# List of top-scoring protein chains for t2k-w0.5 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 1jeoA 180 2.70e-22 c.80.1.3 66611 1moq 368 1.44e-17 1moq c.80.1.1 35302 1jxaA 608 1.73e-17 c.80.1.1 67407 d.153.1.1 67408 1c7qA 445 1.33e-03 2pgi c.80.1.2 35307 2pgi 445 1.33e-03 2pgi c.80.1.2 35308 1e9iD 431 6.19e-02 c.1.11.1 64824 d.54.1.1 64825 1c9jA 269 6.94e-02 1gci c.41.1.1 32507 1c9nA 269 7.00e-02 1gci c.41.1.1 32505 1gci 269 2.30e-01 1gci c.41.1.1 32503 1mpt 269 2.30e-01 1gci c.41.1.1 32541 2tecE 279 2.95e-01 1gci c.41.1.1 32545 1thm 279 2.96e-01 1gci c.41.1.1 32544 1ah2 269 3.41e-01 1gci c.41.1.1 32542 1iavA 269 3.44e-01 1gci c.41.1.1 62125 1dqrA 557 4.36e-01 1dqrA c.80.1.2 35305 1g98A 558 4.36e-01 c.80.1.2 60396 1c9mA 269 5.40e-01 1gci c.41.1.1 32506 1gzdA 557 5.63e-01 1iriA 558 5.66e-01 1iatA 557 5.66e-01 1dqrA c.80.1.2 62123 1cjuC 402 6.76e-01 1cipA a.66.1.1 18207 c.37.1.8 32090 1hyeA 313 6.96e-01 2cmd c.2.1.5 61400 d.162.1.1 61401 1d3yA 301 7.37e-01 1d3yA e.12.1.1 43252 1ddrB 159 8.18e-01 1vdrA c.71.1.1 34857 1dhjB 159 8.19e-01 1vdrA c.71.1.1 34834 1draA 159 8.25e-01 1vdrA c.71.1.1 34831 1tdrB 159 8.26e-01 1vdrA c.71.1.1 34866 1ra9 159 8.36e-01 1vdrA c.71.1.1 34820 6dfr 159 8.36e-01 1vdrA c.71.1.1 34874 2drcB 159 8.36e-01 1vdrA c.71.1.1 34849 1akw 147 8.55e-01 5nul c.23.5.1 31153 1dhiB 159 8.97e-01 1vdrA c.71.1.1 34845 1drbB 159 9.36e-01 1vdrA c.71.1.1 34829 1azl 147 1.00e+00 5nul c.23.5.1 31154 1akr 147 1.06e+00 1rcf c.23.5.1 31152 1akt 147 1.08e+00 5nul c.23.5.1 31157 1aku 147 1.12e+00 5nul c.23.5.1 31161 1meeA 275 1.17e+00 1gci c.41.1.1 32540 1ja1A 622 1.21e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1j9gA 147 1.27e+00 c.23.5.1 62757 1i1oA 147 1.37e+00 5nul c.23.5.1 61542 1scjA 275 1.37e+00 1gci c.41.1.1 32486 1ja0A 620 1.38e+00 1amoA b.43.4.1 62798 c.23.5.2 62799 c.25.1.4 62800 1j9zA 622 1.40e+00 1amoA b.43.4.1 62792 c.23.5.2 62793 c.25.1.4 62794 1f4pA 147 1.41e+00 5nul c.23.5.1 59651 1fx1 148 1.44e+00 1rcf c.23.5.1 31169 1j9eA 147 1.44e+00 c.23.5.1 62756 1bu5A 147 1.46e+00 5nul c.23.5.1 31155 2fx2 147 1.46e+00 1rcf c.23.5.1 31158 1cs4C 394 1.82e+00 1cipA a.66.1.1 18205 c.37.1.8 32088 1amoA 615 2.05e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1c7fA 147 2.06e+00 5nul c.23.5.1 31163 1culB 208 2.10e+00 1azsA d.58.29.1 39424 1azsB 212 2.16e+00 1azsA d.58.29.1 39423 1ab8A 220 2.23e+00 1azsA d.58.29.1 39414 1qgoA 264 2.29e+00 1qgoA c.92.1.2 35596 1eulA 994 2.72e+00 1eulA