Align Trehalose transport system permease protein SugB (characterized)
to candidate WP_004119214.1 RHSP_RS16125 carbohydrate ABC transporter permease
Query= SwissProt::P9WG01 (274 letters) >NCBI__GCF_000359745.1:WP_004119214.1 Length = 295 Score = 171 bits (434), Expect = 1e-47 Identities = 98/268 (36%), Positives = 150/268 (55%), Gaps = 5/268 (1%) Query: 9 WAVLDTLVVGYALLPVLWIFSLSLKPTSTVKD--GKLIPSTVTFDNYRGIFRGDLFSSAL 66 W L LV L P ++I SLK + V + P F+NY + F+SA Sbjct: 31 WIAL-LLVAAIWLAPFVFIVFTSLKTQADVTSTGAFMPPFDPAFENYSNAWGRGNFASAF 89 Query: 67 INSIGIGLITTVIAVVLGAMAAYAVARLEFPGKRLLIGAALLITMFPSISLVTPLFNIER 126 +NS I +I + ++L AMAAYA+A++ ++++ A + TM P ++ PLF + Sbjct: 90 LNSAIITVIKVPLGLILSAMAAYALAKIRMRFSKIMLLAIVFGTMIPFQVMLAPLFTLVN 149 Query: 127 AIGLFDTWPGLILPYITFALPLAIYTLSAFFREIPWDLEKAAKMDGATPGQAFRKVIVPL 186 ++GL DT+PG+ILPYI F +P ++ L FF+ IP +L +AA +DGA+ FR++ +P+ Sbjct: 150 SLGLIDTYPGVILPYIAFGVPYQVFILHGFFKGIPKELSEAALIDGASHFTIFRRIFLPV 209 Query: 187 AAPGLVTAAILVFIFAWNDLLLALSLTATKAAITAPVAIANFTGSSQFEEPTGSIAAGAI 246 P L IL F+ WN+ +AL L + T P+ + +F G QF G + A + Sbjct: 210 CLPVLAALLILDFVSTWNEFAMALVLLQDQHMWTLPLGLMSFQG--QFSNDYGQLNAAIV 267 Query: 247 VITIPIIVFVLIFQRRIVAGLTSGAVKG 274 + +P + LIFQR V+GLTSGAVKG Sbjct: 268 MTVLPATIVYLIFQRYFVSGLTSGAVKG 295 Lambda K H 0.327 0.141 0.418 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: 269 Number of extensions: 11 Number of successful extensions: 2 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: 274 Length of database: 295 Length adjustment: 26 Effective length of query: 248 Effective length of database: 269 Effective search space: 66712 Effective search space used: 66712 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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