Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_007664567.1 BN137_RS17300 putrescine ABC transporter ATP-binding subunit PotG
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000319285.1:WP_007664567.1 Length = 377 Score = 206 bits (524), Expect = 8e-58 Identities = 118/317 (37%), Positives = 188/317 (59%), Gaps = 21/317 (6%) Query: 6 VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65 ++N++K F A+D+V++ I GE F +LG SG GK+T +R++AG + P+TG++ D Sbjct: 22 IRNLTKSFDGQH--AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPTTGQIVLD 79 Query: 66 DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125 ++ VPP R I M+FQ++AL+P++T +NIAF L K+ K EI RVEE+ Sbjct: 80 GVDLSH-----VPPYQRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVEEML 134 Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185 ++ + P +LSGGQ+QRVALAR+L K P LLLLDEP LD ++RD + V + Sbjct: 135 GLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVD 194 Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245 + R+G T ++V+HD + +A R+ ++ +GK VQ+G+PE++Y++P + A IG +N Sbjct: 195 ILERVGATCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVN 254 Query: 246 ELEGKV---TNEGVVIGS--LRFPVSVSSDRAI-------IGIRPEDVKLSKDVIKDDSW 293 +G + +G++I + L P+ V D ++ + +RPE V L + D Sbjct: 255 VFDGLLRERREDGLIIDAPGLVHPLKVDPDASVVDGVPVHVALRPEKVMLCDEPPADG-- 312 Query: 294 ILVGKGKVKVIGYQGGL 310 G G+V I Y G L Sbjct: 313 FNFGVGEVVHIAYLGDL 329 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: 276 Number of extensions: 10 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: 377 Length adjustment: 30 Effective length of query: 323 Effective length of database: 347 Effective search space: 112081 Effective search space used: 112081 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 24 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