***Table 2*** ------------------------------------------------------------------------------------------------------ Align- | | | ment |2' | | Posit- |Struct |Predic | Comments ion |ure |tion | ******** W.R.T. |assign |Confid | A25051 |ed |ence | ------------------------------------------------------------------------------------------------------ 039-071 Unclear Low This region is poorly conserved with many gaps. There is a concentration of aliphatic hydrophobic groups (LIV) in region 044-051 together with minor peak in strand prediction weakly suggestive of strand. 073-076 Strand Medium Highly conserved aliphatic hydrophobic residues (LIV) with high strand prediction and matching low turn prediction are seen. This type of highly conserved hydrophobic strand would be expected to pack in the core of the protein. 077-081 Coil High There is a high turn propensity in this region. A pair of conserved charged groups (R038 and R039) with the highly conserved G040 supports this prediction. The very high conservation here is indicative of an important structural or functional role for this turn. 082-087 Strand High Here we see a low turn prediction mirrored by a high strand prediction. There is a striking alternation of conserved hydrophobic residues with unconserved positions which is typical of strand. The conserved positions would be expected to pack against the core of the protein while the more polar but unconserved positions are likely to be exposed to the solvent. 088-096 Loop Medium This region shows a 3 residue insertion in sequence F13P4.DAT between residues 088 and 089 and a single residue deletion in F13TMP.FA, F13RtK.da and F13HuE.da at position 95. There is a high incidence of small residues (AG), suggesting flexability, and charged or polar residues (EKRHDNQ), including the absolutely conserved R at 089 and the conserved D at 096,suggesting an aqueous environment. These factors together with the high turn prediction are indicative of a surface loop. The alternating pattern of conserved and unconserved residues between R089 and 094 would perhaps argue for a strand in this region. 097-104 Strand High Again, an alternating pattern of conserved, mainly hydrophobic residues with relatively unconserved positions is seen, suggesting a beta strand. This is supported by the low turn propensity and the high beta prediction in this region. 104-113 Loop High A high incidence of G (including the highly conseved G at 105) and of P (especially at 108) together with an unconserved scattering of polar and charged residies and a high turn prediction support the prediction of another surface loop in this region. The 2 residue insertion between 104 and 105 seen in F13ann.da supports this prediction. 114-120 Strand Medium A weak strand-like pattern of alternating conserved and unconserved positions is seen here. The turn prediction is low and the strand propensity is high. 121-128 Loop High Small residues (ASG) are common in this region. The turn prediction is high and two sequences have prominant insertions between 123 and 124 (F13LH.DAT and F13ann.da). A scattering of unconserved charged and polar residues is seen. 129-134 Strand Medium An alternating conservation pattern together with a high strand propensity and matching low turn prediction are seen for this region. 135-139 Loop High Many charges and polar residues are seen here leading to a high turn potential. This region is predicted as surface loop. 140-146 Strand High Alternating Hydrophobic residue conservation with unconserved residues are seen with high strand prediction and low turn prediction. 147-154 Coil High The conserved small residues (AS) and prolines with only one unconserved relatively polar position suggest a turn in this region. The conserved G154 is an example of the observation that conserved glycines often mark the beginning or end of a turn. There is a peak in the turn prediction at the N-terminal end of this region. 155-160 Strand High An alternating pattern of conserved and unconserved positions is again seen here. This strand terminates at the gap caused by the insertion in F13LH.DAT between residues 164 and 165, the deletions between 160 and 164 seen in F13BoE.da, F13TgHu.d, F13TgMs.d and F13TgGp.d and the deletions between 160 and 167 seen in F13P4.DAT and F13TMP.FA. Strand prediction is high and turn prediction is low. 161-178 Loop Medium (Including inserted/deleted positions detailed at the end of the strand 153-160) An unconserved scattering of small and polar residues is seen here together with a large number of gaps (an additional gap is seen in F13TMP.FA between 171 and 178). Coil prediction is high and strand propensity is low. 179-183 Strand High Highly conserved and hydrophobic, this region shows a high propensity for strand and a low turn prediction. This would be predicted to be a burried strand. 184-190 Coil Medium This is a highly conserved region, containing a number of proline and cysteine positions together with small (AS) and charged or polar (DEQ) residues. Coil prediction is maximal and the strand prediction is very low. 191-195 Strand Medium Another highly conserved hydrophobic region with a high strand prediction and low turn propensity. Likely to be burried. 196-201 Loop Medium A predominantly unconserved pattern of mainly charged and polar groups. This region and the following predicted strand predict strongly as helix by both the multiple and Zvelebil methods. This is unsupported by the conservation profile. 202-205 Strand Medium Highly conserved. 203-205 almost identical runs of hydrophobic residues which are likely to be protected from solvent. Weak strand prediction is seen for this region matched by a low turn prediction. 