# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1i12A 160 3.14e-15 1i21A d.108.1.1 61515 1i1dA 161 3.72e-15 1i21A d.108.1.1 61526 1i21A 159 1.20e-14 1i21A d.108.1.1 61549 1qsmA 152 2.53e-14 1qsmA d.108.1.1 40808 1b87A 181 1.08e-13 1b87A d.108.1.1 40797 1cjwA 166 1.59e-13 1cjwA d.108.1.1 40818 1bo4A 168 2.96e-12 1bo4A d.108.1.1 40798 1qstA 160 4.82e-12 1yghA d.108.1.1 40804 1bo4B 168 8.97e-12 1bo4A d.108.1.1 40799 1yghA 164 8.83e-09 1yghA d.108.1.1 40802 1nmtA 392 5.37e-06 1nmtA d.108.1.2 40823 d.108.1.2 40824 1bob 320 4.71e-05 1bob d.108.1.1 40816 1fy7A 278 1.11e-04 1fy7A d.108.1.1 40817 1iicA 422 1.46e-04 1nmtA d.108.1.2 62422 d.108.1.2 62423 1pxtB 390 1.55e-01 1afwA c.95.1.1 35906 c.95.1.1 35907 1j5eK 129 2.51e-01 1gsa 316 6.05e-01 1gsa c.30.1.3 31718 d.142.1.1 41477 1fjgK 129 6.65e-01 1fjfK c.55.4.1 33733 6pfkA 319 1.30e+00 3pfk c.89.1.1 35583 1afwA 393 1.30e+00 1afwA c.95.1.1 35900 c.95.1.1 35901 1k4jA 230 1.32e+00 4pfk 319 1.41e+00 3pfk c.89.1.1 35582 3pfk 319 1.50e+00 3pfk c.89.1.1 35581 1hqsA 423 1.52e+00 1iso c.77.1.1 61154 1pfkA 320 1.87e+00 3pfk c.89.1.1 35575 2pfkA 320 2.02e+00 3pfk c.89.1.1 35577 1han 297 2.36e+00 1han d.32.1.3 38506 d.32.1.3 38507 1j7iA 264 2.55e+00 1j7iA d.144.1.6 62694 1jmrA 249 2.60e+00 1cqqA 180 2.97e+00 1cqqA b.47.1.4 26422 1d5tA 433 2.97e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 1thfD 253 3.15e+00 1thfD c.1.2.1 28535 1dgaA 375 3.20e+00 1yagA c.55.1.1 33441 c.55.1.1 33442 2btfA 375 3.38e+00 1yagA c.55.1.1 33429 c.55.1.1 33430 1ndk 155 3.40e+00 1npk d.58.6.1 39118 1kblA 873 3.63e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1npk 154 3.64e+00 1npk d.58.6.1 39099 1stfI 98 3.66e+00 1stfI d.17.1.2 38006 1d4xA 375 3.73e+00 1yagA c.55.1.1 59107 c.55.1.1 59108 1aa8A 347 3.84e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1shdA 107 3.96e+00 1fmk d.93.1.1 40440 1f5sA 211 4.08e+00 1f5sA c.108.1.4 59656 1j97A 211 4.08e+00 1f5sA c.108.1.4 62753 1aj6 219 4.25e+00 1aj6 d.122.1.2 41106 1jykA 254 4.25e+00 c.68.1.13 67458 1an9A 340 4.34e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1agjA 242 4.42e+00 1agjA b.47.1.1 25827 1rpxA 230 4.84e+00 1rpxA c.1.2.2 28536 1hrkA 359 4.88e+00 1hrkA c.92.1.1 61228 1ffkE 119 5.07e+00 1ffkE d.79.3.1 39812 1j6zA 376 5.22e+00 1yagA c.55.1.1 62667 c.55.1.1 62668 1skyE 473 5.25e+00 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1j7lA 264 5.40e+00 d.144.1.6 62697 1gt8D 1025 5.54e+00 1dik 874 5.95e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1jatA 155 6.23e+00 1u9aA d.20.1.1 62818 1ecsA 126 6.59e+00 1ecsA d.32.1.2 59407 1cr1A 296 6.77e+00 1cr1A c.37.1.11 32286 1gt8B 1025 6.88e+00 1h7xB 1025 6.99e+00 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7xC 