Complet list of 1lfc hssp file
Complete list of 1lfc.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1LFC
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 ANTIMICROBIAL PEPTIDE 24-JUN-98 1LFC
COMPND MOL_ID: 1; MOLECULE: LACTOFERRICIN; CHAIN: A; FRAGMENT: RESIDUES 17 -
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: BOS TAURUS; ORGANISM_COMMON: CATTLE; O
AUTHOR P.M.HWANG,N.ZHOU,X.SHAN,C.H.ARROWSMITH,H.J.VOGEL
DBREF 1LFC A 1 25 UNP P24627 TRFL_BOVIN 36 60
SEQLENGTH 25
NCHAIN 1 chain(s) in 1LFC data set
NALIGN 37
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 : A3QPC0_BOSMU 1.00 1.00 1 25 36 60 25 0 0 708 A3QPC0 Lactoferrin OS=Bos mutus grunniens PE=2 SV=1
2 : A5HLY3_BOBOX 1.00 1.00 1 25 36 60 25 0 0 708 A5HLY3 Lactoferrin OS=Bos indicus x Bos taurus PE=2 SV=1
3 : A8VTA8_BOSIN 1.00 1.00 1 25 21 45 25 0 0 54 A8VTA8 Lactoferrin (Fragment) OS=Bos indicus PE=4 SV=1
4 : A9YTV6_BOSMU 1.00 1.00 1 25 21 45 25 0 0 54 A9YTV6 Lactoferrin (Fragment) OS=Bos mutus grunniens PE=4 SV=1
5 : B2CS79_BOSMU 1.00 1.00 1 25 36 60 25 0 0 708 B2CS79 Lactoferrin OS=Bos mutus grunniens PE=2 SV=1
6 : B2CS80_BOSMU 1.00 1.00 1 25 36 60 25 0 0 708 B2CS80 Lactoferrin OS=Bos mutus grunniens PE=2 SV=1
7 : B3VTM3_BOVIN 1.00 1.00 1 25 36 60 25 0 0 708 B3VTM3 Lactoferrin OS=Bos taurus PE=2 SV=1
8 : B9VPZ5_BOVIN 1.00 1.00 1 25 36 60 25 0 0 708 B9VPZ5 Lactoferrin OS=Bos taurus GN=LF PE=2 SV=1
9 : C7FE01_BOVIN 1.00 1.00 1 25 18 42 25 0 0 690 C7FE01 Lactoferrin (Fragment) OS=Bos taurus PE=2 SV=1
10 : D0VAV0_BOSIN 1.00 1.00 1 25 36 60 25 0 0 708 D0VAV0 Lactoferrin OS=Bos indicus GN=LF PE=2 SV=1
11 : E6YCQ7_BOVIN 1.00 1.00 1 25 22 46 25 0 0 55 E6YCQ7 Lactoferrin (Fragment) OS=Bos taurus GN=lf PE=4 SV=1
12 : G1CW23_BOSIN 1.00 1.00 1 25 36 60 25 0 0 708 G1CW23 Lactoferrin OS=Bos indicus PE=2 SV=1
13 : G1CW25_BOSIN 1.00 1.00 1 25 36 60 25 0 0 708 G1CW25 Lactoferrin OS=Bos indicus PE=2 SV=1
14 : J7K1V4_BOBOX 1.00 1.00 1 25 36 60 25 0 0 708 J7K1V4 Lactoferrin OS=Bos indicus x Bos taurus PE=2 SV=1
15 : L8IBY3_9CETA 1.00 1.00 1 25 31 55 25 0 0 703 L8IBY3 Lactotransferrin (Fragment) OS=Bos mutus GN=M91_11266 PE=4 SV=1
16 : Q19KS1_BOVIN 1.00 1.00 1 25 36 60 25 0 0 352 Q19KS1 Lactoferrin (Fragment) OS=Bos taurus PE=2 SV=1
17 : Q6LBN7_BOVIN 1.00 1.00 1 25 9 33 25 0 0 681 Q6LBN7 Lactoferrin (Fragment) OS=Bos taurus PE=2 SV=1
18 : TRFL_BOVIN 1.00 1.00 1 25 36 60 25 0 0 708 P24627 Lactotransferrin OS=Bos taurus GN=LTF PE=1 SV=2
19 : B2LT73_BUBBU 0.96 1.00 2 25 22 45 24 0 0 200 B2LT73 Lactoferrin (Fragment) OS=Bubalus bubalis PE=4 SV=1
20 : A9QUB1_BUBBU 0.92 1.00 1 25 21 45 25 0 0 54 A9QUB1 Lactoferrin (Fragment) OS=Bubalus bubalis PE=4 SV=1
21 : G9DAR3_BUBBU 0.92 1.00 1 25 36 60 25 0 0 708 G9DAR3 Lactoferrin OS=Bubalus bubalis PE=2 SV=1
