Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_002964709.1 BIBO1_RS11500 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000182725.1:WP_002964709.1 Length = 381 Score = 207 bits (528), Expect = 3e-58 Identities = 121/350 (34%), Positives = 203/350 (58%), Gaps = 21/350 (6%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I +NV+K+F G A+DN+++N+ N E F +LG SG GKTT MR++AG + P++G + Sbjct: 23 ISFENVTKIF--GDFTAVDNLSLNVFNREFFALLGASGCGKTTLMRMLAGFEEPTSGRIT 80 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123 D + + +PP R + M+FQ++AL+P++T +NIAF L M+K EI RV E Sbjct: 81 LDGQDMRG-----IPPYKRPVNMMFQSYALFPHMTVEKNIAFGLKQDGMAKSEIDARVAE 135 Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183 + K++ + P +LSGGQ+QRVALAR++ K P +LLLDEP LD ++R+ + + Sbjct: 136 MLKLVKLEQYGKRKPHQLSGGQRQRVALARSVAKRPKVLLLDEPLGALDKKLREETQFEL 195 Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243 ++Q +LG+T +VV+HD + +ADR+ V+ KG+++QV P ++Y+ P S VA IG Sbjct: 196 MDLQVKLGMTFMVVTHDQEEAMTMADRIAVMDKGRIMQVATPAEVYEAPRSKFVADFIGN 255 Query: 244 INELEG---KVTNEGVVIGSLRFPVSVSSD---------RAIIGIRPEDVKLSKDVIKDD 291 +N +EG K N I + +F + ++ + +RPE ++S++ D+ Sbjct: 256 VNIIEGEVVKAANGEAEIATEKFGFHIHTETREQLNPGQKVWYAVRPEKTRISREK-PDE 314 Query: 292 SWILVGKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEVLVY 341 + + +G++ I Y G + + LD+ + S + + E L Y Sbjct: 315 AAVNAVEGELWDIAYFGDM-TVFHVRLDNGRTVKAASLNAVRKTENPLTY 363 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: 275 Number of extensions: 14 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: 381 Length adjustment: 30 Effective length of query: 323 Effective length of database: 351 Effective search space: 113373 Effective search space used: 113373 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