Align ABC-type transporter, permease components, component of Maltose transporter, MusEFGKI (characterized)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like
Query= TCDB::Q8NMV5 (304 letters) >FitnessBrowser__SynE:Synpcc7942_0471 Length = 276 Score = 122 bits (305), Expect = 1e-32 Identities = 86/279 (30%), Positives = 144/279 (51%), Gaps = 10/279 (3%) Query: 29 SGSAKFVVYAILAFFTIVFLGPILFIFINSFKSKFAISSDPFSLP--IGETWVGFENFMV 86 +G ++Y +L + L P+L++ +FKS D F P T +NF Sbjct: 5 AGFRSLLLYLLLGTIAVAMLIPLLWLVSTAFKSA---GEDIFQFPPQFLPTQPTLDNFRR 61 Query: 87 GLTKQGFLEATLWSFIITILSVIVIVFFSAMTAYYITRVKTWWTNLLYYLFVVSMIIPFQ 146 T+ + L S + +L+V + + F ++ AY + R++ L+ L V +++IPFQ Sbjct: 62 VWTENPLGQYFLNSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQ 121 Query: 147 MVMFPTVKIADMLHLNNP-IGIVVLYLGFGSGLSVFMFAGFVKSIPLDVEEAAMIDGCGP 205 +VM P + L L N +G+V YL S +F+ + IP D+EEAA IDGC Sbjct: 122 VVMIPLYVLIINLGLRNTYLGLVFPYLA--SAFGIFLLRQAFQGIPKDLEEAARIDGCND 179 Query: 206 LQNYFRVVWPMLKPTAITVAILNAMWVWNDYLLPYLVIGLSTRYKTIPVVIQSFVGSNGN 265 L ++ V+ P +P IT+AI + W+D+L P +++ RY T+P+ I + + S + Sbjct: 180 LGVWWNVMIPSARPALITLAIFVFIGSWSDFLWPLIILDEPDRY-TLPLGIAT-LASGFS 237 Query: 266 RDTGAMMAMLVLAIIPIVIFYFSTQRHIIEGVAAGAVKG 304 D + A VL+I+P+ + + QR+I+ AA VKG Sbjct: 238 LDWRLVAAGSVLSILPVFGVFLALQRYIVPSAAASGVKG 276 Lambda K H 0.329 0.141 0.434 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: 290 Number of extensions: 27 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: 304 Length of database: 276 Length adjustment: 26 Effective length of query: 278 Effective length of database: 250 Effective search space: 69500 Effective search space used: 69500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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