Complet list of 1ytr hssp file
Complete list of 1ytr.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1YTR
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 2014-05-14
HEADER ANTIBIOTIC 11-FEB-05 1YTR
COMPND MOL_ID: 1; MOLECULE: BACTERIOCIN PLANTARICIN A; CHAIN: A; ENGINEERED:
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY S
AUTHOR P.E.KRISTIANSEN,G.FIMLAND,D.MANTZILAS,J.NISSEN-MEYER
DBREF 1YTR A 1 26 UNP P80214 PLNA_LACPL 23 48
SEQLENGTH 26
NCHAIN 1 chain(s) in 1YTR data set
NALIGN 11
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 : C1KBG0_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 C1KBG0 Plantaricin A OS=Lactobacillus plantarum GN=plnA PE=4 SV=1
2 : D7V8I1_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 D7V8I1 Bacteriocin plantaricin-A OS=Lactobacillus plantarum subsp. plantarum ATCC 14917 GN=plnA PE=4 SV=1
3 : E1TSU3_LACPS 1.00 1.00 1 26 23 48 26 0 0 48 E1TSU3 Plantaricin A peptide, induction factor OS=Lactobacillus plantarum (strain ST-III) GN=plnA PE=4 SV=1
4 : I6TYV4_9LACO 1.00 1.00 1 26 23 48 26 0 0 48 I6TYV4 Plantaricin A peptide OS=Lactobacillus paraplantarum GN=plnA PE=4 SV=1
5 : I6WB56_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 I6WB56 Putative plantaricin A peptide OS=Lactobacillus plantarum subsp. plantarum GN=plnA PE=4 SV=1
6 : PLNA_LACPL 1YTR 1.00 1.00 1 26 23 48 26 0 0 48 P80214 Bacteriocin plantaricin-A OS=Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) GN=plnA PE=1 SV=2
7 : Q27XH9_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 Q27XH9 Plantaricin A peptide induction factor OS=Lactobacillus plantarum GN=plnA PE=4 SV=1
8 : U2I7T4_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 U2I7T4 Bacteriocin OS=Lactobacillus plantarum 2165 GN=N574_15210 PE=4 SV=1
9 : U2WK23_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 U2WK23 Plantaricin A peptide, induction factor OS=Lactobacillus plantarum AY01 GN=N644_2223 PE=4 SV=1
10 : U6Z7F3_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 U6Z7F3 Plantaricin A peptide, induction factor OS=Lactobacillus plantarum WJL GN=LPLWJ_15910 PE=4 SV=1
11 : V8RQ23_LACPN 1.00 1.00 1 26 23 48 26 0 0 48 V8RQ23 Plantaricin A peptide, induction factor OS=Lactobacillus plantarum 4_3 GN=N654_0219 PE=4 SV=1
## ALIGNMENTS 1 - 11
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A K 0 0 222 12 0 KKKKKKKKKKK
2 2 A S - 0 0 121 12 0 SSSSSSSSSSS
3 3 A S S S+ 0 0 100 12 0 SSSSSSSSSSS
4 4 A A - 0 0 88 12 0 AAAAAAAAAAA
5 5 A Y + 0 0 167 12 0 YYYYYYYYYYY
6 6 A S - 0 0 80 12 0 SSSSSSSSSSS
7 7 A L + 0 0 172 12 0 LLLLLLLLLLL
8 8 A Q - 0 0 91 12 0 QQQQQQQQQQQ
9 9 A M S S+ 0 0 167 12 0 MMMMMMMMMMM
10 10 A G S S+ 0 0 47 12 0 GGGGGGGGGGG
11 11 A A S >> S+ 0 0 42 12 0 AAAAAAAAAAA
12 12 A T H >> S+ 0 0 74 12 0 TTTTTTTTTTT
13 13 A A H >> S+ 0 0 25 12 0 AAAAAAAAAAA
14 14 A I H X> S+ 0 0 117 12 0 IIIIIIIIIII
15 15 A K H XX S+ 0 0 115 12 0 KKKKKKKKKKK
16 16 A Q H XX S+ 0 0 87 12 0 QQQQQQQQQQQ
17 17 A V H XX S+ 0 0 57 12 0 VVVVVVVVVVV
18 18 A K H XX S+ 0 0 116 12 0 KKKKKKKKKKK
19 19 A K H << S+ 0 0 102 12 0 KKKKKKKKKKK
20 20 A L H XX S+ 0 0 53 12 0 LLLLLLLLLLL
21 21 A F H << S+ 0 0 103 12 0 FFFFFFFFFFF
22 22 A K T 3< S+ 0 0 160 12 0 KKKKKKKKKKK
23 23 A K T <4 S+ 0 0 151 12 0 KKKKKKKKKKK
24 24 A W < + 0 0 135 12 0 WWWWWWWWWWW
25 25 A G 0 0 66 12 0 GGGGGGGGGGG
26 26 A W 0 0 307 12 0 WWWWWWWWWWW
## 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 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
7 7 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 12 0 0 0.000 0 1.00
9 9 A 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
14 14 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 12 0 0 0.000 0 1.00
17 17 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
20 20 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
21 21 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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