Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate BPHYT_RS24660 BPHYT_RS24660 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__BFirm:BPHYT_RS24660 Length = 357 Score = 209 bits (533), Expect = 7e-59 Identities = 119/293 (40%), Positives = 183/293 (62%), Gaps = 23/293 (7%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M + ++ V++ F G A+DNV++++ +G+ LGPSG GKTT +R+IAGL+ P++G Sbjct: 1 MTHLTLQAVTRRF--GAAHAVDNVDLSVPDGKLVCFLGPSGCGKTTLLRMIAGLETPTSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 ++F R + +P R GMVFQ+ AL+P++T +NIA+PL K +K++ +R Sbjct: 59 SIHFAGRDITR-----LPANQRDFGMVFQSLALFPHMTVAQNIAYPLKLRKTAKDQQTRR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V E+ +++ + H+ N +LSGGQ+QRVA+ARA+ P LLLLDEP S LDA++R++ + Sbjct: 114 VAELLELIQLPHMANRPVTQLSGGQRQRVAIARAIASQPKLLLLDEPLSALDAKLREAMQ 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 ++ +Q RLG+T ++V+HD + +AD + V+ KG++ QVGKP D+Y +PVS VA Sbjct: 174 VEIRLLQQRLGITTIMVTHDQREAMTMADEIVVMEKGRIAQVGKPLDIYRDPVSEFVADF 233 Query: 241 IGEINELEGKVTNEGV------------VIGSLRFPVSVSSDRAIIGIRPEDV 281 IG N L VT +G V+ R P S S R + IRPEDV Sbjct: 234 IGLGNIL--PVTYDGAGGVSLPGGRRISVVQPARVPESSSDIRLL--IRPEDV 282 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: 267 Number of extensions: 12 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: 357 Length adjustment: 29 Effective length of query: 324 Effective length of database: 328 Effective search space: 106272 Effective search space used: 106272 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