Web document 6.7. APDB server results for five distantly related globins.

 

Contents

[1] Five divergent globin sequences (see Web Document 6.3) with the Protein Data Bank identifiers placed at the beginning of the description line.

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

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

 

[1] Five divergent globin sequences (see Web Document 6.3) with the Protein Data Bank identifiers placed at the beginning of the description line.

 

>2hhbB beta_globin NP_000509.1 [Homo sapiens]

MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG

AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN

ALAHKYH

>2MM1 myoglobin NP_005359.1 [Homo sapiens]

MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVL

TALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFR

KDMASNYKELGFQG

>1OJ6A neuroglobin NP_067080.1 [Homo sapiens]

MERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVML

VIDAAVTNVEDLSSLEEYLASLGRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAV

VQAMSRGWDGE

>1FSL  soybean_globin leghemoglobin P02238 LGBA_SOYBN [Glycine max]

MVAFTEKQDALVSSSFEAFKANIPQYSVVFYTSILEKAPAAKDLFSFLANGVDPTNPKLTGHAEKLFALV

RDSAGQLKASGTVVADAALGSVHAQKAVTDPQFVVVKEALLKTIKAAVGDKWSDELSRAWEVAYDELAAA

IKKA

>1D8U rice_globin  rice Non-Symbiotic Plant Hemoglobin NP_001049476.1 [Oryza sativa (japonica cultivar-group)]

MALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFSFLRNSDVPLEKNPK

LKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDAHFEVVKFALLDTIKEEVPADMWS

PAMKSAWSEAYDHLVAAIKQEMKPAE

 

[2] The following multiple sequence alignment was generated using the default T-Coffee program:

 

1D8U            MALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFS-FLR
2MM1            -----------MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFD-KFK
1FSL            ----------MVAFTEKQDALVSSSFEAFKANIPQYSVVFYTSILEKAPAAKDLFS-FLA
2hhbB           ----------MVHLTPEEKSAVTALWGKVNVD--EVGGEALGRLLVVYPWTQRFFE-SFG
1OJ6A           -------------MERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCR
                             :   :   :   :  .. .    .      ::   *     *.    
 
1D8U            NSDVP--LEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDA
2MM1            HLKSEDEMKASEDLKKHGATVLTAL---GGILKKKGHHEAE---IKPLAQSHATKHKIPV
1FSL            NGVDP----TNPKLTGHAEKLFALVRDSAGQLKASGTVVAD----AALGSVHAQKAVTDP
2hhbB           DLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNL---KGTF---ATLSELHCDKLHVDP
1OJ6A           QFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDL---SSLEEYLASLGRKH-RAVGVKL
                .         . ..  *  .::         :               *.  *        
 
1D8U            H-FEVVKFALLDTIKEEVPADMWSPAMKSAWSEAYDHLVAAIKQE---MKPAE
2MM1            KYLEFISECIIQVLQSKH-PGDFGADAQGAMNKALELFRKDMASNYKELGFQG
1FSL            Q-FVVVKEALLKTIKAAV-GDKWSDELSRAWEVAYDELAAAIKKA--------
2hhbB           ENFRLLGNVLVCVLAHHF-GKEFTPPVQAAYQKVVAGVANALAHKYH------
1OJ6A           SSFSTVGESLLYMLEKCL-GPAFTPATRAAWSQLYGAVVQAMSRGWDG----E
                  :  :   ::  :        :      * .     .   :           

 

 

[3] This alignment was input into the APDB server. The results is as follows:

 

APDB_RESULT_FORMAT_02
 
 
#PAIRWISE: 2MM1 Vs 1D8U
        PAIRWISE EVALUATED:  76.62 %    [2MM1 Vs 1D8U] 
        PAIRWISE APDB:       52.54 %    [2MM1 Vs 1D8U] 
        PAIRWISE iRMSD:       1.00 Angs [2MM1 Vs 1D8U]
        PAIRWISE NiRMSD:      1.30 Angs [2MM1 Vs 1D8U]
 
#PAIRWISE: 1FSL Vs 1D8U
        PAIRWISE EVALUATED:  88.89 %    [1FSL Vs 1D8U] 
        PAIRWISE APDB:       79.69 %    [1FSL Vs 1D8U] 
        PAIRWISE iRMSD:       0.70 Angs [1FSL Vs 1D8U]
        PAIRWISE NiRMSD:      0.78 Angs [1FSL Vs 1D8U]
 
#PAIRWISE: 1FSL Vs 2MM1
        PAIRWISE EVALUATED:  75.69 %    [1FSL Vs 2MM1] 
        PAIRWISE APDB:       40.37 %    [1FSL Vs 2MM1] 
        PAIRWISE iRMSD:       1.17 Angs [1FSL Vs 2MM1]
        PAIRWISE NiRMSD:      1.54 Angs [1FSL Vs 2MM1]
 
