From SMian@lbl.gov Mon May 15 16:08:32 2000 Return-Path: Sender: saira@lbl.gov Date: Mon, 15 May 2000 16:08:09 -0700 From: Saira Mian X-Accept-Language: en To: Kevin Karplus Subject: T88/Ig/all beta fold Content-Type: text/plain; charset=us-ascii Dear Kevin, Just a quick message before I get back to my other work. This first round PSI-BLAST hit, although very statistically insignificant, makes sense. The region of 1A12 that aligns ti T88 is all beta and many domains involved in cell adhesion have this general fold. -saira >pdb|1A12|A Chain A, Regulator Of Chromosome Condensation (Rcc1) Of Human pdb|1A12|B Chain B, Regulator Of Chromosome Condensation (Rcc1) Of Human pdb|1A12|C Chain C, Regulator Of Chromosome Condensation (Rcc1) Of Human Length = 413 Score = 29.7 bits (65), Expect = 15 Identities = 34/111 (30%), Positives = 49/111 (43%), Gaps = 17/111 (15%) Query: 3 SFIGSTENDVGPSQGSYSSTHAMDNLPFVYNTGYNIGYQNANVWRISGGFCVGLDGKV-- 60 SF ST++ VG S G + T MD+ Y+ G A R+ G G + K Sbjct: 280 SFKNSTKSWVGFSGGQHH-TVCMDSEGKAYSLG------RAEYGRL--GLGEGAEEKSIP 330 Query: 61 ----DLPVVGSLD-GQSI-YGLTEEVGLLIWMGDTNYSRGTAMSGNSWENV 105 LP V S+ G S+ Y +T++ + W TNY GT ++W V Sbjct: 331 TLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSPV 381 >pir||S57664 IgA-specific metalloendopeptidase homolog sepA precursor - Shigella flexneri emb|CAA88252.1| (Z48219) sepA [Shigella flexneri] Length = 1366 Score = 33.2 bits (74), Expect = 1.4 Identities = 30/115 (26%), Positives = 51/115 (44%), Gaps = 16/115 (13%) Query: 29 PFVYNTGYNIGYQNANVWRISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGD 88 P++Y+ N G + N+ ++SG + LDG V+LP +G +T++ G LI+ G Sbjct: 620 PYMYHGQLN-GNMDVNIPQLSGKDVLALDGSVNLP-----EG----SITKKSGTLIFQGH 669 Query: 89 TNYSRGTAMSGNSWENVFSGWCVGNYVSTQGLSVHVRPVILKRNSSAQYSVQKTS 143 GT S + S W + + + L + L RN Q + T+ Sbjct: 670 PVIHAGTTTSSSQ-----SDWETRQF-TLEKLKLDAATFHLSRNGKMQGDINATN 718 -- I. Saira Mian Life Sciences Division (Mail Stop 74-197) E-mail: SMian@lbl.gov Lawrence Berkeley National Laboratory Tel: (510) 486-6216 1 Cyclotron Road Fax: (510) 486-6949 Berkeley, California 94720 From karplus@cse.ucsc.edu Mon May 15 16:40:35 2000 Return-Path: Date: Mon, 15 May 2000 16:40:31 -0700 From: Kevin Karplus To: saira@sanger.ac.uk CC: karplus@cse.ucsc.edu Subject: T88-1a12A The T88-1a12A looks to me like an incorrect fold, but a possibly good alignment of a beta-sandwich to part of a beta propeller. Actually, I'm not sure whether the structure is properly called a beta propeller, but it has a lot of beta sheets radiating from a common center. See my notes in t88/README or see for yourself with see-a2m 1a12A/T0088-1a12A-local.pw.a2m.gz from pce/casp4/t88 to view the alignment---press the "Kimmen" button to color conserved positions RED and other aligned positions GREEN.