Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_109969962.1 DK846_RS15735 amino acid ABC transporter permease
Query= TCDB::Q88NY4 (223 letters) >NCBI__GCF_003173355.1:WP_109969962.1 Length = 225 Score = 109 bits (272), Expect = 5e-29 Identities = 66/219 (30%), Positives = 123/219 (56%), Gaps = 12/219 (5%) Query: 8 IIPALPALWEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPL 67 +I P L G+ +T+ L+ + ++ GI+LG +AL ++ L+ ++ YV +FR +P+ Sbjct: 7 LIDWFPYLLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPV 66 Query: 68 LLVITWFYLAVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMG 127 L+++ FY + G + AF V + AAY +I R +QSI++GQM Sbjct: 67 LVLLFLFYFGI------FPGLGLDLPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQMT 120 Query: 128 AAQALGMNYAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARSNGD 187 AA++LGM+ AQ +R IILPQA R P + + ++S+ Y +G+ + L + Sbjct: 121 AARSLGMSRAQAIRSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLT---RSSQ 177 Query: 188 IIGRSH---EFLIFAGVVYFLISFSASWLVKRLQKRISV 223 I+ +++ + V++ L+S++ + L++RL+KRI++ Sbjct: 178 IVSQTYVTMPIYLACAVMFILLSYAGTHLIQRLEKRIAI 216 Lambda K H 0.330 0.141 0.417 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: 9 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: 223 Length of database: 225 Length adjustment: 22 Effective length of query: 201 Effective length of database: 203 Effective search space: 40803 Effective search space used: 40803 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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