#PAIRWISE: 2hhbB Vs 1D8U
        PAIRWISE EVALUATED:  78.23 %    [2hhbB Vs 1D8U] 
        PAIRWISE APDB:       44.35 %    [2hhbB Vs 1D8U] 
        PAIRWISE iRMSD:       1.22 Angs [2hhbB Vs 1D8U]
        PAIRWISE NiRMSD:      1.57 Angs [2hhbB Vs 1D8U]
 
#PAIRWISE: 2hhbB Vs 2MM1
        PAIRWISE EVALUATED:  84.35 %    [2hhbB Vs 2MM1] 
        PAIRWISE APDB:       55.65 %    [2hhbB Vs 2MM1] 
        PAIRWISE iRMSD:       0.92 Angs [2hhbB Vs 2MM1]
        PAIRWISE NiRMSD:      1.09 Angs [2hhbB Vs 2MM1]
 
#PAIRWISE: 2hhbB Vs 1FSL
        PAIRWISE EVALUATED:  75.00 %    [2hhbB Vs 1FSL] 
        PAIRWISE APDB:       40.74 %    [2hhbB Vs 1FSL] 
        PAIRWISE iRMSD:       1.30 Angs [2hhbB Vs 1FSL]
        PAIRWISE NiRMSD:      1.74 Angs [2hhbB Vs 1FSL]
 
#PAIRWISE: 1OJ6A Vs 1D8U
        PAIRWISE EVALUATED:  77.48 %    [1OJ6A Vs 1D8U] 
        PAIRWISE APDB:       52.99 %    [1OJ6A Vs 1D8U] 
        PAIRWISE iRMSD:       1.08 Angs [1OJ6A Vs 1D8U]
        PAIRWISE NiRMSD:      1.40 Angs [1OJ6A Vs 1D8U]
 
#PAIRWISE: 1OJ6A Vs 2MM1
        PAIRWISE EVALUATED:  80.79 %    [1OJ6A Vs 2MM1] 
        PAIRWISE APDB:       48.36 %    [1OJ6A Vs 2MM1] 
        PAIRWISE iRMSD:       1.15 Angs [1OJ6A Vs 2MM1]
        PAIRWISE NiRMSD:      1.43 Angs [1OJ6A Vs 2MM1]
 
#PAIRWISE: 1OJ6A Vs 1FSL
        PAIRWISE EVALUATED:  76.39 %    [1OJ6A Vs 1FSL] 
        PAIRWISE APDB:       55.45 %    [1OJ6A Vs 1FSL] 
        PAIRWISE iRMSD:       1.12 Angs [1OJ6A Vs 1FSL]
        PAIRWISE NiRMSD:      1.47 Angs [1OJ6A Vs 1FSL]
 
#PAIRWISE: 1OJ6A Vs 2hhbB
        PAIRWISE EVALUATED:  80.95 %    [1OJ6A Vs 2hhbB] 
        PAIRWISE APDB:       39.50 %    [1OJ6A Vs 2hhbB] 
        PAIRWISE iRMSD:       1.15 Angs [1OJ6A Vs 2hhbB]
        PAIRWISE NiRMSD:      1.41 Angs [1OJ6A Vs 2hhbB]
 
#AVERAGE For Sequence 1D8U
        AVERAGE  EVALUATED:  80.20 %    [1D8U]
        AVERAGE  APDB:       57.95 %    [1D8U]
        AVERAGE  iRMSD:       0.99 Angs [1D8U]
        AVERAGE  NiRMS:       1.24 Angs [1D8U]
 
#AVERAGE For Sequence 2MM1
        AVERAGE  EVALUATED:  79.36 %    [2MM1]
        AVERAGE  APDB:       49.47 %    [2MM1]
        AVERAGE  iRMSD:       1.05 Angs [2MM1]
        AVERAGE  NiRMS:       1.33 Angs [2MM1]
 
#AVERAGE For Sequence 1FSL
        AVERAGE  EVALUATED:  78.99 %    [1FSL]
        AVERAGE  APDB:       55.16 %    [1FSL]
        AVERAGE  iRMSD:       1.06 Angs [1FSL]
        AVERAGE  NiRMS:       1.34 Angs [1FSL]
 
#AVERAGE For Sequence 2hhbB
        AVERAGE  EVALUATED:  79.66 %    [2hhbB]
        AVERAGE  APDB:       45.28 %    [2hhbB]
        AVERAGE  iRMSD:       1.14 Angs [2hhbB]
        AVERAGE  NiRMS:       1.43 Angs [2hhbB]
 
#AVERAGE For Sequence 1OJ6A
        AVERAGE  EVALUATED:  78.92 %    [1OJ6A]
        AVERAGE  APDB:       48.93 %    [1OJ6A]
        AVERAGE  iRMSD:       1.13 Angs [1OJ6A]
        AVERAGE  NiRMS:       1.43 Angs [1OJ6A]
 
#TOTAL for the Full MSA
        TOTAL     EVALUATED:  79.43 %  
        TOTAL     APDB:       51.37 %  
        TOTAL     iRMSD:       1.07 Angs
        TOTAL     NiRMSD:      1.35 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