Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= uniprot:C8WUQ9 (301 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 119 bits (298), Expect = 8e-32 Identities = 75/270 (27%), Positives = 133/270 (49%), Gaps = 6/270 (2%) Query: 36 WVSRIVIWCVIVMVLL-PMWFVVIASFNPSNSYISFSLFP---SNASLANYKALFQGGQF 91 WV+ + + V VLL P +++ I +F P + S P + A++K L + Sbjct: 26 WVTIYIPLGIFVFVLLFPFYWMAITAFKPDGELLMRSANPFWVMAPTFAHFKKLLFDTPY 85 Query: 92 WTWVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLLQMFPNILAIAAFY 151 W+ N+++V + A + ++A+A +LRF G K + + L + P + Sbjct: 86 PEWLLNTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPPSILFIPLA 145 Query: 152 TALAKLNMIDMLGSYILVM-LGTSAFNIWLLKGYMDSVPKELDEAAVIDGATTWQRFIHV 210 + + +L + D + IL F WLL GY S+P EL+E A+IDGAT W+ + + Sbjct: 146 SIVFQLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKI 205 Query: 211 TLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYNLISGQFAKNWGEFAA 270 LPL+ P ++ ++E+++A T + S T+ VG+ + +WG A Sbjct: 206 ILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEGDVYHWGALMA 265 Query: 271 AALLSAVPLAIVFAVAQRYLTKGLVAGSVK 300 ALL ++P+A+V++ Y G+ G+VK Sbjct: 266 GALLGSLPVALVYSFFVEYYVSGM-TGAVK 294 Lambda K H 0.328 0.136 0.417 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: 207 Number of extensions: 11 Number of successful extensions: 3 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: 301 Length of database: 295 Length adjustment: 26 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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