Align Inner-membrane translocator (characterized, see rationale)
to candidate 18255 b4230 predicted sugar transporter subunit: membrane component of ABC superfamily (RefSeq)
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Keio:18255 Length = 341 Score = 335 bits (858), Expect = 2e-96 Identities = 184/320 (57%), Positives = 234/320 (73%), Gaps = 6/320 (1%) Query: 56 STSMGRYLWP-----LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALL 110 +T R+ WP L+AL ++LL + + F+ + QD RL+GS IDILNR+APVALL Sbjct: 10 TTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALL 69 Query: 111 SIGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGL 170 +IGM+LVIATGGIDLSVGAVMAIAGA A + V SL V+ + L G+LAG NG L Sbjct: 70 AIGMTLVIATGGIDLSVGAVMAIAGATTA-AMTVAGFSLPIVLLSALGTGILAGLWNGIL 128 Query: 171 VSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGM 230 V+ L IQP VATL+LMVAGRGVAQLI GQI+TF P + G G L LP PV I + Sbjct: 129 VAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLT 188 Query: 231 LTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADI 290 L LL RKTALG+FIEAVG N +A++ G+N + I + Y ++GLCAA+AG+I ADI Sbjct: 189 LILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADI 248 Query: 291 QGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKF 350 +G+DANNAGLWLELDA+LAVVIGG +L GGRF+L+LSVVGALIIQ + T I++SG P + Sbjct: 249 RGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEM 308 Query: 351 NLLIKAIVILTVLLLQSAKF 370 N ++KA+V+L VL++QS +F Sbjct: 309 NQVVKAVVVLCVLIVQSQRF 328 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: 399 Number of extensions: 19 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: 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