Complet list of 1nh4 hssp file
Complete list of 1nh4.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1NH4
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 2014-05-04
HEADER VIRUS 18-DEC-02 1NH4
COMPND MOL_ID: 1; MOLECULE: MAJOR COAT PROTEIN; CHAIN: A; MUTATION: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE FD; ORGANISM_TAXI
AUTHOR A.C.ZERI,M.F.MESLEH,A.A.NEVZOROV,S.J.OPELLA
DBREF 1NH4 A 1 50 UNP Q9T0Q9 Q9T0Q9_BPFD 1 50
SEQLENGTH 42
NCHAIN 1 chain(s) in 1NH4 data set
NALIGN 61
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 : CAPSD_BPF1 0.98 0.98 1 42 30 71 42 0 0 73 P69540 Capsid protein G8P OS=Enterobacteria phage f1 GN=VIII PE=1 SV=1
2 : CAPSD_BPFD 1MZT 0.98 0.98 1 42 30 71 42 0 0 73 P69539 Capsid protein G8P OS=Enterobacteria phage fd GN=VIII PE=1 SV=1
3 : D0U160_BPF1 0.98 0.98 1 42 30 71 42 0 0 73 D0U160 VIII OS=Enterobacteria phage f1 GN=VIII PE=4 SV=1
4 : Q9T0Q9_BPFD 1NH4 0.98 0.98 1 42 7 48 42 0 0 50 Q9T0Q9 Gene-8 protein, G8P=MAJOR coat protein OS=Enterobacteria phage fd PE=1 SV=1
5 : Q38211_BPF1 0.97 0.97 1 36 30 65 36 0 0 65 Q38211 Bacteriophage F1 and amber mutant M13-8H1, gene VIII, 5' end. (Precursor) OS=Enterobacteria phage f1 PE=4 SV=1
6 : A7BJW7_BPF1 0.95 0.95 1 42 30 71 42 0 0 73 A7BJW7 Protein VIII OS=Enterobacteria phage f1 GN=VIII PE=4 SV=1
7 : A7BJX7_BPF1 0.95 0.95 1 42 30 71 42 0 0 73 A7BJX7 Protein VIII OS=Enterobacteria phage f1 GN=VIII PE=4 SV=1
8 : CAPSD_BPM13 2CPB 0.95 0.98 1 42 30 71 42 0 0 73 P69541 Capsid protein G8P OS=Enterobacteria phage M13 GN=VIII PE=1 SV=1
9 : CAPSD_BPZJ2 0.95 0.98 1 42 7 48 42 0 0 50 P03618 Capsid protein G8P OS=Enterobacteria phage ZJ/2 GN=VIII PE=1 SV=1
10 : D0U170_BPF1 0.95 0.98 1 42 30 71 42 0 0 73 D0U170 VIII OS=Enterobacteria phage f1 GN=VIII PE=4 SV=1
11 : J7I0P6_BPM13 0.95 0.98 1 42 30 71 42 0 0 73 J7I0P6 Major coat protein OS=Enterobacteria phage M13 GN=VIII PE=4 SV=1
12 : CAPSD_BPIF1 1IFK 0.79 0.90 1 42 31 72 42 0 0 74 P03619 Capsid protein G8P OS=Enterobacteria phage If1 GN=VIII PE=1 SV=2
13 : R8UTJ9_9ENTR 0.79 0.90 1 42 31 72 42 0 0 74 R8UTJ9 Capsid protein G8P OS=Citrobacter sp. KTE32 GN=WEU_04652 PE=4 SV=1
14 : D2U3R5_9ENTR 0.54 0.77 4 42 18 56 39 0 0 58 D2U3R5 Putative uncharacterized protein OS=Arsenophonus nasoniae GN=ARN_33020 PE=4 SV=1
15 : Q1Z2M5_PHOPR 0.52 0.74 1 42 34 75 42 0 0 77 Q1Z2M5 Uncharacterized protein OS=Photobacterium profundum 3TCK GN=P3TCK_08566 PE=4 SV=1
16 : Q1Z9G9_PHOPR 0.52 0.74 1 42 34 75 42 0 0 77 Q1Z9G9 Uncharacterized protein OS=Photobacterium profundum 3TCK GN=P3TCK_19935 PE=4 SV=1
17 : L4KXB1_ECOLX 0.50 0.76 1 42 37 78 42 0 0 80 L4KXB1 Uncharacterized protein OS=Escherichia coli KTE192 GN=A13U_01911 PE=4 SV=1
18 : L4UFI9_ECOLX 0.50 0.76 1 42 37 78 42 0 0 80 L4UFI9 Uncharacterized protein OS=Escherichia coli KTE109 GN=WIA_04448 PE=4 SV=1
19 : B3HXZ5_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 B3HXZ5 Coat protein B OS=Escherichia coli F11 GN=EcF11_4854 PE=4 SV=1
