Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000015985.1:WP_011842387.1 Length = 266 Score = 220 bits (560), Expect = 2e-62 Identities = 114/249 (45%), Positives = 166/249 (66%), Gaps = 8/249 (3%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 ++ L+ + K +G F+VL S +V +GEVV + G SGSGKST ++++N +E Q G + Sbjct: 7 LLRLREIRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMPQAGTMDF 66 Query: 61 D--------GIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAP 112 G + K L KLR+ +GMVFQ + L+PH+++++N+ A + + + +A Sbjct: 67 GDFHFDFRKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTLRRTPRAQ 126 Query: 113 AREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMI 172 A E+A LL R+GL + +PA+LSGGQQQRVAIARAL M P MLFDE TSALDPE++ Sbjct: 127 AVEEAEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTSALDPELV 186 Query: 173 NEVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRA 232 +EVL +M LA +GMTM++VTHE+ FAR V++RV+F D+G + E P D +P+S R Sbjct: 187 HEVLVLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLRNPESPRL 246 Query: 233 KDFLAKILH 241 + FL +ILH Sbjct: 247 RQFLHRILH 255 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: 160 Number of extensions: 5 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: 266 Length adjustment: 24 Effective length of query: 217 Effective length of database: 242 Effective search space: 52514 Effective search space used: 52514 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