GCG V. 9.0-GAP

[Ellis Golub]

I guess it depends on which result you consider more useful:

 
ID   LYG_ANSAN      STANDARD;      PRT;   185 AA.
AC   P00718;
DT   21-JUL-1986 (REL. 01, CREATED)
DT   21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)
DT   01-FEB-1996 (REL. 33, LAST ANNOTATION UPDATE)
DE   LYSOZYME G (EC 3.2.1.17) (1,4-BETA-N-ACETYLMURAMIDASE) (GOOSE-TYPE . . . 
 
 to: kad3_bovin  check: 1291  from: 1  to: 226
 
ID   KAD3_BOVIN     STANDARD;      PRT;   226 AA.
AC   P08760;
DT   01-NOV-1988 (REL. 09, CREATED)
DT   01-APR-1990 (REL. 14, LAST SEQUENCE UPDATE)
DT   01-NOV-1995 (REL. 32, LAST ANNOTATION UPDATE)
DE   GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3). . . . 

 Symbol comparison table: . .gcg90/gcgcore/data/rundata/blosum62.cmp CompCheck: 6430

         Gap Weight:      5      Average Match:  2.912
      Length Weight:      3   Average Mismatch: -2.003

            Quality:      4             Length:    409
              Ratio:  0.022               Gaps:      0
 Percent Similarity: 50.000   Percent Identity: 50.000

        Match display thresholds for the alignment(s):
                    | = IDENTITY
                    : =   2
                    . =   1

 lyg_ansan x kad3_bovin    May 26, 1997 20:47  ..

                                  .
                                  .
                                  .
                  .         .         .         .         .
     151 AGNVRSYARMDIGTTHDDYANDVVARAQYYKQHGY............... 185
                                          |                
       1 .................................GASARLLRAAIMGAPGS 17
                                  .
                                  .
OR                                 .

 Symbol comparison table: . .gcg90/gcgcore/data/moredata/oldpep.cmp
 CompCheck: 2543

         Gap Weight:      5      Average Match:  5.402
      Length Weight:      3   Average Mismatch: -3.964

            Quality:    829             Length:    244
              Ratio:  4.481               Gaps:     35
 Percent Similarity: 64.072   Percent Identity: 31.737

        Match display thresholds for the alignment(s):
                    | = IDENTITY
                    : =   4
                    . =   1

 lyg_ansan x kad3_bovin    May 26, 1997 20:58  ..

                  .         .         .         .         .
       1 .......RTDCYGNVNRIDTTGASCKTAKP.EGLSYCGVSASKKIAERD. 41
                |:.. |..:. .:| .|::.:|. | |..  :| | .:  || 
       1 GASARLLRAAIMGAPGSGKGT.VSSRITKHFE.LKH..LS.SGDLL.RDN 44
                  .         .         .         .         .
      42 .LQA..MDRY.KTIIKKVGEKLCVEPAVIAGIISRESHAGKVLKN..GWG 85
          |::  :: . ||:|.: | || :...|:: :: :|      |||  .: 
      45 MLRGTEIGVLAKTFIDQ.G.KL.IPDDVMTRLVLHE......LKNLTQY. 84
                  .         .         .         .         .
      86 DR.GNGF..GLMQVD..KRSHKPQG..TWNG..EV...HIT.....QGTT 118
         ::  :||  :| |.:  .|:.: ::  .:|.  ||   ::|     .|.:
      85 NWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPGSG 134
                  .         .         .         .         .
     119 .IL.INF..IKT..IQ....KKFPSWTKDQQ...LKGGISAYNAGAGNVR 155
          :. |:|   ||  |:    ..:. :..|:.   :|  :.||:|.:: | 
     135 RVYNIEFNPPKTMGIDDLTGEPLVQREDDRPETVVK.RLKAYEAQTEPVL 183
                  .         .         .         .    
     156 SYAR....MD.I.GT.THDDYANDVVARAQY.YKQHGY...... 185
         .| |    :: : || |:. ::: | |  |  ..|::       
     184 EYYRKKGVLETFSGTETNKIWPH.VYAFLQTKLPQRSQETSVTP 226
     

In article <5me8vi$ngj at rc1.vub.ac.be>, cgovaert at ulb.ac.be (Cedric Govaerts) writes:

|> 
|> 
|> But the renormalized matrix used by GCG 8 has no scientific value, because
|> a conserved Glycine is in fact different than a conserved Tryptophan..
|> Better use Blosum 62 or PAM 250 (not renormalized !!).
|> 
|> Cedric Govaerts
|> 

--
Ellis Golub                  Phone: (215) 898-4629
Biochemistry Department      FAX:   (215) 898-3695
University of Pennsylvania   ellis at biochem.dental.upenn.edu
School of Dental Medicine             
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