Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 118 bits (296), Expect = 9e-32 Identities = 75/243 (30%), Positives = 129/243 (53%), Gaps = 24/243 (9%) Query: 3 YNWDWGVFFKSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVS 62 + +DW S + + I G+ +T+ I+ G +I ALG G++ + Sbjct: 5 FQFDWQAAIDS--------IPFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLR 56 Query: 63 GIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFT 122 ATAY+EIFR P+LVQ+ ++ +PDL+ ++P T+ + + L + Sbjct: 57 WPATAYIEIFRGTPILVQVLFIFYGLPDLIGG--------PIDPLTAG----IAAIALNS 104 Query: 123 AARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKN 182 A + E VR G+Q++ GQT A ++G Q + V+ PQAFR +IPPL ++ + K+ Sbjct: 105 GAYISEVVRGGVQSIDKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKD 164 Query: 183 SSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLIMRLVERKVAVPGL 242 +S+ S+IG+ EL+ Q + + FE + + ++Y + +SL +I+R VER+ GL Sbjct: 165 TSLFSVIGVGELVRQGQIYIANTFTAFEVYFVVAILYLAITLSLSIILRFVERR----GL 220 Query: 243 ISV 245 SV Sbjct: 221 ASV 223 Lambda K H 0.327 0.141 0.433 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: 175 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: 223 Length adjustment: 23 Effective length of query: 225 Effective length of database: 200 Effective search space: 45000 Effective search space used: 45000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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