Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate Dsui_0637 Dsui_0637 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__PS:Dsui_0637 Length = 224 Score = 121 bits (304), Expect = 1e-32 Identities = 71/209 (33%), Positives = 120/209 (57%), Gaps = 6/209 (2%) Query: 28 GLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWYFL 87 GL T+ + +TA ++ + G+LL V R NRL+S +A YV LFR+VPL V + +W++L Sbjct: 19 GLLVTLEVTLTAIVVGIGWGTLLAVARLSSNRLLSFLAAGYVNLFRSVPL-VMVILWFYL 77 Query: 88 VPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARA 147 + +P+ L+ F QD+ L+S ++ LF AA E +R GIQ++PKGQ AA A Sbjct: 78 I---VPQALKGLFGQDIGDIR--LVSALVAFALFEAAYYSEIIRAGIQSVPKGQVAAGLA 132 Query: 148 MGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207 +G + Q V+LPQA+R +IP L ++ + +F+++S+ +IGL + + + Sbjct: 133 LGLTPGQTMRLVVLPQAFRNMIPLLLTQAIILFQDTSLVYVIGLSDFFGTAYKVGDRDGR 192 Query: 208 LFEAFTLATLIYFTLNMGLMLLMRMVEKK 236 L E A YF + + L++ ++ + Sbjct: 193 LVELLLFAGAAYFVICFTVSRLVKHLQAR 221 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: 164 Number of extensions: 9 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