SFESA (Shift to Fix ElementS in Alignment)

Local secondary structure element shifts improve protein alignments
with a combination of sequence and structural scoring


"Helix" alignment blocks are shown alternately in Red and Orange in alignment.
"Strand" alignment blocks are shown alternately in Blue and Darkgreen in alignment.
In SFESA alignment, the alignment blocks shifted are marked with Underscore.

Alignment for d1ja1a3 vs d2piaa2


Starting Pairwise Alignment                                                                                  
PSIPRED : CCC-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEECCC
Number  :          10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
Query   : RLP-FKSTTPVIMVGPGTGIAPFMGFIQERAWLREQGKEVGETLLYYGCRRSDEDYLYREELARFHKDGALTQLNVAFSREQAHKVYVQHLLKRDREHLWKLIHEGGAHIYVAGDARNMAKDVQNTFYDIVAEFGPMEHTQAVDYVKKLMTKGRYSLNVWS
Template: EFPLDKRAKSFILVAGGIGITPMLSMARQLRAEG-----LRSFRLYYLTRDP-EGTAFFDELTSDEWRS-DVKIHHDHGDPT-KAFDFWSVFEKS---------KPAQHVYCCGP--------QALMDTVRDMTGHWPSGTV-------------HFE---
Number  :         10        20        30             40         50        60         70         80                 90               100       110                    120
PALSSE  : CCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHHH-----CEEEEEEEEEEEC-CCCCCCCCCCCCCCCC-EEEEEEEECCCC-CCCHHHHHHHHH---------CCEEEEEEEEH--------HHHHHHHHHHHHCCCCCEE-------------EEE---
DSSP    : CCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHC-----CCEEEEEEEECCH-HHCCCHHHHHCCCCCC-CEEEEECCCCCC-CCCCHHHHHCCC---------CCCEEEEEECC--------HHHHHHHHHHCCCCCCCCE-------------EEC---


Refined Alignment by SFESA (SFESA_O+G+M)                                                
PSIPRED : CCC-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEEEEC--CCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHH-HHHHHCCCCCHHHHHHHHHHHHHCCCEEEECCC
Number  :          10        20        30        40        50        60        70          80        90       100       110       120        130       140       150       160
Query   : RLP-FKSTTPVIMVGPGTGIAPFMGFIQERAWLREQGKEVGETLLYYGCRRSDEDYLYREELARFHKDGALTQLNVAFSR--EQAHKVYVQHLLKRDREHLWKLIHEGGAHIYVAGDARNMAKDVQNTFY-DIVAEFGPMEHTQAVDYVKKLMTKGRYSLNVWS
Cm1     :                                                                         --------                                             +++++                                  
Cm2     : 000 000000000000000000000000000000-----0000000000000-0000000000000000-**22222222  00-000000000000---------0000000000*########77777 *******0000000-------------000---
Template: EFPLDKRAKSFILVAGGIGITPMLSMARQLRAEG-----LRSFRLYYLTRDP-EGTAFFDELTSDEWRS---DVKIHHDHGDPT-KAFDFWSVFEKS---------KPAQHVYCCG-PQALMDTVRDMTG--------HWPSGTV-------------HFE---
Number  :         10        20        30             40         50        60           70         80                 90        100       110                            120
PALSSE  : CCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHHH-----CEEEEEEEEEEEC-CCCCCCCCCCCCCCCC---EEEEEEEECCCC-CCCHHHHHHHHH---------CCEEEEEEEE-HHHHHHHHHHHHH--------CCCCCEE-------------EEE---
DSSP    : CCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHC-----CCEEEEEEEECCH-HHCCCHHHHHCCCCCC---CEEEEECCCCCC-CCCCHHHHHCCC---------CCCEEEEEEC-CHHHHHHHHHHCC--------CCCCCCE-------------EEC---



List of all elements in SFESA                                                                                                              

Element
Number
Template
Start
Template
End
Secondary
Structure
Type
Original Alignment BlockShift by SFESA
(Gap Mode
[Shifting Number])
Refined Alignment Block
1 9 16 Strand TPVIMVGP
KSFILVAG
No Shift -
2 17 34 Helix GTGIAPFMGFIQERAWLR
GIGITPMLSMARQLRAEG
No Shift -
3 36 46 Strand GETLLYYGCRR
RSFRLYYLTRD
No Shift -
4 64 71 Strand LTQLNVAF
DVKIHHDH
Original[-2] QLNVAFSR
DVKIHHDH
5 79 87 Helix YVQHLLKRD
DFWSVFEKS
No Shift -
6 90 97 Strand GAHIYVAG
AQHVYCCG
No Shift -
7 98 110 Helix DARNMAKDVQNTFYDIVAEFG
P--------QALMDTVRDMTG
Left[-1] ARNMAKDVQNTFY
PQALMDTVRDMTG



