# List of top-scoring protein chains for t04-w0.5-1-alpha-0.1-scores 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.
#
#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	SCOP_domain	SCOP_suid
5S	5N	12S	12S	10N
1e54A	332	1.16e-39	f.4.3.1	59258
2fgqX	332	4.53e-39	f.4.3.1	133439
2j1nA	346	6.95e-38		
1hxxA	340	1.43e-37	f.4.3.1	61385
2omf	340	3.29e-37		
2porA	301	4.52e-35	f.4.3.1	43759
2por	301	4.84e-32		
3prn	289	1.96e-30		
3prnA	289	1.37e-29	f.4.3.1	43761
1prn	289	3.26e-12		
2o4vA	411	2.50e-11		
1fepA	724	0.003477	f.4.3.3	43808
1t16A	427	0.01427	f.4.3.4	106242
1nqeA	594	0.03301	f.4.3.3	86027
2gufA	594	0.07189	f.4.3.3	135736
1p4tA	155	0.1403	f.4.1.1	87779
1qfgA	725	0.1731	f.4.3.3	43803
1kmoA	774	0.1734	f.4.3.3	72753
1qjpA	171	0.2255	f.4.1.1	43742
1po0A	751	0.3800	f.4.3.3	94960
2f1vA	197	0.4092		
2odjA	428	0.6887		
2mprA	421	0.7441	f.4.3.2	43788
1a0tP	413	0.9656	f.4.3.2	43794
1xkwA	665	1.009		
2hdiA	639	1.628		
1i78A	297	2.414	f.4.4.1	66046
2mev1	277	2.557		
2iwvA	281	3.384		
1py5A	326	6.651	d.144.1.7	104389
2eh6A	375	7.980		
1xf1A	926	8.055		
1vjyA	303	8.232	d.144.1.7	108633
1v0eA	666	9.884	b.68.1.2,b.108.1.3	113466,113467
2f1cX	286	10.58		
1vjvA	415	11.61	d.3.1.9	108632
2pb2A	420	13.27		
2qv3A	457	15.34		
1qcxA	359	16.48	b.80.1.2	28028
2fuvA	549	16.83		
1qj8A	148	17.06	f.4.1.1	43744
1owqA	361	19.64	c.1.8.5,d.26.3.1	104041,104042
2d1pB	119	22.02	c.114.1.1	131137
1pov1	302	23.26		
1gt91	357	24.50		
2jqyA	280	27.11		
2hp1A	432	27.47		
1vjuA	309	28.07	d.248.1.1	100835
2g3fA	421	32.34		
1zgkA	308	32.50		
1arbA	268	32.50	b.47.1.1	25766
2psoA	237	33.88		
1gkpA	458	37.17	b.92.1.3,c.1.9.6	70231,70232
1aym1	285	38.12		
1qd6C	240	38.25		
3cgvA	397	42.72		
2p0mA	662	45.65		
1pvc1	301	46.89		
1pt6A	213	47.94	c.62.1.1	95091
2hmcA	344	47.99		
1oflA	481	47.99	b.80.1.4	103934
2gcuA	245	50.40		
2a7bA	120	50.42	b.1.10.2	126333
2c9wA	169	53.72		
1rxxA	421	56.22	d.126.1.4	98061
1hurA	180	64.08	c.37.1.8	32052
1qqp1	213	66.23		
1bkcE	256	66.81	d.92.1.10	40333
3bs2A	148	67.57		
2cy8A	453	67.70		
1qg4A	216	67.85	c.37.1.8	32035
1txnA	328	70.78	d.248.1.1	112779
1dtoA	221	76.80	b.91.1.1	28405
1zodA	433	77.55	c.67.1.4	125437
1kcxA	518	77.74	b.92.1.3,c.1.9.6	90953,90954
2d6mA	159	78.92		
2ddxA	333	80.28		
1cs1A	386	83.56	c.67.1.3	34399
2qtcA	886	85.41		
2bjkA	516	87.09		
2nruA	307	87.59		
2ddfA	257	87.71		
2irmA	358	89.87		
2ftwA	521	89.99	b.92.1.3,c.1.9.6	134083,134084