Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate WP_086511010.1 BZY95_RS16615 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >NCBI__GCF_002151265.1:WP_086511010.1 Length = 275 Score = 133 bits (335), Expect = 4e-36 Identities = 84/266 (31%), Positives = 129/266 (48%), Gaps = 6/266 (2%) Query: 15 VAVIILVA---VFPFYYAILTSLKSGTALFRIDYWPTDI-SLANYAGIFSHGTFVRNLGN 70 V V+ILVA + P + K+ L W D + NY IF G F R +GN Sbjct: 12 VIVLILVASLVIGPLLASFFGGFKTNAELRTNPLWLPDAWNPQNYVAIFLDGNFWRYMGN 71 Query: 71 SLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELIRFV 130 S ++++ V ++L++ AAY +++RF G ++ +L MFP A + LF +R + Sbjct: 72 SFFISSMTVLLTLVVGAAAAYVFSQIRFFGSRMIHSYLLLGLMFPFAAAILPLFIKVRDL 131 Query: 131 GIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMPLMW 190 G+ +T A+I F L + + F LP E+ EAA VDG S +PL Sbjct: 132 GLLDTYWAVILPQTAFGLSLAILLFKAFFDQLPKELFEAAYVDGCSYLRFFWSFTLPLST 191 Query: 191 PALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAASVIV 250 P L T G+ F+ +WN FL L + + T P+ + G ++ W I+A + Sbjct: 192 PILATVGVFVFVQSWNNFLLPLVVLNDRSIYTWPLGMMQFQG--EYLTQWNMILAFVTLT 249 Query: 251 TVPLVVLVLIFQRRIISGLTAGGVKG 276 P V+ L Q+ I++GLT G VKG Sbjct: 250 ITPAVIFFLAAQKYIVAGLTGGSVKG 275 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: 171 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: 276 Length of database: 275 Length adjustment: 25 Effective length of query: 251 Effective length of database: 250 Effective search space: 62750 Effective search space used: 62750 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: 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