Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate PfGW456L13_445 Cystine ABC transporter, permease protein
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_445 Length = 221 Score = 110 bits (275), Expect = 2e-29 Identities = 71/212 (33%), Positives = 113/212 (53%), Gaps = 13/212 (6%) Query: 26 ITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLFIWY 85 + G +T+ +++ L++G L +MR +LVS IA YV FR PLLVQLF+ Y Sbjct: 16 LKGAYYTVILSLGGMFFGLVMGFGLALMRLSRFKLVSWIARIYVSFFRGTPLLVQLFVIY 75 Query: 86 FLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAA 145 + +P L GL+ L+P +ALI L AA CE +R I ++ +GQ AA Sbjct: 76 YGLPQL---GLE------LDPLPAALIG----FSLNMAAYACEILRAAISSIERGQWEAA 122 Query: 146 RAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFS 205 ++G + Q +LPQA R +PPL + F+++ K++++A+ I + EL Q + + Sbjct: 123 ASIGMTRAQTLRRAILPQAMRTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITART 182 Query: 206 ANLFEAFTLATLIYFTLNMGLMLLMRMVEKKV 237 +F + A LIY+ L L L +E +V Sbjct: 183 FEIFTMYLAAALIYWVLATVLSHLQNQLEARV 214 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: 133 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: 221 Length adjustment: 23 Effective length of query: 225 Effective length of database: 198 Effective search space: 44550 Effective search space used: 44550 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