Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 140 bits (353), Expect = 2e-38 Identities = 95/228 (41%), Positives = 137/228 (60%), Gaps = 19/228 (8%) Query: 1 MITLKNVSKWYGHFQ----VLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQG 56 +I KN+ K YG + VL + ++K+GE V + GPSG GKSTL+ + L+ +G Sbjct: 17 LIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKG 76 Query: 57 EITVDGIVVNDKKT------DLAKLRSRV-GMVFQHFELFPHLSIIENLTLAQVKVLKRD 109 + + G KKT D A R ++ G +FQ F L L+ +EN+ L V + +++ Sbjct: 77 MVYIKG-----KKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVELPLV-LDEKN 130 Query: 110 KAPAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDP 169 K +KA KLL+ + L N +P QLSGGQQQRVAIARAL +P + DEPT LD Sbjct: 131 KNYRIKKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDS 190 Query: 170 EMINEVLDVMVEL-ANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVE 216 + EV+D++ EL EG+T+++VTHE FA K A+R+I M +G+IVE Sbjct: 191 KNSREVMDILKELNEKEGITVIMVTHEPEFA-KYASRIINMKDGEIVE 237 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: 151 Number of extensions: 9 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: 238 Length adjustment: 23 Effective length of query: 218 Effective length of database: 215 Effective search space: 46870 Effective search space used: 46870 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 Apr 09 2024. 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