Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 194 bits (494), Expect = 2e-54 Identities = 105/272 (38%), Positives = 170/272 (62%), Gaps = 10/272 (3%) Query: 18 VVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIV 77 VV + N+++ ++ GE +LGPSG GK+T +R+IAGLD P++G ++ DR + + + Sbjct: 19 VVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWLGDREITT-----L 73 Query: 78 PPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHF 137 PP DR + MVFQ++ALYP+L +N+ L + S EI +R+++VA L++ H+L+ Sbjct: 74 PPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLELDHLLDRR 133 Query: 138 PRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVV 197 P +LSGGQ+QRVAL RALV+ PS+ LLDEP SNLDA +R+ RA +K + S+ ++ V Sbjct: 134 PAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQQASPVVYV 193 Query: 198 SHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIG--EINELEGKVTNEG 255 +HD + +++ R+ +L G L Q+ P+ +Y P + VA IG +N L + + Sbjct: 194 THDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLLPLPIHSGQ 253 Query: 256 VVIGSLRFPVS---VSSDRAIIGIRPEDVKLS 284 +GS P+ + + + G+RPE +KL+ Sbjct: 254 AWLGSRALPIPSHLAARSQVLWGLRPEHLKLA 285 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: 257 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: 355 Length adjustment: 29 Effective length of query: 324 Effective length of database: 326 Effective search space: 105624 Effective search space used: 105624 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