Details of all elements in SFESA                                                                                                         

Element Number 1: Strand(9:16)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original -4 Yes TTPVIMVGP----GTGIA
A----
KSFILVAGGIGIT
-2.4839 0.4834 0.1273 0.4240
Original -3 Yes STTPVIMVGP---GTGIA
RA---
KSFILVAGGIGIT
-2.0004 0.8168 0.4787 0.7604
Original -2 Yes KSTTPVIMVGP--GTGIA
KRA--
KSFILVAGGIGIT
-1.2976 1.3022 0.9902 1.2502
Original -1 Yes FKSTTPVIMVGP-GTGIA
DKRA-
KSFILVAGGIGIT
0.5952 1.7248 1.5893 1.7022
Original 0 Yes -FKSTTPVIMVGPGTGIA
LDKRA
KSFILVAGGIGIT
4.7124 2.1816 2.4853 2.2322
Original 1 Yes -FKS-TTPVIMVGPGTGI
LDKRA
KSFILVAG-GIGI
1.7248 2.1105 2.0641 2.1028
Original 2 Yes -FK--STTPVIMVGPGTG
LDKRA
KSFILVAG--GIG
-0.8554 1.9630 1.6248 1.9068
Original 3 Yes -F---KSTTPVIMVGPGT
LDKRA
KSFILVAG---GI
-2.0847 1.6716 1.2209 1.5964
Original 4 Yes -----FKSTTPVIMVGPG
LDKRA
KSFILVAG----G
-3.3414 1.2581 0.7061 1.1660



Element Number 2: Helix(17:34)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original -4 Yes PGTGIAPFMGFIQERAWLREQGKEVGET
G----
GIGITPMLSMARQLRAEG-LRSF
-2.2259 1.2769 0.8566 1.2071
Original -3 Yes GPGTGIAPFMGFIQERAWLREQGKEVGE
AG---
GIGITPMLSMARQLRAEG--LRS
-0.5313 1.3784 1.1492 1.3400
Original -2 Yes VGPGTGIAPFMGFIQERAWLREQGKEVG
VAG--
GIGITPMLSMARQLRAEG---LR
-1.7458 0.9766 0.6499 0.9221
Original -1 Yes MVGPGTGIAPFMGFIQERAWLREQGKEV
LVAG-
GIGITPMLSMARQLRAEG----L
-5.9173 1.1848 0.3324 1.0427
Original 0 Yes IMVGPGTGIAPFMGFIQERAWLREQGKE
ILVAG
GIGITPMLSMARQLRAEG-----
9.3262 1.5085 2.4468 1.6647
Original 1 Yes IMVGP-GTGIAPFMGFIQERAWLREQGK
ILVAG
GIGITPMLSMARQLRAEG-----
-5.6844 0.9709 0.1721 0.8379
Original 2 Yes IMVGP--GTGIAPFMGFIQERAWLREQG
ILVAG
GIGITPMLSMARQLRAEG-----
-2.2824 0.9008 0.5186 0.8371
Original 3 Yes IMVGP---GTGIAPFMGFIQERAWLREQ
ILVAG
GIGITPMLSMARQLRAEG-----
-1.1231 1.1967 0.9184 1.1505
Original 4 Yes IMVGP----GTGIAPFMGFIQERAWLRE
ILVAG
GIGITPMLSMARQLRAEG-----
-1.9714 0.9525 0.6016 0.8942



Element Number 3: Strand(36:46)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original -4 Yes VGETLLYYGCRRSDED---YL
L----
RSFRLYYLTRDPEGTA
-3.1772 1.5009 0.9395 1.4073
Original -3 Yes EVGETLLYYGCRRSDE--DYL
-L---
RSFRLYYLTRDPEGTA
-1.8600 1.6194 1.2019 1.5498
Original -2 Yes KEVGETLLYYGCRRSD-EDYL
--L--
RSFRLYYLTRDPEGTA
-0.2225 1.8164 1.5718 1.7757
Original -1 Yes GKEVGETLLYYGCRRS-DEDY
---L-
RSFRLYYLTRDP-EGT
1.2055 1.9256 1.8394 1.9112
Original 0 Yes QGKEVGETLLYYGCRRSDEDY
----L
RSFRLYYLTRDP-EGT
4.4610 2.0803 2.3661 2.1279
Original 1 Yes QGKE-VGETLLYYGCRRSDED
----L
RSFRLYYLTRD-P-EG
0.2821 1.8566 1.6675 1.8250
Original 2 Yes EQGK-EVGETLLYYGCRRSDE
----L
RSFRLYYLTRD--P-E
-0.2760 1.9308 1.6658 1.8866
Original 3 Yes REQG-KEVGETLLYYGCRRSD
G---L
RSFRLYYLTRD---P-
-1.7648 1.7123 1.2950 1.6426
Original 4 Yes LREQ-GKEVGETLLYYGCRRS
EG--L
RSFRLYYLTRD----P
-3.2462 1.5630 0.9862 1.4667



