Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 145 bits (366), Expect = 8e-40 Identities = 92/242 (38%), Positives = 132/242 (54%), Gaps = 12/242 (4%) Query: 5 KNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQ-----QGEIT 59 + V+ +YG Q + D S +V V GPSG GKST ++T+N + +GEIT Sbjct: 32 RGVNVFYGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEIT 91 Query: 60 VDGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLA-QVKVLKRDKAPAREKAL 118 +DG + DK D+ +LR+RVGMVFQ FP SI EN+ ++ L R K + Sbjct: 92 LDGENIYDKSMDVVQLRARVGMVFQKPNPFPK-SIYENVAYGPRIHGLARAKGDMDQIVE 150 Query: 119 KLLERVGL----SAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINE 174 + L+R GL N LSGGQQQR+ IARA+ +DP +L DEP SALDP + Sbjct: 151 RSLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAK 210 Query: 175 VLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKD 234 + +++ EL +++VTH M A +V+ R F G +VE D F P+ +R KD Sbjct: 211 IEELIHELRGR-YAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTKD 269 Query: 235 FL 236 ++ Sbjct: 270 YI 271 Lambda K H 0.320 0.135 0.383 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: 155 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: 241 Length of database: 276 Length adjustment: 24 Effective length of query: 217 Effective length of database: 252 Effective search space: 54684 Effective search space used: 54684 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 (21.8 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