Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate WP_081718345.1 N177_RS02595 ABC transporter permease
Query= uniprot:B2TBJ8 (250 letters) >NCBI__GCF_000496075.1:WP_081718345.1 Length = 248 Score = 152 bits (385), Expect = 5e-42 Identities = 84/226 (37%), Positives = 135/226 (59%), Gaps = 2/226 (0%) Query: 3 FDFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVF 62 F DF ++L+ TT+ L SL++G +SL + R+SP+ + A Y+ F Sbjct: 19 FSTDFAQRYGFRMLSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFF 78 Query: 63 RGSPLLIQMFLVYYGMGQFGVIRESF-LWPVLREPYMCAVLSLALCTAGYTAEIIRGGLM 121 RG+PLL Q FLVYYG G F ++ LW R+ + CAV + +L T+ Y AEI+ G + Sbjct: 79 RGTPLLAQTFLVYYGAGSFRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIR 138 Query: 122 AVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVT 181 VP QIEAG ++GLS + + R++ P AL L Y E VL++K +A+AS++T++++ Sbjct: 139 TVPRSQIEAGQALGLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLM 198 Query: 182 GVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHL 227 G ++ +++ + +I AA++YL L + RL ++E RL+RHL Sbjct: 199 GETRRAFSRSF-DFQTYIWAAILYLVLVETLRRLWDVMERRLTRHL 243 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: 164 Number of extensions: 9 Number of successful extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 226 Effective length of database: 224 Effective search space: 50624 Effective search space used: 50624 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 24 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