Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_004681962.1 BIBO1_RS17100 amino acid ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000182725.1:WP_004681962.1 Length = 253 Score = 197 bits (500), Expect = 2e-55 Identities = 105/245 (42%), Positives = 156/245 (63%), Gaps = 6/245 (2%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 MI L+++ K + +L D + + +G V + GPSG GKSTL++ +N LE G + + Sbjct: 1 MIELQHIVKRFDDAVILNDINITIAEGTVTALVGPSGGGKSTLLRCINLLEIPTSGTLLL 60 Query: 61 DGIVV----NDKKT--DLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAR 114 G + N K + + +R + GMVFQ+F+LFPH + I+N+ V VLK K AR Sbjct: 61 GGQSITFEPNRKPSWQTIQSIRRQTGMVFQNFQLFPHQTAIQNVMEGLVTVLKWPKNKAR 120 Query: 115 EKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINE 174 E+A++LL +VG++ A+ +P+ LSGGQQQR+AIARAL P +L DEPTSALDPE+ +E Sbjct: 121 ERAMELLTKVGMAHKADAWPSTLSGGQQQRIAIARALAPSPRVLLCDEPTSALDPELASE 180 Query: 175 VLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKD 234 V+DV+ +LA EG TM++ TH++ A K+A V+F++ G +VE F P +R K Sbjct: 181 VVDVLSKLAQEGTTMVIATHDLRLASKIAKNVVFLETGNVVETGSAHDVFTHPTRERTKQ 240 Query: 235 FLAKI 239 F+A I Sbjct: 241 FVATI 245 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: 156 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: 241 Length of database: 253 Length adjustment: 24 Effective length of query: 217 Effective length of database: 229 Effective search space: 49693 Effective search space used: 49693 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