Complet list of 1o8t hssp file
Complete list of 1o8t.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1O8T
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 LIPID TRANSPORT 29-NOV-02 1O8T
COMPND MOL_ID: 1; MOLECULE: APOLIPOPROTEIN C-II; CHAIN: A; SYNONYM: APO-CII;
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HOMO SAPIENS; ORGANISM_COMMON: HUMAN;
AUTHOR J.ZDUNEK,G.V.MARTINEZ,J.SCHLEUCHER,P.O.LYCKSELL,Y.YIN, S.NILSSON,Y.SHE
DBREF 1O8T A 1 79 UNP P02655 APC2_HUMAN 23 101
SEQLENGTH 79
NCHAIN 1 chain(s) in 1O8T data set
NALIGN 42
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 : APOC2_HUMAN 1.00 1.00 1 79 23 101 79 0 0 101 P02655 Apolipoprotein C-II OS=Homo sapiens GN=APOC2 PE=1 SV=1
2 : K7ER74_HUMAN 1.00 1.00 1 79 100 178 79 0 0 178 K7ER74 Protein APOC4-APOC2 OS=Homo sapiens GN=APOC4-APOC2 PE=4 SV=1
3 : H2R605_PANTR 0.99 0.99 1 79 23 101 79 0 0 101 H2R605 Uncharacterized protein OS=Pan troglodytes GN=APOC2 PE=4 SV=1
4 : H2NZ65_PONAB 0.90 0.97 1 79 23 101 79 0 0 101 H2NZ65 Uncharacterized protein OS=Pongo abelii GN=APOC2 PE=4 SV=1
5 : APOC2_PAPHA 0.89 0.97 1 79 23 101 79 0 0 101 P0DKY1 Apolipoprotein C-II OS=Papio hamadryas GN=APOC2 PE=3 SV=1
6 : A2V9Y5_MACFA 0.87 0.97 1 79 23 101 79 0 0 101 A2V9Y5 Putative uncharacterized protein OS=Macaca fascicularis PE=4 SV=1
7 : APOC2_COLGU 0.87 0.97 1 79 23 101 79 0 0 101 P0DKU5 Apolipoprotein C-II OS=Colobus guereza GN=APOC2 PE=3 SV=1
8 : APOC2_MACFA 0.87 0.97 1 79 23 101 79 0 0 101 P18658 Apolipoprotein C-II OS=Macaca fascicularis GN=APOC2 PE=1 SV=2
9 : G7NMB2_MACMU 0.87 0.99 1 79 23 101 79 0 0 101 G7NMB2 Uncharacterized protein OS=Macaca mulatta GN=APOC2 PE=4 SV=1
10 : G7PXV6_MACFA 0.87 0.99 1 79 23 101 79 0 0 101 G7PXV6 Putative uncharacterized protein OS=Macaca fascicularis GN=EGM_09851 PE=4 SV=1
11 : V9GYJ8_HUMAN 0.80 0.80 1 79 23 87 79 1 14 87 V9GYJ8 Apolipoprotein C-II OS=Homo sapiens GN=APOC2 PE=4 SV=1
12 : APOC2_AOTNA 0.75 0.96 1 79 23 101 79 0 0 101 P0DKV7 Apolipoprotein C-II OS=Aotus nancymaae GN=APOC2 PE=3 SV=1
13 : APOC2_CALMO 0.75 0.96 1 79 23 101 79 0 0 101 P0DKV9 Apolipoprotein C-II OS=Callicebus moloch GN=APOC2 PE=3 SV=1
14 : I3MTK2_SPETR 0.75 0.92 6 78 25 97 73 0 0 97 I3MTK2 Uncharacterized protein OS=Spermophilus tridecemlineatus GN=APOC2 PE=4 SV=1
