Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 212 bits (539), Expect = 7e-60 Identities = 116/251 (46%), Positives = 160/251 (63%), Gaps = 12/251 (4%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 ++ V+K YG VL ++++GE V + GPSGSGKSTL++ + LE + +G I V Sbjct: 24 LVRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEV 83 Query: 61 DGI-----------VVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRD 109 DG +V L ++R +VGMVFQ F LFPH++ ++N+ A V+VL Sbjct: 84 DGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLS 143 Query: 110 KAPAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDP 169 KA AR +A +LL VGL FPAQLSGGQQQRVAIARAL M P MLFDE TSALDP Sbjct: 144 KAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDP 203 Query: 170 EMINEVLDVMVELAN-EGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPK 228 E+ EVL+V+ L +TM++VTH+MGFAR+ A+RV F +G+I E D F++P+ Sbjct: 204 ELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQ 263 Query: 229 SDRAKDFLAKI 239 +R ++FL+ + Sbjct: 264 EERTREFLSAV 274 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: 206 Number of extensions: 7 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: 278 Length adjustment: 24 Effective length of query: 217 Effective length of database: 254 Effective search space: 55118 Effective search space used: 55118 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: 47 (22.7 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