Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate PfGW456L13_4772 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4772 Length = 223 Score = 122 bits (307), Expect = 5e-33 Identities = 68/212 (32%), Positives = 121/212 (57%), Gaps = 6/212 (2%) Query: 28 GLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWYFL 87 G+ T+ + I ++LG++L +MR N+++S IA AYV FR++PLL+ + +Y Sbjct: 18 GMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVITWFYLA 77 Query: 88 VPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARA 147 VP +L W + P A S ++ +F AA CE VR G+Q++PKGQ AA+A Sbjct: 78 VPFVL-----RWITGEDTPI-GAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQA 131 Query: 148 MGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSAN 207 +G S Q+ ++LPQA+R + P L + + +F+++S+ +GL++ L ++ + + Sbjct: 132 LGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIGR 191 Query: 208 LFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239 E A L+YF ++ L++ ++K+ AV Sbjct: 192 SNEFLIFAGLVYFIISFAASQLVKRLQKRFAV 223 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: 140 Number of extensions: 5 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: 223 Length adjustment: 23 Effective length of query: 225 Effective length of database: 200 Effective search space: 45000 Effective search space used: 45000 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