Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b20327 SM_b20327 trehalosemaltose transporter permease
Query= uniprot:C8WUQ9 (301 letters) >FitnessBrowser__Smeli:SM_b20327 Length = 276 Score = 149 bits (376), Expect = 7e-41 Identities = 80/259 (30%), Positives = 137/259 (52%), Gaps = 2/259 (0%) Query: 45 VIVMVLLPMWFVVIASFNPSNSYISFSLFPSNASLANYKALFQGGQFWTWVRNSLVVGVV 104 +I++ + P ++ ++ S + +P++ SLANY +F G F + NSL+V + Sbjct: 18 IILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSHGTFVRNLGNSLLVATL 77 Query: 105 VAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLLQMFPNILAIAAFYTALAKLNMIDM-L 163 V + +A+A +++RF GR L+T+L + MFP I +A + + + + + L Sbjct: 78 VVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELIRFVGIFNTPL 137 Query: 164 GSYILVMLGTSAFNIWLLKGYMDSVPKELDEAAVIDGATTWQRFIHVTLPLSTPMMVVIF 223 M+ T F +W+L +M +P E++EAA++DGA+ W V +PL P +V Sbjct: 138 ALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMPLMWPALVTTG 197 Query: 224 FLTLVGIFSEYMFAGTILQSPWNYTLGVGMYNLISG-QFAKNWGEFAAAALLSAVPLAIV 282 L + ++E++FA T S T+ V + L G QF WG AA+++ VPL ++ Sbjct: 198 LLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAASVIVTVPLVVL 257 Query: 283 FAVAQRYLTKGLVAGSVKG 301 + QR + GL AG VKG Sbjct: 258 VLIFQRRIISGLTAGGVKG 276 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: 238 Number of extensions: 15 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: 276 Length adjustment: 26 Effective length of query: 275 Effective length of database: 250 Effective search space: 68750 Effective search space used: 68750 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