					***Table 2***

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Align-	|      	|      	|
ment  	|2'    	|      	|
Posit-	|Struct	|Predic	|			Comments
ion   	|ure   	|tion	|			********
W.R.T.	|assign	|Confid	|
A25051	|ed    	|ence 	|
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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.




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