Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate Pf1N1B4_4804 ABC-type polar amino acid transport system protein, ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4804 Length = 254 Score = 244 bits (623), Expect = 1e-69 Identities = 123/244 (50%), Positives = 172/244 (70%), Gaps = 10/244 (4%) Query: 6 NVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDGIVV 65 +++K+Y HF L D + EV++GEV+ + GPSGSGKSTL++ VN LE + +G + VDG +V Sbjct: 9 SLNKYYDHFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWVDGELV 68 Query: 66 NDK----------KTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPARE 115 + ++ +A+ R GMVFQ F LFPH+++++N+ +VLKR A E Sbjct: 69 GYRIVGNKLHELNESQIARQRLATGMVFQRFNLFPHMTVLQNIIEGPCQVLKRSPKEAHE 128 Query: 116 KALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEV 175 +AL+LL RVGL+ N +P +LSGGQQQRVAIARAL M P MLFDEPTSALDPE++ EV Sbjct: 129 EALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALDPELVGEV 188 Query: 176 LDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDF 235 L VM +LA GMTM+VVTHE+GFAR+V+NR++FMDEG+IVE + P++ R + F Sbjct: 189 LSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDEGQIVEAGSPEEILISPQNPRTQSF 248 Query: 236 LAKI 239 ++ + Sbjct: 249 ISAV 252 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: 184 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 217 Effective length of database: 230 Effective search space: 49910 Effective search space used: 49910 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