Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 6938983 Sama_3081 ABC transporter, ATP-binding protein, putative (RefSeq)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__SB2B:6938983 Length = 270 Score = 144 bits (362), Expect = 4e-39 Identities = 88/247 (35%), Positives = 139/247 (56%), Gaps = 23/247 (9%) Query: 45 KDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVR 104 +D SL+I +G++ IMG SG GK+T+++L+ + P G+VL DGV+I IS +EL E+R Sbjct: 25 EDISLSIPKGKVTAIMGPSGIGKTTLLKLIAGQLVPDHGEVLFDGVNIHDISRSELFELR 84 Query: 105 RKKIAMVFQSFALMPHMTVLDNTAFGM-ELAGINAEERREKALDALRQVGLENYAHSYPD 163 K+++M+FQS AL M V DN AF + E +G++ R L L VGL A P Sbjct: 85 -KRMSMLFQSGALFTDMNVFDNIAFALREHSGLDEAIIRRIVLMKLEAVGLRGAAMLMPS 143 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 ELSGGM++RV LARA+A+ P++++ DE F+ DP+ + + +L T V +SH Sbjct: 144 ELSGGMQRRVALARAIALEPEMVMYDEPFAGQDPISMGVLVKLIRELSDALNLTSVVVSH 203 Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNN---------------------PANDYVR 262 D+ E + I D + ++ ++ GTP ++ ++ PANDY++ Sbjct: 204 DVGEVLGIADYVYVIAEKRIIAQGTPAQLKSSHDPRLRQFIGGEPDGPVPFHYPANDYMK 263 Query: 263 TFFRGVD 269 G + Sbjct: 264 ELTGGAN 270 Lambda K H 0.319 0.137 0.378 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: 250 Number of extensions: 15 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: 400 Length of database: 270 Length adjustment: 28 Effective length of query: 372 Effective length of database: 242 Effective search space: 90024 Effective search space used: 90024 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