Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate WP_011648818.1 RL_RS33030 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >NCBI__GCF_000009265.1:WP_011648818.1 Length = 281 Score = 202 bits (515), Expect = 5e-57 Identities = 109/266 (40%), Positives = 163/266 (61%), Gaps = 4/266 (1%) Query: 12 YALVAVIILVAVFPFYYAILTSLKSGTALFRID--YWPTDISLANYAGIFSHGTFVRNLG 69 Y +A+ ++ + FP + +SLKS T +F + P D ++A Y IF+ VR Sbjct: 17 YLGLAIGLVFSAFPIVWMFFSSLKSNTEIFALPPRLLPDDFTVAAYLTIFNDPVKVRFFI 76 Query: 70 NSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELIRF 129 NS VA +V A++L++A+ AY +R +FR + L + I+S P I +L F ++ Sbjct: 77 NSYFVAGVVTALTLVVAIVTAYGFSRYQFRFKNTLNIFIISTQTVPPITLLIPYFGMVVA 136 Query: 130 VGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFMPLM 189 IF+T LALI +Y++FTLP+ V ++T ++ LP E++EA +VDG S W + RV +P+ Sbjct: 137 FRIFDTYLALILTYLVFTLPYAVLLMTGYLNTLPKELDEAVLVDGGSSWTALWRVIVPVS 196 Query: 190 WPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAASVI 249 P +V T + F+ AWNEFLFALT T S RTVP+ I LL G FE W +MA SV+ Sbjct: 197 IPGIVATAVYTFLLAWNEFLFALTLTKSMDLRTVPIGIQLLMGQHAFE--WNEMMAMSVL 254 Query: 250 VTVPLVVLVLIFQRRIISGLTAGGVK 275 ++PL+VL L+ QR ++G+TAG VK Sbjct: 255 GSLPLLVLYLVAQRYFLAGMTAGSVK 280 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: 190 Number of extensions: 7 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: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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