Complet list of 1ryj hssp file
Complete list of 1ryj.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1RYJ
THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5
REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT Maintained at http://www.cmbi.ru.nl/ by Maarten L. Hekkelman
DATE file generated on 2014-05-09
HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 22-DEC-03 1RYJ
COMPND MOL_ID: 1; MOLECULE: UNKNOWN; CHAIN: A; SYNONYM: HYPOTHETICAL PROTEIN
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: METHANOTHERMOCOCCUS THERMOLITHOTROPHIC
AUTHOR A.YEE,X.CHANG,A.PINEDA-LUCENA,B.WU,A.SEMESI,B.LE,T.RAMELOT, G.M.LEE,S.
DBREF 1RYJ A 4 73 UNP O27775 O27775_METTH 1 70
SEQLENGTH 70
NCHAIN 1 chain(s) in 1RYJ data set
NALIGN 10
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
NOTATION : %IDE: percentage of residue identity of the alignment
NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment
NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
NOTATION : LALI: length of the alignment excluding insertions and deletions
NOTATION : NGAP: number of insertions and deletions in the alignment
NOTATION : LGAP: total length of all insertions and deletions
NOTATION : LSEQ2: length of the entire sequence of the aligned protein
NOTATION : ACCNUM: SwissProt accession number
NOTATION : PROTEIN: one-line description of aligned protein
NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence
NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence
NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
NOTATION : acid/amide form in proportion to their database frequencies
NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
NOTATION : NINS: number of sequences with an insertion in the test protein at this position
NOTATION : ENTROPY: entropy measure of sequence variability at this position
NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100
NOTATION : WEIGHT: conservation weight
## PROTEINS : identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : O27775_METTH1RYJ 1.00 1.00 1 70 1 70 70 0 0 70 O27775 Uncharacterized protein OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=MTH_1743 PE=1 SV=1
2 : T2GK66_METTF 0.97 1.00 5 70 1 66 66 0 0 66 T2GK66 Uncharacterized protein OS=Methanothermobacter thermautotrophicus CaT2 GN=MTCT_1594 PE=4 SV=1
3 : D9PUM7_METTM 0.71 0.91 5 70 1 66 66 0 0 66 D9PUM7 Uncharacterized protein OS=Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) GN=MTBMA_c03190 PE=4 SV=1
4 : K6UAI5_9EURY 0.56 0.79 5 70 1 66 66 0 0 66 K6UAI5 Sulfur transfer protein involved in thiamine biosynthesis OS=Methanobacterium sp. Maddingley MBC34 GN=B655_0358 PE=4 SV=1
5 : K2RT11_METFO 0.55 0.73 5 70 1 66 66 0 0 66 K2RT11 Sulfur transfer protein ThiS OS=Methanobacterium formicicum DSM 3637 GN=A994_07210 PE=4 SV=1
6 : F0T9J7_METSL 0.53 0.73 5 70 1 66 66 0 0 66 F0T9J7 ThiamineS protein OS=Methanobacterium sp. (strain AL-21) GN=Metbo_0493 PE=4 SV=1