206-209 Coil Medium Short run of polar residues ending with the absolutely conserved G209, reduced strand prediction, increased turn prediction. 210-213 Strand Medium A strong strand prediction mirrored by a low turn propensity is seen. The region is bounded by absolutely conserved glycines (G209, G214 - glycines often bracket regions of defined secondary structure). The region contains a pair of conserved hydrophobic residues. 214-232 Loop Medium This region has a high turn propensity throughout with low propensity for both helix and strand. The residue composition is of polar and small residues and is relatively unconserved toward the N terminal. The strongly conserved W224 marks the beginning of a relatively highly conserved region of small (GAS) polar (QEDHKRN) and aromatic (WYF) residues, but no structure prediction is made for these positions. A gap is seen at position 230 in F13TMP.FA, supporting the loop hypothesis. 233-242 Strand Medium This region contains a run of highly conserved hydrophobic positions ending in a conserved charged group. In part of the run an alternating pattern of conserved and unconserved positions is seen. Strand and helix predictions are high, turn is low, but the residue composition and conservation pattern is more typical of strand. 243-254 Loop High There is a 6 residue insertion between D/E242 and R/K/243 in F13BoE.da, F13TgHu.d, F13TgMs.d and F13TgGp.d in comparison with A25051. F13ann.da has an insertion in this predicted loop region but the location is unclear due to anomalous alignment. Other sequences have 1 or 2 residue deletions here. The gaps generated by these insertions/deletions together with the high incidence of small residues mark this as a loop. The turn prediction is high and no strand or helix is predicted here. 255-265 Strand High This is a very hydrophobic region with strong strand and low turn propensities. 266-272 Coil High Short run of polar/charged residues ending with the conserved G272. High turn and low strand propensities. 273-275 Strand Medium Short run of hydrophobic residues bracketed by G272 and G276. High strand and low turn prediction. 276-293 Loop High High turn prediction at N-terminal end of this region reduced towards C-terminal while strand and helix predictions low throughout. Many small or charged/polar residues present. 294-301 Helix High Residues 1,4,5 and 8 are conserved. These residues could correspond to conservation of one face of an alpha-helix. The unconserved residues are frequently polar suggestive of solvent exposure, while the conserved positions are aromatic or aliphatic in nature (S294 excepted) suggesting packing with the protein core. The turn prediction begins low at the N terminus but rises towards the C-terminal end, while the helix prediction is high throughout. 302-312 Loop High This region is poorly conserved and contains many gaps. The residues are, on the whole, small or charged/polar and the turn prediction remains high where gaps do not occur. Strand and helix prediction remain low. 313-316 Strand Medium This region predicts as strand, the turn prediction dropping after the polar residue Q312. 317-318 Coil Medium The end of the strand is marked by the two small residues (A/G/S) at positions 317 and 318. 319-327 Strand Medium This region is highly conserved and predicts as strand. 328-331 Coil Medium Coil prediction is relatively high and small residues (G/A/S) are present with proline. ### Start of poorly predicted region 1 ### 332-335 Strand Low A peak in strand prediction is mirrored by a reduced turn prediction. 336-346 Loop Medium Coil prediction is very strong and many polar and charged residues are present. 347-354 Strand Low Low turn prediction, high strand prediction, LIVM are present and conserved. This strand may ends at the gap at 351, but may continue to 354 through the run of aromatic residues at 352 and 353. 355-358 Coil Medium A strong turn prediction is supported by the presence of small, polar and charged residues here. 359-361 V. Low May be a continuation of a loop motif, possibly some helical character. 362-367 Coil Low Charged, polar and small residues with a high turn prediction. 368-372 Strand Medium Highly conserved sequence of residues typical of a burried strand. Strong strand prediction. 373-376 Coil Low Increased turn prediction. 377-379 Strand Low Highly conserved region with the exception of gaps in F13TgGp.d. 380-395 Loop Low Many gaps and, perhaps, poor alignment of sequences in this region make prediction difficult. Many Gly and Pro residues combined with a number of polar and charged positions suggest loop for this region. 396-404 Loop Medium Strongly conserved G and P positions with small, charged and polar positions continue the loop motif. 405-408 Strand Low A conserved region bracketed by G404 and G409 with a high strand prediction. 409-412 Coil Low G409, P410 and P411 suggest a turn. 413-416 Strand Low Low turn prediction and high strand prediction. 417-419 Coil Low Coil prediction peaks here, strand prediction is low. Ends at absolutely conserved G419. 420-425 Strand V. Low Poorly defined in terms of conserved residues, but predicted by Zvelebil method and strand propensity peaks and reduced turn prediction. 426-428 Coil Medium Small and charged residues and prolines occur here. The turn prediction is high and other predictions are low. 429-432 Strand Low Strongly conserved and generally hydrophobic with strand prediction and low turn prediction. This region also predicts strongly as helix, but the residue composition does not resemble helix. 433-437 Coil Low Polar, small and charged residues are seen here suggesting turn. The turn prediction peaks sharply at N435. 438-441 Strand Low The presence of hydrophobic residues, with an alternating conservation pattern suggests strand at this position. 