Complet list of 2gwp hssp file
Complete list of 2gwp.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2GWP
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 2014-05-19
HEADER ANTIBIOTIC 05-MAY-06 2GWP
COMPND MOL_ID: 1; MOLECULE: DEFENSIN-RELATED CRYPTDIN 4; CHAIN: A; FRAGMENT:
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: MUS MUSCULUS; ORGANISM_COMMON: HOUSE M
AUTHOR K.J.ROSENGREN,D.J.CRAIK,H.J.VOGEL,N.L.DALY,A.J.OUELLETTE
DBREF 2GWP A 1 32 UNP P28311 DEF4_MOUSE 61 92
SEQLENGTH 32
NCHAIN 1 chain(s) in 2GWP data set
NALIGN 14
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 : DEFA4_MOUSE 2LEY 0.97 1.00 1 32 61 92 32 0 0 92 P28311 Alpha-defensin 4 OS=Mus musculus GN=Defa4 PE=1 SV=4
2 : DFA20_MOUSE 0.62 0.88 1 32 61 92 32 0 0 95 Q45VN2 Alpha-defensin 20 OS=Mus musculus GN=Defa20 PE=2 SV=2
3 : Q8C1N9_MOUSE 0.62 0.88 1 32 61 92 32 0 0 95 Q8C1N9 Alpha-defensin 2 OS=Mus musculus GN=Defcr20 PE=4 SV=1
4 : Q8C1P0_MOUSE 0.62 0.84 1 32 61 92 32 0 0 95 Q8C1P0 Putative uncharacterized protein OS=Mus musculus PE=4 SV=1
5 : DFA22_MOUSE 0.53 0.72 1 32 61 92 32 0 0 93 Q8C1N8 Alpha-defensin 22 OS=Mus musculus GN=Defa22 PE=2 SV=1
6 : W4VSN6_MOUSE 0.53 0.72 1 32 61 92 32 0 0 93 W4VSN6 Alpha-defensin 22 OS=Mus musculus GN=Defa22 PE=4 SV=1
7 : D3Z0J0_MOUSE 0.50 0.66 2 30 62 93 32 1 3 93 D3Z0J0 Protein Gm15315 OS=Mus musculus GN=Gm15315 PE=4 SV=1
8 : DEFA5_MOUSE 0.50 0.66 2 30 62 93 32 1 3 93 P28312 Alpha-defensin 5 OS=Mus musculus GN=Defa5 PE=1 SV=2
9 : DFA21_MOUSE 0.50 0.72 1 32 61 92 32 0 0 93 Q8C1P2 Alpha-defensin 21 OS=Mus musculus GN=Defa21 PE=3 SV=1
10 : E9QLQ1_MOUSE 0.50 0.66 2 30 62 93 32 1 3 93 E9QLQ1 Protein Gm10104 OS=Mus musculus GN=Gm10104 PE=4 SV=1
11 : K9J724_MOUSE 0.50 0.66 2 30 62 93 32 1 3 93 K9J724 Protein Gm14850 OS=Mus musculus GN=Gm21498 PE=4 SV=1
12 : L7N230_MOUSE 0.50 0.66 2 30 62 93 32 1 3 93 L7N230 Alpha-defensin 5 OS=Mus musculus GN=Defa5 PE=4 SV=1
13 : Q0VDM0_MOUSE 0.50 0.66 2 30 60 91 32 1 3 91 Q0VDM0 Defcr5 protein (Fragment) OS=Mus musculus GN=Defa5 PE=2 SV=1
14 : H0XSF6_OTOGA 0.47 0.56 2 30 70 101 32 1 3 101 H0XSF6 Uncharacterized protein OS=Otolemur garnettii GN=DEFA6 PE=4 SV=1
## ALIGNMENTS 1 - 14
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 33 8 34 GDDDDD D
2 2 A L + 0 0 169 15 0 LLLLLLLLLLLLLL
3 3 A L S S- 0 0 147 15 33 LIIIIIIIIIIIIS
4 4 A a - 0 0 17 15 0 CCCCCCCCCCCCCC
5 5 A Y E -A 28 0A 72 15 34 YYYYLLYYLYYYYY
6 6 A b E +A 27 0A 58 15 0 CCCCCCCCCCCCCC
7 7 A R E -A 26 0A 102 15 0 RRRRRRRRRRRRRR
8 8 A K E S+A 25 0A 140 15 88 KKKKKKIINIIIIR
9 9 A G S S- 0 0 40 15 76 GGGGRRRRRRRRRG
10 10 A H S S- 0 0 123 15 79 HGGGRRGGRGGGGS
11 11 A c - 0 0 20 15 0 CCCCCCCCCCCCCC
12 12 A K > - 0 0 100 15 61 KNNNNNKKNKKKKP
13 13 A R T 3 S+ 0 0 235 15 0 RRRRRRRRRRRRRR
14 14 A G T 3 S+ 0 0 25 15 86 GGGGGGRRGRRRRP
15 15 A D < - 0 0 21 15 5 EEEEEEEEEEEEEE
16 16 A R E -B 29 0A 114 15 75 RQQQLLRRLRRRRR
