Align ABC transporter related (characterized, see rationale)
to candidate AO356_29795 AO356_29795 amino acid transporter
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29795 Length = 268 Score = 305 bits (782), Expect = 5e-88 Identities = 154/247 (62%), Positives = 193/247 (78%), Gaps = 1/247 (0%) Query: 8 ALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSL 67 A++ + + KS+G+ VLKGI A +G+V+SILGASGSGKSTFLRCLNLLE P GS+ + Sbjct: 14 AIATQGLRKSYGEIEVLKGIDFTAREGEVVSILGASGSGKSTFLRCLNLLELPSAGSLDV 73 Query: 68 AGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRS 127 GE +K+K+ G +DR+QVDR+R+Q+ MVFQNF LWSHMTVLENL+E P+ VQ R Sbjct: 74 FGERVKLKQ-GASDAHIADRKQVDRLRTQVAMVFQNFCLWSHMTVLENLMEAPVHVQGRK 132 Query: 128 RAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDP 187 +AE +EA ++L +VGL + YPA LSGGQQQR AIARAL M P+V+LFDEPTSALDP Sbjct: 133 KAEVRDEALSILERVGLTHRADAYPAQLSGGQQQRAAIARALVMKPRVLLFDEPTSALDP 192 Query: 188 ELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKS 247 ELVGEVL+VMR LA EGRTML+VTHEM FAR VSNR++FL QG++EA G P ++F + Sbjct: 193 ELVGEVLKVMRDLATEGRTMLIVTHEMAFARDVSNRILFLDQGRIEAQGQPQQLFAGGVN 252 Query: 248 DRFRQFV 254 +RF QFV Sbjct: 253 ERFDQFV 259 Lambda K H 0.318 0.133 0.377 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: 7 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: 268 Length adjustment: 25 Effective length of query: 238 Effective length of database: 243 Effective search space: 57834 Effective search space used: 57834 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 (21.7 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