Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate 209025 DVU0096 polyamine ABC transporter, permease protein
Query= reanno::Smeli:SMc03063 (380 letters) >MicrobesOnline__882:209025 Length = 257 Score = 81.3 bits (199), Expect = 3e-20 Identities = 64/211 (30%), Positives = 105/211 (49%), Gaps = 5/211 (2%) Query: 149 FTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVV 208 FTLD YA++L+ + + LNSL+VA S + L+ + AA L FPGR VL + + Sbjct: 42 FTLDWYAKLLANTPLVDAALNSLSVATLSATLATLLGSLAAMCLHRYRFPGRKVLHSSIY 101 Query: 209 GLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPR 268 L V P + I LL + + G ++ + +AHT GLP + +A Sbjct: 102 VLTVSPDIVMGISLLIFFIALRMELG-----FVTLLIAHTTLGLPFVTVTVLARLAEFDE 156 Query: 269 EIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVL 328 ++E+AR GAS+ + IILPL+ PA+A+ + F + +D+L++ G + L L Sbjct: 157 HLVEAARDLGASEAAAYRHIILPLTLPAVAAGWLLSFTLSMDDVLISFFVTGPSFEVLPL 216 Query: 329 TGRLVNLLGSRGGNWEILTASAFITIVVPLI 359 + LG + + +TIV+ L+ Sbjct: 217 KIYSMVRLGVKPDINALSAVMFGVTIVLVLL 247 Lambda K H 0.324 0.139 0.418 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: 175 Number of extensions: 12 Number of successful extensions: 2 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: 380 Length of database: 257 Length adjustment: 27 Effective length of query: 353 Effective length of database: 230 Effective search space: 81190 Effective search space used: 81190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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