Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 224 bits (571), Expect = 3e-63 Identities = 133/297 (44%), Positives = 176/297 (59%), Gaps = 7/297 (2%) Query: 22 IDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGER-VNDVPPSKRGIAMV 80 +DLDI GE VV +GPSGCGK+T LR+IAGLE G + + G+ V +P +RG+ MV Sbjct: 26 LDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGDNDVTPLPIEQRGVGMV 85 Query: 81 FQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKALSGGQRQ 140 FQSYAL+P+MTV +N+A+G+R+ R RRV M+ L P+ +R LSGGQRQ Sbjct: 86 FQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRIDQLSGGQRQ 145 Query: 141 RVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTHDQVEAMT 200 RVA+ RAI P+V L DEPL+ LDA LR A R +I +L R T +YVTHDQ EAM Sbjct: 146 RVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLL-RSLHITAVYVTHDQAEAMA 204 Query: 201 LADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQTAVSLAG 260 L DRI+V+ G I Q G P ++Y PAN FVA FIG+ MN +PA + A + L Sbjct: 205 LGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNRLPAVLEADAWRVPGGLVP 262 Query: 261 GKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIVEALGEVTLLYIE 317 + A+ A RPED+ + +A+D G+V LG T L ++ Sbjct: 263 RHGTAASL---AAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTALFLGNYTRLLVD 316 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: 339 Number of extensions: 20 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: 357 Length adjustment: 29 Effective length of query: 333 Effective length of database: 328 Effective search space: 109224 Effective search space used: 109224 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