f.2.1.10 43726 1qmjA 132 2.73e+00 1c1lA b.29.1.3 24210 2fsp 124 2.78e+00 1dz3A c.23.1.1 31119 1qcrB 423 2.93e+00 1be3B d.185.1.1 59027 d.185.1.1 59028 1c3lA 274 2.93e+00 1gci c.41.1.1 32492 1b1cA 181 2.97e+00 1amoA c.23.5.2 31212 1dr9A 201 2.97e+00 1dr9A b.1.1.1 19762 b.1.1.3 21684 1cliA 345 2.97e+00 1cliA d.79.4.1 39816 d.139.1.1 41459 1i8lA 208 2.97e+00 1dr9A b.1.1.1 61970 b.1.1.3 61971 1be3B 439 3.00e+00 1be3B d.185.1.1 58952 d.185.1.1 58953 1kq3A 376 3.08e+00 e.22.1.2 68790 1srrA 124 3.34e+00 1dz3A c.23.1.1 31110 1f51F 119 3.37e+00 1dz3A c.23.1.1 31115 1cseE 274 3.47e+00 1gci c.41.1.1 32481 1scnE 276 3.50e+00 1gci c.41.1.1 32490 1i2mD 402 3.50e+00 1a12A b.69.5.1 61571 1selA 274 3.50e+00 1gci c.41.1.1 32483 1a12A 413 3.51e+00 1a12A b.69.5.1 27663 1bh6A 274 3.73e+00 1gci c.41.1.1 32487 1e2sP 489 3.86e+00 1auk c.76.1.2 35031 1e1zP 489 3.89e+00 1auk c.76.1.2 59158 1e3cP 489 3.90e+00 1auk c.76.1.2 59187 1auk 489 3.94e+00 1auk c.76.1.2 35030 1uok 558 4.02e+00 1uok b.71.1.1 27801 c.1.8.1 28788 1e33P 489 4.16e+00 1auk c.76.1.2 59186 1ag9A 175 4.44e+00 1rcf c.23.5.1 31178 1jqfA 334 4.88e+00 c.94.1.2 67086 1culC 380 5.11e+00 1cipA a.66.1.1 18204 c.37.1.8 32087 1iciA 256 5.14e+00 1iciA c.31.1.5 62266 1aztB 388 5.15e+00 1cipA a.66.1.1 18202 c.37.1.8 32085 1qhtA 775 5.56e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1sbt 275 5.69e+00 1gci c.41.1.1 32538 2sbt 275 5.69e+00 1gci c.41.1.1 32539 1e3lA 376 5.70e+00 2ohxA b.35.1.2 24745 c.2.1.1 29761 1dxy 333 5.78e+00 1dxy c.2.1.4 30094 c.23.12.1 31354 1fqeA 331 5.84e+00 1nnt c.94.1.2 59988 1e3iA 376 5.85e+00 2ohxA b.35.1.2 24741 c.2.1.1 29757 1cf2O 337 6.09e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1dtgA 334 6.28e+00 1nnt c.94.1.2 35896 1jqmB 691 6.32e+00 i.1.1.1 63236 1dar 691 6.34e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1fnmA 691 6.35e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1d4nA 329 6.36e+00 1nnt c.94.1.2 35891 1d3kA 329 6.42e+00 1nnt c.94.1.2 35889 1f2rI 100 6.76e+00 1c9fA d.15.2.1 37641 1qe0A 420 6.96e+00 1adjA c.51.1.1 33186 d.104.1.1 40735 1kxrA 339 6.96e+00 1fqfA 331 6.98e+00 1nnt c.94.1.2 59989 1djnA 729 7.04e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 2tmdA 729 7.04e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1djqA 729 7.07e+00 2tmdA c.1.4.1 28614 c.3.1.1 30315 c.4.1.1 30600 1a8e 329 7.07e+00 1cb6A c.94.1.2 35888 1b4fA 82 7.13e+00 1b4fA a.60.1.2 17934 1b4fG 82 7.13e+00 1b4fA a.60.1.2 17940 