Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_076482473.1 BW971_RS17350 amino acid ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_900156495.1:WP_076482473.1 Length = 250 Score = 233 bits (595), Expect = 2e-66 Identities = 125/250 (50%), Positives = 168/250 (67%), Gaps = 10/250 (4%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 M+ V K +G QVL S EV++GEV + GPSGSGKST ++ VN LE V G + V Sbjct: 1 MVLADRVCKSFGALQVLKGISLEVERGEVTCLIGPSGSGKSTFLRCVNHLESVTAGRLYV 60 Query: 61 DGIVVNDKKT----------DLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDK 110 D ++ ++ D A R +GMVFQHF LFPH + ++N+ A ++V + Sbjct: 61 DDDLIGYREKGGKLYELSAKDAAAQRRDIGMVFQHFNLFPHRTALDNIIEAPIQVKGVVR 120 Query: 111 APAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPE 170 A A E+ LL++VGL+ A+ +PAQLSGGQQQRVAIARAL MDP MLFDEPTSALDPE Sbjct: 121 ARAVERGKDLLDQVGLADKASAYPAQLSGGQQQRVAIARALAMDPKLMLFDEPTSALDPE 180 Query: 171 MINEVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSD 230 ++ +VL VM LA +GMTM+VVTHEMGFAR+VA++++FMD GK+VE + P+ + Sbjct: 181 LVGDVLAVMRNLAKDGMTMVVVTHEMGFAREVADQLVFMDAGKVVEKGDPREVLNSPQHE 240 Query: 231 RAKDFLAKIL 240 R + FL+K+L Sbjct: 241 RTQSFLSKLL 250 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: 187 Number of extensions: 9 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: 241 Length of database: 250 Length adjustment: 24 Effective length of query: 217 Effective length of database: 226 Effective search space: 49042 Effective search space used: 49042 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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