Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_012676168.1 PERMA_RS09515 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000021565.1:WP_012676168.1 Length = 287 Score = 160 bits (405), Expect = 4e-44 Identities = 83/226 (36%), Positives = 140/226 (61%), Gaps = 7/226 (3%) Query: 24 VNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLI-VPPEDR 82 ++++I+ GE + G SG+GKTT +R+I+GL+ P G++ D ++ + K I +PP+ R Sbjct: 21 LDLHIKKGEFVTLFGRSGSGKTTVLRMISGLEKPDRGKIEIDGKVYFDSEKGIDLPPQKR 80 Query: 83 KIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPRELS 142 IG VFQ +AL+PN+T ENI F + R++ E+ K + + + + +P LS Sbjct: 81 NIGFVFQNYALFPNMTVLENILFAMDRPD------REKAIELLKTVHLEDLKDRYPDTLS 134 Query: 143 GGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHDPA 202 GGQQQRVA+ARAL ++PS+LLLDEP S LD +R+ + +K + +T ++VSHD Sbjct: 135 GGQQQRVAVARALAREPSILLLDEPLSALDFSIREKLQEEIKRIHRVFNLTTILVSHDKT 194 Query: 203 DIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELE 248 ++F ++DRV + KG++++ G P ++ S IG + +++ Sbjct: 195 EVFKLSDRVVWIEKGRIIKEGSPRKVFIEKNISGKFSFIGNVLQIK 240 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: 271 Number of extensions: 12 Number of successful extensions: 3 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: 287 Length adjustment: 27 Effective length of query: 326 Effective length of database: 260 Effective search space: 84760 Effective search space used: 84760 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: 48 (23.1 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