1f0mA 82 7.13e+00 1b4fA a.60.1.2 17942 1bp5C 337 7.13e+00 1cb6A c.94.1.2 35894 1hzhH 457 7.18e+00 1igtB b.1.1.1 61437 b.1.1.2 61438 b.1.1.2 61439 b.1.1.2 61440 1efpA 307 7.71e+00 1efvA c.29.1.1 31635 c.31.1.2 31729 1cerP 331 7.76e+00 1dssG c.2.1.3 29988 d.81.1.1 39903 1jr1A 514 7.98e+00 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1flgA 582 8.42e+00 4aahA b.70.1.1 27682 1s01 275 8.48e+00 1gci c.41.1.1 32511 1sbi 275 8.51e+00 1gci c.41.1.1 32533 1sbh 275 8.52e+00 1gci c.41.1.1 32518 1sub 275 8.66e+00 1gci c.41.1.1 32513 1sud 275 8.68e+00 1gci c.41.1.1 32526 1sup 275 8.74e+00 1gci c.41.1.1 32510 2sniE 275 8.75e+00 1gci c.41.1.1 32529 1fxuA 289 8.78e+00 1b8oA c.56.2.1 33772 1ubnA 275 8.83e+00 1gci c.41.1.1 32535 1vfn 281 8.86e+00 1b8oA c.56.2.1 33773 1a9q 282 9.13e+00 1b8oA c.56.2.1 33769 1a9t 284 9.15e+00 1b8oA c.56.2.1 33765 1pbn 289 9.23e+00 1b8oA c.56.2.1 33771 3pnp 289 9.23e+00 1b8oA c.56.2.1 33763 1a9p 289 9.24e+00 1b8oA c.56.2.1 33774 1b8oA 284 9.38e+00 1b8oA c.56.2.1 33762 1b3eA 330 9.53e+00 1nnt c.94.1.2 35897 1s02 275 9.62e+00 1gci c.41.1.1 32525 1hxmA 229 1.09e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1im5A 180 1.11e+01 c.33.1.2 66211 1jq5A 370 1.18e+01 e.22.1.2 67084 1jqaA 370 1.18e+01 e.22.1.2 67085 1qklA 127 1.18e+01 1qklA d.78.1.2 39754 1ak9 275 1.24e+01 1gci c.41.1.1 32517 1aqn 275 1.25e+01 1gci c.41.1.1 32514 1a2q 275 1.25e+01 1gci c.41.1.1 32512 1g6q2 328 1.26e+01 1g6q2 1f6yA 262 1.28e+01 1f6yA c.1.21.2 29673 1lldA 319 1.33e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1bykA 255 1.35e+01 1bykA c.93.1.1 35706 1bhgA 613 1.38e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1gqeA 365 1.41e+01 1fdo 715 1.42e+01 2napA b.52.2.2 26917 c.81.1.1 35325 1fdi 715 1.42e+01 2napA b.52.2.2 26918 c.81.1.1 35326 1aa6 715 1.42e+01 2napA b.52.2.2 26916 c.81.1.1 35324 1ybvA 283 1.43e+01 1ybvA c.2.1.2 29948 1g0oA 283 1.48e+01 1ybvA c.2.1.2 60181 1gnsA 263 1.48e+01 1suc 266 1.48e+01 1gci c.41.1.1 32521 1duiA 266 1.48e+01 1gci c.41.1.1 32530 1sue 266 1.49e+01 1gci c.41.1.1 32520 1spbS 266 1.50e+01 1gci c.41.1.1 32532 1gnvA 266 1.50e+01 1suaA 266 1.51e+01 1gci c.41.1.1 32531 1lbvA 252 1.51e+01 1cdwA 179 1.56e+01 1ytbA d.129.1.1 41212 d.129.1.1 41213 1ibxB 145 1.61e+01 1c9fA d.15.2.1 62232 1bccB 422 1.61e+01 1be3B d.185.1.1 58948 d.185.1.1 58949 1l1fA 505 1.61e+01 1jayA 212 1.63e+01 c.2.1.6 66478 1tgoA 773 1.66e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1lssA 140 1.66e+01 