Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Smeli:SMc03865 Length = 273 Score = 115 bits (289), Expect = 7e-31 Identities = 68/224 (30%), Positives = 122/224 (54%), Gaps = 15/224 (6%) Query: 26 ITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLF--- 82 + GLG T+ + + +++A +LG + +M + ++ IA Y E+ R VP+LV LF Sbjct: 47 LKGLGVTVFVTLVGFVLATVLGLGVALMALSEHVVLRQIARFYTEVIRGVPILVLLFYIA 106 Query: 83 ---------IWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTG 133 + F+ L+ G W + + S + ++ L + +A + E R G Sbjct: 107 FVGAPALVTVANFVAAPLISAG---WIEPFVVRDVSLMWRAIMALMIGYSAFIAEVFRAG 163 Query: 134 IQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLME 193 IQ++ KGQ AA+A+G S Q + V+ PQA R+I+PPL ++F+ + K+SS+ S++G+ + Sbjct: 164 IQSVDKGQVEAAKALGLSRYQRFRLVVFPQAIRVILPPLGNDFVAMVKDSSLVSVLGVAD 223 Query: 194 LLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKV 237 + K A S FE +++ +Y L +GL L +R VE+++ Sbjct: 224 ITQMGKVYASGSFRFFETYSIVAYVYLVLTIGLSLALRAVERRL 267 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: 122 Number of extensions: 8 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: 273 Length adjustment: 24 Effective length of query: 224 Effective length of database: 249 Effective search space: 55776 Effective search space used: 55776 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: 47 (22.7 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