From SMian@lbl.gov Sun May 14 18:35:32 2000 Return-Path: Sender: saira@lbl.gov Date: Sun, 14 May 2000 18:35:12 -0700 From: Saira Mian X-Accept-Language: en To: Kevin Karplus Subject: Re: CASP/t86 Content-Type: multipart/mixed; boundary="------------08F2AE88E2CBC5CD7735F39B" This is a multi-part message in MIME format. --------------08F2AE88E2CBC5CD7735F39B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Kevin, Great! I don't have permission to access /projects/compbio/experiments/casp4. I have some thoughts about the HMM library which I will send tomorrow. Since T86 is due soon, I thought I'd send you an HMM-generated alignment of t86 derived from an initial PSI-BLAST analysis. You might want to take a look at Xue & Lipscomb PNAS 92:10595 (1995) in terms of the types of chorismate binding residues one might expect to be conserved. -saira Kevin Karplus wrote: > > Saira, > > I would be willing to include you on the SAM_T2K team (the SAM_T99 > team is the automatic server). > > The best role for you would be look through various "hit" lists and > give us some hints for functional screening. Because we don't usually > understand the names of the proteins, we often miss relationships that > would be obvious to a real protein person. > > You can also look at alignment predictions and give comments on how > good or bad they look. For example, you are more likely to figure out > whether residues at a binding site are being properly matched than we > are. > > The work will all be done in /projects/compbio/experiments/casp4 > with a subdirectory for each target. There are three targets there > already (t86, t87, t88). None of these have obvious (or even > sam-t99-detectable) homologies, so we are going to be reduced to > secondary structure matching and functional matching. > > Take a look at the files in each of those directories and let me know > if you have any questions about what they mean. As I get a chance to > look at the results, I'll add my working notes as a README file for > each target. > > Kevin -- 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 --------------08F2AE88E2CBC5CD7735F39B Content-Type: text/plain; charset=us-ascii; name="t00861.out" Content-Disposition: inline; filename="t00861.out" Content-Transfer-Encoding: 7bit ; SAM: prettyalign v2.2.1 (October 5, 1998) compiled 10/06/98_16:11:20. ; SAM: Sequence Alignment and Modeling Software System ; (c) 1992-1998 Regents of the University of California, Santa Cruz ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ------ Citations (HMMs, SAM) ------ ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: ; Extension and analysis of the basic method, CABIOS 12:95-107, 1996. ; ----------------------- 10 20 30 40 50 60 70 80 | | | | | | | | T0086 ....SHPALT.QLRALRYCKEIPALDPQLLDWLLLEDSMTKRF-EQQGKTVSVTMIREGFv9eeLPLLPKESR....YWLREILLCADGEPWLAGRTVV AF187880_4 mev.AYRFSQpHLEWNSYGHWRSSIAATQREWLFDRSSLTRRLRTLSDNEFEVIPLREAA....GPMLPEECRv9vtGWIREVYLAGFGRPWVYARSVI T36851 113aFDAGAQ.ALRDRRDSRLRVAASMTIAEYLLPGWLVALRA-QLPDTAVSLLAGNSAAva..ERLLADDADl18iGHDRLIVVTAPGHPWARRRRPL 90 100 110 120 130 140 150 | | | | | | | T0086 PVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRD....AGLWGRRSRLRLSGKPLLLTELFLPASPLY-..... AF187880_4 SHCDVEGSDSALLQLGNIPLGSLLFGENPYKRSEIEVCRYp11aYPLWARRSVFSRRQSRVLVHEMFLPALWEE-ls... T36851 EAAELAATPLILREKGSGTRQVLDAALGGLARPLIELSSTt22gEELTTRRLVSVPVADVVLARD--LRAVWPT-g17a. --------------08F2AE88E2CBC5CD7735F39B Content-Type: text/plain; charset=us-ascii; name="t0086.pep" Content-Disposition: inline; filename="t0086.pep" Content-Transfer-Encoding: 7bit ; ; T0086 Chorismate lyase, E. coli T0086 SHPALTQLRA LRYCKEIPAL DPQLLDWLLL EDSMTKRFEQ QGKTVSVTMI REGFVEQNEI PEELPLLPKE SRYWLREILL CADGEPWLAG RTVVPVSTLS GPELALQKLG KTPLGRYLFT SSTLTRDFIE IGRDAGLWGR RSRLRLSGKP LLLTELFLPA SPLY ; [AF187880_4] ; LOCUS AF187880_4 182 aa BCT 07-OCT-1999 ; DEFINITION unknown [Pseudomonas sp. YH102]. ; ACCESSION AAF01449 ; PID g6014666 ; VERSION AAF01449.1 GI:6014666 ; DBSOURCE locus AF187880 accession AF187880.1 ; KEYWORDS . ; SOURCE Pseudomonas sp. YH102. ; ORGANISM Pseudomonas sp. YH102 ; Bacteria; Proteobacteria; gamma subdivision; Pseudomonas group; ; Pseudomonas. ; REFERENCE 1 (residues 1 to 182) ; AUTHORS Newman,L.M. and Zylstra,G.J. ; TITLE Analysis of genes for p-nitrobenzoate degradation from Pseudomonas ; sp. strain YH102 ; JOURNAL Unpublished ; REFERENCE 2 (residues 1 to 182) ; AUTHORS Newman,L.M. and Zylstra,G.J. ; TITLE Direct Submission ; JOURNAL Submitted (16-SEP-1999) Biotech Center for Agriculture & the ; Environment, Cook College, Rutgers University, 59 Dudley Road, New ; Brunswick, NJ 08901-8520, USA ; COMMENT Method: conceptual translation supplied by author. ; FEATURES Location/Qualifiers ; source 1..182 ; /organism="Pseudomonas sp. YH102" ; /strain="YH102" ; /db_xref="taxon:104926" ; Protein 1..182 ; /product="unknown" ; /name="orf2" ; CDS 1..182 ; /coded_by="AF187880.1:2680..3228" ; /transl_table=11 ; ORIGIN AF187880_4 MEVAYRFSQPHLEWNSYGHWRSSIAATQREWLFDRSSLTRRLRTLSDNEFEVIPLREAAGPMLPEECRVL GLQPGVTGWIREVYLAGFGRPWVYARSVISHCDVEGSDSALLQLGNIPLGSLLFGENPYKRSEIEVCRYP DACNASSRPAYPLWARRSVFSRRQSRVLVHEMFLPALWEELS ; [T36851] ; LOCUS T36851 325 aa BCT 07-DEC-1999 ; DEFINITION probable transcription regulator - Streptomyces coelicolor. ; ACCESSION T36851 ; PID g7481539 ; VERSION T36851 GI:7481539 ; DBSOURCE pir: locus T36851; ; summary: #length 325 #molecular-weight 33489 #checksum 5285; ; genetic: #gene SCOEDB:SCI35.38c; ; PIR dates: 03-Dec-1999 #sequence_revision 03-Dec-1999 #text_change ; 07-Dec-1999. ; KEYWORDS . ; SOURCE Streptomyces coelicolor. ; ORGANISM Streptomyces coelicolor ; Bacteria; Firmicutes; Actinobacteria; Actinobacteridae; ; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces. ; REFERENCE 1 (residues 1 to 325) ; AUTHORS Oliver,K., Harris,D., Parkhill,J., Barrell,B.G. and Rajandream,M.A. ; TITLE Direct Submission ; JOURNAL Submitted (??-SEP-1998) to the EMBL Data Library ; FEATURES Location/Qualifiers ; source 1..325 ; /organism="Streptomyces coelicolor" ; /db_xref="taxon:1902" ; Protein 1..325 ; /product="probable transcription regulator" ; ORIGIN T36851 MGSGAGSSTNGGTGGGTEGGHDTRARQVAGSLAHRVPDLGAMELLLAVARLGSLGGAARELGITQPAASS RIRSMERQLGVALVDRSPRGSRLTDAGALVTDWARRIVEAAEA FDAGAQALRDRRDSRLRVAASMTIAEY LLPGWLVALRAQLPDTAVSLLAGNSAAVAERLLADDADLGFVEGVSVPTGLDSAVIGHDRLIVVTAPGHP WARRRRPLEAAELAATPLILREKGSGTRQVLDAALGGLARPLIELSSTTAVKAAAVGGAGPSVLSELAVG EELTTRRLVSVPVADVVLARDLRAVWPT GHRPTGPARQLLSLTRA ; [S72976] ; LOCUS S72976 353 aa BCT 22-OCT-1999 ; DEFINITION hypothetical protein B229_C1_169 - Mycobacterium leprae. ; ACCESSION S72976 ; PID g2145797 ; VERSION S72976 GI:2145797 ; DBSOURCE pir: locus S72976; ; summary: #length 353 #molecular-weight 39114 #checksum 3066; ; PIR dates: 19-Mar-1997 #sequence_revision 25-Apr-1997 #text_change ; 22-Oct-1999. ; KEYWORDS . ; SOURCE Mycobacterium leprae. ; ORGANISM Mycobacterium leprae ; Bacteria; Firmicutes; Actinobacteria; Actinobacteridae; ; Actinomycetales; Corynebacterineae; Mycobacteriaceae; ; Mycobacterium. ; REFERENCE 1 (residues 1 to 353) ; AUTHORS Smith,D.R. and Robison,K. ; TITLE Direct Submission ; JOURNAL Submitted (??