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101447, , , 19, e-mail: natasha@imb.imb.ac.ru . (095) 135-20-41 - , 119899, Integrated Genomics, , / 348, 117337 , , , 113545, 1- . 1
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. 1. q q kfs. , -- . q q = perij / obij , kfsij = per/li , kfsj i = per/lj , kfs = (kfsij + kfsj i )/ (tmi + tmj ),
i,j i,j i,j i,j

obij -- , perij -- , li -- , lj -- , tmi -- , tmj -- .

( TC.2A . . (http://www-biology.ucsd.edu /msaier/transport/) [1],[2]) : GNTP (2A.8), MHS (2A.1.6), NCS2 (2A.40). , , ERGO (http://ergo.integratedgenomics.com/ERGO/) [3]: -- 40%-60%; -- 60%-80%; -- 80%-100%. 26 . GNTP 1, 2 , . RSAX01242 RZW01701 RZY00850 RBS04001 1 2 3 4 1 100 99 88 62 2 99 100 88 62 3 88 88 100 65 4 62 62 65 100

1. GNTP. ClustalW [4]. : DAS (http://www.sbc.su.se/miklos/DAS/) [5], TMAP (http://www.mbb.ki.se/tmap/) [6], TMHMM1.0 (http://www.cbs.dtu.dk/services /TMHMM-2.0) [7], TMPred (http://www.ch.embnet.org/software/TMPRED_form.html).
2 1 2002

98

, , ,

RBL00061 RBS04001 RSY03952 RTY03814 REC03333 RYP01565 RBPS05419 RBU11141 RAC01503 RPU05135 RBE02868 RPA04265 RCHU01060

1 2 3 4 5 6 7 8 9 10 11 12 13

1 100 85 51 51 50 52 43 42 41 38 43 42 41

2 85 100 52 52 51 53 44 43 42 41 43 43 42

3 51 52 100 99 96 85 45 46 43 42 47 44 42

4 51 52 99 100 96 85 45 46 43 42 47 44 42

5 50 51 96 96 100 84 45 45 43 42 46 44 42

6 52 53 85 85 84 100 46 45 44 43 46 45 42

7 43 44 45 45 45 46 100 83 80 62 60 52 40

8 42 43 46 46 45 45 83 100 73 62 57 51 39

9 41 42 43 43 43 44 80 73 100 60 57 49 38

10 38 41 42 42 42 43 62 62 60 100 54 49 38

11 43 43 47 47 46 46 60 57 57 54 100 54 40

12 42 43 44 44 44 45 52 51 49 49 54 100 41

13 41 42 42 42 42 42 40 39 38 38 40 41 100

2. GNTP. 3. , , . TM.exe CPP. q q kfs . . DAS . . 3 q q kfs GNTP . DAS qq 40-60 0,365 60-80 0,469 80-100 0,827 DAS kfs 0,499 0,692 0,945 TMAP qq 0,564 0,619 0,769 TMAP TMHMM TMHMM TMPRED TMPRED kfs qq kfs qq kfs 0,784 0,551 0,735 0,482 0,671 0,866 0,579 0,842 0,567 0,855 0,916 0,778 0,906 0,828 0,935

3. GNTP . q q kfs. , . . , , . .. , .. .. . (00-15-99362), INTAS (99-1476), HHMI (55000309) LICR (CRDF RBO-1268).
1. Milton H., Saier Jr. A Functional-Phylogenetic System for the Classification of Transport Proteins. J. Cell Biochem., 1999, vol. 75, no. S32, pp. 8494. 2. Milton H., Saier Jr. A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters. Microbiol. Mol. Biol. Rev., 2000, vol. 64, no. 2, pp. 354411.
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3. Overbeek R., Larsen N., Pusch G.D., D'Souza M., Selkov E.Jr, Kyrpides N., Fonstein M., Maltsev N., Selkov E. WIT: Integrated System for High-Throughput Genome Sequence Analysis and Metabolic Reconstruction. Nucleic Acids Res., 2000, vol. 28, pp. 123125. 4. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Res., 1994, vol. 22, pp. 46734680. 5. Cserzo M., Wallin E., Simon I., von Heijne G., Elofsson A. Prediction of Transmembrane Alpha-Helices in Prokaryotic Membrane Proteins: the Dense Alignment Surface Method. Protein Eng., 1997, vol. 10, pp. 673676. 6. Persson B., Argos P. Topology Prediction of Membrane Proteins. Protein Sci., 1996, vol. 5, pp. 363371. 7. Sonnhammer E.L., von Heijne G., Krogh A. A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 1998, vol. 6, pp. 175182.

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2

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2002