Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_043917275.1 jaqu_RS02045 ABC transporter permease subunit
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_000877395.1:WP_043917275.1 Length = 237 Score = 172 bits (435), Expect = 7e-48 Identities = 90/229 (39%), Positives = 138/229 (60%), Gaps = 1/229 (0%) Query: 3 LIQMLGFGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYT 62 + + L F GWGG LL + T+ + L A A+G G L A K+ LR ++YT Sbjct: 4 VFEYLAFSAPGWGGNLLRGLVSTLQIALGAYALGMSIGILGALGKIHGGPILRGALEVYT 63 Query: 63 TVFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVY 122 T+ R VPEL++I L ++ G + + G E + + VG +G + GAY EV+ Sbjct: 64 TLIRAVPELVLILLLFYAGQDAINVILTSLGFERVI-LDGLWVGIYVIGFVQGAYSTEVF 122 Query: 123 RSAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTG 182 R A AV+ G++EAAR+IGM L + R++IP +L FALPG+ N+W ++ KD+AL++V G Sbjct: 123 RGAFGAVAPGQIEAARAIGMSRLKVQTRVVIPLMLPFALPGLANLWLITTKDTALLAVVG 182 Query: 183 LAELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGR 231 ++EL ++ AAG+T YF F+V G LYL++T +SN++F E + R Sbjct: 183 VSELALETRQAAGATRAYFLFYVAAGCLYLLVTLVSNQIFAWLERRLRR 231 Lambda K H 0.327 0.141 0.403 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: 134 Number of extensions: 4 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: 240 Length of database: 237 Length adjustment: 23 Effective length of query: 217 Effective length of database: 214 Effective search space: 46438 Effective search space used: 46438 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 (21.7 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