15 : U3CZH0_CALJA 0.73 0.95 3 79 25 101 77 0 0 101 U3CZH0 Apolipoprotein C-II OS=Callithrix jacchus GN=APOC2 PE=4 SV=1
16 : APOC2_SAIBB 0.72 0.95 1 79 23 101 79 0 0 101 P0DKW0 Apolipoprotein C-II OS=Saimiri boliviensis boliviensis GN=APOC2 PE=3 SV=1
17 : L9L886_TUPCH 0.70 0.99 4 79 26 101 76 0 0 101 L9L886 Apolipoprotein C-II OS=Tupaia chinensis GN=TREES_T100011512 PE=4 SV=1
18 : APOC2_BOVIN 0.68 0.92 1 79 23 101 79 0 0 101 P19034 Apolipoprotein C-II OS=Bos taurus GN=APOC2 PE=1 SV=2
19 : APOC2_TUPGL 0.68 0.99 4 79 26 101 76 0 0 101 Q9BG58 Apolipoprotein C-II OS=Tupaia glis GN=APOC2 PE=2 SV=1
20 : G3HPD1_CRIGR 0.68 0.95 5 78 27 100 74 0 0 100 G3HPD1 Apolipoprotein C-II OS=Cricetulus griseus GN=I79_012641 PE=4 SV=1
21 : APOC2_CAVPO 0.67 0.95 20 79 41 100 60 0 0 100 P27916 Apolipoprotein C-II OS=Cavia porcellus GN=APOC2 PE=2 SV=1
22 : D2HPB4_AILME 0.67 0.89 1 79 23 101 79 0 0 101 D2HPB4 Putative uncharacterized protein (Fragment) OS=Ailuropoda melanoleuca GN=PANDA_013607 PE=4 SV=1
23 : F7A1W7_HORSE 0.67 0.88 1 78 23 100 78 0 0 101 F7A1W7 Uncharacterized protein OS=Equus caballus GN=APOC2 PE=4 SV=1
24 : M3Y458_MUSPF 0.67 0.94 1 79 23 101 79 0 0 101 M3Y458 Uncharacterized protein OS=Mustela putorius furo GN=APOC2 PE=4 SV=1
25 : G5CBM3_HETGA 0.66 0.87 1 79 23 101 79 0 0 101 G5CBM3 Apolipoprotein C-II OS=Heterocephalus glaber GN=GW7_18157 PE=4 SV=1
26 : L8ID36_9CETA 0.66 0.92 1 79 23 101 79 0 0 101 L8ID36 Apolipoprotein C-II OS=Bos mutus GN=M91_05709 PE=4 SV=1
27 : H0VEB5_CAVPO 0.65 0.94 18 79 36 97 62 0 0 97 H0VEB5 Uncharacterized protein OS=Cavia porcellus GN=Apoc2 PE=4 SV=1
28 : S7MRF2_MYOBR 0.65 0.92 1 79 23 101 79 0 0 101 S7MRF2 Apolipoprotein C-II OS=Myotis brandtii GN=D623_10006035 PE=4 SV=1
29 : D3Y264_PIG 0.63 0.90 1 79 23 101 79 0 0 101 D3Y264 Apolipoprotein C-II OS=Sus scrofa GN=APOC2 PE=4 SV=1
30 : W5PIA1_SHEEP 0.63 0.94 1 79 112 190 79 0 0 190 W5PIA1 Uncharacterized protein OS=Ovis aries GN=APOC2 PE=4 SV=1
31 : G3V8D4_RAT 0.62 0.87 2 78 21 97 77 0 0 97 G3V8D4 Apolipoprotein C-II (Predicted) OS=Rattus norvegicus GN=Apoc2 PE=4 SV=1
32 : L5M6T0_MYODS 0.61 0.86 1 79 23 101 79 0 0 101 L5M6T0 Apolipoprotein C-II OS=Myotis davidii GN=MDA_GLEAN10005802 PE=4 SV=1
33 : APOC2_CANFA 0.60 0.91 1 78 23 100 78 0 0 101 P12278 Apolipoprotein C-II OS=Canis familiaris GN=APOC2 PE=1 SV=1
34 : APOC2_MOUSE 0.60 0.82 2 78 21 97 77 0 0 97 Q05020 Apolipoprotein C-II OS=Mus musculus GN=Apoc2 PE=2 SV=1
