Align ATPase (characterized, see rationale)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 240 bits (613), Expect = 2e-68 Identities = 130/257 (50%), Positives = 174/257 (67%), Gaps = 9/257 (3%) Query: 12 TAIASAPETMIYAE-------GVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTF 64 T +A A + ++ E + K YG+ + L G+ L VQRGEV+ ++G SGSGKST Sbjct: 7 TTLAPAHDGIVVGEPPIVDITALRKSYGSN-EVLKGIDLKVQRGEVIAIIGKSGSGKSTL 65 Query: 65 LRTLNALESHQRGEIWIEGHRLSHDRRD-IATIRQEVGMVFQQFNLFPHLTVLQNLMLAP 123 LR +N LE Q G + + G +L HD + +RQ+VGM+FQ FNLFPHL+V +N+MLAP Sbjct: 66 LRCVNGLEEFQEGALSVNGKKLLHDSPTAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAP 125 Query: 124 VQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDE 183 V+ AE AR+LLERV +AE+ D P QLSGGQQQRVAIARALAM+P++LL DE Sbjct: 126 TLVKARDAKTAETQARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDE 185 Query: 184 PTSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDR 243 TSALDPE+V EVL V+ LA EGMT+++ THE+ FAR+V DRV+ M G++ E+ P Sbjct: 186 ITSALDPELVGEVLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAA 245 Query: 244 FFTAPQSDRAKQFLAQI 260 F PQ+ +QFL+ + Sbjct: 246 LFGNPQTPELQQFLSSL 262 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: 211 Number of extensions: 5 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: 264 Length adjustment: 25 Effective length of query: 236 Effective length of database: 239 Effective search space: 56404 Effective search space used: 56404 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