# List of top-scoring protein chains for t2k-100-30-str2 hidden Markov model. # HMM and HMM E-value scores computed by SAM (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. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1egr 85 1.32e-04 1kte c.47.1.1 32765 1fo5A 85 4.83e-04 1fo5A c.47.1.1 59922 1hyuA 521 6.10e-04 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1ego 85 1.40e-03 1kte c.47.1.1 32767 1grx 85 2.46e-03 1kte c.47.1.1 32766 1kte 105 4.09e-03 1kte c.47.1.1 32771 1gseA 221 5.77e-03 1pgtA a.45.1.1 17667 c.47.1.5 32961 1k3lA 221 6.33e-03 a.45.1.1 77229 c.47.1.5 77230 1f3aA 222 8.94e-03 1pgtA a.45.1.1 17701 c.47.1.5 32995 1k3yA 221 1.40e-02 a.45.1.1 77245 c.47.1.5 77246 1qfnA 85 1.67e-02 1qfnA c.47.1.1 32768 1jhb 106 2.03e-02 1kte c.47.1.1 32772 1ksiB 642 4.81e-02 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1ksiA 642 5.02e-02 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1iloA 77 1.39e-01 c.47.1.1 66205 1t1vA 93 1.48e-01 1gulA 222 1.71e-01 1pgtA a.45.1.1 17675 c.47.1.5 32969 1gumA 222 1.71e-01 1pgtA a.45.1.1 17683 c.47.1.5 32977 1r26A 125 2.95e-01 c.47.1.1 -7389 1f37A 110 3.18e-01 1f37A c.47.1.11 33088 1thx 115 3.55e-01 1thx c.47.1.1 32732 1fw1A 216 4.04e-01 a.45.1.1 60051 c.47.1.5 60052 1o0wA 252 4.90e-01 a.149.1.1 80751 d.50.1.1 80752 1xgsA 295 5.36e-01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1oyjA 231 5.62e-01 a.45.1.1 87597 c.47.1.5 87598 1j0fA 100 6.83e-01 unknown_sccs -7483 1h75A 81 9.99e-01 1h75A c.47.1.1 60716 1m2dA 110 1.01e+00 c.47.1.11 78476 1erv 105 1.08e+00 1erv c.47.1.1 32743 1gwcA 230 1.17e+00 a.45.1.1 70660 c.47.1.5 70661 1oktA 211 1.30e+00 a.45.1.1 -942 c.47.1.5 -7467 1jtdB 273 1.31e+00 b.69.5.2 67265 1j3vA 289 1.36e+00 a.100.1.1 -1303 c.2.1.6 -5947 1s6yA 450 1.51e+00 1dd9A 338 1.60e+00 1dd9A e.13.1.1 43254 1m2aA 110 1.72e+00 c.47.1.11 78472 1ej6A 1289 1.86e+00 i.7.1.1 45967 1hyhA 309 1.88e+00 1hyhA c.2.1.5 30150 d.162.1.1 42117 1m2bA 110 1.90e+00 c.47.1.11 78474 1eqnA 321 1.93e+00 1dd9A e.13.1.1 43256 3grx 82 2.00e+00 1aba c.47.1.1 32769 1aiu 105 2.02e+00 1erv c.47.1.1 32746 1r5tA 142 2.20e+00 1gnwA 211 2.31e+00 1gnwA a.45.1.1 17727 c.47.1.5 33021 2trxA 108 2.35e+00 1thx c.47.1.1 32719 1k0nA 241 2.37e+00 a.45.1.1 67953 c.47.1.5 67954 1ddeA 338 2.37e+00 1dd9A e.13.1.1 43255 1dp0A 1023 2.51e+00 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1jz8A 1023 2.54e+00 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1gky 187 2.60e+00 1gky c.37.1.1 31839 1wkqA 164 2.61e+00 1nkqA 259 2.76e+00 1tiyA 164 2.88e+00 1k0mA 241 2.94e+00 a.45.1.1 67949 c.47.1.5 67950 1ghsA 306 3.24e+00 1aq0A c.1.8.3 28840 1ytbB 180 3.79e+00 1ytbA d.129.1.1 41278 d.129.1.1 41279 1bglA 1023 3.87e+00 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1kebA 108 3.99e+00 c.47.1.1 77341 1pvyA 227 4.19e+00 d.115.1.2 -10937 1ytbA 180 4.30e+00 1ytbA d.129.1.1 41276 d.129.1.1 41277 1e6bA 221 4.50e+00 1e6bA a.45.1.1 59294 c.47.1.5 59295 1gajA 257 4.82e+00 1gajA c.37.1.12 60416 1m4jA 142 5.25e+00 d.109.1.2 78602 1rch 155 5.28e+00 2rn2 c.55.3.1 33570 1g65K 211 5.29e+00 d.153.1.4 41907 