% (null) % (c) 1992-2001 Regents of the University of California, Santa Cruz % % Sequence Alignment and Modeling Software System % http://www.cse.ucsc.edu/research/compbio/sam.html % % ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- % R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: % Extension and analysis of the basic method, CABIOS 12:95-107, 1996. % K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % T0139.t2k Host: cc62 Sun Aug 11 17:25:44 2002 % karplus Dir: /projects/compbio/experiments/casp5/t0139 % --------------------------------------------------------------------- % Sequence-model (global) (SW = 0) % Track 0 Coeff 1.000 File T0139.t2k-w0.5.mod % Track 1 Coeff 0.300 File T0139.t2k.str.mod 1fe6A.1.1 52 -120.54 -120.54 1fe6A.1.0 52 -118.22 -118.22 1fe6C.1.1 52 -115.98 -115.98 1fe6C.1.0 52 -115.12 -115.12 1c8oA.1.1 300 -115.07 -115.07 1wdcC.1.0 156 -114.96 -114.96 1fe6A.2.2 52 -130.71 -130.71 1kafA.2.2 108 -119.47 -119.47 1b5l.2.2 172 -116.85 -116.85 1hsm.2.2 79 -116.85 -116.85 1c8oA.2.2 300 -116.62 -116.62 1avoA.2.2 60 -115.87 -115.87 1fe6A.3.3 52 -129.81 -129.81 1bhdA.3.3 118 -118.62 -118.62 1hsm.3.3 79 -117.82 -117.82 2trcP.3.3 217 -117.11 -117.11 1kafA.3.3 108 -116.32 -116.32 1bhdA.3.2 118 -113.45 -113.45 1fe6A.4.4 52 -131.33 -131.33 1bhdA.4.4 118 -123.32 -123.32 1hsm.4.4 79 -118.83 -118.83 2trcP.4.4 217 -118.66 -118.66 1kafA.4.4 108 -114.53 -114.53 1bhdA.4.3 118 -114.18 -114.18 1fe6A.5.5 52 -130.69 -130.69 1bhdA.5.5 118 -124.46 -124.46 2trcP.5.5 217 -117.83 -117.83 1hsm.5.5 79 -117.56 -117.56 1dp3A.5.5 55 -116.01 -116.01 1bhdA.5.4 118 -114.49 -114.49 1fe6A.6.6 52 -130.99 -130.99 1bhdA.6.6 118 -122.89 -122.89 1dp3A.6.6 55 -119.54 -119.54 1hulA.6.6 108 -116.50 -116.50 2trcP.6.6 217 -115.75 -115.75 1hsm.6.6 79 -114.29 -114.29 1fe6A.7.7 52 -129.57 -129.57 1dp3A.7.7 55 -119.33 -119.33 1bhdA.7.7 118 -118.52 -118.52 1hulA.7.7 108 -118.39 -118.39 1fexA.7.7 59 -115.99 -115.99 1avoA.7.7 60 -114.59 -114.59 1fe6A.8.8 52 -128.66 -128.66 1dp3A.8.8 55 -120.55 -120.55 1hulA.8.8 108 -120.14 -120.14 1dulA.8.8 69 -115.35 -115.35 1avoA.8.8 60 -114.18 -114.18 1fexA.8.8 59 -114.10 -114.10 1fe6A.9.9 52 -128.15 -128.15 1dp3A.9.9 55 -121.58 -121.58 1hulA.9.9 108 -121.27 -121.27 1dulA.9.9 69 -118.48 -118.48 1avoA.9.9 60 -114.10 -114.10 1fexA.9.9 59 -113.29 -113.29 1fe6A.10.10 52 -125.77 -125.77 1hulA.10.10 108 -122.00 -122.00 1dp3A.10.10 55 -120.12 -120.12 1dulA.10.10 69 -119.81 -119.81 1d06A.10.10 130 -115.74 -115.74 1fe6A.10.11 52 -113.32 -113.32 1fe6A.11.11 52 -124.97 -124.97 1hulA.11.11 108 -120.80 -120.80 1dulA.11.11 69 -120.08 -120.08 1dp3A.11.11 55 -119.67 -119.67 1d06A.11.11 130 -117.64 -117.64 1fe6A.11.12 52 -115.86 -115.86 1fe6A.12.12 52 -123.30 -123.30 1dulA.12.12 69 -120.02 -120.02 1hulA.12.12 108 -119.60 -119.60 1d06A.12.12 130 -119.12 -119.12 1dp3A.12.12 55 -118.86 -118.86 1jr8A.12.12 117 -117.27 -117.27 1fe6A.13.13 52 -122.32 -122.32 1d06A.13.13 130 -119.83 -119.83 1dulA.13.13 69 -118.74 -118.74 1hulA.13.13 108 -118.73 -118.73 1jr8A.13.13 117 -118.27 -118.27 1jraA.13.13 117 -118.24 -118.24 1fe6A.14.14 52 -122.08 -122.08 1d06A.14.14 130 -121.48 -121.48 1jr8A.14.14 117 -119.50 -119.50 1jraA.14.14 117 -119.49 -119.49 1hulA.14.14 108 -118.73 -118.73 1dulA.14.14 69 -117.54 -117.54 1d06A.15.15 130 -122.08 -122.08 1fe6A.15.15 52 -121.13 -121.13 1jraA.15.15 117 -120.08 -120.08 1jr8A.15.15 117 -120.06 -120.06 1sra.15.19 151 -119.08 -119.08 1hulA.15.15 108 -119.05 -119.05 1d06A.16.16 130 -124.85 -124.85 1dulA.16.18 69 -123.08 -123.08 1sra.16.20 151 -122.84 -122.84 1jraA.16.16 117 -121.61 -121.61 1jr8A.16.16 117 -121.53 -121.53 1b5l.16.16 172 -121.46 -121.46 1sra.17.21 151 -127.79 -127.79 1dulA.17.19 69 -127.35 -127.35 1d06A.17.17 130 -126.95 -126.95 1jraA.17.17 117 -124.45 -124.45 1jr8A.17.17 117 -124.36 -124.36 1hsm.17.17 79 -124.18 -124.18 1dulA.18.20 69 -132.28 -132.28 1sra.18.22 151 -131.62 -131.62 1d06A.18.18 130 -129.89 -129.89 1hsm.18.18 79 -128.93 -128.93 1ew0A.18.18 130 -127.01 -127.01 1jraA.18.18 117 -126.85 -126.85 1dulA.19.21 69 -137.30 -137.30 1sra.19.23 151 -131.93 -131.93 1hsm.19.19 79 -131.10 -131.10 1d06A.19.19 130 -128.67 -128.67 1bl8A.19.24 97 -128.15 -128.15 1hm6A.19.22 346 -128.00 -128.00 1dulA.20.22 69 -141.97 -141.97 1sra.20.24 151 -130.45 -130.45 1hsm.20.20 79 -129.71 -129.71 1b2sD.20.20 90 -127.48 -127.48 1hm6A.20.23 346 -127.25 -127.25 1bl8A.20.25 97 -126.86 -126.86 1dulA.21.23 69 -145.29 -145.29 1a16.21.24 440 -126.67 -126.67 1hsm.21.21 79 -126.25 -126.25 1sra.21.25 151 -125.70 -125.70 1hm6A.21.24 346 -124.05 -124.05 1b2sD.21.21 90 -123.98 -123.98 1dulA.22.24 69 -149.00 -149.00 1a16.22.25 440 -127.76 -127.76 1e6uA.22.23 321 -124.27 -124.27 1hsm.22.22 79 -122.18 -122.18 1b2sD.22.22 90 -121.19 -121.19 1p32C.22.24 209 -120.89 -120.89 1dulA.23.25 69 -150.35 -150.35 1a16.23.26 440 -128.97 -128.97 1e6uA.23.24 321 -122.67 -122.67 3kvt.23.24 115 -120.79 -120.79 1kuuA.23.23 202 -120.40 -120.40 1p32C.23.25 209 -120.35 -120.35 1dulA.24.26 69 -150.07 -150.07 1a16.24.27 440 -130.79 -130.79 1qqvA.24.25 67 -124.23 -124.23 1kuuA.24.24 202 -120.69 -120.69 1msi.24.25 70 -120.34 -120.34 1p32C.24.26 209 -120.12 -120.12 1dulA.25.27 69 -151.26 -151.26 1a16.25.28 440 -131.40 -131.40 1qqvA.25.26 67 -129.41 -129.41 1msi.25.26 70 -121.60 -121.60 1hg7A.25.26 66 -120.57 -120.57 1kuuA.25.25 202 -120.08 -120.08 1dulA.26.28 69 -150.95 -150.95 1qqvA.26.27 67 -134.49 -134.49 1a16.26.29 440 -130.29 -130.29 1msi.26.27 70 -122.00 -122.00 1hg7A.26.27 66 -120.99 -120.99 1a53.26.26 247 -120.56 -120.56 1dulA.27.29 69 -146.97 -146.97 1qqvA.27.28 67 -138.58 -138.58 1a16.27.30 440 -127.76 -127.76 1msi.27.28 70 -123.21 -123.21 1hulA.27.27 108 -123.06 -123.06 1a53.27.27 247 -122.64 -122.64 1qqvA.28.29 67 -144.57 -144.57 1dulA.28.30 69 -141.52 -141.52 1irsA.28.28 112 -126.45 -126.45 1msi.28.29 70 -126.29 -126.29 1hulA.28.28 108 -125.90 -125.90 1a16.28.31 440 -125.52 -125.52 1qqvA.29.30 67 -148.37 -148.37 1dulA.29.31 69 -134.44 -134.44 1dgnA.29.31 89 -130.82 -130.82 1hulA.29.29 108 -128.59 -128.59 1msi.29.30 70 -128.50 -128.50 1irsA.29.29 112 -128.40 -128.40 1qqvA.30.31 67 -148.67 -148.67 1dgnA.30.32 89 -133.58 -133.58 1hulA.30.30 108 -131.50 -131.50 1fe6A.30.30 52 -130.44 -130.44 1dulA.30.32 69 -130.17 -130.17 1hdoA.30.30 206 -129.42 -129.42 1qqvA.31.32 67 -146.77 -146.77 1hulA.31.31 108 -134.00 -134.00 1dgnA.31.33 89 -132.95 -132.95 1fe6A.31.31 52 -131.02 -131.02 1hdoA.31.31 206 -129.76 -129.76 1he2A.31.31 206 -129.61 -129.61 1qqvA.32.33 67 -146.76 -146.76 1hulA.32.32 108 -135.21 -135.21 1dgnA.32.34 89 -133.36 -133.36 1fe6A.32.32 52 -131.78 -131.78 1hdoA.32.32 206 -131.18 -131.18 1he2A.32.32 206 -131.03 -131.03 1qqvA.33.34 67 -145.58 -145.58 1hulA.33.33 108 -135.81 -135.81 1dgnA.33.35 89 -134.77 -134.77 1hdoA.33.33 206 -133.54 -133.54 1he2A.33.33 206 -133.37 -133.37 1fe6A.33.33 52 -132.39 -132.39 1qqvA.34.35 67 -142.17 -142.17 1hulA.34.34 108 -136.68 -136.68 1hdoA.34.34 206 -135.17 -135.17 1dgnA.34.36 89 -135.01 -135.01 1he2A.34.34 206 -134.99 -134.99 1fe6A.34.34 52 -132.95 -132.95 1qqvA.35.36 67 -138.96 -138.96 1hdoA.35.35 206 -137.88 -137.88 1he2A.35.35 206 -137.69 -137.69 1hulA.35.35 108 -137.62 -137.62 1dgnA.35.37 89 -134.62 -134.62 1ngr.35.36 85 -134.54 -134.54 1hdoA.36.36 206 -139.63 -139.63 1he2A.36.36 206 -139.44 -139.44 