17 17 A V E +B 28 0A 96 15 51 VVVVFFVVFVVVVT
18 18 A R E - 0 0A 175 15 45 RYYYYYFFYFFFFY
19 19 A G E -B 27 0A 29 15 0 GGGGGGGGGGGGGG
20 20 A T E -B 26 0A 124 15 0 TTTTTTTTTTTTTT
21 21 A b E - 0 0A 63 15 0 CCCCCCCCCCCCCC
22 22 A G E > S-B 25 0A 44 15 95 GSSSAARRARRRRT
23 23 A I T 3 S- 0 0 157 15 81 IGGGGGnnGnnnns
24 24 A R T 3 S+ 0 0 190 15 81 RRRRPPttPttttr
25 25 A F E < -AB 8 22A 77 15 10 FLLLFFFFFFFFFY
26 26 A L E -AB 7 20A 45 15 46 LLLLLLVVLVVVVT
27 27 A Y E +AB 6 19A 97 15 66 YFFLRRFFRFFFFL
28 28 A c E -AB 5 17A 0 15 0 CCCCCCCCCCCCCC
29 29 A a E - B 0 16A 4 15 0 CCCCCCCCCCCCCC
30 30 A P - 0 0 22 15 73 PRRRRRSSRSSSSR
31 31 A R 0 0 155 8 0 RRRRRR R
32 32 A R 0 0 238 8 0 RRRRRR R
## 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 25 0 0 0 0 0 0 0 0 0 0 0 75 8 0 0 0.562 18 0.66
2 2 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
3 3 A 0 13 80 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 15 0 0 0.628 20 0.66
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
5 5 A 0 20 0 0 0 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.500 16 0.65
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 15 0 0 0.000 0 1.00
8 8 A 0 0 40 0 0 0 0 0 0 0 0 0 0 0 7 47 0 0 7 0 15 0 0 1.083 36 0.12
9 9 A 0 0 0 0 0 0 0 40 0 0 0 0 0 0 60 0 0 0 0 0 15 0 0 0.673 22 0.24
10 10 A 0 0 0 0 0 0 0 60 0 0 7 0 0 13 20 0 0 0 0 0 15 0 0 1.078 35 0.20
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 53 0 0 40 0 15 0 0 0.882 29 0.38
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 15 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 53 0 7 0 0 0 0 40 0 0 0 0 0 15 0 0 0.882 29 0.13
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 0 7 15 0 0 0.245 8 0.95
16 16 A 0 20 0 0 0 0 0 0 0 0 0 0 0 0 60 0 20 0 0 0 15 0 0 0.950 31 0.24
17 17 A 73 0 0 0 20 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 15 0 0 0.730 24 0.48
18 18 A 0 0 0 0 40 0 47 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 0.991 33 0.55
19 19 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 13 20 0 20 7 0 0 40 0 0 0 0 0 15 0 0 1.459 48 0.04
23 23 A 0 0 13 0 0 0 0 40 0 0 7 0 0 0 0 0 0 0 40 0 15 0 7 1.182 39 0.19
24 24 A 0 0 0 0 0 0 0 0 0 20 0 40 0 0 40 0 0 0 0 0 15 0 0 1.055 35 0.18
25 25 A 0 20 0 0 73 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.730 24 0.89
26 26 A 40 53 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 15 0 0 0.882 29 0.54
27 27 A 0 13 0 0 53 0 13 0 0 0 0 0 0 0 20 0 0 0 0 0 15 0 0 1.194 39 0.34
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 13 40 0 0 0 47 0 0 0 0 0 15 0 0 0.991 33 0.26
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 8 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 8 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
7 23 84 3 nLFLt
8 23 84 3 nLFLt
10 23 84 3 nLFLt
11 23 84 3 nLFLt
12 23 84 3 nLFLt
13 23 82 3 nLFLt
14 23 92 3 sGGLr
//