Element Number 4: Strand(64:71)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original -4 Yes ALTQLNVAFSREQ----A
-----
DVKIHHDHGDPT-
0.5110 0.7999 0.7653 0.7940
Original -3 Yes GALTQLNVAFSRE---QA
S----
DVKIHHDHGDPT-
0.0422 0.8231 0.7294 0.8074
Original -2 Yes DGALTQLNVAFSR--EQA
RS---
DVKIHHDHGDPT-
1.7973 0.8078 0.9265 0.8276
Original -1 Yes KDGALTQLNVAFS-REQA
WRS--
DVKIHHDHGDPT-
-0.9663 0.6966 0.4970 0.6634
Original 0 Yes HKDGALTQLNVAFSREQA
EWRS-
DVKIHHDHGDPT-
0.1343 0.7539 0.6795 0.7414
Original 1 Yes FHKDGALTQLNVAFSREQ
DEWRS
DVKIHHDH-GDPT
-0.6102 0.7326 0.5715 0.7057
Original 2 Yes FHKD-GALTQLNVAFSRE
DEWRS
DVKIHHDH--GDP
-0.8445 0.6599 0.4793 0.6298
Original 3 Yes FHK--DGALTQLNVAFSR
DEWRS
DVKIHHDH---GD
-0.9510 0.6068 0.4200 0.5757
Original 4 Yes FH---KDGALTQLNVAFS
DEWRS
DVKIHHDH----G
-1.5960 0.5539 0.2958 0.5109



Element Number 5: Helix(79:87)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original -4 Yes VYVQHLLKRDREHLWKLIH
F----
DFWSVFEKS-----
0.4818 0.6642 0.6424 0.6605
Original -3 Yes KVYVQHLLKRDREHLWKLI
AF---
DFWSVFEKS-----
-0.8200 0.5005 0.3420 0.4741
Original -2 Yes HKVYVQHLLKRDREHLWKL
KAF--
DFWSVFEKS-----
-1.6644 0.4322 0.1805 0.3903
Original -1 Yes AHKVYVQHLLKRDREHLWK
-KAF-
DFWSVFEKS-----
0.0194 0.6339 0.5601 0.6218
Original 0 Yes QAHKVYVQHLLKRDREHLW
T-KAF
DFWSVFEKS-----
1.1459 0.8686 0.9018 0.8742
Original 1 Yes QAHK-VYVQHLLKRDREHL
T-KAF
DFWSVFEKS-----
-1.2009 0.6140 0.3962 0.5777
Original 2 Yes QAH--KVYVQHLLKRDREH
T-KAF
DFWSVFEKS-----
-2.3547 0.4443 0.1085 0.3884
Original 3 Yes QA---HKVYVQHLLKRDRE
T-KAF
DFWSVFEKS-----
-0.6974 0.5659 0.4142 0.5407
Original 4 Yes EQ---AHKVYVQHLLKRDR
PTKAF
DFWSVFEKS-----
0.2520 0.7242 0.6676 0.7147



Element Number 6: Strand(90:97)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original -4 Yes GGAHIYVAG----DARNM
P----
AQHVYCCGP----
-1.9751 0.3222 0.0464 0.2763
Original -3 Yes EGGAHIYVAG---DARNM
KP---
AQHVYCCGP----
-2.4131 0.5551 0.1990 0.4957
Original -2 Yes HEGGAHIYVAG--DARNM
-KP--
AQHVYCCGP----
-0.8821 0.8168 0.6129 0.7827
Original -1 Yes IHEGGAHIYVAG-DARNM
--KP-
AQHVYCCGP----
0.4406 1.0160 0.9469 1.0045
Original 0 Yes LIHEGGAHIYVAGDARNM
---KP
AQHVYCCGP----
5.3850 1.2091 1.7102 1.2926
Original 1 Yes LIHE-GGAHIYVAGDARN
---KP
AQHVYCCG-P---
0.8681 1.0407 1.0201 1.0372
Original 2 Yes LIH--EGGAHIYVAGDAR
---KP
AQHVYCCG--P--
-0.7646 0.9415 0.7367 0.9074
Original 3 Yes KLI--HEGGAHIYVAGDA
---KP
AQHVYCCG---P-
-2.5758 0.7752 0.3731 0.7082
Original 4 Yes WKL--IHEGGAHIYVAGD
---KP
AQHVYCCG----P
-3.8301 0.6607 0.1218 0.5710



