Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_044621445.1 H744_RS06410 ribose ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >NCBI__GCF_000940995.1:WP_044621445.1 Length = 327 Score = 180 bits (456), Expect = 6e-50 Identities = 104/306 (33%), Positives = 182/306 (59%), Gaps = 14/306 (4%) Query: 66 LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125 L+AL L++ F++ +FF + ++++IL +++ A++++GM+LVI T GIDL Sbjct: 29 LIALIFLIVVVSFLNPNFFTVD--------NILNILRQTSVNAIIAVGMTLVILTAGIDL 80 Query: 126 SVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLL 185 SVG+V+A+ GA A+L+ + ++ ++ + L+ G G I+G +++ +Q +ATL+ Sbjct: 81 SVGSVLALCGAFAASLIAM-EVPVMIAVPTALLAGAALGAISGVIIAKGKVQAFIATLVT 139 Query: 186 MVAGRGVAQLINQGQII----TFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKT 241 M RGV + G+ I T FA G G +G+P+P+W+++ + LL T Sbjct: 140 MTLLRGVTMVYTDGRPISTGFTDVADSFAWFGTGYAMGIPVPIWLMVIVFAAVWYLLNHT 199 Query: 242 ALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLW 301 G +I A+G N A+R GIN +K+ Y I GL AALAG+I T+ + + AG+ Sbjct: 200 RFGRYIYALGGNESAARLSGINVDRVKIGVYAICGLLAALAGIIVTSRLSSAQP-TAGMG 258 Query: 302 LELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILT 361 ELDA+ AVV+GG +L GG+ ++ +++GALII L + + + + + ++ KA+VIL Sbjct: 259 YELDAIAAVVLGGTSLAGGKGRIMGTLIGALIIGFLNNALNLLDVSSYYQMIAKAVVILL 318 Query: 362 VLLLQS 367 +L+ + Sbjct: 319 AVLVDN 324 Lambda K H 0.323 0.136 0.379 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: 300 Number of extensions: 18 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: 405 Length of database: 327 Length adjustment: 29 Effective length of query: 376 Effective length of database: 298 Effective search space: 112048 Effective search space used: 112048 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 (22.0 bits) S2: 49 (23.5 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