1go3E 187 5.83e+00 b.40.4.5 83054 d.230.1.1 83055 1djnA 729 5.90e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1aw9 216 5.97e+00 1gnwA a.45.1.1 17736 c.47.1.5 33030 1f21A 155 6.06e+00 2rn2 c.55.3.1 33550 1nmoA 247 6.24e+00 unknown_sccs -8746 2rn2 155 6.34e+00 2rn2 c.55.3.1 33551 2tmdA 729 6.37e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1rypL 212 6.39e+00 d.153.1.4 41880 1qh3A 260 6.42e+00 1qh5A d.157.1.2 42059 1jkgA 140 6.50e+00 d.17.4.2 66795 1aba 87 6.71e+00 1aba c.47.1.1 32760 1tbaB 180 6.73e+00 1ytbA d.129.1.1 41286 d.129.1.1 41287 1idm 343 6.84e+00 1cnzA c.77.1.1 35035 1eejA 216 6.86e+00 1eejA c.47.1.9 33057 d.17.3.1 38071 1m0uA 249 6.86e+00 a.45.1.1 78359 c.47.1.5 78360 1hmcB 148 6.88e+00 1hmcB a.26.1.2 16868 1qh5A 260 6.91e+00 1qh5A d.157.1.2 42057 1se8A 301 6.91e+00 1zfjA 491 7.08e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1ex7A 186 7.11e+00 1gky c.37.1.1 59537 1ipd 345 7.13e+00 1cnzA c.77.1.1 35038 1o94A 729 7.21e+00 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1r8sA 164 7.34e+00 c.37.1.8 -7082 1dr8B 344 7.54e+00 1cnzA c.77.1.1 35052 1ubeA 349 7.74e+00 c.37.1.11 88412 d.48.1.1 88413 1jl1A 155 7.86e+00 c.55.3.1 66821 1g7eA 122 8.08e+00 1g7eA c.47.1.7 33055 1jp4A 308 8.63e+00 1jp4A e.7.1.1 63223 1j2iA 166 9.62e+00 1o3yA 166 9.62e+00 c.37.1.8 86618 1j79A 347 9.71e+00 1j79A c.1.9.4 62675 1g19A 350 9.84e+00 2reb c.37.1.11 32284 d.48.1.1 38770 1ljrA 244 9.90e+00 1ljrA a.45.1.1 17707 c.47.1.5 33001 1awe 130 1.00e+01 1awe b.55.1.1 26968 1qb0A 211 1.02e+01 1c25 c.46.1.1 32699 1aq0A 306 1.02e+01 1aq0A c.1.8.3 28842 1hmcA 148 1.08e+01 1hmcB a.26.1.2 16867 1o0pA 104 1.09e+01 d.58.7.1 86535 1b87A 181 1.10e+01 1b87A d.108.1.1 40797 1s96A 219 1.11e+01 c.37.1.1 -6972 1r9dA 787 1.11e+01 1iyhA 198 1.14e+01 a.45.1.1 83790 c.47.1.5 83791 1ip9A 85 1.19e+01 1ip9A d.15.2.2 62638 1gsa 316 1.20e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1hv8A 367 1.21e+01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1ci8A 392 1.23e+01 e.3.1.1 64765 1ci9A 392 1.24e+01 e.3.1.1 64767 1bu8A 452 1.26e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1c25 161 1.26e+01 1c25 c.46.1.1 32698 1quqB 121 1.28e+01 1quqB b.40.4.3 25305 1erw 105 1.28e+01 1erv c.47.1.1 32745 1vjqA 79 1.31e+01 unknown_sccs -13478 1uiuA 502 1.33e+01 c.94.1.1 -8674 1faaA 124 1.41e+01 1erv c.47.1.1 32738 1s4nA 348 1.41e+01 unknown_sccs -8262 1nycA 111 1.42e+01 unknown_sccs -4522 1f2dA 341 1.44e+01 1f2dA c.79.1.1 35298 1f9mA 112 1.44e+01 1erv c.47.1.1 32736 1cne 270 1.46e+01 1ndh b.43.4.2 25661 c.25.1.1 31551 1pms 136 1.46e+01 1awe b.55.1.1 26966 1ffkI 194 1.50e+01 1ffkI d.12.1.2 37494 1ax4A 467 1.53e+01 1ax4A c.67.1.2 34391 1s1hM 132 1.55e+01 1be1 137 1.57e+01 1be1 c.23.6.1 31237 1g6hA 257 1.58e+01 1gajA c.37.1.12 60318 1jn5A 140 1.59e+01 d.17.4.2 66921 1pbjA 125 1.60e+01 d.37.1.1 -9608 d.37.1.1 -9609 1vhvA 268 1.67e+01 c.90.1.1 -8619 1uouA 474 1.72e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1o6aA 96 1.74e+01 unknown_sccs -4101 1exqA 154 1.75e+01 1b9dA c.55.3.2 33646 2trcP 217 1.75e+01 1b9yC c.47.1.6 33051 1b1cA 181 1.78e+01 