Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate BWI76_RS09465 BWI76_RS09465 polyamine ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Koxy:BWI76_RS09465 Length = 392 Score = 213 bits (542), Expect = 7e-60 Identities = 122/317 (38%), Positives = 189/317 (59%), Gaps = 21/317 (6%) Query: 6 VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65 ++N++K F A+D+VN+ I GE F +LG SG GK+T +R++AG + P+ G++ D Sbjct: 37 IRNLTKSFDGQH--AVDDVNLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPTAGQIVLD 94 Query: 66 DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125 +A VPP R I M+FQ++AL+P++T +NIAF L K+ K EI RV+E+ Sbjct: 95 GVDLAR-----VPPYQRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEITSRVQEML 149 Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185 ++ + P +LSGGQ+QRVALAR+L K P LLLLDEP LD ++RD + V + Sbjct: 150 ALVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVD 209 Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245 + R+GVT ++V+HD + +A R+ ++ +GK VQ+G+PE++Y++P + A IG +N Sbjct: 210 ILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVN 269 Query: 246 ELEGKV---TNEGVVIGS--LRFPVSVSSDRAI-------IGIRPEDVKLSKDVIKDDSW 293 EG V +G+V+ S L P+ V D ++ + +RPE + L +D D Sbjct: 270 VFEGLVKERQEDGLVLDSPGLTHPLKVDPDASVVDNVPVWVALRPEKIMLCEDPPADGYN 329 Query: 294 ILVGKGKVKVIGYQGGL 310 V G+V I Y G L Sbjct: 330 FAV--GEVIYIAYLGDL 344 Lambda K H 0.319 0.139 0.390 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: 316 Number of extensions: 15 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: 353 Length of database: 392 Length adjustment: 30 Effective length of query: 323 Effective length of database: 362 Effective search space: 116926 Effective search space used: 116926 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 (21.7 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