Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b21343 SM_b21343 sugar uptake ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Smeli:SM_b21343 Length = 334 Score = 207 bits (527), Expect = 4e-58 Identities = 118/297 (39%), Positives = 183/297 (61%), Gaps = 8/297 (2%) Query: 78 FIDSSFFNISYQDDRLYGSLIDI-LNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGA 136 F+ FN+ + + L +++ L + A + +++IGM+LVIATGGIDLSVG++MAI GA Sbjct: 32 FLALILFNVVFTPNFLSLQTLNVNLTQVATIVIVAIGMTLVIATGGIDLSVGSLMAIGGA 91 Query: 137 VCANLL---LVPDISLVTVIAAGLIVGLLA----GCINGGLVSFLGIQPIVATLLLMVAG 189 + + L P S+ +A ++ ++A G NG LV+ IQPI+ATL+L +AG Sbjct: 92 LAPMIFMGTLFPVSSMPVAVALAFVLPVVATGLLGLFNGLLVTRFAIQPIIATLVLFIAG 151 Query: 190 RGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTALGLFIEA 249 RG+AQ++ G + F++ GF I +G+ G+P V ++I + + +R T G + A Sbjct: 152 RGIAQVMTNGNLQVFRNEGFQFIALGRVAGIPAQVILMIAIAAIAWAAIRYTVFGRQVIA 211 Query: 250 VGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLWLELDAVLA 309 VG N KASR GI +KL Y I+G A +AG+I A SDAN GL +ELDA+ A Sbjct: 212 VGGNEKASRLTGIPVHRVKLLVYMISGALAGVAGLIVVARNSASDANLVGLGMELDAIAA 271 Query: 310 VVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILTVLLLQ 366 V +GG LTGGR +++ +V+GAL+IQ + T++ +G+P L++KA +IL + +Q Sbjct: 272 VAVGGTLLTGGRANIVGTVIGALVIQLVRYTLLANGVPDAAALIVKAALILLAVFIQ 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: 341 Number of extensions: 26 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: 334 Length adjustment: 30 Effective length of query: 375 Effective length of database: 304 Effective search space: 114000 Effective search space used: 114000 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