Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate GFF2693 PGA1_c27350 ABC transporter, permease protein
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__Phaeo:GFF2693 Length = 294 Score = 142 bits (357), Expect = 1e-38 Identities = 97/280 (34%), Positives = 141/280 (50%), Gaps = 32/280 (11%) Query: 19 ILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSHGTFVRNLG--------- 69 +++A FPF + S K F I W +L +HG+ V +G Sbjct: 25 LILAAFPFLWTFWGSFKVELDFFSIADWTN--ALTGTLTKATHGSSVTGVGYEGAWIQEE 82 Query: 70 ------NSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAG- 122 N+ LV VV SL + YAL+R +R LL+T L P I ++AG Sbjct: 83 FWKAGINTTLVCIFVVMTSLTIGTLGGYALSRSGYRYTFWLLITALIFRAMPPITLVAGY 142 Query: 123 ---LFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWV 179 FE + + T + L+ PFT+W+L +F + +P E++E+A VDG + + Sbjct: 143 LLPFFEWNLWGHLATTVIVLV----AINQPFTLWMLHSFFQSIPKELDESAKVDGCTQFQ 198 Query: 180 VITRVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIP 239 V +P+MWP ++TTGL +F+ A+N+F S + Q +P IA G +Q E Sbjct: 199 AFRHVIIPVMWPGVITTGLFSFLLAYNDFAVTSMLLSKDNQTMIP-KIASFMGTTQTE-- 255 Query: 240 WGNIM---AASVIVTVPLVVLVLIFQRRIISGLTAGGVKG 276 GN+M AA V T PL VLV+ FQR+I+SGLTAG VKG Sbjct: 256 -GNVMFAVAAVVSATAPLFVLVMFFQRQIVSGLTAGAVKG 294 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: 203 Number of extensions: 14 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: 294 Length adjustment: 26 Effective length of query: 250 Effective length of database: 268 Effective search space: 67000 Effective search space used: 67000 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 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