Align ATPase (characterized, see rationale)
to candidate AZOBR_RS08670 AZOBR_RS08670 arginine ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__azobra:AZOBR_RS08670 Length = 258 Score = 302 bits (774), Expect = 4e-87 Identities = 152/243 (62%), Positives = 189/243 (77%), Gaps = 1/243 (0%) Query: 19 ETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGE 78 E +I +GV KWYG +F L + L+V +GE +V+ GPSGSGKST +R LN LE HQ+G Sbjct: 15 EPIIQCQGVHKWYG-EFHVLKNIDLSVAKGERIVICGPSGSGKSTMIRCLNRLEEHQKGS 73 Query: 79 IWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATA 138 I ++G L+ + ++I +R+EVGMVFQ FNLFPHLTVL+N LAP+ VR+ P A+AE A Sbjct: 74 IVVDGIELTGNLKNIELVRREVGMVFQHFNLFPHLTVLENCTLAPIWVRKKPKAEAEEMA 133 Query: 139 RQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLD 198 + L+RVRIAEQA KYPGQLSGGQQQRVAIAR+L M P+++LFDEPTSALDPEMV+EVLD Sbjct: 134 MRYLKRVRIAEQAHKYPGQLSGGQQQRVAIARSLCMSPKVMLFDEPTSALDPEMVKEVLD 193 Query: 199 VMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLA 258 VM LA +GMTML THE+GFA+ VADRV+ M G+IVE+ P+ FF PQSDR K FL+ Sbjct: 194 VMIGLAEDGMTMLCVTHEMGFAKSVADRVIFMDRGEIVEQNTPNEFFNHPQSDRTKLFLS 253 Query: 259 QIL 261 QIL Sbjct: 254 QIL 256 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: 219 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: 258 Length adjustment: 24 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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