TOPOFIT Referece: Valentin A. Ilyin, Alexej Abyzov, and Chesley M.Leslin, Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. (preprint) Protein Science (2004), 13:1865-1874.
Alignment for 1d2rA and 1mawC

1d2rA HEADER LIGASE 27-SEP-99 1D2R 
1mawC HEADER LIGASE 02-AUG-02 1MAW 

              Ne
              RMSD
              Z-Score
              Seq. %
              Pos. %
              nFrg
              Contact match
              Contact1
              Contact2
              Backbone match
              Backbone1
              Backbone2
              Fragments
               
3210.63666.84498.1399.075198220432044316316318(0,0,108)
(109,108,3)
(113,111,1)
(116,116,63)
(180,180,146)



ALIGNMENT FASTA
1d2rAMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQ
1mawCMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQ
CONSERVED RESIDUESMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQ
1d2rASEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGAA----AAAAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRD
1mawCSEVPAHAQAAWMLQCIVYIGELERMTQF-KEK-S--AGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRD
CONSERVED RESIDUESSEVPAHAQAAWMLQCIVYIGELERMTQF------------A--AGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRD
1d2rALAERFNKRYGELFTIPEARIPKVG-ARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAK
1mawCLAERFNKRYGELFTIPEARIPKV-GARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAK
CONSERVED RESIDUESLAERFNKRYGELFTIPEARIPKV--ARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAK
1d2rAPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMV
1mawCPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMV
CONSERVED RESIDUESPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMV
1d2rARKMEQAMGLGR
1mawCRKMEQAMGLGR
CONSERVED RESIDUESRKMEQAMGLGR


 Fragment notation: (n1,n2,l)
n1 - residue number in 1d2rA
n2 - residue number in 1mawC
l - fragment length (is negative when residues are aligned in reverse order)
***Negative Fragments (non-sequential alignments) can not be shown in a sequential alignment, so they are removed, which could lead to fewer aligned residues then shown by Ne 
 See Alignment plot below