Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= uniprot:B2TBJ8 (250 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 113 bits (282), Expect = 4e-30 Identities = 68/211 (32%), Positives = 118/211 (55%), Gaps = 10/211 (4%) Query: 22 TLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLVYYGMGQF 81 TL + S+ +G LL L+ R+S + A AY+ FRG+PLL+Q+F+VY+G+ + Sbjct: 19 TLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFGIPKL 78 Query: 82 GVIRESFL------WPVLRE----PYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAG 131 + +SF+ PV ++ AV++ +L + Y AEI R G+ ++ GQ+EA Sbjct: 79 LMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIERGQMEAA 138 Query: 132 YSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQT 191 S+G++ +R VI P A ++ +P E + ++K T+L S++ E+T Q II +T Sbjct: 139 RSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNGQLIIART 198 Query: 192 YRTTEVFICAALIYLFLNFVIVRLLGMLETR 222 Y + +++ IYL + F + R++ LE R Sbjct: 199 YESFAIWLTVGFIYLIMTFTLSRIVDYLERR 229 Lambda K H 0.331 0.143 0.431 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: 122 Number of extensions: 6 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: 250 Length of database: 234 Length adjustment: 23 Effective length of query: 227 Effective length of database: 211 Effective search space: 47897 Effective search space used: 47897 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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