442-447 Loop Medium Low conservation and the insertions between 445 and 446 in F13LH.DAT, F13ann.da and F13TMP.FA indicate this region as a likely loop. 448-454 Strand Low In this region, an alternating pattern of generally hydrophobic and generally polar positions coincide with a small peak in strand and helix predictions and a minima in the turn prediction. 454-460 Loop Medium Many gaps, an unconserved scattering of polar and charged residues and peaks in the turn prediction suggest turn. 461-468 Strand Low High strand and low turn predictions matched by high conservation. 469-485 Loop Medium An insertion in F13LH.DAT between 473 and 474 and the high frequency of polar and charged residues including the charged pair of residues E474 and D475 together with high turn predictions at the N-terminal end of the region suggest loop as an apropriate prediction. ### End of pooly predicted region ### 486-496 Helix Medium A pattern of conserved residues at 1,4,5,7,8,10,11 is compatible with a stripe of conserved residues proceeding anti-clockwise around a helix. Helix prediction is high, turn prediction is low. 497-516 Loop High This region contains many gaps, charged, polar and small residues and is predicted as turn where gaps are not present. 517-523 Strand Medium A dip in turn prediction is matched by an increased prediction of both strand and helix. Although the helical prediction is stronger, there is an alternating pattern of conserved hydrophobic residues and unconserved positions which supports a strand prediction. 524-531 Loop High This region shows gap at two positions (523a and 524) and is predicted as turn. 532-541 Strand High This region displays a strong pattern of conserved hydrophobic residues alternating with unconserved positions. It predicts very strongly as strand and the turn prediction is minimal. 542-546 Coil High A high turn prediction and the occurence of an unconserved scattering of polar and residues mark this region as turn. 547-555 Strand High This region displays a strong pattern of conserved hydrophobic residues alternating with unconserved positions. It predicts very strongly as strand and the turn prediction is minimal. 556-561 Loop Medium This region shows weak prediction for each of the three states, despite high conservation. The prediction trends show a decreasing strand propensity with increasing turn prediction and the absolutely conserved G561 is supportive of this prediction. ### Start of second pooly predicted region ### 562-585 Loop Low Very low levels of conservation in this region, together with a number of polar and charged residues, a scattering of small residues and a number of insertions and deletions suggest this region as a loop. A generally high turn prediction is seen thoughout. 586-590 Strand Low Generally hydrophobic region with a peak in strand prediction and a turn minimum. 591-596 Coil V. Low Charged, small and polar redidues in an unconserved scatter. 597-600 Strand V. Low Weakly hydrophobic. This region co-incides with a turn minimum, but there is a generally low strand prediction and the helix prediction is relatively high. The length of helix prediction is, however, not supported by the seies of turn predictions in this region.` 601-607 Coil Low There is an insertion of generally small residues (GA) between 606 and 607 in many sequences. This, together with the usual polar/charged scattering of residues leads to the prediction of turn here. 608-610 Strand Low Alternating pattern of hydrophobic and small residues with unconserved positions is suggestive of a strand packing closely to the core. 611-613 Coil Low Small or charged residues with a high turn prediction. 614-624 Helix Low A 1,5,8 conservation pattern. These residues could correspond to conservation of one face of an alpha-helix. The helix prediction is high and the turn prediction is minimum. 625-629 Loop Medium The deletion at 626 in many sequences and the unconserved positions in this region suggest a loop here, ending at the relatively conserved P629. ### End of pooly predicted region ### 630-635 Strand High This region displays a strong pattern of conserved hydrophobic residues alternating with unconserved positions. It predicts very strongly as strand and the turn prediction is low. 636-644 Loop Medium An unconserved region with a scattering of small, polar and charged residues and prolines. 645-651 Strand High This region displays a pattern of conserved non-polar residues alternating with unconserved positions. It predicts strongly as strand and the turn prediction is low. 652-662 Loop Medium An unconserved region with a scattering of small, polar and charged residues and prolines. 663-668 Strand High This region displays a clear pattern of conserved non-polar residues alternating with unconserved positions. It predicts very strongly as strand and the turn prediction is low. 669-685 Loop Medium This region contains many gaps, charged, polar and small residues and is predicted as turn where gaps are not present. 686-695 Strand Medium This region displays a pattern of non-polar residues alternating with more predominantly polar positions. It predicts very strongly as strand and the turn prediction is low. 696-702 Loop Medium This region contains a conserved gap, a conserved glycine (G700) and a conserved proline (P696) charged predicted as turn where gaps are not present. 703-710 Strand High A highly conserved region, containing many non-polar residues, strongly predicted as strand with a low turn prediction. 711-END Unclear Low A poorly conserved region leading up to the end of the sequences with some suggestion of a strand at 722-724, if shorter sequences are discounted. *************************** ***************************