Element Number 7: Helix(98:110)

Gap ModeShifting
Number
Unique?Alignment VariantsSequence
Score
Structure
Score
Combined
Score 1
Combined
Score 2
Original 0 Yes IYVAGDARNMAKDVQNTFYDIVAEFGPMEHT
VYCCG
P--------QALMDTVRDMTGHWPSG
0.6499 0.7502 0.7383 0.7483
Left -4 Yes GDARNMAKDVQNTFYDIVAEFGP
G----
PQALMDTVRDMTG----H
-1.2385 0.7075 0.4741 0.6685
Left -3 Yes AGDARNMAKDVQNTFYDIVAEFG
CG---
PQALMDTVRDMTG-----
-4.1876 0.4400 -0.1152 0.3475
Left -2 Yes VAGDARNMAKDVQNTFYDIVAEF
CCG--
PQALMDTVRDMTG-----
-1.5047 0.7423 0.4727 0.6972
Left -1 Yes YVAGDARNMAKDVQNTFYDIVAE
YCCG-
PQALMDTVRDMTG-----
3.5244 0.9698 1.2764 1.0209
Left 0 Yes IYVAGDARNMAKDVQNTFYDIVA
VYCCG
PQALMDTVRDMTG-----
-0.4545 0.5669 0.4443 0.5464
Left 1 Yes IYVAG-DARNMAKDVQNTFYDIV
VYCCG
PQALMDTVRDMTG-----
-4.0623 0.4020 -0.1338 0.3127
Left 2 Yes IYVAG--DARNMAKDVQNTFYDI
VYCCG
PQALMDTVRDMTG-----
-0.7444 0.7050 0.5311 0.6759
Left 3 Yes IYVAG---DARNMAKDVQNTFYD
VYCCG
PQALMDTVRDMTG-----
0.2014 0.6984 0.6387 0.6885
Left 4 Yes IYVAG----DARNMAKDVQNTFY
VYCCG
PQALMDTVRDMTG-----
-2.5181 0.3073 -0.0318 0.2509
Right -4 Yes DVQNTFYDIVAEFGPMEH----T
-----
PQALMDTVRDMTGHWPSG
-1.5580 0.6650 0.3981 0.6205
Right -3 Yes KDVQNTFYDIVAEFGPME---HT
-----
PQALMDTVRDMTGHWPSG
-3.2416 0.5023 0.0532 0.4275
Right -2 Yes AKDVQNTFYDIVAEFGPM--EHT
-----
PQALMDTVRDMTGHWPSG
-2.9057 0.5634 0.1472 0.4940
Right -1 Yes MAKDVQNTFYDIVAEFGP-MEHT
-----
PQALMDTVRDMTGHWPSG
0.3572 0.8525 0.7930 0.8426
Right 0 Yes NMAKDVQNTFYDIVAEFGPMEHT
-----
PQALMDTVRDMTGHWPSG
-0.7925 0.7553 0.5697 0.7245
Right 1 Yes RNMAKDVQNTFYDIVAEFGPMEH
-----
PQALMDTVRDMTG-HWPS
-4.3579 0.4490 -0.1279 0.3528
Right 2 Yes ARNMAKDVQNTFYDIVAEFGPME
-----
PQALMDTVRDMTG--HWP
-2.0214 0.6884 0.3633 0.6342
Right 3 Yes DARNMAKDVQNTFYDIVAEFGPM
-----
PQALMDTVRDMTG---HW
1.3146 1.0088 1.0456 1.0151
Right 4 Left[-4] GDARNMAKDVQNTFYDIVAEFGP
G----
PQALMDTVRDMTG----H
-1.2385 0.7075 0.4741 0.6685





References:
Jing Tong, Jimin Pei and Nick Grishin. Local secondary structure element shifts improve protein alignments with a combination of sequence and structural scoring. (In preparing) 2013

Comments, suggestions and bug reports to: jing.tong at utsouthwestern.edu