Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__SynE:Synpcc7942_0471 Length = 276 Score = 132 bits (332), Expect = 9e-36 Identities = 82/271 (30%), Positives = 141/271 (52%), Gaps = 12/271 (4%) Query: 23 IILAILVVLTLGPIVFMVLTSLMD--HNAIARGKWIAPTR--FSNYVEVFQKLPFGIYFR 78 ++L + V L P++++V T+ + PT+ N+ V+ + P G YF Sbjct: 14 LLLGTIAVAMLIPLLWLVSTAFKSAGEDIFQFPPQFLPTQPTLDNFRRVWTENPLGQYFL 73 Query: 79 NSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVK 138 NS V + + + L+ +LA Y LA+ +F G +LI+AT L+P + ++PLY+ + Sbjct: 74 NSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQVVMIPLYVLIIN 133 Query: 139 IKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLR 198 + L N+ GLV Y A F I+++R F IP +LEEAARIDGCN + Sbjct: 134 LG------LRNTYLGLVFPYLAS--AFGIFLLRQAFQGIPKDLEEAARIDGCNDLGVWWN 185 Query: 199 VMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTARYDLLMA 258 VM+P A P ++ AI++F+ +W + ++ ++L + T+P GI + + + L+ A Sbjct: 186 VMIPSARPALITLAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATLASGFSLDWRLVAA 245 Query: 259 AGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 + +PV +F +Q+ + A VKG Sbjct: 246 GSVLSILPVFGVFLALQRYIVPSAAASGVKG 276 Lambda K H 0.332 0.145 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: 251 Number of extensions: 17 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: 289 Length of database: 276 Length adjustment: 26 Effective length of query: 263 Effective length of database: 250 Effective search space: 65750 Effective search space used: 65750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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