Align ATPase (characterized, see rationale)
to candidate PP_3597 PP_3597 Amino-acid ABC transporter, ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Putida:PP_3597 Length = 260 Score = 272 bits (696), Expect = 4e-78 Identities = 144/257 (56%), Positives = 180/257 (70%), Gaps = 6/257 (2%) Query: 10 PVTAIASAPE-----TMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTF 64 P++ APE +I EG+ K YG F L + L V+ GE +V+ GPSGSGKST Sbjct: 4 PLSLATLAPEPDPRPVLIRIEGLNKHYG-AFHVLRDIDLQVREGERIVLCGPSGSGKSTL 62 Query: 65 LRTLNALESHQRGEIWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPV 124 +R +N LE Q+G I ++G L+ R+ A +R ++GMVFQ FNLFPH++VL N +LAP Sbjct: 63 IRCINRLEVAQQGSIQVDGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPT 122 Query: 125 QVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEP 184 VR AE AR L +V I QA KYP QLSGGQQQRVAIARAL M+PRI+LFDEP Sbjct: 123 SVRGLSRKDAEERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEP 182 Query: 185 TSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRF 244 TSALDPEMV EVLDV+ LA GMTML THE+GFAR+VA+RV+ + GQI+E++PP F Sbjct: 183 TSALDPEMVAEVLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVF 242 Query: 245 FTAPQSDRAKQFLAQIL 261 F P+++RAK FLAQIL Sbjct: 243 FNQPRTERAKAFLAQIL 259 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: 226 Number of extensions: 8 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: 261 Length of database: 260 Length adjustment: 25 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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