Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 143 bits (360), Expect = 4e-39 Identities = 85/236 (36%), Positives = 135/236 (57%), Gaps = 12/236 (5%) Query: 11 FGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNG-----GTITIKDTEI 65 +G+ + ++++S + V A IGPSG GKSTFLR LN + G IT+ I Sbjct: 38 YGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEITLDGENI 97 Query: 66 TKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAP-VNVKKESKQAAQEKAEDLLRKV 124 + +++R +GMVFQ + FP K++ EN+ Y P ++ +K + E L++ Sbjct: 98 YDKSMDVVQLRARVGMVFQKPNPFP-KSIYENVAYGPRIHGLARAKGDMDQIVERSLKRA 156 Query: 125 GLFE----KRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMK 180 GL+E + ND LSGGQ+QR+ IARA+A++P+++L DEP SALDP ++ +++ Sbjct: 157 GLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIEELIH 216 Query: 181 ELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFL 236 EL +VIVTH M A V+ R F G +VE G + F +P+ +R +D++ Sbjct: 217 EL-RGRYAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTKDYI 271 Lambda K H 0.317 0.134 0.368 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: 139 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: 240 Length of database: 276 Length adjustment: 24 Effective length of query: 216 Effective length of database: 252 Effective search space: 54432 Effective search space used: 54432 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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