Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_041670877.1 RSPH17029_RS18130 amino acid ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000015985.1:WP_041670877.1 Length = 242 Score = 283 bits (724), Expect = 2e-81 Identities = 139/240 (57%), Positives = 179/240 (74%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 MI + +VSKWYGHFQVL D S +V+KGE VVVCGPSGSGKSTLI+ +N LE Q G+I V Sbjct: 1 MIRMSHVSKWYGHFQVLHDVSLDVRKGERVVVCGPSGSGKSTLIRCINRLEVHQSGQIFV 60 Query: 61 DGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKL 120 G+ + D ++ +R +GMVFQ+F LFPHL+++ENLTL + + K+ A + A+ Sbjct: 61 KGLEMTDNVKNIDTIRRHIGMVFQNFNLFPHLTVLENLTLGPMLTRQMKKSAAEDLAMHF 120 Query: 121 LERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMV 180 L +V + + K+P QLSGGQQQRVAIAR+LCM+P MLFDEPTSALDPEMI EVLD M+ Sbjct: 121 LRKVRIPEQSGKYPLQLSGGQQQRVAIARSLCMEPEIMLFDEPTSALDPEMIKEVLDTMI 180 Query: 181 ELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKIL 240 ELA GMTM+VVTHEMGFAR VA+ V+FM +G+ VE P + FF +P+ +R + FL +IL Sbjct: 181 ELAESGMTMIVVTHEMGFARTVADNVVFMADGRKVESGPPEEFFGNPREERTRAFLDQIL 240 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: 179 Number of extensions: 6 Number of successful extensions: 1 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: 242 Length adjustment: 23 Effective length of query: 218 Effective length of database: 219 Effective search space: 47742 Effective search space used: 47742 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 Apr 09 2024. 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