Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate H281DRAFT_05872 H281DRAFT_05872 amino acid ABC transporter membrane protein 2, PAAT family
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__Burk376:H281DRAFT_05872 Length = 214 Score = 128 bits (321), Expect = 9e-35 Identities = 66/206 (32%), Positives = 122/206 (59%), Gaps = 3/206 (1%) Query: 9 NIEFLMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLW 68 ++ L+QGL TL +++A + S + G A+ +++G + +A Y ++FR TP+L+ Sbjct: 9 SLSILLQGLVTTLLLSIAAIVGSTLIGLLAAVLRSFGPWGTDRIAKLYTELFRGTPVLIT 68 Query: 69 MLAACFVLPVFFGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKF 128 ++ F + F G IG S+Y + +AE+ R G+ S+PKGQ+E + G + Sbjct: 69 LMFIYFGVSYFGYAIDVFAAGVIGLSVYQGAYIAEVFRAGIESVPKGQWEVSQILGLSRI 128 Query: 129 FTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILA 188 T ++LPQT R ++P L+ Q ++ +KDT+ ++ +G++EL + + I+ ++ EI Sbjct: 129 QTFASVVLPQTGRIVLPPLVGQYLSLIKDTSIVSMIGMSELMHGGQAIVDRVGKPVEI-- 186 Query: 189 MIGVVAGIYFIICFSLSMLVRYYAKK 214 G+VA IYF++CF LS VR++ ++ Sbjct: 187 -YGLVALIYFVVCFPLSQWVRHHDRR 211 Lambda K H 0.331 0.144 0.428 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: 135 Number of extensions: 11 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: 219 Length of database: 214 Length adjustment: 22 Effective length of query: 197 Effective length of database: 192 Effective search space: 37824 Effective search space used: 37824 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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