVFSLMGLLAG+AALFQISRLE Sbjct: 181 FVAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKVLVFSLMGLLAGVAALFQISRLE 240 Query: 241 AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR 300 AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR Sbjct: 241 AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR 300 Query: 301 IITGAVIVVAVVLDTYRSQRASRRT 325 IITGAVIVVAVVLDTYRSQRASRRT Sbjct: 301 IITGAVIVVAVVLDTYRSQRASRRT 325 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: 443 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: 325 Length adjustment: 28 Effective length of query: 297 Effective length of database: 297 Effective search space: 88209 Effective search space used: 88209 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: 48 (23.1 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