Complet list of 1cw5 hssp file
Complete list of 1cw5.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1CW5
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 2014-04-27
HEADER TOXIN 25-AUG-99 1CW5
COMPND MOL_ID: 1; MOLECULE: TYPE IIA BACTERIOCIN CARNOBACTERIOCIN B2; CHAIN:
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CARNOBACTERIUM MALTAROMATICUM; ORGANIS
AUTHOR Y.WANG,M.E.HENZ,N.L.F.GALLAGHER,S.CHAI,L.Z.YAN,A.C.GIBBS, M.E.STILES,D
DBREF 1CW5 A 1 48 UNP P38580 CBB2_CARPI 19 66
SEQLENGTH 48
NCHAIN 1 chain(s) in 1CW5 data set
NALIGN 33
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 : CBB2_CARML 1.00 1.00 1 48 19 66 48 0 0 66 P38580 Bacteriocin carnobacteriocin B2 OS=Carnobacterium maltaromaticum GN=cbnB2 PE=1 SV=1
2 : Q8GR37_ENTFL 0.47 0.66 2 39 32 69 38 0 0 72 Q8GR37 Uncharacterized protein OS=Enterococcus faecalis GN=orf8 PE=4 SV=1
3 : S4D7Y2_ENTFL 0.47 0.66 2 39 15 52 38 0 0 55 S4D7Y2 Putative bacteriocin carnobacteriocin BM1 (Fragment) OS=Enterococcus faecalis F01966 GN=D921_01283 PE=4 SV=1
4 : R2PMD9_ENTFC 0.46 0.73 3 39 32 68 37 0 0 71 R2PMD9 Bacteriocin enterocin-P OS=Enterococcus faecium EnGen0263 GN=UA3_02560 PE=4 SV=1
5 : B6DSR2_ENTFC 0.45 0.68 3 40 18 55 38 0 0 58 B6DSR2 MundKS OS=Enterococcus faecium GN=mundKS PE=4 SV=1
6 : B6DSR9_ENTMU 0.45 0.74 2 39 30 67 38 0 0 70 B6DSR9 EntP (Fragment) OS=Enterococcus mundtii GN=entP PE=4 SV=1
7 : D2DXK5_ENTAV 0.45 0.68 3 40 21 58 38 0 0 61 D2DXK5 Avicin A OS=Enterococcus avium GN=avcA PE=4 SV=1
8 : D4QJK6_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 D4QJK6 Enterocin P OS=Enterococcus faecium E980 GN=EfmE980_0977 PE=4 SV=1
9 : D4SN36_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 D4SN36 Enterocin P OS=Enterococcus faecium E1039 GN=EfmE1039_1851 PE=4 SV=1
10 : ETCP_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 O30434 Bacteriocin enterocin-P OS=Enterococcus faecium GN=entP PE=1 SV=1
11 : F3R8A4_ENTFL 0.45 0.66 2 39 32 69 38 0 0 72 F3R8A4 Bacteriocin enterocin-P OS=Enterococcus faecalis TX1467 GN=HMPREF9520_03246 PE=4 SV=1
12 : J6L5V8_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 J6L5V8 Bacteriocin enterocin-P OS=Enterococcus faecium 504 GN=HMPREF1347_01499 PE=4 SV=1
13 : L2N0X6_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 L2N0X6 Bacteriocin enterocin-P OS=Enterococcus faecium EnGen0039 GN=OIU_04864 PE=4 SV=1
14 : L2NY07_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 L2NY07 Bacteriocin enterocin-P OS=Enterococcus faecium EnGen0033 GN=OK9_05650 PE=4 SV=1
15 : L2PNS6_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 L2PNS6 Bacteriocin enterocin-P OS=Enterococcus faecium EnGen0043 GN=OKE_05098 PE=4 SV=1
16 : L2QXX5_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 L2QXX5 Bacteriocin enterocin-P OS=Enterococcus faecium EnGen0052 GN=OKQ_04945 PE=4 SV=1
