Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate HSERO_RS19245 HSERO_RS19245 glutamate/aspartate transporter permease GltK
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__HerbieS:HSERO_RS19245 Length = 231 Score = 129 bits (324), Expect = 5e-35 Identities = 74/217 (34%), Positives = 127/217 (58%), Gaps = 7/217 (3%) Query: 25 YITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIW 84 + TGL +T+ + +A ++LG+LL +MR N+ +S IAT YV L R++PL++ +F + Sbjct: 18 FTTGLKFTLILTFSAMAGGIILGTLLAMMRLSSNKPLSFIATTYVNLIRSIPLVLVIFWF 77 Query: 85 YFLVPDLLPEGLQEWFKQDLNPT-TSALISVVICLGLFTAARVCEQVRTGIQALPKGQEA 143 YFLVP + W P A S +I LF AA CE +R+GIQ++P+GQ Sbjct: 78 YFLVPFI-----GAWMIGASEPIQVGAFQSALITFILFEAAYYCEIMRSGIQSIPRGQVF 132 Query: 144 AARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIG-LMELLAQTKQTA 202 A A+G + Q+ NV+LPQA+R + P L ++ + +F++ S+ ++G + + + + A Sbjct: 133 AGYAIGMNYWQMMGNVVLPQAFRNMTPILLTQTIVLFQDVSLVYVLGSVPDFVTSASKIA 192 Query: 203 EFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239 + L E + ++YF L+ GL L++ +KK+A+ Sbjct: 193 QRDGRLVEMYLFVAVVYFVLSFGLSTLVKRFQKKIAI 229 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: 151 Number of extensions: 8 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: 231 Length adjustment: 23 Effective length of query: 225 Effective length of database: 208 Effective search space: 46800 Effective search space used: 46800 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