Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_157619716.1 N825_RS33165 ATP-binding cassette domain-containing protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000576635.1:WP_157619716.1 Length = 243 Score = 291 bits (745), Expect = 8e-84 Identities = 154/243 (63%), Positives = 186/243 (76%), Gaps = 2/243 (0%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 MI NV+K YG FQ L D + EV +GEVVVVCGPSGSGKSTLI+TVN LE + G IT Sbjct: 1 MIRFSNVNKNYGGFQALVDINAEVARGEVVVVCGPSGSGKSTLIRTVNRLEEIHSGTITF 60 Query: 61 DGIVVNDKK--TDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKAL 118 DG V+ K ++L LRSR+G VFQ F LFPHLS +EN+T++ VKV D+ AR++A+ Sbjct: 61 DGRSVHGKMRGSELNHLRSRIGFVFQSFNLFPHLSALENVTISPVKVNGVDREQARDRAM 120 Query: 119 KLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDV 178 +LL+RVGLSA AN +PAQLSGGQQQRVAIARAL M+P AMLFDEPTSALDPEM+ EVL V Sbjct: 121 RLLDRVGLSAKANAYPAQLSGGQQQRVAIARALAMEPPAMLFDEPTSALDPEMVGEVLAV 180 Query: 179 MVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAK 238 M LA +GMTMM VTHEMGFAR+VA+RV FMD G+I+E + FF DP+ RA+ FL+ Sbjct: 181 MRGLAADGMTMMCVTHEMGFAREVADRVWFMDAGQILETAEPSVFFGDPQHARAQRFLSD 240 Query: 239 ILH 241 + H Sbjct: 241 LRH 243 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: 185 Number of extensions: 8 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: 243 Length adjustment: 23 Effective length of query: 218 Effective length of database: 220 Effective search space: 47960 Effective search space used: 47960 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