20 : D8BBY2_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 D8BBY2 Phage major coat protein, Gp8 OS=Escherichia coli MS 200-1 GN=HMPREF9553_00470 PE=4 SV=1
21 : E1S287_ECOUM 0.48 0.76 1 42 37 78 42 0 0 80 E1S287 Uncharacterized protein OS=Escherichia coli (strain UM146) GN=UM146_09465 PE=4 SV=1
22 : E9TNQ4_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 E9TNQ4 Phage major coat protein, Gp8 OS=Escherichia coli MS 60-1 GN=HMPREF9533_00002 PE=4 SV=1
23 : F0KSK7_YERE3 0.48 0.76 1 42 37 78 42 0 0 80 F0KSK7 Coat protein B OS=Yersinia enterocolitica subsp. palearctica serotype O:9 / biotype 3 (strain 105.5R(r)) GN=YE105_C2156 PE=4 SV=1
24 : F4N6M3_YEREN 0.48 0.76 1 42 37 78 42 0 0 80 F4N6M3 Capsid protein G8P OS=Yersinia enterocolitica W22703 GN=VIII PE=4 SV=1
25 : G9UD57_SALMO 0.48 0.76 1 42 37 78 42 0 0 80 G9UD57 Uncharacterized protein OS=Salmonella enterica subsp. enterica serovar Montevideo str. SARB30 GN=SEEM030_18899 PE=4 SV=1
26 : I4T142_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 I4T142 Uncharacterized protein OS=Escherichia coli 541-15 GN=EC54115_07707 PE=4 SV=1
27 : L3DQ15_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 L3DQ15 Uncharacterized protein OS=Escherichia coli KTE206 GN=A15M_01727 PE=4 SV=1
28 : L4QUF1_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 L4QUF1 Uncharacterized protein OS=Escherichia coli KTE215 GN=A175_04714 PE=4 SV=1
29 : L4YAV4_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 L4YAV4 Uncharacterized protein OS=Escherichia coli KTE131 GN=WIU_04681 PE=4 SV=1
30 : L4ZX73_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 L4ZX73 Uncharacterized protein OS=Escherichia coli KTE145 GN=WK5_04654 PE=4 SV=1
31 : L6YUM1_SALEN 0.48 0.76 1 42 37 78 42 0 0 80 L6YUM1 Coat protein B OS=Salmonella enterica subsp. enterica serovar Enteritidis str. 81-2625 GN=SEEE2625_18953 PE=4 SV=1
32 : M8SUX6_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 M8SUX6 Capsid protein G8P OS=Escherichia coli 2872000 GN=EC2872000_1771 PE=4 SV=1
33 : M8T8W9_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 M8T8W9 Capsid protein G8P OS=Escherichia coli 2871950 GN=EC2871950_1646 PE=4 SV=1
34 : N1AP57_SALET 0.48 0.76 1 42 37 78 42 0 0 80 N1AP57 Coat protein B OS=Salmonella enterica subsp. enterica serovar Agona str. 15.H.03 GN=SA15_4636 PE=4 SV=1
35 : N2E758_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 N2E758 Capsid protein G8P OS=Escherichia coli 2846750 GN=EC2846750_1459 PE=4 SV=1
36 : S1V122_KLEPN 0.48 0.76 1 42 37 78 42 0 0 80 S1V122 Phage major coat protein, Gp8 OS=Klebsiella pneumoniae UHKPC81 GN=H232_0512 PE=4 SV=1
37 : T6DZG4_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T6DZG4 Uncharacterized protein OS=Escherichia coli HVH 56 (4-2153033) GN=G728_01402 PE=4 SV=1
38 : T6NXN3_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T6NXN3 Uncharacterized protein OS=Escherichia coli HVH 100 (4-2850729) GN=G761_04629 PE=4 SV=1
39 : T6SUQ3_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T6SUQ3 Uncharacterized protein OS=Escherichia coli HVH 112 (4-5987253) GN=G773_04746 PE=4 SV=1
