Align ATPase (characterized, see rationale)
to candidate 7025948 Shewana3_3096 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__ANA3:7025948 Length = 378 Score = 152 bits (384), Expect = 1e-41 Identities = 86/243 (35%), Positives = 143/243 (58%), Gaps = 7/243 (2%) Query: 19 ETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGE 78 + ++ E V K + + +A+ VSLT+ +GE+ ++G SGSGKST LR L E G Sbjct: 18 KVLLKIERVSKLF-DDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGR 76 Query: 79 IWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATA 138 I+++G D D+ + + M+FQ + LFPH+TV QN+ Q + P A+ E Sbjct: 77 IFLDGE----DITDLPPYERPINMMFQSYALFPHMTVAQNIAFGLKQ-DKLPKAEIEQRV 131 Query: 139 RQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREV-L 197 +++L+ V + + + P QLSGGQ+QRVA+AR+LA +P++LL DEP ALD ++ ++ L Sbjct: 132 QEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQL 191 Query: 198 DVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFL 257 +V+ L G+T ++ TH+ A +A R+ +M+DG I + P + +P S +F+ Sbjct: 192 EVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFI 251 Query: 258 AQI 260 + Sbjct: 252 GSV 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: 213 Number of extensions: 12 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: 378 Length adjustment: 27 Effective length of query: 234 Effective length of database: 351 Effective search space: 82134 Effective search space used: 82134 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