Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate PP_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Putida:PP_3817 Length = 382 Score = 211 bits (537), Expect = 3e-59 Identities = 123/317 (38%), Positives = 176/317 (55%), Gaps = 20/317 (6%) Query: 6 LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 L+ + K YG + +DL+I++GEF+ F+G SG GKST L M+AG E + G++ +DG+ Sbjct: 17 LRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEILVDGQ 76 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125 + +VPP KR I MVFQ Y+L+PH+ V DN+AF + I + E +RV ++QL Sbjct: 77 SLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLVQLEQ 136 Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185 + R P +SGGQ+QRVAI RA+ P++ L DEPL LD LR + E+ +L R+ Sbjct: 137 FAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHRRLG- 195 Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245 T++YVTHDQ EAM L+ RI + S G I +G +LY+ P N FVA F+G+ I A Sbjct: 196 ITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAFVASFLGNSNFLRIKA 255 Query: 246 TITAT----GQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE-- 299 + GQ A+ L G + + D A VRPE A+ + E Sbjct: 256 SSNGAGSFEGQPVAIRLTPGLAASQD-----------ALIMVRPEKAVAMSAEQAMREPL 304 Query: 300 --GTVSIVEALGEVTLL 314 G + +GEV L Sbjct: 305 PAGWNEVTAKVGEVLFL 321 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: 307 Number of extensions: 10 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: 362 Length of database: 382 Length adjustment: 30 Effective length of query: 332 Effective length of database: 352 Effective search space: 116864 Effective search space used: 116864 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