22 : Q0PGA5_BUBBU 0.92 1.00 2 25 7 30 24 0 0 30 Q0PGA5 Lactoferrin (Fragment) OS=Bubalus bubalis PE=1 SV=1
23 : Q19KS4_BUBBU 0.92 1.00 1 25 36 60 25 0 0 352 Q19KS4 Lactoferrin (Fragment) OS=Bubalus bubalis PE=2 SV=1
24 : TRFL_BUBBU 0.92 1.00 1 25 36 60 25 0 0 708 O77698 Lactotransferrin OS=Bubalus bubalis GN=LTF PE=1 SV=1
25 : C7DZZ8_BUBBU 0.85 0.95 6 25 1 20 20 0 0 69 C7DZZ8 Lactoferrin (Fragment) OS=Bubalus bubalis GN=LF PE=2 SV=1
26 : A3QPC1_CAPHI 0.78 0.96 2 24 37 59 23 0 0 708 A3QPC1 Lactoferrin OS=Capra hircus PE=2 SV=1
27 : B6ZCR1_CAPHI 0.78 0.96 2 24 37 59 23 0 0 708 B6ZCR1 Lactoferrin (Precursor) OS=Capra hircus GN=ltf PE=2 SV=1
28 : C6K2K5_CAPHI 0.78 0.96 2 24 40 62 23 0 0 711 C6K2K5 Lactoferrin OS=Capra hircus GN=Lf PE=2 SV=1
29 : D3G9G3_SHEEP 0.78 0.96 2 24 37 59 23 0 0 708 D3G9G3 Lactoferrin OS=Ovis aries GN=LF PE=4 SV=1
30 : Q19KS3_CAPHI 0.78 0.96 2 24 37 59 23 0 0 352 Q19KS3 Lactoferrin (Fragment) OS=Capra hircus PE=2 SV=1
31 : Q5MJE8_SHEEP 0.78 0.96 2 24 37 59 23 0 0 708 Q5MJE8 Lactoferrin OS=Ovis aries PE=1 SV=1
32 : R9QXS6_SHEEP 0.78 0.96 2 24 37 59 23 0 0 708 R9QXS6 Lactoferrin (Precursor) OS=Ovis aries PE=2 SV=1
33 : W5PFP1_SHEEP 0.78 0.96 2 24 37 59 23 0 0 708 W5PFP1 Uncharacterized protein OS=Ovis aries GN=LTF PE=4 SV=1
34 : TRFL_CAPHI 0.74 0.96 2 24 37 59 23 0 0 708 Q29477 Lactotransferrin OS=Capra hircus GN=LTF PE=1 SV=1
35 : S9XE70_9CETA 0.57 0.91 2 24 37 59 23 0 0 693 S9XE70 Lactotransferrin OS=Camelus ferus GN=CB1_008058008 PE=4 SV=1
36 : TRFL_CAMDR 0.57 0.91 2 24 37 59 23 0 0 708 Q9TUM0 Lactotransferrin OS=Camelus dromedarius GN=LTF PE=1 SV=1
37 : W6GH05_CAMDR 0.57 0.91 2 24 37 59 23 0 0 708 W6GH05 Lactoferrin OS=Camelus dromedarius PE=2 SV=1
## ALIGNMENTS 1 - 37
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A F 0 0 150 23 19 FFFFFFFFFFFFFFFFFF LL LL
2 2 A K B -A 24 0A 145 37 4 KKKKKKKKKKKKKKKKKKKKKQKK KKKKKKKKKKKK
3 3 A a - 0 0 15 37 0 CCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCC
4 4 A R S S+ 0 0 157 37 116 RRRRRRRRRRRRRRRRRRHHHHHH YYYYYYYYYAAA
5 5 A R - 0 0 171 37 59 RRRRRRRRRRRRRRRRRRRRRRRR QQQQQQQQQQQQ
6 6 A W - 0 0 123 38 0 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
7 7 A Q E -B 19 0B 132 38 0 QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
8 8 A W E -B 18 0B 154 38 5 WWWWWWWWWWWWWWWWWWWWWWWWWRRRRRRRRRRRR
9 9 A R E -B 17 0B 154 38 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
10 10 A M + 0 0 183 38 0 MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
11 11 A K - 0 0 112 38 26 KKKKKKKKKKKKKKKKKKKKKKKKKRRRRRRRRRKKK
12 12 A K S > S- 0 0 157 38 0 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
13 13 A L T 3 S- 0 0 160 38 18 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLVVV
