Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate Ac3H11_4901 amino acid ABC transporter, permease protein
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4901 Length = 224 Score = 99.0 bits (245), Expect = 7e-26 Identities = 72/219 (32%), Positives = 112/219 (51%), Gaps = 19/219 (8%) Query: 26 ITGLGWTIAIAITAWIIALLLGSLLGVMRTV-----PNRLVSGIATAYVELFRNVPLLVQ 80 + G+ WTI + I + LLLG+ R P L +A+ YVEL RN P +VQ Sbjct: 18 VRGVVWTIGLTIVGTGLGLLLGTACAWARARNLGHRPTALRWAVAS-YVELVRNTPFIVQ 76 Query: 81 LFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKG 140 LF +F +P L GL+ L+P ++++++VI LG ++A E +R GI+A P+G Sbjct: 77 LFFLFFGLPAL---GLK------LSPEFASVLAMVINLGAYSA----EIIRAGIEATPRG 123 Query: 141 QEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQ 200 Q AA ++ + Q + V+LP A + + P + S+ + V S+V I EL Sbjct: 124 QIEAAHSLALTPGQTFRRVVLPPALQKVWPAMVSQIIIVMLGSAVCGQISTPELSYAANL 183 Query: 201 TAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239 + + FEAF LAT +Y L+M L+ V + V Sbjct: 184 ISSNTFRAFEAFILATAVYLVLSMLTRRLLMWVGARFLV 222 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: 126 Number of extensions: 10 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: 224 Length adjustment: 23 Effective length of query: 225 Effective length of database: 201 Effective search space: 45225 Effective search space used: 45225 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