Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 232 bits (592), Expect = 1e-65 Identities = 131/316 (41%), Positives = 196/316 (62%), Gaps = 9/316 (2%) Query: 7 KDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 + ++KSY G ++ ++LDI++GEF+ +GPSG GK+T L M+AG E T G++ + G Sbjct: 18 RGVQKSYDGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGR 77 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125 +N+VPP KR I MVFQ+YAL+PHMTV +N+AF + + SK +I RV+ +M+QL Sbjct: 78 SINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQLDA 137 Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185 + R P LSGGQ+QRVA+ RA+ P++ L DEPL LD LR ++EI + +R+ Sbjct: 138 FAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLG- 196 Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245 T++YVTHDQ EA+T++DR+ V G I+Q+ P LYE P N FVA FIG N I Sbjct: 197 VTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGE--NNRISG 254 Query: 246 TITAT-GQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRV---TEADDFLFEGT 301 T+ A+ G++ V L G+ V + N + G+ + +RPE +R+ +E+ F G Sbjct: 255 TLLASDGKRCQVQLPRGERVEA-LAVNVGQAGEPVTLSIRPERVRLNGHSESCVNRFSGR 313 Query: 302 VSIVEALGEVTLLYIE 317 V+ LG+ + +E Sbjct: 314 VAEFIYLGDHVRVRLE 329 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: 355 Number of extensions: 14 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: 374 Length adjustment: 30 Effective length of query: 332 Effective length of database: 344 Effective search space: 114208 Effective search space used: 114208 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