40 : T7P632_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T7P632 Uncharacterized protein OS=Escherichia coli HVH 185 (4-2876639) GN=G837_01484 PE=4 SV=1
41 : T8EDV1_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T8EDV1 Uncharacterized protein OS=Escherichia coli KOEGE 30 (63a) GN=G881_01479 PE=4 SV=1
42 : T8HSY1_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T8HSY1 Uncharacterized protein OS=Escherichia coli KOEGE 70 (185a) GN=G892_01406 PE=4 SV=1
43 : T8QJF9_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T8QJF9 Uncharacterized protein OS=Escherichia coli UMEA 3113-1 GN=G909_01488 PE=4 SV=1
44 : T9KX77_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T9KX77 Uncharacterized protein OS=Escherichia coli UMEA 3490-1 GN=G976_04870 PE=4 SV=1
45 : T9LSI9_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 T9LSI9 Uncharacterized protein OS=Escherichia coli UMEA 3617-1 GN=G980_01531 PE=4 SV=1
46 : V0UUN9_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 V0UUN9 Phage major coat protein, Gp8 OS=Escherichia coli 907710 GN=HMPREF1598_00807 PE=4 SV=1
47 : V1D241_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 V1D241 Phage major coat protein, Gp8 OS=Escherichia coli A35218R GN=HMPREF1622_00923 PE=4 SV=1
48 : V2RIA3_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 V2RIA3 Uncharacterized protein OS=Escherichia coli UMEA 3290-1 GN=G959_04714 PE=4 SV=1
49 : V2S0W4_ECOLX 0.48 0.76 1 42 37 78 42 0 0 80 V2S0W4 Uncharacterized protein OS=Escherichia coli UMEA 3426-1 GN=G974_01712 PE=4 SV=1
50 : V7QD36_SALET 0.48 0.76 1 42 37 78 42 0 0 80 V7QD36 Capsid protein OS=Salmonella enterica subsp. enterica serovar Cerro str. CFSAN001691 GN=CFSAN001691_22650 PE=4 SV=1
51 : V7R433_SALET 0.48 0.76 1 42 37 78 42 0 0 80 V7R433 Capsid protein OS=Salmonella enterica subsp. enterica serovar Cerro str. CFSAN001690 GN=CFSAN001690_22615 PE=4 SV=1
52 : V7SBK1_SALET 0.48 0.76 1 42 37 78 42 0 0 80 V7SBK1 Capsid protein OS=Salmonella enterica subsp. enterica serovar Cerro str. CFSAN001692 GN=CFSAN001692_22620 PE=4 SV=1
53 : V7T744_SALET 0.48 0.76 1 42 37 78 42 0 0 80 V7T744 Capsid protein OS=Salmonella enterica subsp. enterica serovar Cerro str. CFSAN001697 GN=CFSAN001697_22635 PE=4 SV=1
54 : V7VU65_SALET 0.48 0.76 1 42 37 78 42 0 0 80 V7VU65 Capsid protein OS=Salmonella enterica subsp. enterica serovar Cerro str. CFSAN001587 GN=CFSAN001587_22880 PE=4 SV=1
55 : V7YKX0_SALET 0.48 0.76 1 42 37 78 42 0 0 80 V7YKX0 Capsid protein OS=Salmonella enterica subsp. enterica serovar Cerro str. 5569 GN=SEEC5569_17025 PE=4 SV=1
56 : CAPSD_BPIKE 1IFL 0.45 0.74 1 42 39 80 42 0 0 82 P03620 Capsid protein G8P OS=Enterobacteria phage IKe GN=VIII PE=1 SV=1
57 : Q9T0Q8_BPIKE 0.45 0.71 1 42 10 51 42 0 0 53 Q9T0Q8 Gene-8 protein, G8P=MAJOR coat protein OS=Enterobacteria phage IKe PE=1 SV=1
58 : CAPSD_BPI22 0.43 0.76 1 42 41 82 42 0 0 84 P15416 Capsid protein G8P OS=Enterobacteria phage I2-2 GN=VIII PE=3 SV=1
