Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 125 bits (314), Expect = 1e-33 Identities = 83/283 (29%), Positives = 143/283 (50%), Gaps = 15/283 (5%) Query: 13 KKKIKDTIANIILAILVVLTLGPIVFMVLTSLM---DHNAIARGKWIAPTRFSNYVEVFQ 69 K + + IA + L++ +L PI++ +LTS+ D AI W +Y ++Q Sbjct: 2 KPRFRWAIAALALSLF---SLAPILWQLLTSIKVNADIAAIPTIYWPRQWTVEHYQALWQ 58 Query: 70 KLP-FGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMF 128 + P FG Y NS +V +I + AL+I T Y++A+ + S +L L P ++ Sbjct: 59 QTPAFGRYLLNSAVVSAIATLAALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLL 118 Query: 129 LLPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARID 188 L ++ +Q N+ LV+ Y+A +P I ++R FF +P ELEEAA+ID Sbjct: 119 FQGL------LEVVRWLQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQID 172 Query: 189 GCNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIR--GFI 246 G + +++PL P +V I F+ +W+E + A + + T+P + G I Sbjct: 173 GLSLGQRLWLILVPLTAPALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGI 232 Query: 247 AYTTARYDLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 + Y + AA + T+P++ + Q++ + G+TAGAVKG Sbjct: 233 SIFDVPYGDIAAATVVATLPLIGLVLVAQRRILEGLTAGAVKG 275 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: 194 Number of extensions: 7 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: 275 Length adjustment: 26 Effective length of query: 263 Effective length of database: 249 Effective search space: 65487 Effective search space used: 65487 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