-NOV-1993) to the EMBL Data Library ; FEATURES Location/Qualifiers ; source 1..353 ; /organism="Mycobacterium leprae" ; /db_xref="taxon:1769" ; Protein 1..353 ; /product="hypothetical protein B229_C1_169" ; ORIGIN ; Saira: may be missing N-terminal 50 residues ;; S72976* ;; MKWSPVYAGGSPERTARPKPLTDDEIRRRRNGRPWLAGGTGLVPVATIVGALSLRSIFERDNACRDPYVD ;; RDFEKLGDERRCWVTISGGMALVVREEGAVKAPVAMVFAYGFYLRMDSFHFQRKRFGKRWGPQVRMVFYD ;OMIT; HCGHVQSSEVALDTYTLTQLGQDLRTVLQTVTPHGMIVLVGHSMEGILKSPALEAVRLTSRSASKLMHRG ;OMIT; SIASQSLIGPILRAASYSDLRVSRGLDAFSQRIMNDTLIAILVSFLHALELHEETAGLWPLLRVPALIAC ;OMIT; GDHDLLTSDERSRGMAAVLPLLALVIVSGASRLALLDKPGAINDGLVRLVNRAVPGKAALRYRRFKERLQ ;OMIT; RHG ; [CAB59810] ; LOCUS CAB59810 441 aa BCT 29-OCT-1999 ; DEFINITION putative aminotransferase [Streptomyces coelicolor A3(2)]. ; ACCESSION CAB59810 ; PID g6165436 ; VERSION CAB59810.1 GI:6165436 ; DBSOURCE embl locus SCF62, accession AL121855.2 ; KEYWORDS . ; SOURCE Streptomyces coelicolor A3(2). ; ORGANISM Streptomyces coelicolor A3(2) ; Bacteria; Firmicutes; Actinobacteria; Actinobacteridae; ; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces. ; REFERENCE 1 (residues 1 to 441) ; AUTHORS Redenbach,M., Kieser,H.M., Denapaite,D., Eichner,A., Cullum,J., ; Kinashi,H. and Hopwood,D.A. ; TITLE A set of ordered cosmids and a detailed genetic and physical map ; for the 8 Mb Streptomyces coelicolor A3(2) chromosome ; JOURNAL Mol. Microbiol. 21 (1), 77-96 (1996) ; MEDLINE 97000351 ; REFERENCE 2 (residues 1 to 441) ; AUTHORS Murphy,L. and Harris,D. ; JOURNAL Unpublished ; REFERENCE 3 (residues 1 to 441) ; AUTHORS Thomson,N.R., Parkhill,J., Barrell,B.G. and Rajandream,M.A. ; TITLE Direct Submission ; JOURNAL Submitted (29-OCT-1999) Streptomyces coelicolor sequencing project, ; Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge ; CB10 1SA E-mail: barrell@sanger.ac.uk Cosmids supplied by Prof. ; David A. Hopwood, [3] John Innes Centre, Norwich Research Park, ; Colney, Norwich, Norfolk NR4 7UH, UK ; COMMENT Notes: ; Streptomyces coelicolor sequencing at The Sanger Centre is funded ; by the BBSRC and Beowulf Genomics ; Details of S. coelicolor sequencing at the Sanger Centre are ; available on the World Wide Web. ; (URL; http://www.sanger.ac.uk/Projects/S_coelicolor/) ; CDS are numbered using the following system eg SC7B7.01c. SC (S. ; coelicolor), 7B7 (cosmid name), .01 (first CDS), c (complementary ; strand). ; The more significant matches with motifs in the PROSITE database ; are also included but some of these may be fortuitous. ; The length in codons is given for each CDS. ; Usually the highest scoring match found by fasta -o is given for ; CDS which show significant similarity to other CDS in the database. ; The position of possible ribosome binding site sequences are given ; where these have been used to deduce the initiation codon. ; Gene prediction is based on positional base preference in codons ; using a specially developed Hidden Markov Model (Krogh et al., ; Nucleic Acids Research, 22(22):4768-4778(1994)) and the FramePlot ; program of Bibb et al., Gene 30:157-66(1984) as implemented at ; http://www.nih.go.jp/ ; jun/cgi-bin/frameplot.pl. CAUTION: We may not have predicted the ; correct initiation codon. Where possible we choose an initiation ; codon (atg, gtg, ttg or (att)) which is preceded by an upstream ; ribosome binding site sequence (optimally 5-13bp before the ; initiation codon). If