Align ATPase (characterized, see rationale)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 140 bits (354), Expect = 2e-38 Identities = 88/254 (34%), Positives = 137/254 (53%), Gaps = 19/254 (7%) Query: 17 APETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALE---- 72 A + A GV +YG + QA+ VS+ V V +GPSG GKSTFLRTLN + Sbjct: 24 AEHAKMAARGVNVFYGEK-QAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVA 82 Query: 73 -SHQRGEIWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPV 131 + GEI ++G + D+ +R VGMVFQ+ N FP ++ +N+ P R + Sbjct: 83 SARVEGEITLDGENIYDKSMDVVQLRARVGMVFQKPNPFPK-SIYENVAYGP---RIHGL 138 Query: 132 AQAEATARQLLERV--------RIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDE 183 A+A+ Q++ER + ++ + LSGGQQQR+ IARA+A+ P ++L DE Sbjct: 139 ARAKGDMDQIVERSLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDE 198 Query: 184 PTSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDR 243 P SALDP ++ +++ +L +++ TH + A V+ R G +VE D+ Sbjct: 199 PCSALDPIATAKIEELIHELRGR-YAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQ 257 Query: 244 FFTAPQSDRAKQFL 257 FTAP+ +R K ++ Sbjct: 258 IFTAPRQERTKDYI 271 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: 159 Number of extensions: 9 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: 276 Length adjustment: 25 Effective length of query: 236 Effective length of database: 251 Effective search space: 59236 Effective search space used: 59236 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