Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate BPHYT_RS21915 BPHYT_RS21915 ABC transporter permease
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__BFirm:BPHYT_RS21915 Length = 222 Score = 118 bits (295), Expect = 1e-31 Identities = 75/220 (34%), Positives = 119/220 (54%), Gaps = 22/220 (10%) Query: 30 GWTIAIAITAWIIAL--LLGSLLGVMRTVPNR-LVSGIATAYVELFRNVPLLVQLFIWYF 86 G + + +TA +AL +LG L+G+ R P R +V G TAY+ FR PLLVQLF+ +F Sbjct: 18 GAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYLTFFRGTPLLVQLFLLFF 77 Query: 87 LVPD---LLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEA 143 +P LLP A + ++ LGL++AA V E VR IQ++ +GQ Sbjct: 78 GLPQFGILLP----------------AFVCGMLGLGLYSAAYVSEIVRGAIQSVDRGQME 121 Query: 144 AARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAE 203 AAR++G S Q ++LPQA +IPPL +EF+ + KNS++ SL+ + +L+ + ++ Sbjct: 122 AARSIGMSSGQAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQKIIS 181 Query: 204 FSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAVPGLI 243 S E + L+Y L + VE+ + G++ Sbjct: 182 VSYRSLEVYLAIALVYLVLTQATNYALHRVERHLRAGGMV 221 Lambda K H 0.325 0.139 0.425 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: 151 Number of extensions: 5 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: 248 Length of database: 222 Length adjustment: 23 Effective length of query: 225 Effective length of database: 199 Effective search space: 44775 Effective search space used: 44775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 46 (22.3 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