Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_069333385.1 C8J29_RS07090 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_003046325.1:WP_069333385.1 Length = 332 Score = 213 bits (543), Expect = 4e-60 Identities = 130/354 (36%), Positives = 204/354 (57%), Gaps = 33/354 (9%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M +I ++NV K F G+ V + +++++IE+GE +GPSG GK+T +R+IAGL+ S G Sbjct: 1 MGKITLRNVQKRF--GEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 ++ D R +PP R + MVFQ++ALYP++T +NIAFPL KM +EI +R Sbjct: 59 QIMIDGRDATE-----MPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V AKIL++ + L+ P +LSGGQ+QRVA+ RA+V++P+ L DEP SNLDA +R + R Sbjct: 114 VSNAAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 + E+ L T++ V+HD + +AD++ VL G++ QVG P LY NP ++ VA Sbjct: 174 LEITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGF 233 Query: 241 IG--EINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGK 298 IG ++N +EG P + IGIRPE + LS++ +W + Sbjct: 234 IGSPKMNLIEG--------------PEAAKHGATTIGIRPEHIDLSRET---GAW----Q 272 Query: 299 GKVKVIGYQGG--LFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRKDKIKVF 350 G+V V + G + + + + + T + +H G+ V + + DKI F Sbjct: 273 GEVGVSEHLGSDTFLHVHVAGMPT-LTVRTGGEFGVHHGDRVWLTPQADKIHRF 325 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: 10 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: 332 Length adjustment: 29 Effective length of query: 324 Effective length of database: 303 Effective search space: 98172 Effective search space used: 98172 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