1025 7.00e+00 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1h7xA 1025 7.05e+00 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1flcA 432 7.07e+00 1flcA b.19.1.3 23837 c.23.10.2 31337 1gteA 1025 7.18e+00 1gthC 1025 7.28e+00 1gthA 1025 7.28e+00 1h7wB 1025 7.29e+00 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1g8mA 593 7.30e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1h7wA 1025 7.31e+00 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1h7wD 1025 7.38e+00 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1pot 325 7.47e+00 1pot c.94.1.1 35807 1gthD 1025 7.63e+00 1gt8A 1025 7.64e+00 1jatB 138 7.66e+00 1jatB d.20.1.1 62819 1gthB 1025 7.70e+00 1dxrH 258 7.96e+00 6prcH b.41.1.1 25456 f.2.1.2 43433 6prcH 258 8.21e+00 6prcH b.41.1.1 25457 f.2.1.2 43436 2aop 497 8.39e+00 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1l7mA 211 8.40e+00 1gr8A 412 8.44e+00 1aop 497 8.46e+00 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1gt8C 1025 8.57e+00 1ak1 310 8.59e+00 1ak1 c.92.1.1 35594 1gqeA 365 8.76e+00 1b34B 118 9.15e+00 1b34B b.38.1.1 24797 1fsgA 233 9.26e+00 1qk3A c.61.1.1 34029 1ysc 421 9.32e+00 1ivyA c.69.1.5 34652 1cvl 319 9.42e+00 1cvl c.69.1.18 34786 1h75A 81 9.59e+00 1h75A c.47.1.1 60716 1gox 370 9.83e+00 1gox c.1.4.1 28607 1l1nA 183 9.83e+00 1tahA 318 1.01e+01 1cvl c.69.1.18 34775 1dozA 309 1.02e+01 1ak1 c.92.1.1 35592 1a8l 226 1.04e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1fl2A 310 1.05e+01 1hyuA c.3.1.5 59869 c.3.1.5 59870 1pbp 321 1.08e+01 1ixh c.94.1.1 35768 1ixh 321 1.13e+01 1ixh c.94.1.1 35761 1h8eD 482 1.17e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1a0i 348 1.17e+01 1a0i b.40.4.6 25363 d.142.2.1 41577 1yagA 375 1.18e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 2cpl 165 1.23e+01 2cpl b.62.1.1 27420 1i0rA 169 1.23e+01 1i0rA b.45.1.2 61489 1i0sA 169 1.23e+01 1i0rA b.45.1.2 61491 1avmA 201 1.24e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 2std 172 1.26e+01 3stdA d.17.4.1 38085 1gpwB 201 1.26e+01 c.23.16.1 65461 1e79D 482 1.27e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1dorA 311 1.28e+01 2dorA c.1.4.1 28595 1d3bA 75 1.31e+01 1d3bA b.38.1.1 24798 1ihgA 370 1.36e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 3minC 491 1.37e+01 1qguA c.92.2.3 35607 1bsmA 201 1.42e+01 1avmA a.2.11.1 15780 d.44.1.1 38743 1cg2A 393 1.47e+01 1cg2A c.56.5.4 33844 d.58.19.1 39360 1std 172 1.48e+01 3stdA d.17.4.1 38089 1hvc 203 1.48e+01 1hvc b.50.1.1 26614 1tib 269 1.50e+01 3tgl c.69.1.17 34738 1cwoA 165 1.50e+01 2cpl b.62.1.1 27445 1j8mF 297 1.57e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1edzA 320 1.59e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1gteD 