Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 8502447 DvMF_3153 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Miya:8502447 Length = 233 Score = 103 bits (257), Expect = 5e-27 Identities = 73/183 (39%), Positives = 99/183 (54%), Gaps = 5/183 (2%) Query: 240 AVQEATGTRPTTWWPSLLILF---APISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTA 296 AV + RP W+ + F P+ ++ F D T + ++ F A Sbjct: 45 AVMRLSAVRPLVWFSAGFTEFFRNTPLLVQIFFWYFGSDAVLPTAVN-QWLYKQNFEFAA 103 Query: 297 LLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLI 356 +I+L +YTAAFIAE +R+GI +I R Q EA+ A GL + M V+LPQA R+IVPPLI Sbjct: 104 GVISLAVYTAAFIAEEIRSGIFSIPRTQLEASRACGLTFLQAMRYVVLPQAFRIIVPPLI 163 Query: 357 SQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNL 416 SQ LNL KNSSL + + M+L I + T E + LIYLTISL +S + Sbjct: 164 SQALNLFKNSSLCMTIGVMELTYMARQIE-SYTFHGFEAFTVSTLIYLTISLLVSFSITQ 222 Query: 417 YNK 419 YNK Sbjct: 223 YNK 225 Score = 42.4 bits (98), Expect = 1e-08 Identities = 23/57 (40%), Positives = 34/57 (59%) Query: 88 LIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWI 144 +I+G++ T +S L +LA LGT+I V+RLS + + E FRN PLL+ I Sbjct: 19 IIDGVVVTCQISALSLVLAMALGTLIAVMRLSAVRPLVWFSAGFTEFFRNTPLLVQI 75 Lambda K H 0.326 0.139 0.419 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: 230 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 426 Length of database: 233 Length adjustment: 27 Effective length of query: 399 Effective length of database: 206 Effective search space: 82194 Effective search space used: 82194 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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