Complet list of 2f40 hssp file
Complete list of 2f40.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2F40
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 2014-05-18
HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 22-NOV-05 2F40
COMPND MOL_ID: 1; MOLECULE: HYPOTHETICAL PROTEIN PF1455; CHAIN: A; ENGINEERED
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; ORGANISM_TAXID: 1
AUTHOR S.BANSAL,J.H.PRESTEGARD,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMIC
DBREF 2F40 A 2 88 GB 18977827 NP_579184 2 88
SEQLENGTH 74
NCHAIN 1 chain(s) in 2F40 data set
NALIGN 12
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 : I6V2A6_9EURY 1.00 1.00 2 74 2 74 73 0 0 88 I6V2A6 Uncharacterized protein OS=Pyrococcus furiosus COM1 GN=PFC_06510 PE=4 SV=1
2 : Q8U0X6_PYRFU2F40 1.00 1.00 2 74 2 74 73 0 0 88 Q8U0X6 Uncharacterized protein OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=PF1455 PE=1 SV=1
3 : I3RF57_9EURY 0.64 0.83 5 74 5 74 70 0 0 86 I3RF57 Uncharacterized protein OS=Pyrococcus sp. ST04 GN=Py04_1293 PE=4 SV=1
4 : H3ZJR0_THELN 0.52 0.69 11 74 12 78 67 1 3 90 H3ZJR0 Uncharacterized protein OS=Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C) GN=OCC_02109 PE=4 SV=1
5 : G8ZJG8_PYRAB 0.49 0.73 13 74 14 76 63 1 1 88 G8ZJG8 Uncharacterized protein OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=PAB0482.1n PE=4 SV=1
6 : I3ZUL0_9EURY 0.47 0.68 12 74 21 86 66 1 3 99 I3ZUL0 Uncharacterized protein OS=Thermococcus sp. CL1 GN=CL1_1191 PE=4 SV=1
7 : F0LL32_THEBM 0.45 0.67 11 74 16 82 67 1 3 98 F0LL32 Uncharacterized protein OS=Thermococcus barophilus (strain DSM 11836 / MP) GN=TERMP_01965 PE=4 SV=1
8 : F8AEZ9_PYRYC 0.45 0.68 12 74 14 79 66 1 3 92 F8AEZ9 Uncharacterized protein OS=Pyrococcus yayanosii (strain CH1 / JCM 16557) GN=PYCH_11550 PE=4 SV=1
9 : F4HNI8_PYRSN 0.44 0.68 5 74 7 79 73 1 3 91 F4HNI8 Uncharacterized protein OS=Pyrococcus sp. (strain NA2) GN=PNA2_0047 PE=4 SV=1
10 : W0IA32_9EURY 0.44 0.70 5 74 11 82 73 2 4 98 W0IA32 Uncharacterized protein OS=Thermococcus sp. ES1 GN=TES1_1918 PE=4 SV=1
11 : C6A2T9_THESM 0.43 0.69 11 74 12 78 67 1 3 90 C6A2T9 Uncharacterized protein OS=Thermococcus sibiricus (strain MM 739 / DSM 12597) GN=TSIB_0874 PE=4 SV=1
12 : G0HLJ2_THES4 0.38 0.65 12 74 22 87 66 1 3 100 G0HLJ2 Uncharacterized protein OS=Thermococcus sp. (strain CGMCC 1.5172 / 4557) GN=GQS_07845 PE=4 SV=1
## ALIGNMENTS 1 - 12
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A S 0 0 101 1 0
2 2 A K - 0 0 13 3 0 KK
3 3 A W E +A 43 0A 23 3 0 WW
4 4 A I E -A 42 0A 6 3 0 II
5 5 A K E +A 41 0A 58 6 0 KKK KK
6 6 A F - 0 0 10 6 9 FFF LF
7 7 A T - 0 0 4 6 82 TTE NS
8 8 A T + 0 0 50 5 91 TTI N.
