Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__Phaeo:GFF1143 Length = 259 Score = 217 bits (552), Expect = 2e-61 Identities = 109/246 (44%), Positives = 162/246 (65%), Gaps = 10/246 (4%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82 ++I ++K YG+ V++ +++T HRG+ + + G SGSGKST++RC N LE+ Q G I+ Sbjct: 8 LEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQEGDILFK 67 Query: 83 GIELT----------SDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKR 132 G + SD K + ++R+ + MVFQ FNL+ H+TIL+N+ AP+ V + Sbjct: 68 GEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLTVLGRDRA 127 Query: 133 EAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEM 192 E E+ A YL KV I ++ YP QLSGGQQQR AIAR+LCM+P+ +LFDEPTSALDPE+ Sbjct: 128 EVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPTSALDPEL 187 Query: 193 IKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSER 252 +EV+ + LA EG TM+ VTH+M A V++ ++F+ G I E+ P + F + +SER Sbjct: 188 EQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVFGSTRSER 247 Query: 253 TKQFLS 258 + FL+ Sbjct: 248 LRGFLA 253 Lambda K H 0.320 0.134 0.391 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: 166 Number of extensions: 5 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: 263 Length of database: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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