Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SMc01979 SMc01979 sugar transport system permease ABC transporter protein
Query= uniprot:C8WUQ9 (301 letters) >FitnessBrowser__Smeli:SMc01979 Length = 277 Score = 149 bits (376), Expect = 7e-41 Identities = 87/270 (32%), Positives = 156/270 (57%), Gaps = 12/270 (4%) Query: 39 RIVIWCVIVMVLLPMWFVVIASFNPSNSYIS--FSLFPSNASLANYKALFQGGQFWTWVR 96 R+ + I L P+++++ + P++ S L+PS ASL ++ + + F + R Sbjct: 13 RLAVLAYIAFALFPLFWLLKVAVTPNDLLYSEGIRLWPSRASLEHFDFVLRHSAFPVFFR 72 Query: 97 NSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLL-QMFPNILAIAAFYTALA 155 NSL+V A+ + + ++S +A S+ RF G KY L+TL+LL QMFP ++ +A + L+ Sbjct: 73 NSLIVSGSTAVIVTILASLSGYALSRFRFRG-KYWLVTLMLLTQMFPLVMLVAPIFKILS 131 Query: 156 KLNMIDMLGSYILVMLGTSAFNI----WLLKGYMDSVPKELDEAAVIDGATTWQRFIHVT 211 L + + L ++V +AFN+ +L++ + D +PK+L+EAA+IDGAT + F + Sbjct: 132 PLGLTNSLTGLVVVY---TAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQFVAFRQII 188 Query: 212 LPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYNLISGQFAKNWGEFAAA 271 LPL+ P + +SE +F+ ++ T VG+ + +S +F+ ++G+ AA Sbjct: 189 LPLTLPGIAATLGFVFTAAWSELLFSLMLISGNAQATFPVGLLSFVS-KFSVDFGQMMAA 247 Query: 272 ALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301 +L+ +P + F + QRYL +GL AG+VKG Sbjct: 248 GVLALIPACLFFLLIQRYLVQGLTAGAVKG 277 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: 209 Number of extensions: 9 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: 277 Length adjustment: 26 Effective length of query: 275 Effective length of database: 251 Effective search space: 69025 Effective search space used: 69025 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