Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 14790 b0653 glutamate and aspartate transporter subunit (NCBI)
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Keio:14790 Length = 224 Score = 119 bits (297), Expect = 7e-32 Identities = 71/236 (30%), Positives = 124/236 (52%), Gaps = 13/236 (5%) Query: 3 YNWDWGVFFKSTGVGSETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVS 62 Y +DW S L + + GL T+ I +TA +I +L G++L VMR V+ Sbjct: 2 YEFDWSSIVPS--------LPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVA 53 Query: 63 GIATAYVELFRNVPLLVQLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFT 122 A AYV +FR++PL++ L +Y +VP L L K D+ LIS ++ +F Sbjct: 54 WFAKAYVNVFRSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIR-----LISAMVAFSMFE 108 Query: 123 AARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKN 182 AA E +R GIQ++ +GQ +AA A+G + Q ++LPQA+R ++P L ++ + +F++ Sbjct: 109 AAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQD 168 Query: 183 SSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVA 238 +S+ ++ L + E E A +YF +++ LL+ ++++ A Sbjct: 169 TSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRRTA 224 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: 146 Number of extensions: 7 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