9 9 A N S S+ 0 0 103 6 81 NNA SK
10 10 A L >> - 0 0 78 6 33 LLL II
11 11 A T T 34 S+ 0 0 72 9 17 TTTT T TAT
12 12 A P T 34 S+ 0 0 77 12 16 PPPP PPPHPPP
13 13 A E T <> S+ 0 0 34 13 27 EEEDEDQEEQED
14 14 A E T < S+ 0 0 4 13 9 EEEEEDEEEDEE
15 15 A A T >> S+ 0 0 47 13 0 AAAAAAAAAAAA
16 16 A K H >> S+ 0 0 113 13 56 KKMRMRMKMMRR
17 17 A I H 3X S+ 0 0 16 13 84 IIVEEVDDADRA
18 18 A V H <4 S+ 0 0 58 13 48 VVIMVVLIVLMR
19 19 A Q H < S+ 0 0 62 13 0 YYYYYYYYYYYY
21 21 A E T 3< S+ 0 0 6 13 49 EEEKEEKREKKE
22 22 A L T >4 S+ 0 0 82 13 0 LLLLLLLLLLLL
23 23 A S T << S+ 0 0 104 13 48 SSSSSLSSSSAL
24 24 A T T >> S+ 0 0 12 13 80 TTKLKKVLKVIK
25 25 A R T <4 + 0 0 181 13 75 RREDMDNHENND
26 26 A D T 34 S+ 0 0 167 13 71 DDDLDEPEDSLG
27 27 A E T <4 S+ 0 0 84 13 75 EESAQRAGAAAR
28 28 A F B < +B 46 0B 34 13 64 FFIVVVTTVTVV
29 29 A Y + 0 0 149 13 8 YYYYYWYYYYYW
30 30 A R - 0 0 120 13 0 RRRRRRRRRRRR
31 31 A V + 0 0 40 13 44 VVVVAAVVAVVA
32 32 A F + 0 0 135 13 0 FFFFFFFFFFFF
33 33 A I - 0 0 39 13 11 IIIIIIIVIILI
34 34 A N >>> + 0 0 80 13 0 NNNNNNNNNNNN
35 35 A P T 345S+ 0 0 54 13 47 PPPGPGGGPGGG
36 36 A Y T 345S+ 0 0 194 13 0 YYYYYYYYYYYY
37 37 A A T <45S- 0 0 27 13 48 AAASQASAASSA
38 38 A K T <5S+ 0 0 147 13 23 KKKKRKKRRKKR
39 39 A V < - 0 0 62 13 88 VVININRTMTSS
40 40 A A + 0 0 1 13 32 AAAGAGGAAGGG
41 41 A E E -A 5 0A 95 13 100 EEKYRFMRKMYF
42 42 A V E -A 4 0A 9 13 13 VVVVVVIVIIIV
43 43 A V E +A 3 0A 44 13 14 VVIIIVIVIVIV
44 44 A I - 0 0 7 13 40 IIFFAFFFFFFF
45 45 A D + 0 0 68 13 9 DDDDDDDNDDDD
46 46 A D B -B 28 0B 12 13 38 DDDEgEEPEEEE
47 47 A S + 0 0 83 13 70 SSSTkEEKNGSE
48 48 A K S S- 0 0 67 13 40 KKKKTAKKKKKT
49 49 A V - 0 0 114 13 58 VVILELLLKLLI
50 50 A N S > S+ 0 0 16 13 70 NNSPEPPSEPSS
51 51 A I H > S+ 0 0 113 13 83 IIAKLRKKTKRK
52 52 A E H > S+ 0 0 64 13 42 EEEELEEDKEED
53 53 A E H > S+ 0 0 5 13 61 EEQKKEKFDEEE
54 54 A L H X S+ 0 0 62 13 26 LLILFLLILLIV
55 55 A K H < S+ 0 0 98 13 63 KKALFLLLLLLL
56 56 A E H >< S+ 0 0 45 13 45 EEEEEEEKSRQE
57 57 A K H >X S+ 0 0 0 13 62 KKKMKKMELMMK
58 58 A L T 3< S+ 0 0 69 13 8 LLLLFLLFLFLL
59 59 A K T <4 S+ 0 0 117 13 58 KKKKKKSEESER
60 60 A G T <4 S+ 0 0 20 13 69 GGGpPsepksed
61 61 A E < + 0 0 100 13 22 EEReEeqeeeee
62 62 A V S S- 0 0 118 13 29 VVKVVVIVIIII
63 63 A I S S+ 0 0 88 13 34 IIIIVVIVITIT
64 64 A E + 0 0 18 13 55 EEESEGESEERA
65 65 A E + 0 0 114 13 19 EEEEEEEEEEEI
66 66 A K - 0 0 93 13 35 KKRKKVKRRKKK
67 67 A E + 0 0 62 13 65 EEDEDYEESETR
68 68 A I - 0 0 75 13 26 IIILVLIIIILL
69 69 A T + 0 0 51 13 23 TTTTSTSTTTTT
70 70 A L - 0 0 81 13 54 LLLPLVILVIPV
71 71 A Q S S- 0 0 120 13 31 QQEQEEEEDEDE
72 72 A E S S- 0 0 111 13 5 EEEEEEEEDEEE
73 73 A L 0 0 115 13 14 LLLLVLLLVLLL
74 74 A I 0 0 176 13 7 IIIIIIVIIIIV
## 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 1 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
4 4 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 6 0 0 0.000 0 1.00
