Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= TCDB::P48245 (273 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 101 bits (251), Expect = 3e-26 Identities = 71/224 (31%), Positives = 122/224 (54%), Gaps = 18/224 (8%) Query: 17 INSQTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAI 76 ++S W+ GL TL +A+ S++ +L +G L LGR S + +RW IE FR + Sbjct: 183 VSSNDWS-----GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGL 237 Query: 77 PVLILMIFAYQMFAQYNIVPSSQLAFAAV---VFGLTMYNGSVIAEILRSGIASLPKGQK 133 P++ ++ F M ++ S+ + + GLT++ + +AE +R G+ ++P+GQ Sbjct: 238 PLVTILFFGQVMVP---LMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQF 294 Query: 134 EAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGI-QS 192 EAA ALG++ QT I+LPQA+ +PA++ + L+D+ L +G +E++ GI +S Sbjct: 295 EAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELL--GISRS 352 Query: 193 ASVNRNYLAALFVVALIMIVLN----FSLTALASRIERQLRAGR 232 N YL V L + VL + L L+ R+E++L R Sbjct: 353 ILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRLTPQR 396 Lambda K H 0.323 0.136 0.395 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: 291 Number of extensions: 13 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: 273 Length of database: 396 Length adjustment: 28 Effective length of query: 245 Effective length of database: 368 Effective search space: 90160 Effective search space used: 90160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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