Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate GFF3090 HP15_3033 amino acid ABC transporter, inner membrane subunit
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__Marino:GFF3090 Length = 240 Score = 165 bits (417), Expect = 9e-46 Identities = 86/225 (38%), Positives = 138/225 (61%), Gaps = 14/225 (6%) Query: 11 TIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRV-------SPHWLPNRFARAYILVFR 63 TI + + TT+ L F SL++G L+++ + +R P WL Y +FR Sbjct: 19 TIMEYWDGMVTTVHLVFLSLVIGLLVAVPLAILRTVRNPFVSGPVWL-------YTYLFR 71 Query: 64 GSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAV 123 G+PLLIQ++++YYG+ Q I+E+F W + REP+ A+L+ L TA YT EIIRG +++ Sbjct: 72 GTPLLIQLYIIYYGLAQIEGIQETFWWEIFREPFYPALLAFTLNTAAYTTEIIRGAIIST 131 Query: 124 PVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGV 183 P G+IEA + G++ F +RR++ P A R+ + AYS E + ++ ++A+AS+VT+ ++TG Sbjct: 132 PNGEIEAAKAYGMNWFMRMRRIVLPSAARRAVQAYSNEVIFMLHASAIASVVTIVDLTGA 191 Query: 184 AQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLR 228 A+ I + Y + FI AL Y+ L F++V LET L +H R Sbjct: 192 ARNIYSRFYAPFDAFIFVALCYMALTFILVFAFRKLETHLLKHQR 236 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: 160 Number of extensions: 9 Number of successful extensions: 1 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: 240 Length adjustment: 24 Effective length of query: 226 Effective length of database: 216 Effective search space: 48816 Effective search space used: 48816 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 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