this cannot be identified we choose the most ; upstream initiation codon. ; IMPORTANT: This sequence MAY NOT be the entire insert of the ; sequenced clone. It may be shorter because we only sequence ; overlapping sections once, or longer, because we arrange for a ; small overlap between neighbouring submissions. ; Cosmid F62 Lies on the AseI-F genomic restriction fragment. ; FEATURES Location/Qualifiers ; source 1..441 ; /organism="Streptomyces coelicolor A3(2)" ; /strain="A3(2)" ; /db_xref="taxon:100226" ; /clone="cosmid F62" ; Protein 1..441 ; /product="putative aminotransferase" ; CDS 1..441 ; /gene="SCF62.27" ; /coded_by="AL121855.2:32366..33691" ; /transl_table=11 ; /note="SCF62.27, possible aminotransferase, len: 441 aa. ; Similar to many including Pseudomonas aeruginosa ; SW:GSA_PSEAE (EMBL:X82072) glutamate-1-semialdehyde ; 2,1-aminomutase (EC 5.4.3.8) (glutamate-1-semialdehyde ; aminotransferase) (427 aa), fasta scores opt: 475 ; z-score: 540.8 E(): 9.5e-23 34.8% identity in 434 aa ; overlap and Streptomyces coelicolor TR:CAB39702 (EMBL: ; AL049485) probable aminotransferase SC6A5.18 (461 aa), ; fasta scores opt: 464 z-score: 527.9 E(): 4.9e-22 32.4% ; identity in 407 aa overlap. Contains 2xPfam matches to ; entry PF00202 aminotran_3, Aminotransferases class-III ; pyridoxal-phosphate." ; ORIGIN ; Saira: may be missing C-terminal residues ;OMIT; CAB59810* ;OMIT; MNAEELGLPRSRQANERLHALVPGGAHTYAKGDDQYPENLAPVISHGRGAHVWDVDGNRYVEYGSGLRSV ;OMIT; SLGHAHPRVTEAVRRELDRGSNFVRPSIVEVDAAERFLATVPTAEMVKFAKNGSDATTAAVRLARAATGR ;OMIT; PRVAVCADHPFFSVDDWFIGTTPMSAGIPAATNELTVAFPYGDLAATEDLLARHEGEVACLILEPATHTE ;OMIT; PPPGYLAGLRELADRHGCVLVFDEMITGFRWSEAGAQGLYGVVPDLSTFGKALGNGFAVAALAGRRELME ;OMIT; LGGLRHSGDRVFLLSTTHGAETHALAAAMAVQGTYVEEGVTARLHALGDRLAAGVREAAASMGVGDHVVV ;; CAB59810* ;; RGRASNLVFATLDENGQPSQRYRTLFLRQLLAGGVLAPSFVVSSALGDADLDHTVDVVAEACAVYRKALD ;; AADPTPWMAGRPVKPVFRRLV --------------08F2AE88E2CBC5CD7735F39B Content-Type: text/plain; charset=us-ascii; name="t00861.a2m" Content-Disposition: inline; filename="t00861.a2m" Content-Transfer-Encoding: 7bit >T0086, 337 bases, D5F233E3 checksum. .................................................. .................................................. .............SHPALT.QLRALRYCKEIPALDPQLLDWLLLEDSMTK RF-EQQGKTVSVTMIREGFveqneipeeLPLLPKESR............. .....YWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRY LFTSSTLTRDFIEIGRD......................AGLWGRRSRLR LSGKPLLLTELFLPASPLY-................. >AF187880_4, 337 bases, D7CC0B61 checksum. mev............................................... .................................................. .............AYRFSQpHLEWNSYGHWRSSIAATQREWLFDRSSLTR RLRTLSDNEFEVIPLREAA.........GPMLPEECRvlglqpgvt.... .....GWIREVYLAGFGRPWVYARSVISHCDVEGSDSALLQLGNIPLGSL LFGENPYKRSEIEVCRYpdacnassrpa...........YPLWARRSVFS RRQSRVLVHEMFLPALWEE-ls............... >T36851, 337 bases, 49E624D5 checksum. mgsgagsstnggtgggtegghdtrarqvagslahrvpdlgamelllavar lgslggaarelgitqpaassrirsmerqlgvalvdrsprgsrltdagalv tdwarriveaaeaFDAGAQ.ALRDRRDSRLRVAASMTIAEYLLPGWLVAL RA-QLPDTAVSLLAGNSAAva.......ERLLADDADlgfvegvsvptgl dsaviGHDRLIVVTAPGHPWARRRRPLEAAELAATPLILREKGSGTRQVL DAALGGLARPLIELSSTtavkaaavggagpsvlselavgEELTTRRLVSV PVADVVLARD--LRAVWPT-ghrptgparqllsltra --------------08F2AE88E2CBC5CD7735F39B-- From karplus@cse.ucsc.edu Mon May 15 08:23:07 2000 Return-Path: Date: Mon, 15 May 2000 08:23:05 -0700 From: Kevin Karplus To: SMian@lbl.gov CC: karplus@cse.ucsc.edu In-reply-to: <391F5450.BE756769@lbl.gov> (message from Saira Mian on Sun, 14 