Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b21589 SM_b21589 sugar uptake ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Smeli:SM_b21589 Length = 341 Score = 339 bits (870), Expect = 6e-98 Identities = 185/337 (54%), Positives = 246/337 (72%), Gaps = 7/337 (2%) Query: 57 TSMGRYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSL 116 T GR L L+AL+ +++A + F N+ Q+ RLYGS++DILNR APV LL+IGM++ Sbjct: 7 TYAGRLLPQLIALAAIVVAISIVFPGFLNLQIQNGRLYGSMVDILNRGAPVVLLAIGMTV 66 Query: 117 VIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGI 176 VIAT GIDLSVGAVMAI GAV A+L+ SL + A L VG++ G NG LV+ L I Sbjct: 67 VIATKGIDLSVGAVMAICGAVAASLI-TSGHSLAETLLATLAVGIVCGIWNGVLVAVLDI 125 Query: 177 QPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMP--VWIVIGMLTFS 234 QPI+ATL+LMVAGRG+AQLI +G I+TF PG IG G F GLPMP +W+V G+L Sbjct: 126 QPIIATLVLMVAGRGIAQLITEGTILTFNDPGLIFIGSGSFAGLPMPLVIWLVFGLLV-- 183 Query: 235 QLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSD 294 LL+R+TALG+ IEA+G N +AS G+ + + AY ++GLCAA+AG+I+ ADI+G+D Sbjct: 184 ALLVRRTALGMLIEAIGINRQASTLSGVLTPVLLVAAYVLSGLCAAIAGIIAAADIRGAD 243 Query: 295 ANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLI 354 ANNAGLWLELDA+LAVV+GG +L GGRFS+ SV+GA+IIQ + T I++SG P +FNL+I Sbjct: 244 ANNAGLWLELDAILAVVVGGTSLLGGRFSIAASVLGAVIIQAINTGILLSGFPPEFNLII 303 Query: 355 KAIVILTVLLLQSAKFRRQLSALFKSKRHADAKPAEK 391 KA +I+ +L+LQS +FR +S F S A +KP E+ Sbjct: 304 KAAIIIFILVLQSPRFRTGVS--FLSIPKAASKPTER 338 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: 394 Number of extensions: 21 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: 405 Length of database: 341 Length adjustment: 30 Effective length of query: 375 Effective length of database: 311 Effective search space: 116625 Effective search space used: 116625 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 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