1hulA.36.36 108 -137.60 -137.60 1qqvA.36.37 67 -136.73 -136.73 1ngr.36.37 85 -136.71 -136.71 1fe6A.36.36 52 -135.59 -135.59 1hdoA.37.37 206 -140.20 -140.20 1he2A.37.37 206 -140.01 -140.01 1ngr.37.38 85 -138.15 -138.15 1bs2A.37.43 607 -136.58 -136.58 1hulA.37.37 108 -136.30 -136.30 1fe6A.37.37 52 -135.75 -135.75 1hdoA.38.38 206 -139.91 -139.91 1he2A.38.38 206 -139.74 -139.74 1ngr.38.39 85 -138.37 -138.37 1bs2A.38.44 607 -137.40 -137.40 1jykA.38.40 254 -136.78 -136.78 1hulA.38.38 108 -135.80 -135.80 1hdoA.39.39 206 -140.34 -140.34 1he2A.39.39 206 -140.17 -140.17 1jykA.39.41 254 -139.30 -139.30 1ngr.39.40 85 -138.79 -138.79 1bs2A.39.45 607 -138.40 -138.40 1hulA.39.39 108 -133.97 -133.97 1hdoA.40.40 206 -142.47 -142.47 1he2A.40.40 206 -142.33 -142.33 1bs2A.40.46 607 -141.82 -141.82 1jykA.40.42 254 -140.97 -140.97 1ngr.40.41 85 -139.26 -139.26 1fe6A.40.40 52 -132.52 -132.52 1hdoA.41.41 206 -145.52 -145.52 1he2A.41.41 206 -145.40 -145.40 1bs2A.41.47 607 -143.82 -143.82 1jykA.41.43 254 -141.60 -141.60 1ngr.41.42 85 -141.02 -141.02 1fe6A.41.41 52 -133.91 -133.91 1hdoA.42.42 206 -146.52 -146.52 1he2A.42.42 206 -146.43 -146.43 1bs2A.42.48 607 -143.65 -143.65 1ngr.42.43 85 -142.47 -142.47 1jykA.42.44 254 -139.24 -139.24 1uch.42.44 230 -138.75 -138.75 1bs2A.43.49 607 -142.12 -142.12 1ngr.43.44 85 -141.52 -141.52 1hdoA.43.43 206 -140.30 -140.30 1he2A.43.43 206 -140.24 -140.24 1uch.43.45 230 -138.38 -138.38 1jykA.43.45 254 -132.42 -132.42 1ngr.44.45 85 -141.94 -141.94 1bs2A.44.50 607 -141.81 -141.81 1ois.44.44 223 -135.37 -135.37 1uch.44.46 230 -134.74 -134.74 1ppfE.44.47 218 -129.73 -129.73 1hdoA.44.44 206 -128.72 -128.72 1ngr.45.46 85 -145.73 -145.73 1bs2A.45.51 607 -141.77 -141.77 1ois.45.45 223 -138.22 -138.22 1uch.45.47 230 -131.81 -131.81 1ppfE.45.48 218 -126.50 -126.50 1kb0A.45.52 677 -125.71 -125.71 1ngr.46.47 85 -147.57 -147.57 1ois.46.46 223 -143.32 -143.32 1bs2A.46.52 607 -141.18 -141.18 1uch.46.48 230 -130.00 -130.00 1dtdA.46.51 303 -125.65 -125.65 1ppfE.46.49 218 -124.47 -124.47 1ngr.47.48 85 -150.72 -150.72 1ois.47.47 223 -146.18 -146.18 1bs2A.47.53 607 -139.22 -139.22 1nkl.47.51 78 -130.13 -130.13 1dtdA.47.52 303 -129.39 -129.39 1uch.47.49 230 -129.28 -129.28 1ngr.48.49 85 -150.09 -150.09 1ois.48.48 223 -147.40 -147.40 1nkl.48.52 78 -136.72 -136.72 1bs2A.48.54 607 -135.49 -135.49 1dtdA.48.53 303 -131.99 -131.99 1uch.48.50 230 -128.01 -128.01 1ois.49.49 223 -147.91 -147.91 1ngr.49.50 