Sample Output

Explanations/Comments

SEQUENCE sars15 NUMBER of RESIDUES: 1255 NUMBER of TM HELICES: 1 N-TERMINAL outside MEMBRANE ---------------------------------------------- Helix # Starting Ending # of Residues ---------------------------------------------- Helix 1 : 1197 1224 28 ============================================== SEQUENCE sars3 NUMBER of RESIDUES: 2422 NUMBER of TM HELICES: 11 N-TERMINAL inside MEMBRANE --------------------------------------------- Helix # Starting Ending # of Residues ---------------------------------------------- Helix 1 : 1327 1333 7 Helix 2 : 1388 1413 26 Helix 3 : 1481 1499 19 Helix 4 : 1509 1527 19 Helix 5 : 1537 1555 19 Helix 6 : 1932 1954 23 Helix 7 : 2178 2186 9 Helix 8 : 2205 2223 19 Helix 9 : 2237 2255 19 Helix 10 : 2265 2283 19 Helix 11 : 2294 2312 19 ============================================== ************ SUMMARY *************** total proteins: 2 proteins have helix segments: 2 100.% proteins have single segment: 1 50.% predicted to be TM proteins: 2 100.% ####################################### THUMBUP version 1.0 Hongyi Zhou and Yaoqi Zhou Oct. 2002, hzhou2@acsu.buffalo.edu Reference: H. Zhou and Y. Zhou, Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model based method, Protein Science 12:1547-1555 (2003) #######################################

The name of the first sequence given in input file is sars15 1255 The number of residues for the first sequence in input file is 1255. The number of transmembrane helices found is 1. N-terminal is predicted to be outside membrane. The table for predicted transmembrane helices (if any). The four columns are 1) Index for the transmembrane helix 2) The starting residue # 3) The ending residue # 4) The number residue for the TM helix. The result for the 2nd sequence if any Explaination as above. Presentation of summary information The total number of sequences in input file is 2 The number and fraction of input sequences with TM helix segments The number and fraction of input sequences with single TM segment The number and fraction of input sequences are TM proteins. Other informations about programs used.