1025 1.62e+01 1h7xD 1025 1.62e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1eulA 994 1.63e+01 1eulA f.2.1.10 43726 2dorA 311 1.66e+01 2dorA c.1.4.1 28593 1cvrA 435 1.66e+01 1cvrA b.1.1.5 21949 c.17.1.2 31006 1brwA 433 1.66e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1i0vA 104 1.67e+01 9rnt d.1.1.1 36054 9rnt 104 1.69e+01 9rnt d.1.1.1 36055 1awqA 164 1.74e+01 2cpl b.62.1.1 27461 1jotA 133 1.74e+01 1jotA 1gk8I 140 1.78e+01 d.73.1.1 65242 3rnt 104 1.81e+01 9rnt d.1.1.1 36069 1ecfA 504 1.82e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1nhkL 144 1.83e+01 1npk d.58.6.1 39142 1isaA 192 1.84e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1hzmA 154 1.86e+01 c.46.1.1 65975 1iscA 192 1.87e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1ewjA 126 1.87e+01 1ecsA d.32.1.2 59526 1awsA 164 1.87e+01 2cpl b.62.1.1 27431 1jdw 423 1.97e+01 1jdw d.126.1.2 41129 1kafA 108 1.99e+01 d.199.1.1 68372 1fn8A 224 2.06e+01 5ptp b.47.1.2 26012 1i8fA 81 2.06e+01 1i8fA b.38.1.1 61959 1ezwA 349 2.11e+01 1ezwA c.1.16.3 29558 1k9vF 201 2.13e+01 c.23.16.1 68365 1rgs 288 2.13e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1gefA 123 2.14e+01 1gefA c.52.1.18 60465 2eng 210 2.22e+01 2eng b.52.1.1 26895 1rpl 251 2.22e+01 1bpyA e.9.1.1 43212 1qcsA 211 2.28e+01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1f75A 249 2.28e+01 1f75A c.101.1.1 59662 1qflA 389 2.29e+01 1afwA c.95.1.1 35908 c.95.1.1 35909 1ee9A 320 2.30e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1befA 181 2.30e+01 1befA b.47.1.3 26419 1a53 247 2.31e+01 1a53 c.1.2.4 28564 1ei1A 391 2.31e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1a58 177 2.33e+01 2cpl b.62.1.1 27495 1dywA 173 2.37e+01 2cpl b.62.1.1 27505 1ao0A 459 2.38e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 1bvoA 175 2.38e+01 1a3qA b.2.5.1 22457 1kwsA 261 2.39e+01 1fggA 261 2.39e+01 1fggA c.68.1.7 34576 1yrgB 385 2.41e+01 1yrgA c.10.1.2 30855 1hi0P 664 2.47e+01 1hi0P e.8.1.6 61051 1e0tA 470 2.48e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1hhsA 664 2.51e+01 1hi0P e.8.1.6 61045 1bib 321 2.51e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1fxqA 267 2.53e+01 1d9eA c.1.10.4 60108 1fcbA 511 2.54e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1whtB 153 2.54e+01 1whtB 1spa 396 2.55e+01 1ajsA c.67.1.1 34291 1jflA 228 2.58e+01 1bia 321 2.59e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1ku8A 133 2.62e+01 1jacA 133 2.65e+01 1jotA 1din 236 2.67e+01 1din c.69.1.9 34682 1uae 419 2.72e+01 1uae d.68.2.2 39574 1a73A 163 2.77e+01 1a73A d.4.1.3 37145 1fwsA 267 2.78e+01 1d9eA c.1.10.4 60063 1g6q2 328 2.78e+01 1g6q2 1pkp 150 2.81e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 