14 14 A G T 3 S+ 0 0 90 38 48 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGRRR
15 15 A A < - 0 0 38 38 21 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGG
16 16 A P - 0 0 66 38 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
17 17 A S E -B 9 0B 37 38 4 SSSSSSSSSSSSSSSSSSSSSSSSCSSSSSSSSSSSS
18 18 A I E +B 8 0B 61 38 10 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIVVV
19 19 A T E -B 7 0B 49 38 6 TTTTTTTTTTTTTTTTTTTTTTTTSTTTTTTTTTTTT
20 20 A a + 0 0 33 38 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
21 21 A V + 0 0 57 38 5 VVVVVVVVVVVVVVVVVVVVVVVVLVVVVVVVVIVVV
22 22 A R - 0 0 113 38 18 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRKKK
23 23 A R + 0 0 188 38 18 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRKKK
24 24 A A B A 2 0A 35 38 58 AAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTT
25 25 A F 0 0 239 26 0 FFFFFFFFFFFFFFFFFFFFFFFFF
## 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 17 0 0 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.462 15 0.80
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 97 3 0 0 0 37 0 0 0.124 4 0.96
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 37 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 24 0 8 0 0 0 0 16 51 0 0 0 0 0 37 0 0 1.185 39 -0.16
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 68 0 32 0 0 0 37 0 0 0.630 21 0.40
6 6 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 38 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 68 0 0 0 0 0 0 0 0 32 0 0 0 0 0 38 0 0 0.624 20 0.95
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 38 0 0 0.000 0 1.00
10 10 A 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 76 0 0 0 0 38 0 0 0.547 18 0.73
12 12 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 38 0 0 0.000 0 1.00
13 13 A 8 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0.276 9 0.81
14 14 A 0 0 0 0 0 0 0 92 0 0 0 0 0 0 8 0 0 0 0 0 38 0 0 0.276 9 0.52
15 15 A 0 0 0 0 0 0 0 8 92 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0.276 9 0.79
16 16 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 97 0 3 0 0 0 0 0 0 0 38 0 0 0.122 4 0.96
18 18 A 8 0 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0.276 9 0.89
19 19 A 0 0 0 0 0 0 0 0 0 0 3 97 0 0 0 0 0 0 0 0 38 0 0 0.122 4 0.94
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
21 21 A 95 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0.243 8 0.95
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 8 0 0 0 0 38 0 0 0.276 9 0.81
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 8 0 0 0 0 38 0 0 0.276 9 0.81
24 24 A 0 0 0 0 0 0 0 0 68 0 0 32 0 0 0 0 0 0 0 0 38 0 0 0.624 20 0.42
25 25 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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