Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 225 bits (574), Expect = 1e-63 Identities = 134/313 (42%), Positives = 189/313 (60%), Gaps = 15/313 (4%) Query: 3 GLLLKDIRKSYG----AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58 G++ ++I K YG A + GI ++ G +GPSGCGK+T LRMIAGLE T G Sbjct: 7 GIVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSG 66 Query: 59 DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118 ++FI G+ V + P++R ++M+FQSYAL+PHM V +N+ +G+R++ + KE+ + A Sbjct: 67 EIFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEAL 126 Query: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178 + L + DRLP LSGGQ+QRVA+ RA+ P+V LFDEPLSNLDA LR R EI Sbjct: 127 RGVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRA 186 Query: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSP 238 L +R+S T+ YVTHDQ EAM ++D+I+V++ G I Q G+P LYE P + FVA F+G Sbjct: 187 LQQRLS-LTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEA 245 Query: 239 AMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLF 298 + PA A G ++A G V P A ++G VRPE R+T + L Sbjct: 246 ML--FPAVADADG-----TVALGPLVLR--PRVAVKSG-PVKVAVRPEAWRITRQGEGLL 295 Query: 299 EGTVSIVEALGEV 311 ++ LG V Sbjct: 296 PARLAKSAYLGAV 308 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: 318 Number of extensions: 13 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: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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