May 2000 18:35:12 -0700) Subject: Re: CASP/t86 Saira, You should have access to all the /projects/compbio/experiments/casp4/t* directories now. You are in the protein group, and the directories are now group-writable (they were only group-readable/executable before). Let me know if you have any further problems. The alignment you got from PSI-BLAST is a bit different than the one from T2K, though both have essentially 3 sequences (T0086+two others---the T2K alignment has some close duplicates). Both include AF187880_4, but the third sequence is different. I'll look at the article you mention. From karplus@cse.ucsc.edu Wed May 17 12:25:48 2000 Return-Path: Date: Wed, 17 May 2000 12:25:45 -0700 From: Kevin Karplus To: saira@sanger.ac.uk Cc: karplus@cse.ucsc.edu Subject: T0086-2chsA What do you think of the aligment of T0086 to 2chsA (see the notes in pce/casp4/t86/README)? From SMian@lbl.gov Thu May 18 10:41:54 2000 Return-Path: Sender: saira@lbl.gov Date: Thu, 18 May 2000 10:41:51 -0700 From: Saira Mian X-Accept-Language: en To: karplus@cse.ucsc.edu Subject: T0086: T0089 & T0090 Content-Type: text/plain; charset=us-ascii Dear Kevin, Since T0089 and T0090 are each listed as having a "Homologous sequence of known structure", I assume that both will be picked with the automated scanning of the library. Unless I hear otherwise, I won't think about these two targets. I've created casp4/t86/saira which contains an archaeal sequence (B69085) that could be a structural (not biochemical) homologue. Rather than adding to the README files (I don't know what the etiquette for writing to them is and I'm not present during your discussions with everyone else on the team), I'll send you e-mail. A reasonable rule of thumb is to look at structures/active sites, if known, for enzymes that precede and follow the one of interest in the pathway under consideration. In terms of T0086, the flanking enzymes should recognise the substrate (chorismate) using similar types of residues. -saira -- 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 cline@cse.ucsc.edu Thu May 18 13:47:59 2000 Return-Path: From: Melissa Cline Content-Type: text/plain; charset=us-ascii Date: Thu, 18 May 2000 13:47:57 -0700 (PDT) To: Kevin Karplus Subject: T0086 tasks In-Reply-To: <200005180028.RAA21406@purr.cse.ucsc.edu> > I think it would be valuable to build an active-site model of > chorismate mutase by running T2K on a structural alignment of 1ecmA > and 5csmA. This alignment may have to be done with the Yale aligner, > not DALI or VAST, since the active sites are alignable, but the > scaffolding that supports them has different secondary structure elements. > > Melissa, could you produce this structural alignment? The Yale aligner seems to be blowing up on 1ecmA and 5csmA. Would you like me to keep hunting for a different tool to align them? Melissa From karplus@cse.ucsc.edu Thu May 18 13:53:06 2000 Return-Path: Date: Thu, 18 May 2000 13:53:05 -0700 From: Kevin Karplus To: cline@cse.ucsc.edu Cc: karplus@cse.ucsc.edu In-reply-to: <14628.22166.387111.409716@oink> (message from Melissa Cline on Thu, 18 May 2000 13:47:57 -0700 (PDT)) Subject: Re: T0086 tasks Sigh, maybe we should have created our own iterated superposition aligner. The problem may be coming from the interrupted chain in 5csmA. We have an fssp alignment, plus an extra helix from the Xue and Lipscomb paper, so the Yale alignment is not critical. Perhaps you should focus on T89 and T90 for a while, where the probable templates are clearer.