Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate RR42_RS31740 RR42_RS31740 ABC transporter permease
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Cup4G11:RR42_RS31740 Length = 222 Score = 122 bits (306), Expect = 6e-33 Identities = 75/222 (33%), Positives = 122/222 (54%), Gaps = 20/222 (9%) Query: 26 ITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNR-LVSGIATAYVELFRNVPLLVQLFIW 84 + G G T+ + A ++ ++G L+G+ R P R +V G+ TAYV R PLLVQLF+ Sbjct: 16 VRGAGVTVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVTAIRGTPLLVQLFLL 75 Query: 85 YFLVPD---LLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQ 141 +F +P LLP A + VI LG+++ A V E VR IQ++ KGQ Sbjct: 76 FFGLPQFDILLP----------------AFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQ 119 Query: 142 EAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQT 201 AAR++G S Q V+LPQA +IPPL +EF+ + KNS++ SL+ + +++ + ++ Sbjct: 120 MEAARSIGMSSGQAMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKI 179 Query: 202 AEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAVPGLI 243 S E + L+Y L L +R +E+++ + G++ Sbjct: 180 ISVSYRSLEVYLAIALVYLLLTSAAGLFLRHMEQRLRMGGMV 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: 137 Number of extensions: 4 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: 222 Length adjustment: 23 Effective length of query: 225 Effective length of database: 199 Effective search space: 44775 Effective search space used: 44775 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