Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= TCDB::P0AAG3 (241 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 216 bits (551), Expect = 3e-61 Identities = 120/251 (47%), Positives = 160/251 (63%), Gaps = 12/251 (4%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 M+ +V+K YG VL +V++GE V + GPSGSGKSTL++ + LE + G I V Sbjct: 25 MVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGIDDGLIEV 84 Query: 61 DGI-----------VVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRD 109 DG +V L ++R +VGMVFQ F LFPH++ ++N+ A V+VL Sbjct: 85 DGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLS 144 Query: 110 KAPAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDP 169 K ARE+A +LL VGL FPAQLSGGQQQRVAIARAL M P MLFDE TSALDP Sbjct: 145 KREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDP 204 Query: 170 EMINEVLDVMVELAN-EGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPK 228 E+ EVL V+ L +TM++VTH+MGFAR+ A+RV F +G+I E DA F++P+ Sbjct: 205 ELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDALFNNPQ 264 Query: 229 SDRAKDFLAKI 239 DR ++FL+ + Sbjct: 265 EDRTREFLSAV 275 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: 208 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: 279 Length adjustment: 24 Effective length of query: 217 Effective length of database: 255 Effective search space: 55335 Effective search space used: 55335 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 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