Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate BPHYT_RS34460 BPHYT_RS34460 glutamate/aspartate transporter permease GltK
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__BFirm:BPHYT_RS34460 Length = 225 Score = 121 bits (304), Expect = 1e-32 Identities = 72/236 (30%), Positives = 123/236 (52%), Gaps = 13/236 (5%) Query: 3 YNWDWGVFFKSTGVGSETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVS 62 +N DW S G+ + G+G T+ I A + LL G++L V+ P R V Sbjct: 2 FNIDWQALADSKGI--------VLAGMGVTLQITFVAILCGLLWGTVLAVLHRSPQRAVR 53 Query: 63 GIATAYVELFRNVPLLVQLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFT 122 A YV LFR++PL V L +W+FL+ +P+ L+ F LIS ++ L Sbjct: 54 VFAQGYVALFRSIPL-VMLLLWFFLI---VPQFLKALFNLPAGVDVR-LISAMVAYSLLE 108 Query: 123 AARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKN 182 AA CE +R GI++LP+GQ AA A+G + Q V+LPQA+R ++P ++ + +F++ Sbjct: 109 AAFFCEIIRAGIESLPRGQAQAALALGMTAGQTMRYVILPQAFRAMVPVALTQCIVIFQD 168 Query: 183 SSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVA 238 +S+ +I L + + E + A + Y+++ GL + +++V ++A Sbjct: 169 TSLVYVIALGDFFRRVSAIGERDGTVVPMLLFAGVAYWSITTGLTVTVKVVRTRLA 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: 130 Number of extensions: 5 Number of successful extensions: 3 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: 225 Length adjustment: 23 Effective length of query: 225 Effective length of database: 202 Effective search space: 45450 Effective search space used: 45450 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