17 : MUTI_ENTMU 0.45 0.68 3 40 3 40 38 0 0 43 P80925 Bacteriocin mundticin OS=Enterococcus mundtii PE=1 SV=1
18 : Q6SZ94_ENTMU 0.45 0.68 3 40 18 55 38 0 0 58 Q6SZ94 MundKS OS=Enterococcus mundtii GN=mundKS PE=4 SV=1
19 : Q6TGQ7_ENTMU 0.45 0.68 3 40 18 55 38 0 0 58 Q6TGQ7 Enterocin CRL35 OS=Enterococcus mundtii GN=munA PE=4 SV=1
20 : Q8RR65_ENTMU 0.45 0.68 3 40 10 47 38 0 0 50 Q8RR65 Mundticin KS OS=Enterococcus mundtii GN=munA PE=4 SV=1
21 : R1I2Z1_ENTFL 0.45 0.66 2 39 32 69 38 0 0 72 R1I2Z1 Bacteriocin carnobacteriocin BM1 OS=Enterococcus faecalis EnGen0059 GN=Q9E_00877 PE=4 SV=1
22 : R2UQ23_ENTFL 0.45 0.66 2 39 32 69 38 0 0 72 R2UQ23 Bacteriocin carnobacteriocin BM1 OS=Enterococcus faecalis EnGen0301 GN=UK1_01813 PE=4 SV=1
23 : R3JPG3_ENTFL 0.45 0.66 2 39 32 69 38 0 0 72 R3JPG3 Bacteriocin carnobacteriocin BM1 OS=Enterococcus faecalis EnGen0359 GN=WOK_02016 PE=4 SV=1
24 : R3NMB2_ENTFL 0.45 0.66 2 39 32 69 38 0 0 72 R3NMB2 Bacteriocin carnobacteriocin BM1 OS=Enterococcus faecalis EnGen0062 GN=Q95_01265 PE=4 SV=1
25 : R3P8I8_ENTFL 0.45 0.66 2 39 32 69 38 0 0 72 R3P8I8 Bacteriocin carnobacteriocin BM1 OS=Enterococcus faecalis EnGen0063 GN=Q9C_01894 PE=4 SV=1
26 : S4FNS1_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 S4FNS1 Bacteriocin enterocin-P OS=Enterococcus faecium SD2A-2 GN=D356_00215 PE=4 SV=1
27 : U2NG86_ENTFC 0.45 0.74 2 39 31 68 38 0 0 71 U2NG86 Bacteriocin OS=Enterococcus faecium CRL1879 GN=I131_10085 PE=4 SV=1
28 : V5XTD9_ENTMU 0.45 0.68 3 40 18 55 38 0 0 58 V5XTD9 Mundticin OS=Enterococcus mundtii QU 25 GN=EMQU_3203 PE=4 SV=1
29 : W7BE23_9LIST 0.45 0.71 3 40 21 58 38 0 0 61 W7BE23 PapA OS=Listeriaceae bacterium FSL S10-1188 GN=MAQA_09646 PE=4 SV=1
30 : Q8GR39_ENTFL 0.44 0.69 3 47 32 76 45 0 0 76 Q8GR39 Enterocin SE-K4 OS=Enterococcus faecalis GN=orf6 PE=4 SV=1
31 : R3FL89_ENTFL 0.44 0.69 3 47 32 76 45 0 0 76 R3FL89 Uncharacterized protein OS=Enterococcus faecalis ATCC 35038 GN=WMK_02870 PE=4 SV=1
32 : S4BPA3_ENTFL 0.44 0.69 3 47 32 76 45 0 0 76 S4BPA3 Bacteriocin hiracin-JM79 OS=Enterococcus faecalis 02-MB-BW-10 GN=D927_02919 PE=4 SV=1
33 : S4CPK4_ENTFL 0.44 0.69 3 47 15 59 45 0 0 59 S4CPK4 Bacteriocin hiracin-JM79 domain protein (Fragment) OS=Enterococcus faecalis F01966 GN=D921_02247 PE=4 SV=1
## ALIGNMENTS 1 - 33
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A V 0 0 151 2 0 V
2 2 A N + 0 0 139 21 40 NSS S SSSSSSSSS SSSSSSS
3 3 A Y + 0 0 205 34 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
4 4 A G S S- 0 0 53 34 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
5 5 A N S S+ 0 0 164 34 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
6 6 A G S S+ 0 0 70 34 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
7 7 A V S S+ 0 0 89 34 0 VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV
8 8 A S S S- 0 0 98 34 81 SYYYSYSYYYYYYYYYSSSSYYYYYYYSSYYYY
9 9 A a - 0 0 82 34 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
10 10 A S S > S+ 0 0 85 34 13 SNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
11 11 A K T 3 S- 0 0 136 34 39 KKKNKNKNNNKNNNNNKKKKKKKKKNNKKKKKK
12 12 A T T 3 S+ 0 0 145 34 81 TQQSKSKSSSQSSSSSKKKKQQQQQSSKKQQQQ
13 13 A K < - 0 0 140 34 52 KKKKGKGKKKKKKKKKGGGGKKKKKKKGKKKKK
14 14 A a + 0 0 53 34 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
15 15 A S S S- 0 0 108 34 51 SWWWSWSWWWWWWWWWSSSSWWWWWWWSSWWWW
16 16 A V - 0 0 96 34 0 VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV
17 17 A N >> - 0 0 110 34 37 NNNNDNDNNNNNNNNNDDDDNNNNNNNDDDDDD
18 18 A W H 3> S+ 0 0 214 34 0 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
19 19 A G H 3> S+ 0 0 53 34 44 GNNGGGGGGGNGGGGGGGGGNNNNNGGGGSSSS
20 20 A Q H <> S+ 0 0 123 34 69 QEEEKEKEEEEEEEEEKKKKEEEEEEEKKRRRR
21 21 A A H >X S+ 0 0 39 34 5 AAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAA
22 22 A F H 3X S+ 0 0 132 34 89 FKKKIKIKKKKKKKKKIIIIKKKKKKKIIRRRR
23 23 A Q H 3X S+ 0 0 117 34 72 QQQEGESEEEQEEEEEGGGGQQQQQEEGGSSSS
24 24 A E H << S+ 0 0 139 34 93 EQQNININNNQNNNNNIIIIQQQQQNNIIEEEE
25 25 A R H X S+ 0 0 195 34 19 RIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
26 26 A Y H X S+ 0 0 89 34 74 YAAAGAGAAAAAAAAAGGGGAAAAAAAGGIIII
27 27 A T H X S+ 0 0 45 34 60 TGGGNGNGGGGGGGGGNNNNGGGGGGGNNDDDD
28 28 A A H > S+ 0 0 54 34 101 AIIININIIIIIIIIINNNNIIIIIIINNRRRR
29 29 A G H X S+ 0 0 49 34 80 GVVVSVSVVVVVVVVVSSSSVVVVVVVSSGGGG
30 30 A I H X S+ 0 0 96 34 61 IIIIAIAIIIIIIIIIAAAAIIIIIIIAAVVVV
31 31 A N H >X S+ 0 0 97 34 75 NGGSASASSSGSSSSSAAAAGGGGGSSAAKKKK
32 32 A S H 3X S+ 0 0 79 34 61 SGGGNGNGGGGGGGGGNNNNGGGGGGGNNAAAA
33 33 A F H 3X S+ 0 0 121 34 43 FWWWLWLWWWWWWWWWLLLLWWWWWWWLLYYYY
34 34 A V H X S+ 0 0 44 34 24 GSSGGGGGGGSGGGGGGGGGSSSSSGGGGGGGG
37 37 A V H 3X S+ 0 0 73 34 84 VLLLGLGLLLLLLLLLGGGGLLLLLLLGGFFFF
38 38 A A H 3X S+ 0 0 58 34 41 AAAAAAAAAASAAAAAAAAASSSSSAAAATTTT
39 39 A S H << S+ 0 0 108 34 70 SSSGAGAGGGSGGGGGAAAASSSSSGGAAKKKK
40 40 A G H < S- 0 0 67 14 62 G G G GGGG GGVVVV
41 41 A A H < + 0 0 65 6 106 A LLLL
42 42 A G < + 0 0 26 6 0 G GGGG
43 43 A S S S+ 0 0 104 6 60 S GGGG
44 44 A I S S+ 0 0 129 6 0 I IIII
45 45 A G + 0 0 56 6 0 G GGGG
46 46 A R + 0 0 213 6 120 R GGGG
47 47 A R 0 0 192 6 0 R RRRR
48 48 A P 0 0 203 2 0 P
## 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 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 90 0 0 0 0 0 0 0 10 0 21 0 0 0.314 10 0.60
3 3 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 34 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 0 100 0 34 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
7 7 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 71 0 0 0 29 0 0 0 0 0 0 0 0 0 34 0 0 0.606 20 0.18
