Align ATPase (characterized, see rationale)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000015985.1:WP_011842387.1 Length = 266 Score = 237 bits (604), Expect = 2e-67 Identities = 126/243 (51%), Positives = 170/243 (69%), Gaps = 9/243 (3%) Query: 27 VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEI------- 79 + K +G F+ L GVSL V +GEVV ++G SGSGKSTFLR++N +E Q G + Sbjct: 13 IRKSFGT-FEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMPQAGTMDFGDFHF 71 Query: 80 -WIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATA 138 + +G + + +R E+GMVFQ +NL+PH+TVLQN++ AP+ +RR P AQA A Sbjct: 72 DFRKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTLRRTPRAQAVEEA 131 Query: 139 RQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLD 198 LL R+ + E+ D YP +LSGGQQQRVAIARALAM+PR++LFDE TSALDPE+V EVL Sbjct: 132 EALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTSALDPELVHEVLV 191 Query: 199 VMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLA 258 +M LA++GMTML+ THE+ FAR+V+ RV+ G + E+ PPDR P+S R +QFL Sbjct: 192 LMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLRNPESPRLRQFLH 251 Query: 259 QIL 261 +IL Sbjct: 252 RIL 254 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: 212 Number of extensions: 7 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: 266 Length adjustment: 25 Effective length of query: 236 Effective length of database: 241 Effective search space: 56876 Effective search space used: 56876 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 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