6 6 A 0 17 0 0 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.451 15 0.91
7 7 A 0 0 0 0 0 0 0 0 0 0 17 50 0 0 0 0 0 17 17 0 6 1 0 1.242 41 0.17
8 8 A 0 0 20 0 0 0 0 0 0 0 0 60 0 0 0 0 0 0 20 0 5 0 0 0.950 31 0.08
9 9 A 0 0 0 0 0 0 0 0 17 0 17 0 0 0 0 17 0 0 50 0 6 0 0 1.242 41 0.19
10 10 A 0 67 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.637 21 0.66
11 11 A 0 0 0 0 0 0 0 0 11 0 0 89 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.82
12 12 A 0 0 0 0 0 0 0 0 0 92 0 0 0 8 0 0 0 0 0 0 12 0 0 0.287 9 0.84
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 62 0 23 13 0 0 0.925 30 0.73
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 0 15 13 0 0 0.429 14 0.90
15 15 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
16 16 A 0 0 0 38 0 0 0 0 0 0 0 0 0 0 31 31 0 0 0 0 13 0 0 1.093 36 0.43
17 17 A 15 0 23 0 0 0 0 0 15 0 0 0 0 0 8 0 0 15 0 23 13 0 0 1.738 58 0.15
18 18 A 46 15 15 15 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 13 0 0 1.418 47 0.52
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 13 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 31 0 62 0 0 13 0 0 0.859 28 0.50
22 22 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
23 23 A 0 15 0 0 0 0 0 0 8 0 77 0 0 0 0 0 0 0 0 0 13 0 0 0.687 22 0.51
24 24 A 15 15 8 0 0 0 0 0 0 0 0 23 0 0 0 38 0 0 0 0 13 0 0 1.479 49 0.19
25 25 A 0 0 0 8 0 0 0 0 0 0 0 0 0 8 23 0 0 15 23 23 13 0 0 1.698 56 0.24
26 26 A 0 15 0 0 0 0 0 8 0 8 8 0 0 0 0 0 0 15 0 46 13 0 0 1.525 50 0.28
27 27 A 0 0 0 0 0 0 0 8 38 0 8 0 0 0 15 0 8 23 0 0 13 0 0 1.586 52 0.24
28 28 A 46 0 8 0 23 0 0 0 0 0 0 23 0 0 0 0 0 0 0 0 13 0 0 1.231 41 0.35
29 29 A 0 0 0 0 0 15 85 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.92
30 30 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 13 0 0 0.000 0 1.00
31 31 A 69 0 0 0 0 0 0 0 31 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.617 20 0.56
32 32 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
33 33 A 8 8 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.536 17 0.88
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 13 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 54 0 46 0 0 0 0 0 0 0 0 0 0 13 0 0 0.690 23 0.52
36 36 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
37 37 A 0 0 0 0 0 0 0 0 62 0 31 0 0 0 0 0 8 0 0 0 13 0 0 0.859 28 0.52
38 38 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 69 0 0 0 0 13 0 0 0.617 20 0.76
39 39 A 23 0 15 8 0 0 0 0 0 0 15 15 0 0 8 0 0 0 15 0 13 0 0 1.885 62 0.11
40 40 A 0 0 0 0 0 0 0 46 54 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.690 23 0.68
41 41 A 0 0 0 15 15 0 15 0 0 0 0 0 0 0 15 15 0 23 0 0 13 0 0 1.778 59 -0.00
