Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Miya:8500595 Length = 337 Score = 131 bits (330), Expect = 2e-35 Identities = 73/211 (34%), Positives = 123/211 (58%), Gaps = 4/211 (1%) Query: 26 ITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWY 85 + GL T+ +++ A I +++G + G+ R N ++ A Y+E+ R PLLVQ+F+WY Sbjct: 128 LEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFLWY 187 Query: 86 FLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAA 145 F+V L+ L+ ++P L V+ L LFT A V E VR GIQ++ +GQ AA Sbjct: 188 FVVGTLINALLEHVGLGGISP----LWYGVMALALFTGAYVAEIVRAGIQSVHRGQMEAA 243 Query: 146 RAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFS 205 R++G + Q V+LPQA+R I+PPL +F+++ K+SS+ +I + EL T++ S Sbjct: 244 RSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRELTKATREVVTTS 303 Query: 206 ANLFEAFTLATLIYFTLNMGLMLLMRMVEKK 236 FE + + ++Y L L L ++ +E++ Sbjct: 304 LQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334 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: 188 Number of extensions: 4 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: 248 Length of database: 337 Length adjustment: 26 Effective length of query: 222 Effective length of database: 311 Effective search space: 69042 Effective search space used: 69042 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: 48 (23.1 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