7 : U6EEV9_9EURY 0.53 0.79 5 70 1 66 66 0 0 66 U6EEV9 Uncharacterized protein OS=Methanobacterium sp. MB1 GN=MBMB1_1535 PE=4 SV=1
8 : F6D5V8_METSW 0.47 0.68 5 70 1 66 66 0 0 66 F6D5V8 ThiamineS protein OS=Methanobacterium sp. (strain SWAN-1) GN=MSWAN_1902 PE=4 SV=1
9 : R9SNV4_9EURY 0.47 0.73 5 70 1 66 66 0 0 66 R9SNV4 Thiamine biosynthesis protein ThiS OS=Methanobrevibacter sp. AbM4 GN=thiS PE=4 SV=1
10 : Q2NHY6_METST 0.45 0.67 5 70 1 66 66 0 0 66 Q2NHY6 Uncharacterized protein OS=Methanosphaera stadtmanae (strain ATCC 43021 / DSM 3091 / JCM 11832 / MCB-3) GN=Msp_0330 PE=4 SV=1
## ALIGNMENTS 1 - 10
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 4 A M 0 0 225 2 0 M
2 5 A V - 0 0 123 2 0 V
3 6 A I + 0 0 121 2 0 I
4 7 A G - 0 0 41 2 0 G
5 8 A M E -A 20 0A 3 11 0 MMMMMMMMMM
6 9 A K E +A 19 0A 90 11 67 KKKEEKEEST
7 10 A F E -A 18 0A 5 11 55 FFFVVIVVYI
8 11 A T E -Ab 17 60A 14 11 45 TTTTTNTKTK
9 12 A V E -Ab 16 61A 19 11 15 VVVVVVVIVL
10 13 A I E +Ab 15 62A 46 11 27 IIIIIKIVII
11 14 A T E > S-A 14 0A 30 11 85 TTTVIVNIYN
12 15 A D T 3 S+ 0 0 117 11 59 DDDGGGGGKK
13 16 A D T 3 S- 0 0 117 11 41 DDDEENEEDK
14 17 A G E < -A 11 0A 27 11 57 GGGDDNDNKD
15 18 A K E -A 10 0A 157 11 67 KKKKEEETKI
16 19 A K E -A 9 0A 83 11 60 KKRNNDKEEK
17 20 A I E +A 8 0A 120 11 80 IIVINTKIED
18 21 A L E -A 7 0A 63 11 64 LLMMMVIRRI
19 22 A E E -A 6 0A 135 11 45 EEEKTTDEEE
20 23 A S E -A 5 0A 41 11 71 SSSVIIVILI
21 24 A G S S+ 0 0 51 11 62 GGEDESENNS
22 25 A A S S- 0 0 49 11 50 AAEEEGGEGE
23 26 A P + 0 0 77 11 80 PPTGGEDNKN
24 27 A R - 0 0 123 11 74 RRKKKKKQYT
25 28 A R B >> -E 54 0B 77 11 58 RRKTTTTTTT
26 29 A I H 3> S+ 0 0 6 11 14 IIIVVIVVII
27 30 A K H 3> S+ 0 0 96 11 37 KKKKKKKKQA
28 31 A D H <> S+ 0 0 34 11 12 DDDDDDDDND
29 32 A V H X S+ 0 0 30 11 34 VVILLLIMLI
30 33 A L H <>S+ 0 0 22 11 0 LLLLLLLLLL
31 34 A G H <5S+ 0 0 41 11 62 GGQQQEQEDK
32 35 A E H <5S+ 0 0 166 11 88 EEEIISMIDK
33 36 A L T <5S- 0 0 116 11 32 LLLMLMMMLE
34 37 A E T 5 - 0 0 156 11 20 EEQEEEEDDE
35 38 A I < - 0 0 52 11 5 IIIIIIIVII
36 39 A P >> - 0 0 70 11 28 PPPPPAPPSP
37 40 A I T 34 S+ 0 0 74 11 75 IILLTAVSSI
38 41 A E T 34 S+ 0 0 178 11 0 EEEEEEEEEE
39 42 A T T <4 S+ 0 0 63 11 0 TTTTTTTTTT
40 43 A V E < S-C 65 0A 12 11 21 VVAVVVVVIV
41 44 A V E -C 64 0A 55 11 0 VVVVVVVVVV
42 45 A V E -C 63 0A 4 11 21 VVVVVVVVPV
43 46 A K E -CD 62 48A 50 11 0 KKKKKKKKKK
44 47 A K E > S-CD 61 47A 27 11 47 KKRKKKKKQL
45 48 A N T 3 S- 0 0 120 11 0 NNNNNNNNNN
46 49 A G T 3 S+ 0 0 21 11 65 GGSHQDQNGG
47 50 A Q E < S-D 44 0A 146 11 91 QEESTYSYDD
48 51 A I E +D 43 0A 113 11 27 IIIIIILIIT
49 52 A V - 0 0 32 11 12 VVVIIVIVVV
50 53 A I > - 0 0 102 11 24 IIIIIIIIVT
51 54 A D T 3 S+ 0 0 33 11 14 DEEEEDEEEE
52 55 A E T 3 S+ 0 0 100 11 7 EEEEEEEEED
53 56 A E S < S- 0 0 84 11 20 EEEEEEEESE
54 57 A E B -E 25 0B 97 11 71 EEESSIEPEK
55 58 A I - 0 0 4 11 23 IIIVVLVVIV
56 59 A F > - 0 0 119 11 101 FFSEEEEAHK
57 60 A D T 3 S+ 0 0 107 11 11 DDDDDDDDDN
58 61 A G T 3 S+ 0 0 55 11 0 GGGGGGGGGG
59 62 A D < - 0 0 24 11 0 DDDDDDDDDD