1amoA c.23.5.2 31212 1q2yA 140 1.82e+01 d.108.1.1 -10791 1itg 166 1.84e+01 1b9dA c.55.3.2 33661 1ghr 306 1.85e+01 1aq0A c.1.8.3 28844 1imdA 277 1.88e+01 1imbA e.7.1.1 42968 1r5pA 108 1.89e+01 unknown_sccs -7487 1f61A 429 1.95e+01 1dquA c.1.12.7 29319 1bed 181 1.96e+01 1fvkA unknown_sccs -7444 1jagA 241 2.06e+01 c.37.1.1 66463 1dypA 271 2.07e+01 1dypA b.29.1.2 24185 1cnv 299 2.10e+01 1cnv c.1.8.5 28989 1aszB 490 2.11e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1mdiA 105 2.12e+01 1erv c.47.1.1 32755 1qpsA 261 2.17e+01 1ckqA c.52.1.1 33234 1mtpB 43 2.20e+01 1jx4A 352 2.21e+01 unknown_sccs -10188 unknown_sccs -11898 1us5A 314 2.21e+01 c.94.1.1 -8686 1fx2A 235 2.25e+01 1fx2A d.58.29.1 39430 1danH 254 2.28e+01 5ptp b.47.1.2 26292 1qstA 160 2.29e+01 1yghA d.108.1.1 40804 1g66A 207 2.31e+01 1bs9 unknown_sccs 31329 1mek 120 2.37e+01 1erv c.47.1.2 32775 1eriA 276 2.39e+01 1ckqA c.52.1.1 33231 1n71A 180 2.42e+01 d.108.1.1 85370 1bs9 207 2.42e+01 1bs9 unknown_sccs 31330 1kk9A 221 2.51e+01 d.115.1.1 77432 1kliH 254 2.53e+01 b.47.1.2 77435 1s3zA 165 2.53e+01 2dabA 282 2.62e+01 1daaA e.17.1.1 43274 1fc6A 388 2.67e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1kf6A 602 2.68e+01 a.7.3.1 72394 c.3.1.4 72395 d.168.1.1 72396 1pb1A 416 2.70e+01 c.77.1.1 88014 1cl8A 276 2.71e+01 1ckqA c.52.1.1 33230 1b6sA 355 2.73e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 7icd 416 2.74e+01 1iso c.77.1.1 35072 1ckqA 276 2.78e+01 1ckqA c.52.1.1 33229 1gmiA 136 2.79e+01 b.7.1.1 65309 1hph 37 2.81e+01 1hph j.15.1.1 46159 1uyrA 737 2.84e+01 c.14.1.4 -6258 c.14.1.4 -6259 1glv 303 2.85e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 3daaA 277 2.86e+01 1daaA e.17.1.1 43272 1fvyA 31 2.89e+01 1fvyA j.15.1.1 46157 1cdwA 179 2.95e+01 1ytbA d.129.1.1 41212 d.129.1.1 41213 1qc9A 276 2.98e+01 1ckqA c.52.1.1 33235 1daaA 282 3.02e+01 1daaA e.17.1.1 43270 1eu8A 409 3.03e+01 1eu8A c.94.1.1 59502 1a8l 226 3.06e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1k4nA 192 3.07e+01 d.32.1.5 72059 1pd21 199 3.09e+01 1pd21 1pmt 203 3.10e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1fgyA 127 3.13e+01 1faoA b.55.1.1 26976 1o0yA 260 3.14e+01 c.1.10.1 80756 1fx4A 231 3.15e+01 1fx2A d.58.29.1 39431 1b6rA 355 3.20e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1jhnA 424 3.25e+01 b.29.1.12 70060 b.104.1.1 66722 1fn9A 365 3.33e+01 1fn9A d.196.1.1 59894 1qk3A 233 3.33e+01 1qk3A c.61.1.1 34031 1r4aA 165 3.36e+01 c.37.1.8 -7089 1rjdA 334 3.36e+01 unknown_sccs -8079 1gcb 454 3.37e+01 3gcb d.3.1.1 37034 1igwA 434 3.41e+01 c.1.12.7 62370 1qipA 183 3.42e+01 1qipA d.32.1.1 38470 1iso 416 3.44e+01 1iso c.77.1.1 35065 3gcb 470 3.45e+01 3gcb d.3.1.1 37032 1j08A 226 3.48e+01 c.47.1.2 83855 c.47.1.2 83856 1bh5A 183 3.54e+01 1qipA d.32.1.1 38476 1nnwA 252 3.58e+01 d.159.1.5 80674 1uxoA 192 3.62e+01 1gpl 432 3.88e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1ek4A 418 3.91e+01 1dd8A c.95.1.1 59436 c.95.1.1 59437 1imbA 277 3.91e+01 1imbA e.7.1.1 42957 1jvwA 167 3.96e+01 d.26.1.1 71907 1oeqA 418 3.97e+01 2hhmA 276 3.98e+01 1imbA e.7.1.1 42955