Web document 6.6. Evaluation of the multiple sequence alignment of five closely related beta globin orthologs using the iRMSD-APDB web server at www.tcoffee.org.

 

Contents

[1] Five closely related globins; for three, the Protein Data Bank accessions are provided.

[2] A multiple sequence alignment of these sequences created using T-Coffee.

[3] The i-RMSD APDB server results showing an evaluation of the multiple sequence alignment based on structural information.

 

[1] Five closely related globins; for three, the Protein Data Bank accessions are provided.

 

>2hhbB human_NP_000509
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN
ALAHKYH
>Pan_troglodytes_XP_508242
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN
ALAHKYH
>Canis_familiaris_XP_537902
MVHLTAEEKSLVSGLWGKVNVDEVGGEALGRLLIVYPWTQRFFDSFGDLSTPDAVMSNAKVKAHGKKVLN
SFSDGLKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVAN
ALAHKYH
>1DXT Mus_musculus_NP_058652
MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIT
AFNEGLKNLDNLKGTFASLSELHCDKLHVDPENFRLLGNAIVIVLGHHLGKDFTPAAQAAFQKVVAGVAT
ALAHKYH
>Gallus_gallus_XP_444648
MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT
SFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAH
ALARKYH

 

[2] A multiple sequence alignment of these sequences created using T-Coffee.

 

CLUSTAL FORMAT for T-COFFEE Version_5.13 [http://www.tcoffee.org], CPU=0.20 sec, SCORE=82, Nseq=5, Len=147 
 
1DXT                        MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPK
Gallus_gallus_XP_444648     MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPM
Canis_familiaris_XP_537902  MVHLTAEEKSLVSGLWGKVNVDEVGGEALGRLLIVYPWTQRFFDSFGDLSTPDAVMSNAK
Pan_troglodytes_XP_508242   MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK
2hhbB                       MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK
                            *** *  **. :: **.***  * *.***.***:*******:* ***:**:. *::.*. 
 
1DXT                        VKAHGKKVITAFNEGLKNLDNLKGTFASLSELHCDKLHVDPENFRLLGNAIVIVLGHHLG
Gallus_gallus_XP_444648     VRAHGKKVLTSFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFS
Canis_familiaris_XP_537902  VKAHGKKVLNSFSDGLKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFG
Pan_troglodytes_XP_508242   VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG
2hhbB                       VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG
                            *:******: :*.:.: :***:*.**: ****************:***: :: **. *:.
 
1DXT                        KDFTPAAQAAFQKVVAGVATALAHKYH
Gallus_gallus_XP_444648     KDFTPECQAAWQKLVRVVAHALARKYH
Canis_familiaris_XP_537902  KEFTPQVQAAYQKVVAGVANALAHKYH
Pan_troglodytes_XP_508242   KEFTPPVQAAYQKVVAGVANALAHKYH
2hhbB                       KEFTPPVQAAYQKVVAGVANALAHKYH
                            *:***  ***:**:*  ** ***:***

 

[3] The iRMSD-APDB server results showing an evaluation of the multiple sequence alignment based on structural information.

 

APDB_RESULT_FORMAT_02
 
 
#PAIRWISE: 2hhbB Vs 1DXT
        PAIRWISE EVALUATED:  25.17 %    [2hhbB Vs 1DXT] 
        PAIRWISE APDB:       59.46 %    [2hhbB Vs 1DXT] 
        PAIRWISE iRMSD:       0.95 Angs [2hhbB Vs 1DXT]
        PAIRWISE NiRMSD:      3.76 Angs [2hhbB Vs 1DXT]
 
#AVERAGE For Sequence 1DXT
        AVERAGE  EVALUATED:  25.17 %    [1DXT]
        AVERAGE  APDB:       59.46 %    [1DXT]
        AVERAGE  iRMSD:       0.95 Angs [1DXT]
        AVERAGE  NiRMS:       3.76 Angs [1DXT]
 
#AVERAGE For Sequence 2hhbB
        AVERAGE  EVALUATED:  25.17 %    [2hhbB]
        AVERAGE  APDB:       59.46 %    [2hhbB]
        AVERAGE  iRMSD:       0.95 Angs [2hhbB]
        AVERAGE  NiRMS:       3.76 Angs [2hhbB]
 
#TOTAL for the Full MSA
        TOTAL     EVALUATED:  25.17 %  
        TOTAL     APDB:       59.46 %  
        TOTAL     iRMSD:       0.95 Angs
        TOTAL     NiRMSD:      3.76 Angs
 
# EVALUATED: Fraction of Pairwise Columns Evaluated
# APDB:      Fraction of Correct Columns according to APDB
# iRMDS:     Average iRMSD over all evaluated columns
# NiRMDS:    iRMSD*MIN(L1,L2)/Number Evaluated Columns
# Main Parameter: -maximum_distance 10.00 Angstrom
# Undefined values are set to -1 and indicate LOW Alignment Quality
# Results Produced with T-COFFEE (Version_5.13)
# T-COFFEE is available from http://www.tcoffee.org