Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_051511316.1 N825_RS00145 ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000576635.1:WP_051511316.1 Length = 269 Score = 225 bits (573), Expect = 8e-64 Identities = 117/249 (46%), Positives = 171/249 (68%), Gaps = 10/249 (4%) Query: 2 ITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVD 61 + ++++ K +G +VL S +G+V+ + G SGSGKST ++ +N LE +G + V+ Sbjct: 21 VVVEDLHKRFGQLEVLKGVSLVAHEGDVISMIGSSGSGKSTFLRCINLLETPDEGRVWVN 80 Query: 62 GIVVNDKK----------TDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKA 111 G ++ K+ + ++RS +GMVFQ F L+ H+++++N+ A V VL KA Sbjct: 81 GELIRMKQGRHHAVPADAKQVDRIRSGLGMVFQGFNLWTHMTVLQNVIEAPVHVLGVPKA 140 Query: 112 PAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEM 171 A ++A LL++VGL A A+ +P+ LSGGQQQRVAIARAL M P MLFDEPTSALDPE+ Sbjct: 141 EAIDRAEALLQKVGLEAKASSYPSHLSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEL 200 Query: 172 INEVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDR 231 + EVL VM +LA+EGMTM++VTHEMGFAR+V++ VIF+ +G+I E P D +P+SDR Sbjct: 201 VGEVLRVMRQLADEGMTMIIVTHEMGFAREVSSEVIFLHQGRIEEQGPPDQVLANPRSDR 260 Query: 232 AKDFLAKIL 240 + FLA+ L Sbjct: 261 CRQFLARNL 269 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: 162 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: 269 Length adjustment: 24 Effective length of query: 217 Effective length of database: 245 Effective search space: 53165 Effective search space used: 53165 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: 47 (22.7 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