Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_047092042.1 AAV99_RS00435 ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_001013305.1:WP_047092042.1 Length = 233 Score = 127 bits (319), Expect = 2e-34 Identities = 79/208 (37%), Positives = 120/208 (57%), Gaps = 9/208 (4%) Query: 15 QVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDG---IVVNDKKTD 71 ++L +V +GE + + GPSGSGKS+L+ ++GLE G++TV G +N+ Sbjct: 28 EILRGIDLDVARGETLALLGPSGSGKSSLMSVLSGLERATSGKLTVAGEDFTALNEDALA 87 Query: 72 LAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKLLERVGLSAHAN 131 +A+ R R+G+V Q F L P ++ +EN+ +++ D A E+A LE VGL Sbjct: 88 MAR-RGRIGIVLQAFHLLPTMTAVENVA-TPLELAGEDGA--WERATAELEAVGLGHRLT 143 Query: 132 KFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMVE-LANEGMTMM 190 +PAQLSGG+QQRVAIARA+ P + DEPT LD V D + E A G T++ Sbjct: 144 HYPAQLSGGEQQRVAIARAIVSRPPLIFADEPTGNLDTNTGASVEDALFERRAETGATLI 203 Query: 191 VVTHEMGFARKVANRVIFMDEGKIVEDS 218 ++TH+ A + NRV+ + +G I D+ Sbjct: 204 IITHDRKLAER-CNRVVTLGDGLIATDT 230 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: 116 Number of extensions: 4 Number of successful extensions: 3 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: 233 Length adjustment: 23 Effective length of query: 218 Effective length of database: 210 Effective search space: 45780 Effective search space used: 45780 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