Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate GFF3854 PGA1_78p00180 putative sn-glycerol-3-phosphate transport system permease protein UgpE
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Phaeo:GFF3854 Length = 309 Score = 122 bits (305), Expect = 2e-32 Identities = 68/224 (30%), Positives = 119/224 (53%), Gaps = 9/224 (4%) Query: 158 LSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQM 217 ++ G+ R F NS+ + VPS + I IA+ YALA F G +++ +P Q Sbjct: 93 INCDGLSRGFGNSIKILVPSVALSIAIASVNGYALANWRFKGSETFFTILIIGAFIPYQT 152 Query: 218 SLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVD 277 L P++ + + + G+ L H+ FG+P+ L RNY + LP E+ ++ARVD Sbjct: 153 MLYPIVIILRELKLMGSL-----WGLVLVHSIFGMPILTLLFRNYFSSLPEELFKAARVD 207 Query: 278 GASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLG 337 GA + I++++++P+S P I Q WND L +++ + +T +L N++ Sbjct: 208 GAGFWGIYLRVMVPMSIPIFVVAMILQVTGIWNDFLFGVIY--TKPETYPMTVQLNNIVN 265 Query: 338 SRGG--NWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 S G + + A+ +T +VPL+++ + VRG+ AG+VKG Sbjct: 266 SVQGVKEYNVNMAATLLTGLVPLVIYLVSGKLFVRGIAAGAVKG 309 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: 275 Number of extensions: 11 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: 380 Length of database: 309 Length adjustment: 29 Effective length of query: 351 Effective length of database: 280 Effective search space: 98280 Effective search space used: 98280 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: 49 (23.5 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