Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_05299 H281DRAFT_05299 amino acid ABC transporter membrane protein 1, PAAT family
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__Burk376:H281DRAFT_05299 Length = 216 Score = 122 bits (306), Expect = 6e-33 Identities = 76/210 (36%), Positives = 110/210 (52%), Gaps = 12/210 (5%) Query: 17 VLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYL 76 +LL AAL T+ ++L L +G V AA+LS R R G Y FRGVP L+ + L Sbjct: 13 LLLHAALATIGVSLTGLFIGFFVAVGVCAARLSPNRAARRFGGAYVFFFRGVPMLVQLLL 72 Query: 77 FYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEA 136 Y+ L+ G + V P V AV + S +Y AE+ R L++ G +EA Sbjct: 73 VYY----LLPFAG--------INVSPLVAAISAVSLCSASYIAEILRGGFLSIPPGHIEA 120 Query: 137 ARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVAAGS 196 AR +G+ RRIL+PQ R LP + N L +K S+LISV G+AEL RT+Q A S Sbjct: 121 ARMLGLSPFDTLRRILVPQAFRLTLPSLVNEMVLLIKASSLISVVGVAELTRTAQNIAAS 180 Query: 197 THQYFTFFVVGGALYLIMTSISNRVFNRAE 226 T++ ++ G +Y ++ + + AE Sbjct: 181 TYRPLEAYLAAGLIYFVICGALALIAHAAE 210 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: 105 Number of extensions: 4 Number of successful extensions: 1 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: 216 Length adjustment: 23 Effective length of query: 217 Effective length of database: 193 Effective search space: 41881 Effective search space used: 41881 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 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