Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 176 bits (447), Expect = 6e-49 Identities = 107/296 (36%), Positives = 171/296 (57%), Gaps = 15/296 (5%) Query: 4 LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFID 63 L L + Y V+ G+DL + +GE + +GPSGCGK+TLLR +AGL+ I+ G++ I+ Sbjct: 5 LNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQIN 64 Query: 64 GERVND----VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 G+ V+ VP +RGI M+FQ YAL+PH+TV +N+ FG +A+ + + R+ Sbjct: 65 GKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG--VAKLTPAQRKARLDDMLA 122 Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 +++L R P LSGGQ+QRV+I RA+ P++ L DEP SN+DA +R + EI + Sbjct: 123 LVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSI 182 Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPA 239 + + + ++VTH + EA AD + + + G I Q G LY P + +VA F+GS Sbjct: 183 L-KQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSG- 240 Query: 240 MNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADD 295 N +PA + G + +S+T + + + NG+ +RP+ L ++ ADD Sbjct: 241 -NYLPAEV-IDGHSVVTPIGELRSLT-PLSQSHAFNGQVF---LRPQQLALS-ADD 289 Lambda K H 0.320 0.137 0.387 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: 285 Number of extensions: 9 Number of successful extensions: 4 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: 362 Length of database: 349 Length adjustment: 29 Effective length of query: 333 Effective length of database: 320 Effective search space: 106560 Effective search space used: 106560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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