Align ATPase (characterized, see rationale)
to candidate GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Marino:GFF3087 Length = 256 Score = 226 bits (576), Expect = 4e-64 Identities = 117/236 (49%), Positives = 161/236 (68%), Gaps = 11/236 (4%) Query: 33 NQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI----------- 81 +Q + L G+SL ++G+VV ++G SGSGKSTFLR +N LE+ G+I + Sbjct: 17 DQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSGDIIVHGDPIRFTTNR 76 Query: 82 EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQL 141 +G R+ D + + IR ++ MVFQ FNL+ H+TVL+N++ APV V + P +A A Sbjct: 77 KGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHVLKVPKKEAIERAEAY 136 Query: 142 LERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMR 201 L +V I E+ D YP Q+SGGQQQR AIARALAM+P ++LFDEPTSALDPE+V EVL VM+ Sbjct: 137 LNKVGIYERKDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTSALDPELVGEVLKVMQ 196 Query: 202 DLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFL 257 LA EG TM+V THE+ FAR+V+ +V+ + G I E+ P++ F P S+R KQFL Sbjct: 197 GLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFDHPDSERMKQFL 252 Lambda K H 0.321 0.134 0.387 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: 192 Number of extensions: 3 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: 261 Length of database: 256 Length adjustment: 24 Effective length of query: 237 Effective length of database: 232 Effective search space: 54984 Effective search space used: 54984 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 (21.9 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