Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= TCDB::P48243 (242 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 238 bits (608), Expect = 7e-68 Identities = 125/251 (49%), Positives = 165/251 (65%), Gaps = 12/251 (4%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 +++ GV K +G+ L +DL+I G+ V ++GPSGSGKSTL R + LE I+EG IE+ Sbjct: 24 LVRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEV 83 Query: 61 DGKVL-----------PEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMK 109 DG+ L P + L +R VGMVFQSFNLFPH+ NV AP++V + Sbjct: 84 DGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLS 143 Query: 110 KSEAEKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDP 169 K+EA A LL VG+ ++ + +PAQLSGGQQQRVAIARALAM PK+MLFDE TSALDP Sbjct: 144 KAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDP 203 Query: 170 EMVNEVLDVMASLAK-EGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPK 228 E+ EVL+V+ L + +TM+ VTH+MGFAR+ ADRV F G I E PD F NP+ Sbjct: 204 ELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQ 263 Query: 229 SDRAKDFLGKI 239 +R ++FL + Sbjct: 264 EERTREFLSAV 274 Lambda K H 0.319 0.135 0.379 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: 211 Number of extensions: 6 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: 242 Length of database: 278 Length adjustment: 24 Effective length of query: 218 Effective length of database: 254 Effective search space: 55372 Effective search space used: 55372 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