Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_085219126.1 B9N75_RS12690 ATP-binding cassette domain-containing protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_900177405.1:WP_085219126.1 Length = 252 Score = 152 bits (384), Expect = 6e-42 Identities = 89/227 (39%), Positives = 136/227 (59%), Gaps = 3/227 (1%) Query: 2 ITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVD 61 I +K+V+K +G VL S +VK GE + + G SG+GKS LIK + GL G I +D Sbjct: 7 IAIKDVAKAFGENVVLDGVSLDVKTGESLAIIGQSGTGKSVLIKCILGLLTPDAGSIRID 66 Query: 62 G-IVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKL 120 G VV + + ++R + GM+FQ LF L I N+T + ++ A R+ A + Sbjct: 67 GQEVVGASEREQERIRRKTGMLFQGGALFDSLPIWRNVTFGLTRGAYKNPAKMRDIAAEN 126 Query: 121 LERVGLSAH-ANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVM 179 LERVGL A + P+ LSGG Q+RVA+ARA+ P + FDEPT+ LDP + + D++ Sbjct: 127 LERVGLGADILDLRPSALSGGMQKRVALARAVAPRPEILFFDEPTTGLDPIRADVINDLI 186 Query: 180 VELANE-GMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFD 225 + L ++ G+T + +TH+M ARK+A+RV + G+I+ P+D +D Sbjct: 187 MSLVDDLGITALTITHDMASARKIAHRVAMLYRGRIIWCGPRDRLYD 233 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: 143 Number of extensions: 12 Number of successful extensions: 4 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: 252 Length adjustment: 24 Effective length of query: 217 Effective length of database: 228 Effective search space: 49476 Effective search space used: 49476 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