1jr2A 286 1.66e+01 c.113.1.1 67111 1c9bB 180 1.66e+01 1ytbA d.129.1.1 41216 d.129.1.1 41217 1ipcA 217 1.68e+01 1jt9A 266 1.68e+01 c.35.1.1 67259 1dd8A 406 1.68e+01 1dd8A c.95.1.1 35932 c.95.1.1 35933 2rslA 140 1.69e+01 2rslA c.53.1.1 33345 1fj8A 406 1.69e+01 1dd8A c.95.1.1 35948 c.95.1.1 35949 1f91A 406 1.72e+01 1dd8A c.95.1.1 59713 c.95.1.1 59714 1eehA 437 1.72e+01 4uagA c.5.1.1 30654 c.59.1.1 33955 c.72.2.1 34958 1ek4A 418 1.73e+01 1dd8A c.95.1.1 59436 c.95.1.1 59437 3uagA 437 1.73e+01 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 4uagA 437 1.73e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1uag 437 1.73e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1tmhA 254 1.77e+01 1amk c.1.1.1 28507 1ulb 289 1.79e+01 1b8oA c.56.2.1 33760 1fs5A 266 1.80e+01 c.35.1.1 65044 1fsfA 266 1.80e+01 c.35.1.1 65047 1deaA 266 1.80e+01 1deaA c.35.1.1 31760 1l8bA 190 1.80e+01 1ej1A 190 1.80e+01 1ejhA d.86.1.1 40144 1ejhA 190 1.80e+01 1ejhA d.86.1.1 40147 1l9fA 389 1.80e+01 1el5A 389 1.80e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1jfiC 185 1.83e+01 1ytbA d.129.1.1 62938 d.129.1.1 62939 1dtwB 342 1.85e+01 1qs0B c.36.1.3 31828 c.48.1.2 33102 1ihfB 94 1.86e+01 1huuA a.55.1.1 17894 1hyuA 521 1.87e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 5reqA 727 1.89e+01 1reqA c.1.19.1 29632 c.23.6.1 31259 1e1cA 727 1.89e+01 1reqA c.1.19.1 29636 c.23.6.1 31263 1reqA 727 1.90e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 1i94K 128 1.90e+01 1fjfK c.55.4.1 62002 1fjgK 129 1.91e+01 1fjfK c.55.4.1 33733 1e52A 63 1.96e+01 1e52A a.2.9.1 59256 1g5rA 196 1.97e+01 1g5rA c.37.1.11 32367 1qojA 63 2.00e+01 1qojA a.2.9.1 15716 1tghA 185 2.01e+01 1ytbA d.129.1.1 41214 d.129.1.1 41215 6ldh 330 2.19e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1ldm 329 2.20e+01 3ldh c.2.1.5 30160 d.162.1.1 42127 1eliA 389 2.20e+01 1b3mA c.3.1.2 30375 d.16.1.3 37943 1dbiA 280 2.21e+01 1gci c.41.1.1 32543 1ng1 294 2.24e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 2napA 723 2.26e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1fveB 223 2.29e+01 1igtB b.1.1.1 19871 b.1.1.2 20967 1jw9B 249 2.32e+01 c.111.1.1 67377 1gajA 257 2.32e+01 1gajA c.37.1.12 60416 1g6hA 257 2.35e+01 1gajA c.37.1.12 60318 1gw5A 621 2.36e+01 1f9aA 168 2.38e+01 1f9aA c.26.1.3 31602 1jpnA 296 2.39e+01 a.24.13.1 67039 c.37.1.10 67040 1ghtA 105 2.45e+01 2rslA c.53.1.1 60526 1a06 332 2.53e+01 1tkiA d.144.1.1 41634 1hueA 90 2.54e+01 1huuA a.55.1.1 