Align ATPase (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 152 bits (384), Expect = 1e-41 Identities = 92/238 (38%), Positives = 136/238 (57%), Gaps = 9/238 (3%) Query: 27 VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86 + K +G QFQAL ++L +Q GE++ ++GPSGSGK+T LR + LE G+I H Sbjct: 8 ISKKFG-QFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQI----HFG 62 Query: 87 SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQV---RRWPVAQAEATARQLLE 143 + D + + VG VFQ + LF H+TV N+ + +R A+ + LLE Sbjct: 63 NRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLE 122 Query: 144 RVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDL 203 V++ A +YP QLSGGQ+QR+A+ARALA QP +LL DEP ALD ++ +E+ +R L Sbjct: 123 MVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSL 182 Query: 204 ASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 E T + TH+ A E++DRVV+M++G I + P + P S FL + Sbjct: 183 HDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGNV 240 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: 269 Number of extensions: 8 Number of successful extensions: 4 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: 376 Length adjustment: 27 Effective length of query: 234 Effective length of database: 349 Effective search space: 81666 Effective search space used: 81666 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: 48 (23.1 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