1igs 248 2.82e+01 1a53 c.1.2.4 28565 1nom 248 2.85e+01 1bpyA e.9.1.1 43220 1feuA 206 2.93e+01 1feuA b.53.1.1 59801 1jcxA 267 2.93e+01 c.1.10.4 66510 1e1aA 314 2.94e+01 1e1aA b.68.6.1 59155 1evxA 162 2.97e+01 1a73A d.4.1.3 37149 1jacC 133 2.98e+01 1jotA 1jilA 420 2.98e+01 c.26.1.1 66745 1g2qA 187 2.99e+01 c.61.1.1 65117 1juk 248 3.03e+01 1a53 c.1.2.4 28567 1jj2F 119 3.04e+01 1ffkE d.79.3.1 63091 1poiA 317 3.09e+01 1poiA c.63.1.1 34153 1vkxA 273 3.09e+01 1a3qA b.1.1.5 21941 b.2.5.1 22454 1iso 416 3.11e+01 1iso c.77.1.1 35065 1ars 396 3.13e+01 1ajsA c.67.1.1 34287 1qo7A 394 3.14e+01 1qo7A c.69.1.11 34697 5hvpA 99 3.15e+01 1fmb b.50.1.1 26605 1i6wA 181 3.16e+01 1i6wA c.69.1.18 61859 1i7xB 151 3.20e+01 1i7xB j.71.1.1 61914 1fr9A 194 3.22e+01 1fr9A c.68.1.8 34579 1fmtB 314 3.23e+01 1fmtA b.46.1.1 25759 c.65.1.1 34175 2tbs 222 3.33e+01 5ptp b.47.1.2 26009 7icd 416 3.33e+01 1iso c.77.1.1 35072 1lvl 458 3.38e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 2bbkH 355 3.39e+01 2bbkH b.69.2.1 27634 1cr0A 296 3.40e+01 1cr1A c.37.1.11 32287 1im4A 221 3.47e+01 e.8.1.5 62581 1yrgA 385 3.48e+01 1yrgA c.10.1.2 30854 1whsB 153 3.49e+01 1whtB 1fmtA 314 3.52e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1crzA 403 3.53e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1ecfB 504 3.53e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 8cho 125 3.53e+01 1opy d.17.4.3 38108 1k47A 337 3.55e+01 1fpzA 212 3.55e+01 1fpzA c.45.1.1 59976 1yptA 305 3.56e+01 1ytw c.45.1.2 32686 1hrdA 449 3.58e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1zfjA 491 3.59e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1qjgA 125 3.59e+01 1opy d.17.4.3 38102 1hj8A 222 3.61e+01 b.47.1.2 65844 1e19A 314 3.62e+01 1b7bA c.73.1.1 34967 1qcwA 410 3.66e+01 1gox c.1.4.1 28622 1try 224 3.69e+01 5ptp b.47.1.2 26017 1ytn 306 3.69e+01 1ytw c.45.1.2 32688 1dkrA 317 3.74e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1jyeA 349 3.75e+01 c.93.1.1 67455 1e58A 249 3.81e+01 1qhfA c.60.1.1 59262 1k1tA 99 3.81e+01 1bvzA 585 3.83e+01 1bvzA b.1.1.5 21856 b.71.1.1 27783 c.1.8.1 28770 1qunB 279 3.87e+01 b.2.3.2 22411 b.2.3.2 22412 1ejdA 419 3.87e+01 1uae d.68.2.2 39576 1clc 639 3.89e+01 1clc a.102.1.2 18835 b.1.1.5 21872 1fr1A 361 3.90e+01 1gceA e.3.1.1 42734 1fjcA 96 3.93e+01 1fjcA d.58.7.1 39212 1dhy 292 3.94e+01 1han d.32.1.3 38504 d.32.1.3 38505 1g4uS 383 3.95e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1bt3A 345 3.96e+01 1bt3A a.86.1.2 18507 1thm 279 3.96e+01 1gci c.41.1.1 32544 1cqzA 554 3.99e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1qoiA 177 3.99e+01 2cpl b.62.1.1 27490 1bs2A 607 4.00e+01 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563