17900 1huuA 90 2.54e+01 1huuA a.55.1.1 17897 1cs1A 386 2.54e+01 1ibjA c.67.1.3 34399 1cs1C 386 2.54e+01 1ibjA c.67.1.3 34401 1gdtA 183 2.54e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1gcxA 774 2.60e+01 1tgoA c.55.3.5 33725 e.8.1.1 43014 1a9nA 176 2.67e+01 1a9nA c.10.2.4 30875 1atg 231 2.68e+01 1atg c.94.1.1 35834 1b3oB 514 2.70e+01 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 1cr1A 296 2.70e+01 1cr1A c.37.1.11 32286 1cr0A 296 2.70e+01 1cr1A c.37.1.11 32287 1e0jB 289 2.73e+01 1cr1A c.37.1.11 32291 1b8zA 90 2.73e+01 1huuA a.55.1.1 17902 2pgd 482 2.80e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1lnrR 94 2.84e+01 1kxhA 448 2.88e+01 1b3qA 379 2.89e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1aqm 453 2.89e+01 1smd b.71.1.1 27717 c.1.8.1 28704 1g94A 448 2.89e+01 b.71.1.1 65169 c.1.8.1 65170 1c0pA 363 2.90e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1cpt 412 2.97e+01 1cpt a.104.1.1 18968 1b48A 221 2.97e+01 1pgtA a.45.1.1 17703 c.47.1.5 32997 1gukA 222 2.97e+01 1pgtA a.45.1.1 17705 c.47.1.5 32999 1grj 158 3.08e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1brwA 433 3.08e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 9ldtA 332 3.11e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 1tmy 120 3.13e+01 1dbwA c.23.1.1 31083 1bjt 793 3.15e+01 1bjt e.11.1.1 43249 1c44A 123 3.16e+01 1qndA d.106.1.1 40795 1jm0A 50 3.22e+01 k.8.1.1 66870 2pfkC 302 3.33e+01 3pfk c.89.1.1 35579 1dkrA 317 3.40e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1dkuA 317 3.40e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1c41A 200 3.51e+01 1di0A c.16.1.1 30962 1fvdB 223 3.56e+01 1igtB b.1.1.1 19867 b.1.1.2 20963 2ng1 293 3.59e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1eq2A 310 3.59e+01 1eq2A c.2.1.2 29814 1g60A 260 3.60e+01 1b0aA 288 3.67e+01 1a4iA c.2.1.7 30286 c.58.1.2 33934 1a6dA 545 3.68e+01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1ffh 294 3.74e+01 1ng1 a.24.13.1 16960 c.37.1.10 32271 1b77A 228 3.75e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1h5xA 247 3.77e+01 1lnrS 115 3.83e+01 1lnrJ 156 3.85e+01 1btu 240 3.87e+01 5ptp b.47.1.2 26241 1esb 241 3.88e+01 5ptp b.47.1.2 26276 1d8lA 149 3.91e+01 1hjp a.60.2.1 17948 b.40.4.2 25267 1ez4B 318 3.91e+01 c.2.1.5 64919 d.162.1.1 64920 1bg4 302 3.97e+01 1taxA c.1.8.3 28806 1ciu 683 3.97e+01 1cxlA b.1.1.5 21852 b.3.1.1 22521 b.71.1.1 27759 c.1.8.1 28746 1hjrA 158 3.98e+01 1hjrA c.55.3.6 33727