Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate BWI76_RS05950 BWI76_RS05950 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Koxy:BWI76_RS05950 Length = 250 Score = 127 bits (319), Expect = 2e-34 Identities = 81/225 (36%), Positives = 121/225 (53%), Gaps = 11/225 (4%) Query: 15 GVGSETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRN 74 GV S L W I+G T+ +++ I+A +L LL +R R + A+V LFRN Sbjct: 9 GVLSGQPLQWIISGFLTTVWVSVAGMILATVLAILLLALRLGGGRPGRWLVAAWVSLFRN 68 Query: 75 VPLLVQLFIWYFLVPDLLPEGLQEWFKQD-----LNPTTSALISVVIC----LGLFTAAR 125 PLLVQL WYF +LLP G +++ D L L +C LG+FT+A Sbjct: 69 TPLLVQLLFWYFAAWNLLPLGARDFINDDHSWSILPGNVWWLTPEFLCSMWGLGVFTSAF 128 Query: 126 VCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSV 185 + E++ +G++A+ GQ AA + GF+ Q ++LLPQ P+ ++LN+ K SS+ Sbjct: 129 LIEEIASGLRAVSHGQREAALSQGFTPWQELRHILLPQGLANAWQPIIGQYLNLMKLSSL 188 Query: 186 ASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLN--MGLML 228 AS IG EL Q +Q ++A+ EAF + T +Y L MG+ L Sbjct: 189 ASGIGFAELTYQVRQIESYNAHALEAFAVGTALYLALGVVMGVAL 233 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: 156 Number of extensions: 6 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: 250 Length adjustment: 24 Effective length of query: 224 Effective length of database: 226 Effective search space: 50624 Effective search space used: 50624 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