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 94 0 34 0 0 0.224 7 0.87
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 0 0 35 0 34 0 0 0.649 21 0.60
12 12 A 0 0 0 0 0 0 0 0 0 0 35 6 0 0 0 24 35 0 0 0 34 0 0 1.242 41 0.19
13 13 A 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 79 0 0 0 0 34 0 0 0.508 16 0.47
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 71 0 0 0 0 29 0 0 0 0 0 0 0 0 0 34 0 0 0.606 20 0.48
16 16 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 35 34 0 0 0.649 21 0.63
18 18 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 65 0 0 12 0 0 0 0 0 0 0 24 0 34 0 0 0.874 29 0.56
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 24 6 59 0 0 34 0 0 1.071 35 0.31
21 21 A 0 0 0 0 0 0 0 0 97 0 0 3 0 0 0 0 0 0 0 0 34 0 0 0.133 4 0.95
22 22 A 0 0 24 0 6 0 0 0 0 0 0 0 0 0 12 59 0 0 0 0 34 0 0 1.071 35 0.11
23 23 A 0 0 0 0 0 0 0 21 0 0 15 0 0 0 0 0 29 35 0 0 34 0 0 1.335 44 0.27
24 24 A 0 0 24 0 0 0 0 0 0 0 0 0 0 0 0 0 24 18 35 0 34 0 0 1.355 45 0.07
25 25 A 0 0 94 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 34 0 0 0.224 7 0.80
26 26 A 0 0 12 0 0 0 6 24 59 0 0 0 0 0 0 0 0 0 0 0 34 0 0 1.071 35 0.25
27 27 A 0 0 0 0 0 0 0 59 0 0 0 6 0 0 0 0 0 0 24 12 34 0 0 1.071 35 0.40
28 28 A 0 0 59 0 0 0 0 0 6 0 0 0 0 0 12 0 0 0 24 0 34 0 0 1.071 35 -0.01
29 29 A 59 0 0 0 0 0 0 18 0 0 24 0 0 0 0 0 0 0 0 0 34 0 0 0.959 32 0.19
30 30 A 12 0 65 0 0 0 0 0 24 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.874 29 0.39
31 31 A 0 0 0 0 0 0 0 24 24 0 35 0 0 0 0 12 0 0 6 0 34 0 0 1.467 48 0.24
32 32 A 0 0 0 0 0 0 0 59 12 0 6 0 0 0 0 0 0 0 24 0 34 0 0 1.071 35 0.39
33 33 A 0 24 0 0 6 59 12 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 1.071 35 0.56
34 34 A 18 0 0 0 0 0 0 0 82 0 0 0 0 0 0 0 0 0 0 0 34 0 0 0.466 15 0.62
35 35 A 0 0 0 0 0 0 0 0 0 0 65 24 0 0 0 0 0 0 12 0 34 0 0 0.874 29 0.36
36 36 A 0 0 0 0 0 0 0 76 0 0 24 0 0 0 0 0 0 0 0 0 34 0 0 0.546 18 0.76
37 37 A 6 59 0 0 12 0 0 24 0 0 0 0 0 0 0 0 0 0 0 0 34 0 0 1.071 35 0.15
38 38 A 0 0 0 0 0 0 0 0 71 0 18 12 0 0 0 0 0 0 0 0 34 0 0 0.804 26 0.58
39 39 A 0 0 0 0 0 0 0 35 24 0 29 0 0 0 0 12 0 0 0 0 34 0 0 1.320 44 0.29
40 40 A 29 0 0 0 0 0 0 71 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0.598 19 0.38
41 41 A 0 67 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.637 21 -0.07
42 42 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
43 43 A 0 0 0 0 0 0 0 67 0 0 33 0 0 0 0 0 0 0 0 0 6 0 0 0.637 21 0.40
44 44 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
45 45 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
46 46 A 0 0 0 0 0 0 0 67 0 0 0 0 0 0 33 0 0 0 0 0 6 0 0 0.637 21 -0.20
47 47 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 6 0 0 0.000 0 1.00
48 48 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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