Complet list of 1loi hssp file
Complete list of 1loi.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1LOI
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 2014-05-03
HEADER HYDROLASE 21-MAY-96 1LOI
COMPND MOL_ID: 1; MOLECULE: CYCLIC 3',5'-AMP SPECIFIC PHOSPHODIESTERASE RD1;
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; ORGANISM_COMMON: NO
AUTHOR K.J.SMITH,G.SCOTLAND,J.BEATTIE,I.P.TRAYER,M.D.HOUSLAY
DBREF 1LOI A 1 25 UNP P54748 PDE4A_RAT 1 25
SEQLENGTH 25
NCHAIN 1 chain(s) in 1LOI data set
NALIGN 8
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 : A6QQQ0_BOVIN 1.00 1.00 1 25 1 25 25 0 0 635 A6QQQ0 PDE4A protein OS=Bos taurus GN=PDE4A PE=2 SV=1
2 : C9K100_MOUSE 1.00 1.00 1 25 1 25 25 0 0 610 C9K100 Phosphodiesterase 4A OS=Mus musculus GN=Pde4a PE=2 SV=1
3 : H9FVH8_MACMU 1.00 1.00 1 25 1 25 25 0 0 647 H9FVH8 cAMP-specific 3',5'-cyclic phosphodiesterase 4A isoform 4 OS=Macaca mulatta GN=PDE4A PE=2 SV=1
4 : K7EKV1_HUMAN 1.00 1.00 1 25 1 25 25 0 0 96 K7EKV1 cAMP-specific 3',5'-cyclic phosphodiesterase 4A OS=Homo sapiens GN=PDE4A PE=2 SV=1
5 : Q684M5_PIG 1.00 1.00 1 25 1 25 25 0 0 620 Q684M5 Phosphodiesterase 4A, cAMP-specific OS=Sus scrofa GN=PDE4A PE=3 SV=1
6 : U3D7J0_CALJA 1.00 1.00 1 25 1 25 25 0 0 639 U3D7J0 cAMP-specific 3',5'-cyclic phosphodiesterase 4A isoform 4 OS=Callithrix jacchus GN=PDE4A PE=2 SV=1
7 : U3ECG3_CALJA 1.00 1.00 1 25 1 25 25 0 0 639 U3ECG3 cAMP-specific 3',5'-cyclic phosphodiesterase 4A isoform 4 OS=Callithrix jacchus GN=PDE4A PE=2 SV=1
8 : H2TMV0_TAKRU 0.88 1.00 2 25 2 25 24 0 0 453 H2TMV0 Uncharacterized protein (Fragment) OS=Takifugu rubripes GN=PDE4A (1 of 2) PE=3 SV=1
## ALIGNMENTS 1 - 8
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A M 0 0 173 8 0 MMMMMMM
2 2 A P >> + 0 0 107 9 0 PPPPPPPP
3 3 A L H 3> S+ 0 0 127 9 0 LLLLLLLL
4 4 A V H 3> S+ 0 0 80 9 0 VVVVVVVV
5 5 A D H <> S+ 0 0 94 9 0 DDDDDDDD
6 6 A F H X S+ 0 0 146 9 20 FFFFFFFL
7 7 A F H < S+ 0 0 126 9 0 FFFFFFFF
8 8 A C H >< S+ 0 0 105 9 0 CCCCCCCC
9 9 A E H 3< S- 0 0 100 9 0 EEEEEEEE
10 10 A T T 3< S+ 0 0 85 9 0 TTTTTTTT
11 11 A C S < S+ 0 0 58 9 0 CCCCCCCC
12 12 A S S S+ 0 0 99 9 0 SSSSSSSS
13 13 A K >> + 0 0 29 9 46 KKKKKKKR
14 14 A P T 34 S+ 0 0 68 9 0 PPPPPPPP
15 15 A W T >4 S+ 0 0 182 9 0 WWWWWWWW
16 16 A L G X4 S+ 0 0 59 9 0 LLLLLLLL
17 17 A V G >X S+ 0 0 75 9 26 VVVVVVVI
18 18 A G G X4 S+ 0 0 55 9 0 GGGGGGGG
19 19 A W G <> S+ 0 0 135 9 0 WWWWWWWW
20 20 A W H <> S+ 0 0 87 9 0 WWWWWWWW
21 21 A D H X< S+ 0 0 115 9 0 DDDDDDDD
22 22 A Q H >4 S+ 0 0 96 9 0 QQQQQQQQ
23 23 A F H 3< + 0 0 149 9 0 FFFFFFFF
24 24 A K T << 0 0 151 9 0 KKKKKKKK
25 25 A R < 0 0 198 9 0 RRRRRRRR
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
3 3 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
4 4 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 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 0 0 0 0 100 9 0 0 0.000 0 1.00
6 6 A 0 11 0 0 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.80
7 7 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 9 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 89 0 0 0 0 9 0 0 0.349 11 0.53
14 14 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
16 16 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
17 17 A 89 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.73
18 18 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 9 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 9 0 0 0.000 0 1.00
23 23 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 9 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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