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Parts of the TniQ protein appear in Foldit the CRISPR-Cas Transposase series of puzzles.

Puzzle 1787 first presented the sequence shown below, which is roughly the second half of TniQ. (See TniQ part 1 for the first half.)

Primary sequence in FolditEdit

The primary sequence has a length of 202 residues (segments).

The overall Foldit sequence is:

gheaactvsnwlagheskplpnlpksyrwglvhwwmgikdsefdhfsfvqffsnwprsfhsiiedevefnlehavvstselrlkdllgrlffgsirlpernlqhniilgellcylenrlwqdkglianlkmnaleatvmlncsldqiasmveqrilkpnrkskpnspldvtdylfhfgdifclwlaefqsdefnrsfyvsrw

With rulers, the Foldit sequence is:

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
gheaactvsnwlagheskplpnlpksyrwglvhwwmgikdsefdhfsfvqffsnwprsfhsiiedevefnlehavvstse

0                  1         1         1         1         1         1         1
8        9         0         1         2         3         4         5         6
12345678901234567890123456789012345678901234567890123456789012345678901234567890
lrlkdllgrlffgsirlpernlqhniilgellcylenrlwqdkglianlkmnaleatvmlncsldqiasmveqrilkpnr

1        1         1         1         2 2
6        7         8         9         0 0
123456789012345678901234567890123456789012
kskpnspldvtdylfhfgdifclwlaefqsdefnrsfyvsrw

PDB MatchesEdit

As described in CRISPR-Cas Transposase, the sequence matches chains I and J of these three PDB entries:

In these three PDB entries, chain I is referred to as "TniQ monomer 1", and chain J is "TniQ monomer 2". The two chains start out with identical sequences, but then diverge.

While the two chains have different primary sequences, the sequence of each chain I is identical in all three PDB entries, and each chain J is also identical to the other chains J.

Chains I and J together form a dimer that makes the complete TniQ.

The identical chains in the three PDB entries mean matches to Foldit are also identical.

(The 3D structure (tertiary structure of the TniQ protein is likely to be at least somewhat different between 6PIF, 6PIG, and 6PIJ.)

The online tool JPred can be used to match a primary structure to the PDB.

Combining three reports, the JPred results for chain I of the three PDB entries is:

>6pif_I, 6pig_j, 6pij_J mol:protein length:358  TniQ monomer 1
          Length = 358

 Score =  400 bits (1027), Expect = e-111
 Identities = 195/202 (96%), Positives = 195/202 (96%), Gaps = 7/202 (3%)

Query: 1   GHEAACTVSNWLAGHESKPLPNLPKSYRWGLVHWWMGIKDSEFDHFSFVQFFSNWPRSFH 60
           GHEAACTVSNWLAGHESKPLPNLPKSYRWGLVHWWMGIKDS  DHFSFVQFFSNWPRSFH
Sbjct: 164 GHEAACTVSNWLAGHESKPLPNLPKSYRWGLVHWWMGIKDS--DHFSFVQFFSNWPRSFH 221

Query: 61  SIIEDEVEFNLEHAVVSTSELRLKDLLGRLFFGSIRLPERNLQHNIILGELLCYLENRLW 120
           SIIEDEVEFNLEHAVVSTSELRLKDLLGRLFFGSIRLPERNLQHNIILGELLCYLENRLW
Sbjct: 222 SIIEDEVEFNLEHAVVSTSELRLKDLLGRLFFGSIRLPERNLQHNIILGELLCYLENRLW 281

Query: 121 QDKGLIANLKMNALEATVMLNCSLDQIASMVEQRILKPNRKSKPNSPLDVTDYLFHFGDI 180
           QDKGLIANLKMNALEATVMLNCSLDQIASMVEQRILKPNRKSK     DVTDYLFHFGDI
Sbjct: 282 QDKGLIANLKMNALEATVMLNCSLDQIASMVEQRILKPNRKSK-----DVTDYLFHFGDI 336

Query: 181 FCLWLAEFQSDEFNRSFYVSRW 202
           FCLWLAEFQSDEFNRSFYVSRW
Sbjct: 337 FCLWLAEFQSDEFNRSFYVSRW 358

Combining the matches for chain J shows:

>6pif_I, 6pig_j, 6pij_J mol:protein length:369  TniQ monomer 2
          Length = 369

 Score =  385 bits (988), Expect = e-107
 Identities = 187/199 (93%), Positives = 189/199 (94%), Gaps = 3/199 (1%)

Query: 3   EAACTVSNWLAGHESKPLPNLPKSYRWGLVHWWMGIKDSEFDHFSFVQFFSNWPRSFHSI 62
           EAACTVSNWLAGHESKPLPNLPKSYRWGLVHWWMGIKD   DHFSFVQFFSNWPRSFHSI
Sbjct: 174 EAACTVSNWLAGHESKPLPNLPKSYRWGLVHWWMGIKD---DHFSFVQFFSNWPRSFHSI 230

Query: 63  IEDEVEFNLEHAVVSTSELRLKDLLGRLFFGSIRLPERNLQHNIILGELLCYLENRLWQD 122
           IEDEVEFNLEHAVVSTSELRLKDLLGRLFFGSIRLPERNLQHNIILGELLCYLENRLWQD
Sbjct: 231 IEDEVEFNLEHAVVSTSELRLKDLLGRLFFGSIRLPERNLQHNIILGELLCYLENRLWQD 290

Query: 123 KGLIANLKMNALEATVMLNCSLDQIASMVEQRILKPNRKSKPNSPLDVTDYLFHFGDIFC 182
           KGLIANLKMNALEATVMLNCSLDQIASMVEQRILKPN  +   +  DVTDYLFHFGDIFC
Sbjct: 291 KGLIANLKMNALEATVMLNCSLDQIASMVEQRILKPNAAAAAAAAADVTDYLFHFGDIFC 350

Query: 183 LWLAEFQSDEFNRSFYVSR 201
           LWLAEFQSDEFNRSFYVSR
Sbjct: 351 LWLAEFQSDEFNRSFYVSR 369

Chain I matches the Foldit protein starting with first segment, but chain J skips the first two segments.

Chain I has two gaps, spots where Foldit has segments that aren't found in the PDB. The first gap skips two Foldit segments, the second gap skips 5 segments.

The match to chain J starts at a different point in the PDB the match to chain J. Chain J shows a gap of three segments near the same spot as the first gap in the chain I match. Then chain J shows a nine-segment mismatch, where the PDB segment is all alanine (nine As in a row). The mismatch with chain J occurs near where the second match appears in the match with chain I.

Neither chain I or chain J match the complete Foldit protein. Chain I matches 195 out of 202 Foldit segments. The two gaps account for the difference of 7 segments. Chain J matches 187 out of 202 segments. In the mismatched section, two Foldit serines are counted as "positives", meaning they are (weak) matches for the alanines found in the PDB sequence. Overall, chain J positives cover 189 of the 202 Foldit segments.

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