Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >NCBI__GCF_003217355.1:WP_110804034.1 Length = 382 Score = 122 bits (305), Expect = 2e-32 Identities = 84/245 (34%), Positives = 131/245 (53%), Gaps = 11/245 (4%) Query: 37 GTALFRIDYWPTDISLANYAGIFSHGTFVRNLGNSLLVATLVVAISLLLAVTAAYALARV 96 G +F P ++ NYA + + R N++ V I +L+A AAYALA + Sbjct: 143 GMRIFVTTVAPPRLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWM 202 Query: 97 RFRGRGLLLLTILSVSMFPQIAVLAGLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLT 156 RF GR LL+ TI+ + + P L L +L +G+ + L + ++ F LP +++L Sbjct: 203 RFPGRALLVATIVGLLVVPLQLALIPLLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLR 262 Query: 157 TFMRDLPIEIEEAAIVDGASPWVVITRVFMPLMWPALVTTGLLAFIAAWNEFLFALTF-- 214 +M LP EI E+A VDGA+ + + R+ +PL +PAL + + F+ WN+ L A F Sbjct: 263 NYMVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLG 322 Query: 215 TSSNTQRTVPVAIALL-SGGSQFEIPWGNIMAAS--VIVTVPLVVLVLIFQRRIISGLTA 271 +++TQ ALL S G +E I+AAS V + VPL+V + Q+ ++ GL A Sbjct: 323 NATDTQVMTGALRALLGSRGGDWE-----ILAASAFVSIAVPLIVFFAL-QKYLVRGLLA 376 Query: 272 GGVKG 276 G VKG Sbjct: 377 GSVKG 381 Lambda K H 0.332 0.143 0.426 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: 246 Number of extensions: 16 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: 276 Length of database: 382 Length adjustment: 28 Effective length of query: 248 Effective length of database: 354 Effective search space: 87792 Effective search space used: 87792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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