Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate PP_3597 PP_3597 Amino-acid ABC transporter, ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__Putida:PP_3597 Length = 260 Score = 286 bits (733), Expect = 2e-82 Identities = 140/241 (58%), Positives = 184/241 (76%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 +I ++ ++K YG F VL D +V++GE +V+CGPSGSGKSTLI+ +N LE QQG I V Sbjct: 20 LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79 Query: 61 DGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKL 120 DGI + + A++RS +GMVFQHF LFPH+S+++N LA V + A E+A Sbjct: 80 DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139 Query: 121 LERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMV 180 L +VG+ + A+K+P+QLSGGQQQRVAIARALCM P MLFDEPTSALDPEM+ EVLDV+V Sbjct: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199 Query: 181 ELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKIL 240 +LA GMTM+ VTHEMGFAR+VA RV+F++ G+I+EDSP FF+ P+++RAK FLA+IL Sbjct: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQIL 259 Query: 241 H 241 H Sbjct: 260 H 260 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: 180 Number of extensions: 4 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 217 Effective length of database: 236 Effective search space: 51212 Effective search space used: 51212 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