85 -146.77 -146.77 1nkl.49.53 78 -138.51 -138.51 1dtdA.49.54 303 -134.71 -134.71 1bs2A.49.55 607 -129.39 -129.39 1thm.49.51 279 -128.23 -128.23 1ois.50.50 223 -148.92 -148.92 1ngr.50.51 85 -142.52 -142.52 1nkl.50.54 78 -140.18 -140.18 1dtdA.50.55 303 -137.80 -137.80 1thm.50.52 279 -128.81 -128.81 1uch.50.52 230 -124.85 -124.85 1ois.51.51 223 -149.42 -149.42 1dtdA.51.56 303 -140.45 -140.45 1nkl.51.55 78 -140.37 -140.37 1ngr.51.52 85 -137.19 -137.19 1thm.51.53 279 -130.09 -130.09 1bdb.51.55 277 -126.91 -126.91 1ois.52.52 223 -149.25 -149.25 1dtdA.52.57 303 -140.99 -140.99 1nkl.52.56 78 -137.76 -137.76 1ngr.52.53 85 -129.36 -129.36 1thm.52.54 279 -128.88 -128.88 1bdb.52.56 277 -128.12 -128.12 1ois.53.53 223 -148.26 -148.26 1dtdA.53.58 303 -141.24 -141.24 1nkl.53.57 78 -133.41 -133.41 1chrA.53.54 370 -132.43 -132.43 1bdb.53.57 277 -128.88 -128.88 1cxzB.53.55 86 -128.37 -128.37 1ois.54.54 223 -146.72 -146.72 1dtdA.54.59 303 -140.07 -140.07 1chrA.54.55 370 -135.73 -135.73 1cxzB.54.56 86 -130.29 -130.29 1nkl.54.58 78 -128.46 -128.46 1qopA.54.56 268 -127.10 -127.10 1ois.55.55 223 -144.98 -144.98 1dtdA.55.60 303 -138.99 -138.99 1chrA.55.56 370 -136.44 -136.44 1cxzB.55.57 86 -132.38 -132.38 1qopA.55.57 268 -131.69 -131.69 1bksA.55.57 268 -128.28 -128.28 1ois.56.56 223 -142.63 -142.63 1chrA.56.57 370 -137.41 -137.41 1dtdA.56.61 303 -136.08 -136.08 1cxzB.56.58 86 -133.33 -133.33 1qopA.56.58 268 -132.87 -132.87 1bksA.56.58 268 -129.92 -129.92 1ois.57.57 223 -142.18 -142.18 1chrA.57.58 370 -136.09 -136.09 1cxzB.57.59 86 -134.46 -134.46 1qopA.57.59 268 -133.70 -133.70 1dtdA.57.62 303 -132.46 -132.46 1bksA.57.59 268 -131.19 -131.19 1ois.58.58 223 -140.05 -140.05 1cxzB.58.60 86 -136.86 -136.86 1chrA.58.59 370 -134.54 -134.54 1qopA.58.60 268 -134.09 -134.09 1kptA.58.59 105 -133.66 -133.66 1bksA.58.60 268 -131.82 -131.82 1cxzB.59.61 86 -138.61 -138.61 1ois.59.59 223 -137.43 -137.43 1kptA.59.60 105 -133.98 -133.98 1qopA.59.61 268 -133.43 -133.43 1chrA.59.60 370 -131.92 -131.92 1bksA.59.61 268 -131.30 -131.30 1cxzB.60.62 86 -141.66 -141.66 1ois.60.60 223 -134.45 -134.45 1kptA.60.61 105 -132.71 -132.71 1qopA.60.62 268 -131.82 -131.82 1chrA.60.61 370 -130.44 -130.44 2trcP.60.65 217 -130.01 -130.01 1cxzB.61.63 86 -144.02 -144.02 1kptA.61.62 105 -131.24 -131.24 2trcP.61.66 217 -130.05 -130.05 1gk4A.61.61 84 -130.02 -130.02 1qopA.61.63 268 -129.78 -129.78 1ois.61.61 223 -129.28 -129.28 1cxzB.62.64 86 -148.70 -148.70 2trcP.62.67 217 -131.24 -131.24 1gk4A.62.62 84 -130.63 -130.63 1kptA.62.63 105 -129.90 -129.90 1qopA.62.64 268 -128.49 -128.49 1jplA.62.73 171 -128.46 -128.46 1cxzB.63.65 86 -152.37 -152.37 2trcP.63.68 217 -134.63 -134.63 1gk4A.63.63 84 -130.52 -130.52 1cc5.63.66 83 -127.29 -127.29 1qopA.63.65 268 -127.15 -127.15 1kptA.63.64 105 -127.02 -127.02 1cxzB.64.66 86 -155.34 -155.34 2trcP.64.69 217 -140.40 -140.40 1gk4A.64.64 84 -130.86 -130.86 1cc5.64.67 83 -128.03 -128.03 1prgA.64.65 270 -126.74 -126.74 1qopA.64.66 268 -126.67 -126.67 1cxzB.65.67 86 -156.70 -156.70 2trcP.65.70 217 -143.37 -143.37 1gk4A.65.65 84 -130.98 -130.98 1prgA.65.66 270 -129.17 -129.17 1cc5.65.68 83 -126.26 -126.26 1an2A.65.66 86 -125.80 -125.80 1cxzB.66.68 86 -158.85 -158.85 2trcP.66.71 217 -141.35 -141.35 1gk4A.66.66 84 -131.04 -131.04 1prgA.66.67 270 -128.28 -128.28 1an2A.66.67 86 -127.47 -127.47 1cc5.66.69 83 -124.52 -124.52 1cxzB.67.69 86 -163.16 -163.16 2trcP.67.72 217 -139.63 -139.63 1gk4A.67.67 84 -131.45 -131.45 1an2A.67.68 86 -129.64 -129.64 1prgA.67.68 270 -126.85 -126.85 1cc5.67.70 83 -123.43 -123.43 1cxzB.68.70 86 -170.12 -170.12 2trcP.68.73 217 -138.43 -138.43 1an2A.68.69 86 -132.95 -132.95 1gk4A.68.68 84 -131.22 -131.22 1prgA.68.69 270 -126.71 -126.71 1cc5.68.71 83 -124.25 -124.25 1cxzB.69.71 86 -177.01 -177.01 2trcP.69.74 217 -137.16 -137.16 1an2A.69.70 86 -135.92 -135.92 1gk4A.69.69 84 -131.15 -131.15 1prgA.69.70 270 -127.00 -127.00 1cc5.69.72 83 -125.04 -125.04 1cxzB.70.72 86 -180.45 -180.45 1an2A.70.71 86 -136.63 -136.63 2trcP.70.75 217 -133.59 -133.59 1gk4A.70.70 84 -131.23 -131.23 1prgA.70.71 270 -126.43 -126.43 1cc5.70.73 83 -125.89 -125.89 1cxzB.71.73 86 -182.01 -182.01 1an2A.71.72 86 -136.74 -136.74 1gk4A.71.71 84 -131.77 -131.77 2trcP.71.76 217 -131.02 -131.02 1cc5.71.74 83 -126.71 -126.71 1prgA.71.72 270 -124.22 -124.22 1cxzB.72.74 86 -182.10 -182.10 1an2A.72.73 86 -137.37 -137.37 1gk4A.72.72 84 -131.45 -131.45 2trcP.72.77 217 -128.73 -128.73 1br0A.72.72 120 -124.10 -124.10 1prgA.72.73 270 -122.28 -122.28 1cxzB.73.75 86 -186.80 -186.80 1an2A.73.74 86 -138.45 -138.45 1gk4A.73.73 84 -131.79 -131.79 2trcP.73.78 217 -127.67 -127.67 1br0A.73.73 120 -126.98 -126.98 1a32.73.77 88 -124.32 -124.32 1cxzB.74.76 86 -189.06 -189.06 1an2A.74.75 86 -138.44 -138.44 1gk4A.74.74 84 -133.44 -133.44 1mho.74.78 88 -128.91 -128.91 1br0A.74.74 120 -127.80 -127.80 1a32.74.78 88 -127.61 -127.61