Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_019388681.1 P735_RS0114015 ATP-binding cassette domain-containing protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000283015.1:WP_019388681.1 Length = 227 Score = 140 bits (352), Expect = 3e-38 Identities = 79/217 (36%), Positives = 130/217 (59%), Gaps = 1/217 (0%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGE-IT 59 ++ LK+ S + G VL++ + E+ KGE V + G +G+GKS+ +KT+ G P+ +GE Sbjct: 5 ILQLKDASIFQGDSLVLSNVNVEINKGEFVYLIGKTGTGKSSFMKTLYGDLPLTEGEGHI 64 Query: 60 VDGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALK 119 VD + N K+ D+ LR ++G+VFQ F+L +I +NL +DK + + + Sbjct: 65 VDFDLKNLKEKDIPYLRRKLGVVFQDFKLLTDRTINDNLLFVLKATGWKDKDKMKTRVEE 124 Query: 120 LLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVM 179 +L +V + KFP +LSGG+QQRVAIARAL +P +L DEPT LDP+ EV++V+ Sbjct: 125 VLTKVDMKTKGFKFPHELSGGEQQRVAIARALLNNPELILADEPTGNLDPQTSVEVMEVL 184 Query: 180 VELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVE 216 ++ G T+++ TH+ K ++ + DE ++ E Sbjct: 185 QDINKNGNTILMATHDYALLLKYPSKTLKCDENQVYE 221 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: 130 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: 227 Length adjustment: 23 Effective length of query: 218 Effective length of database: 204 Effective search space: 44472 Effective search space used: 44472 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