Complet list of 1jdm hssp file
Complete list of 1jdm.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1JDM
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 2014-05-02
HEADER MEMBRANE PROTEIN 14-JUN-01 1JDM
COMPND MOL_ID: 1; MOLECULE: SARCOLIPIN; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS SEQUENCE OCCURS NATURAL
AUTHOR G.VEGLIA,A.MASCIONI
DBREF 1JDM A 1 31 UNP O00631 SARCO_HUMAN 1 31
SEQLENGTH 31
NCHAIN 1 chain(s) in 1JDM data set
NALIGN 19
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 : F6ZI62_MACMU 1.00 1.00 1 31 1 31 31 0 0 31 F6ZI62 Sarcolipin OS=Macaca mulatta GN=LOC100424360 PE=4 SV=1
2 : G3SAS6_GORGO 1.00 1.00 1 31 1 31 31 0 0 31 G3SAS6 Uncharacterized protein OS=Gorilla gorilla gorilla GN=101148498 PE=4 SV=1
3 : G7PNQ4_MACFA 1.00 1.00 1 31 1 31 31 0 0 31 G7PNQ4 Putative uncharacterized protein OS=Macaca fascicularis GN=EGM_06188 PE=4 SV=1
4 : H2NF64_PONAB 1.00 1.00 1 31 1 31 31 0 0 31 H2NF64 Uncharacterized protein OS=Pongo abelii GN=SLN PE=4 SV=1
5 : H2Q4P5_PANTR 1.00 1.00 1 31 1 31 31 0 0 31 H2Q4P5 Uncharacterized protein OS=Pan troglodytes GN=SLN PE=4 SV=1
6 : SARCO_HUMAN 1.00 1.00 1 31 1 31 31 0 0 31 O00631 Sarcolipin OS=Homo sapiens GN=SLN PE=1 SV=1
7 : D2I1Y5_AILME 0.97 1.00 1 31 1 31 31 0 0 31 D2I1Y5 Uncharacterized protein (Fragment) OS=Ailuropoda melanoleuca GN=LOC100466949 PE=4 SV=1
8 : M3W000_FELCA 0.97 1.00 1 31 1 31 31 0 0 31 M3W000 Uncharacterized protein OS=Felis catus GN=SLN PE=4 SV=1
9 : F7H6B8_CALJA 0.94 0.97 1 31 1 31 31 0 0 31 F7H6B8 Uncharacterized protein OS=Callithrix jacchus PE=4 SV=1
10 : F7CIP7_HORSE 0.92 1.00 6 30 1 25 25 0 0 25 F7CIP7 Uncharacterized protein (Fragment) OS=Equus caballus PE=4 SV=1
11 : I3LY83_SPETR 0.87 0.97 1 30 1 30 30 0 0 30 I3LY83 Uncharacterized protein OS=Spermophilus tridecemlineatus PE=4 SV=1
12 : G3SQ37_LOXAF 0.81 0.90 1 31 1 31 31 0 0 31 G3SQ37 Uncharacterized protein OS=Loxodonta africana GN=LOC100663349 PE=4 SV=1
13 : H0VT96_CAVPO 0.81 0.94 1 31 1 31 31 0 0 31 H0VT96 Uncharacterized protein OS=Cavia porcellus GN=Sln PE=4 SV=1
14 : Q1W0X9_PIG 0.81 0.90 1 31 1 31 31 0 0 31 Q1W0X9 Sarcolipin OS=Sus scrofa GN=SLN PE=4 SV=1
15 : SARCO_RABIT 0.81 0.90 1 31 1 31 31 0 0 31 P42532 Sarcolipin OS=Oryctolagus cuniculus GN=SLN PE=1 SV=1
16 : G1P313_MYOLU 0.77 0.97 1 30 1 30 30 0 0 30 G1P313 Uncharacterized protein OS=Myotis lucifugus PE=4 SV=1
17 : SARCO_MOUSE 0.77 0.94 1 31 1 31 31 0 0 31 Q9CQD6 Sarcolipin OS=Mus musculus GN=Sln PE=1 SV=1
18 : SARCO_RAT 0.77 0.94 1 31 1 31 31 0 0 31 Q6SLE7 Sarcolipin OS=Rattus norvegicus GN=Sln PE=3 SV=1
19 : W5Q669_SHEEP 0.74 0.90 1 31 1 31 31 0 0 31 W5Q669 Uncharacterized protein OS=Ovis aries GN=SLN PE=4 SV=1
## ALIGNMENTS 1 - 19
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A M 0 0 190 19 0 MMMMMMMMM MMMMMMMMM
2 2 A G - 0 0 57 19 48 GGGGGGGGE EEEEEDEEE
3 3 A I S S+ 0 0 175 19 93 IIIIIIIIV LRRRRLRRR
4 4 A N - 0 0 81 19 51 NNNNNNSSN SSSSSSSSS
5 5 A T S S+ 0 0 129 19 22 TTTTTTTTT TTTTTATTA
6 6 A R S S+ 0 0 184 20 19 RRRRRRRRRRRRRRRRQQR
7 7 A E S S+ 0 0 68 20 0 EEEEEEEEEEEEEEEEEEE
8 8 A L S > S+ 0 0 95 20 7 LLLLLLLLLLLLLLLLLLI
9 9 A F H >> + 0 0 106 20 60 FFFFFFFFFFFCFCCCFFC
10 10 A L H >5S+ 0 0 87 20 12 LLLLLLLLLLLLLLLLIIL
11 11 A N H >5S+ 0 0 108 20 0 NNNNNNNNNNNNNNNNNNN
12 12 A F H X5S+ 0 0 128 20 0 FFFFFFFFFFFFFFFFFFF
13 13 A T H X5S+ 0 0 76 20 0 TTTTTTTTTTTTTTTTTTT
14 14 A I H XS+ 0 0 74 20 22 IIIIIIIIILLILIIILLI
21 21 A L I X>S+ 0 0 44 20 0 LLLLLLLLLLLLLLLLLLL
22 22 A M I X5S+ 0 0 126 20 32 MMMMMMMMMMMIIIIMMMI
23 23 A W I <5S+ 0 0 214 20 0 WWWWWWWWWWWWWWWWWWW
24 24 A L I X5S+ 0 0 56 20 0 LLLLLLLLLLLLLLLLLLL
25 25 A L I <