60 63 A I E -b 8 0A 45 11 73 IIIIISVTEE
61 64 A I E -bC 9 44A 7 11 10 IIIIIIIIIL
62 65 A E E -bC 10 43A 57 11 18 EEEEEEEEKE
63 66 A V E + C 0 42A 5 11 14 VVIVVVVIII
64 67 A I E - C 0 41A 83 11 0 IIIIIIIIII
65 68 A R E - C 0 40A 139 11 50 RRRKKQKQQK
66 69 A V > - 0 0 82 11 6 VVVVVVVVIV
67 70 A I T 3 S+ 0 0 155 11 0 IIIIIIIIII
68 71 A Y T 3 S+ 0 0 225 11 0 YYYYYYYYYY
69 72 A G < 0 0 34 11 0 GGGGGGGGGG
70 73 A G 0 0 143 11 0 GGGGGGGGGG
## SEQUENCE PROFILE AND ENTROPY
SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT
1 4 A 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
2 5 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
3 6 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
4 7 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
5 8 A 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
6 9 A 0 0 0 0 0 0 0 0 0 0 9 9 0 0 0 45 0 36 0 0 11 0 0 1.162 38 0.33
7 10 A 36 0 18 0 36 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 1.264 42 0.45
8 11 A 0 0 0 0 0 0 0 0 0 0 0 73 0 0 0 18 0 0 9 0 11 0 0 0.760 25 0.54
9 12 A 82 9 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.600 20 0.85
10 13 A 9 0 82 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 11 0 0 0.600 20 0.73
11 14 A 18 0 18 0 0 0 9 0 0 0 0 36 0 0 0 0 0 0 18 0 11 0 0 1.516 50 0.15
12 15 A 0 0 0 0 0 0 0 45 0 0 0 0 0 0 0 18 0 0 0 36 11 0 0 1.036 34 0.41
13 16 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 36 9 45 11 0 0 1.162 38 0.59
14 17 A 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 9 0 0 18 36 11 0 0 1.264 42 0.43
15 18 A 0 0 9 0 0 0 0 0 0 0 0 9 0 0 0 55 0 27 0 0 11 0 0 1.121 37 0.33
16 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 45 0 18 18 9 11 0 0 1.414 47 0.40
17 20 A 9 0 45 0 0 0 0 0 0 0 0 9 0 0 0 9 0 9 9 9 11 0 0 1.666 55 0.19
18 21 A 9 27 18 27 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 11 0 0 1.547 51 0.36
19 22 A 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 9 0 64 0 9 11 0 0 1.034 34 0.55
20 23 A 18 9 36 0 0 0 0 0 0 0 36 0 0 0 0 0 0 0 0 0 11 0 0 1.264 42 0.28
21 24 A 0 0 0 0 0 0 0 27 0 0 18 0 0 0 0 0 0 27 18 9 11 0 0 1.547 51 0.38
22 25 A 0 0 0 0 0 0 0 27 27 0 0 0 0 0 0 0 0 45 0 0 11 0 0 1.067 35 0.49
23 26 A 0 0 0 0 0 0 0 18 0 27 0 9 0 0 0 9 0 9 18 9 11 0 0 1.846 61 0.20
24 27 A 0 0 0 0 0 0 9 0 0 0 0 9 0 0 27 45 9 0 0 0 11 0 0 1.367 45 0.26
25 28 A 0 0 0 0 0 0 0 0 0 0 0 64 0 0 27 9 0 0 0 0 11 0 0 0.860 28 0.42
26 29 A 36 0 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.655 21 0.85
27 30 A 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 82 9 0 0 0 11 0 0 0.600 20 0.63
28 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 91 11 0 0 0.305 10 0.88
29 32 A 27 36 27 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 1.295 43 0.66
30 33 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
31 34 A 0 0 0 0 0 0 0 27 0 0 0 0 0 0 0 9 36 18 0 9 11 0 0 1.468 49 0.38
32 35 A 0 0 27 9 0 0 0 0 0 0 9 0 0 0 0 9 0 36 0 9 11 0 0 1.594 53 0.12
