Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 221 bits (563), Expect = 2e-62 Identities = 127/289 (43%), Positives = 182/289 (62%), Gaps = 8/289 (2%) Query: 4 LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFID 63 L +K I K++ + IDL +++GE + F+GPSGCGK+TLLR+IAGLE T G + Sbjct: 20 LEIKGIHKNFENFSALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIVQS 79 Query: 64 GERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQL 123 G ++ +P S+R +VFQSYAL+P++T+ +N+A+G+ + K EI RV M L Sbjct: 80 GRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMAGL 139 Query: 124 TPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERM 183 + P LSGGQ+QRVA+ RA+ NP + L DEPLS LDA +RV R EI +L +++ Sbjct: 140 PTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQKQV 199 Query: 184 SDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVI 243 TT I VTHDQ EA++++DRIVV++ G IEQVG P+E+YERPA+ FVA F+G +NV+ Sbjct: 200 GITT-IMVTHDQEEALSMSDRIVVMNHGVIEQVGTPMEIYERPASPFVANFVGK--VNVL 256 Query: 244 PATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTE 292 G++ V G + + + G+ S +RPED RV E Sbjct: 257 RGQALG-GKRFRV---GKMEIECEASEGSFRLGEDVSLYLRPED-RVAE 300 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: 343 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: 377 Length adjustment: 30 Effective length of query: 332 Effective length of database: 347 Effective search space: 115204 Effective search space used: 115204 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 Apr 09 2024. 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