Table 4

Evolutionary trace residues in ISDR and V3 region of NS5A from genotype 1b, 3a and 2a
Genotype 1b Vs 3a Genotype 1b Vs 2a Genotype 1b Vs 3a and 2a
Trace residues (NS5A -1b) Trace residues (NS5A -3A) Blosum-62 substitution score Trace residues (NS5A -1b) Trace residues (NS5A -2A) BLOSUM-62 substitution score Trace residues (NS5A-1b) Trace residues in (NS5A -3a and 2a) BLOSUM-62 Substitution score
T244 Q244 0 K240 R240 2 I255 V255 V255 1
H247 R247 0 H247 G247 −2 E256 D256 D256 2
D248 P248 −1 P250 Y250 −3 N276 T276 S272 0,1
S249 H249 −1 A252 V252 −2 E293 D293 D289 2
D253 E253 2 L254 M254 2 - K384 P380
I255 V255 1 I255 V255 1 - P385 P381
E256 D256 2 E256 D256 2 - Q386 S382
G267 S267 0 L260 F260 0 - E387 G383
N276 T276 0 W261 - - E388 D384
E293 D293 2 R262 - A387 G394 G390 0
I302 C302 −1 Q263 - T292 S399 D395 1,1
G381 P381 −2 E264 - A293 S400 S396 1
- K384 I269 V265 1 - V405 T400
- P385 V272 I268 3 S401 - -
- Q386 N276 S272 1 D402 - -
- E387 I280 V276 1 G404 - -
- E388 F284 L280 0 D405 - -
A387 G394 0 L287 M283 2
S390 T397 1 A289 E285 −1
G391 Q398 −2 D292 S288 0
T392 S399 1 E293 D289 2
A393 S400 1 R294 L290 −2
P396 S403 −1 V298 I294 3
P397 K404 −1 A300 S296 1
D398 V405 −3 I302 Y298 −1
Q399 P406 −1 - Q378
D402 P409 −1 - P379
D405 E412 2 - P380
G407 - - P381
- S382
- G383
- D384
- S385
- G386
- L387
T389 1
A391 1
D392 0
-
E404 2
-
-
-
-
L407 −4

Trace residues are picked up if complete/ high conservation (mostly >90% and very few residues showing >80%) or conservative substitution of two different residues or a residue and a gap from both multiple sequence alignment are being compared. The extent of amino acid substitution across genotypes in NS5A has been shown using BLOSUM – 62 substitution score. The trace residues from NS5A genotype1b are predicted to be PKR interacting residues.

Sudha et al.

Sudha et al. BMC Structural Biology 2012 12:28   doi:10.1186/1472-6807-12-28

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