Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF3854 PGA1_78p00180 putative sn-glycerol-3-phosphate transport system permease protein UgpE
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Phaeo:GFF3854 Length = 309 Score = 117 bits (294), Expect = 3e-31 Identities = 66/217 (30%), Positives = 112/217 (51%), Gaps = 3/217 (1%) Query: 170 NSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLA 229 N +G++R F N++ + +P+ + I +A+ YALA F G +++ +P Q Sbjct: 94 NCDGLSRGFGNSIKILVPSVALSIAIASVNGYALANWRFKGSETFFTILIIGAFIPYQTM 153 Query: 230 LIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQ 289 L P++ + + + G L H+ FGMP+ L RNY LP ++ + A+VDGA + Sbjct: 154 LYPIVIILRELKLMGSLWGLVLVHSIFGMPILTLLFRNYFSSLPEELFKAARVDGAGFWG 213 Query: 290 IFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIV-ELLGTRGG 348 I+ ++++P+S P I Q WND L ++ T TV N IV + G + Sbjct: 214 IYLRVMVPMSIPIFVVAMILQVTGIWNDFLFGVIYTKPETYPMTVQLNNIVNSVQGVKEY 273 Query: 349 NWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 N + AT ++ VPL+++ + VRG+ AG+VK Sbjct: 274 NVNMAAT--LLTGLVPLVIYLVSGKLFVRGIAAGAVK 308 Lambda K H 0.323 0.138 0.419 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: 278 Number of extensions: 9 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: 385 Length of database: 309 Length adjustment: 29 Effective length of query: 356 Effective length of database: 280 Effective search space: 99680 Effective search space used: 99680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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