42 42 A 69 0 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.617 20 0.87
43 43 A 54 0 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.690 23 0.85
44 44 A 0 0 23 0 69 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.790 26 0.59
45 45 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 92 13 0 0 0.271 9 0.91
46 46 A 0 0 0 0 0 0 0 8 0 8 0 0 0 0 0 0 0 54 0 31 13 0 1 1.091 36 0.61
47 47 A 0 0 0 0 0 0 0 8 0 0 38 8 0 0 0 15 0 23 8 0 13 0 0 1.586 52 0.30
48 48 A 0 0 0 0 0 0 0 0 8 0 0 15 0 0 0 77 0 0 0 0 13 0 0 0.687 22 0.60
49 49 A 23 46 15 0 0 0 0 0 0 0 0 0 0 0 0 8 0 8 0 0 13 0 0 1.378 45 0.41
50 50 A 0 0 0 0 0 0 0 0 0 31 31 0 0 0 0 0 0 15 23 0 13 0 0 1.352 45 0.30
51 51 A 0 8 23 0 0 0 0 0 8 0 0 8 0 0 15 38 0 0 0 0 13 0 0 1.586 52 0.17
52 52 A 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 69 0 15 13 0 0 0.937 31 0.58
53 53 A 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 23 8 54 0 8 13 0 0 1.264 42 0.38
54 54 A 8 62 23 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 1.032 34 0.73
55 55 A 0 62 0 0 8 0 0 0 8 0 0 0 0 0 0 23 0 0 0 0 13 0 0 1.032 34 0.37
56 56 A 0 0 0 0 0 0 0 0 0 0 8 0 0 0 8 8 8 69 0 0 13 0 0 1.044 34 0.54
57 57 A 0 8 0 31 0 0 0 0 0 0 0 0 0 0 0 54 0 8 0 0 13 0 0 1.091 36 0.38
58 58 A 0 77 0 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.540 18 0.92
59 59 A 0 0 0 0 0 0 0 0 0 0 15 0 0 0 8 54 0 23 0 0 13 0 0 1.157 38 0.42
60 60 A 0 0 0 0 0 0 0 31 0 23 15 0 0 0 0 8 0 15 0 8 13 0 8 1.672 55 0.30
61 61 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 8 85 0 0 13 0 0 0.536 17 0.78
62 62 A 54 0 38 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 13 0 0 0.898 29 0.70
63 63 A 23 0 62 0 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 13 0 0 0.925 30 0.65
64 64 A 0 0 0 0 0 0 0 8 8 0 15 0 0 0 8 0 0 62 0 0 13 0 0 1.179 39 0.44
65 65 A 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 0 0 13 0 0 0.271 9 0.81
66 66 A 8 0 0 0 0 0 0 0 0 0 0 0 0 0 23 69 0 0 0 0 13 0 0 0.790 26 0.65
67 67 A 0 0 0 0 0 0 8 0 0 0 8 8 0 0 8 0 0 54 0 15 13 0 0 1.411 47 0.34
68 68 A 8 31 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.859 28 0.74
69 69 A 0 0 0 0 0 0 0 0 0 0 15 85 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.76
70 70 A 23 46 15 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 13 0 0 1.271 42 0.46
71 71 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 54 0 15 13 0 0 0.984 32 0.69
72 72 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 0 8 13 0 0 0.271 9 0.94
73 73 A 15 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.85
74 74 A 15 0 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.92
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
4 51 62 3 pFEPe
5 35 48 1 gMk
6 50 70 3 sLEPe
7 51 66 3 eLNPq
8 50 63 3 pYGYe
9 57 63 3 kFKPe
10 56 66 3 sHEPe
11 51 62 3 eFKPe
12 50 71 3 dFEPe
//