59 : F9S7V9_9VIBR 0.43 0.76 1 42 30 71 42 0 0 73 F9S7V9 Uncharacterized protein OS=Vibrio ichthyoenteri ATCC 700023 GN=VII00023_20732 PE=4 SV=1
60 : K8W5V2_9ENTR 0.43 0.79 1 42 36 77 42 0 0 78 K8W5V2 Uncharacterized protein OS=Providencia sneebia DSM 19967 GN=OO7_16330 PE=4 SV=1
61 : U4ZPR2_9VIBR 0.43 0.76 1 42 35 76 42 0 0 78 U4ZPR2 Uncharacterized protein OS=Vibrio cyclitrophicus FF75 GN=M565_ctg5P0626 PE=4 SV=1
## ALIGNMENTS 1 - 61
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 7 A A > 0 0 115 61 0 AAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2 8 A K H > + 0 0 184 61 89 KKKKKKKKKKKKK AAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTTEQE
3 9 A A H > S+ 0 0 70 61 74 AAAAAAAAAAAAA AAQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQEEEADA
4 10 A A H > S+ 0 0 66 62 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5 11 A F H X S+ 0 0 153 62 59 FFFFFFFFFFFFFMFFMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMFIA
6 12 A D H X S+ 0 0 96 62 32 DDDDDDDNDDNDDDTTDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDNTTT
7 13 A S H X S+ 0 0 66 62 51 SSSSSSSSSSSSSSAASSAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASSSASA
8 14 A L H X S+ 0 0 115 62 12 LLLLLLLLLLLLLLVVLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLVIM
9 15 A Q H X S+ 0 0 104 62 106 QQQQQQQQQQQTTLGGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLKKKSGT
10 16 A A H X S+ 0 0 33 62 54 AAAAAAAAATAAATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTET
11 17 A S H X S+ 0 0 64 62 78 SSSSSSSSSSSQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQFTA
12 18 A A H X S+ 0 0 59 62 10 AAAAAAAAAAAAAAVVAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13 19 A T H X S+ 0 0 75 62 74 TTTTTTNTTTTTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNIITTTT
14 20 A E H X S+ 0 0 123 62 28 EEEEEEEEEEEEETEEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDGD
15 21 A M H >X S+ 0 0 122 62 57 YYYYYYYYYYYMMLYYLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLVMY
16 22 A I H 3X S+ 0 0 115 62 24 IIIIIIIIIIISSIEEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
17 23 A G H 3X S+ 0 0 38 62 19 GGGGGGGGGGGGGGGGAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGSSDADA
18 24 A Y H S+ 0 0 67 62 4 VVVVVVVVVVVVVVIIVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIV
24 30 A V I X>S+ 0 0 57 62 33 VVVVVVVVVVVVVVLLVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVTTTTAP
25 31 A V I X>S+ 0 0 81 62 78 VVVVVVVVVVVLLAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTSLLI
26 32 A I I <>S+ 0 0 73 62 18 IIIIIIIIIIIVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVLVV
27 33 A V I <5S+ 0 0 67 62 19 VVVVVVVVVVVVVVTTVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVATVV
28 34 A G I XX S+ 0 0 100 62 4 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIMII
34 40 A K H >X S+ 0 0 145 62 38 KKKKKKKKKKKKKRKKRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRKRKKK
35 41 A L H 3X>S+ 0 0 96 62 36 LLLLLLLLLLLLLLLLLLIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIILLLLLL
36 42 A F H