Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate 8502445 DvMF_3151 ABC transporter related (RefSeq)
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__Miya:8502445 Length = 242 Score = 295 bits (754), Expect = 7e-85 Identities = 143/240 (59%), Positives = 185/240 (77%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 MI +V KWYG F VL + +V+KGEV+V+CGPSGSGKS+ I+ +N LEP+Q+G+I + Sbjct: 3 MIEFHDVHKWYGEFHVLKGITQKVEKGEVLVICGPSGSGKSSFIRCLNRLEPIQKGQILL 62 Query: 61 DGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKL 120 +G ++DK D+ +LR+ VG+VFQ F L+PHLS++ N+TLA KV K KA A A++L Sbjct: 63 EGKSIHDKGVDVNELRTEVGIVFQQFNLYPHLSVLHNVTLAPTKVRKMPKAKAESIAMEL 122 Query: 121 LERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMV 180 LERVG+ A K+P +LSGGQQQRVAIARAL M P MLFDEPTSALDPEMINEVL+ M Sbjct: 123 LERVGIHDQARKYPVELSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEMINEVLNAMK 182 Query: 181 ELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKIL 240 +LA GMTM+ VTHEMGFAR+VA+RV+FMD GK++E++P D FF PK +R + FL +IL Sbjct: 183 DLARAGMTMLCVTHEMGFAREVADRVVFMDGGKVIEEAPPDVFFSSPKHERTQAFLREIL 242 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: 204 Number of extensions: 8 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 Sep 17 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