Align ATPase (characterized, see rationale)
to candidate GFF3910 PGA1_65p00130 putative amino-acid ABC transporter, ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Phaeo:GFF3910 Length = 251 Score = 213 bits (543), Expect = 2e-60 Identities = 113/240 (47%), Positives = 160/240 (66%), Gaps = 8/240 (3%) Query: 26 GVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG-----EIW 80 G+ K +G+ L G+ LT+Q GE +V++GPSG+GKST LR LN L++ G ++ Sbjct: 14 GLRKTFGDSV-VLDGIDLTIQPGERIVIIGPSGTGKSTLLRCLNFLDAPDAGLVRIGDLD 72 Query: 81 IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140 ++ R S + +I +R+ VFQ + LF + T +N+M A + V++ P A+AEA AR+ Sbjct: 73 VDAARAS--KAEILALRRRTAFVFQNYALFANKTAAENIMEALITVQKQPRAEAEARARE 130 Query: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200 +L +A++AD YP LSGGQQQRV I RA+A+ ++LFDEPTSALDPE V EVL +M Sbjct: 131 ILAETGLADKADAYPASLSGGQQQRVGIGRAMALGAELMLFDEPTSALDPEWVGEVLALM 190 Query: 201 RDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 +A E TML+ THE+ FARE+ADRVV M G+IVE+ PP + F APQ R + FL ++ Sbjct: 191 HKVAEERQTMLIVTHEMQFAREIADRVVFMEGGRIVEQGPPTQIFDAPQDPRTRAFLRRV 250 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: 189 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: 251 Length adjustment: 24 Effective length of query: 237 Effective length of database: 227 Effective search space: 53799 Effective search space used: 53799 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