Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= TCDB::Q88NY5 (256 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 142 bits (357), Expect = 1e-38 Identities = 82/227 (36%), Positives = 128/227 (56%), Gaps = 6/227 (2%) Query: 11 LRMISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDI 70 + + +KNV+K+YG + S E++ GE +V GPSG GKSTL++ + LE G + Sbjct: 1 MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60 Query: 71 VVDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGL 130 ++DG I T +P + + MVFQ + L+PH+T+ EN++ A R + A +K Sbjct: 61 ILDGRDI----TEVPPSQRDLAMVFQSYALYPHMTVEENMSFALR-LAKVDPAIIQEKVK 115 Query: 131 ALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDV 190 D++ L+A+ ++ P LSGGQ+QRVAI R++ P V LFDEP S LD + Sbjct: 116 MAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVE 175 Query: 191 MVQLAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFF 236 + L +E G T + VTH+ A +A+RV+ + G I + T E + Sbjct: 176 IASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELY 222 Lambda K H 0.319 0.134 0.383 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: 187 Number of extensions: 9 Number of successful extensions: 4 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: 256 Length of database: 348 Length adjustment: 27 Effective length of query: 229 Effective length of database: 321 Effective search space: 73509 Effective search space used: 73509 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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