33 36 A 0 55 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 11 0 0 0.916 30 0.68
34 37 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 73 0 18 11 0 0 0.760 25 0.79
35 38 A 9 0 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.305 10 0.95
36 39 A 0 0 0 0 0 0 0 0 9 82 9 0 0 0 0 0 0 0 0 0 11 0 0 0.600 20 0.71
37 40 A 9 18 36 0 0 0 0 0 9 0 18 9 0 0 0 0 0 0 0 0 11 0 0 1.642 54 0.25
38 41 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 11 0 0 0.000 0 1.00
39 42 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
40 43 A 82 0 9 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.600 20 0.79
41 44 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
42 45 A 91 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 11 0 0 0.305 10 0.78
43 46 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 11 0 0 0.000 0 1.00
44 47 A 0 9 0 0 0 0 0 0 0 0 0 0 0 0 9 73 9 0 0 0 11 0 0 0.886 29 0.52
45 48 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 11 0 0 0.000 0 1.00
46 49 A 0 0 0 0 0 0 0 45 0 0 9 0 0 9 0 0 18 0 9 9 11 0 0 1.540 51 0.35
47 50 A 0 0 0 0 0 0 18 0 0 0 18 9 0 0 0 0 18 18 0 18 11 0 0 1.768 59 0.09
48 51 A 0 9 82 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 11 0 0 0.600 20 0.73
49 52 A 73 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.586 19 0.88
50 53 A 9 0 82 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 11 0 0 0.600 20 0.75
51 54 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 73 0 27 11 0 0 0.586 19 0.86
52 55 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 0 9 11 0 0 0.305 10 0.93
53 56 A 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 91 0 0 11 0 0 0.305 10 0.80
54 57 A 0 0 9 0 0 0 0 0 0 9 18 0 0 0 0 9 0 55 0 0 11 0 0 1.295 43 0.28
55 58 A 45 9 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.935 31 0.77
56 59 A 0 0 0 0 27 0 0 0 9 0 9 0 0 9 0 9 0 36 0 0 11 0 0 1.594 53 -0.01
57 60 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 91 11 0 0 0.305 10 0.88
58 61 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
59 62 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 11 0 0 0.000 0 1.00
60 63 A 9 0 55 0 0 0 0 0 0 0 9 9 0 0 0 0 0 18 0 0 11 0 0 1.295 43 0.26
61 64 A 0 9 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.305 10 0.90
62 65 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 91 0 0 11 0 0 0.305 10 0.81
63 66 A 64 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.655 21 0.85
64 67 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
65 68 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 36 27 0 0 0 11 0 0 1.090 36 0.49
66 69 A 91 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.305 10 0.94
67 70 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
68 71 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
69 72 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
70 73 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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