35 : J9NWJ6_CANFA 0.60 0.91 1 78 78 155 78 0 0 156 J9NWJ6 Apolipoprotein C-II OS=Canis familiaris GN=APOC2 PE=4 SV=1
36 : M3WNX1_FELCA 0.60 0.86 2 78 24 100 77 0 0 101 M3WNX1 Uncharacterized protein OS=Felis catus GN=APOC2 PE=4 SV=1
37 : Q3UJG0_MOUSE 0.60 0.82 2 78 21 97 77 0 0 97 Q3UJG0 Apoc2 protein OS=Mus musculus GN=Apoc2 PE=4 SV=1
38 : G3TW86_LOXAF 0.55 0.83 4 79 26 101 76 0 0 101 G3TW86 Uncharacterized protein OS=Loxodonta africana GN=APOC2 PE=4 SV=1
39 : G1M234_AILME 0.52 0.77 1 62 23 84 62 0 0 92 G1M234 Uncharacterized protein OS=Ailuropoda melanoleuca GN=APOC2 PE=4 SV=1
40 : G3VHQ0_SARHA 0.47 0.84 12 79 33 100 68 0 0 100 G3VHQ0 Uncharacterized protein OS=Sarcophilus harrisii GN=APOC2 PE=4 SV=1
41 : F6PKW1_ORNAN 0.46 0.80 11 79 35 103 69 0 0 103 F6PKW1 Uncharacterized protein (Fragment) OS=Ornithorhynchus anatinus GN=APOC2 PE=4 SV=1
42 : F6PLB0_ORNAN 0.46 0.80 11 79 29 97 69 0 0 97 F6PLB0 Uncharacterized protein OS=Ornithorhynchus anatinus GN=APOC2 PE=4 SV=1
## ALIGNMENTS 1 - 42
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A T 0 0 142 28 30 TTTAAAAAAATAA A A ATATA AAA AA A A
2 2 A Q - 0 0 136 32 46 QQQPQQQQQQQHH P H HHHHH PHHQPHQHDQ H
3 3 A Q - 0 0 63 33 80 QQQPLLLLLLQLL LL V VEVLV TVVGTEGEMG V
4 4 A P - 0 0 103 36 38 PPPPPPSPPPPPP PPSPS PPPPP PPPTPSNSANPP
5 5 A Q - 0 0 40 37 19 QQQQQQQQQQQQQ QQRQRQ QQQQQ QPQEQQQQRQQQ
6 6 A Q S S+ 0 0 166 38 19 QQQQQQQQQQQQQQQQQQQQ QEQQQ QQQEQQEQQEAQ
7 7 A D S S- 0 0 38 38 8 DDDDDDDDDDDEEDEEDDDD DDDDD DDDDDDDDDDED
8 8 A E S S+ 0 0 158 38 7 EEEEEEEEEEEEEEEEEEED EEEEE EEEDEEDEEDEE
9 9 A M S S- 0 0 113 38 72 MMTLRPPPLLMSSPSSPAPP AAAPA APAPATSTASAA
10 10 A P - 0 0 101 38 64 PPPPPPPPPPPAAAAAASAG TAATS ADSGATGTTGDT
11 11 A S > - 0 0 28 40 22 SSSSSSSSSSSSGSSGSSSS SSSSS SSSSSSSSGSGS PP
12 12 A P H > S+ 0 0 96 41 52 PPPPPPPPPPPPPPPPPPPP STPPP APPSASLSPLSSPQQ
13 13 A T H > S+ 0 0 84 41 46 TTTAAAAAAATAAPAAAAAA TPAHA TAAATAAATATTGTT
14 14 A F H > S+ 0 0 51 41 6 FFFFLLLLLLFLLLLLLLLL LLLML LLLLLLLLLLFLLLL
15 15 A L H >< S+ 0 0 100 41 2 LLLLLLLLLLLLLLLLLLLF LLLLL FLLLFLLLLLLLLLL
16 16 A T H >< S+ 0 0 106 41 52 TTTTSSTSSSTTTATTATAG GTTTT STTDSTGTSGTGSSS
17 17 A Q H >X S+ 0 0 17 41 53 QQQQQRQRRRQQQQQQQQQK QKQQQ QKKTQQTQKTWQRRR
18 18 A V H S+ 0 0 133 42 30 KKKQQQQQQQKQQKQRRQRQ QQQQQLQQQQQQQQQQQQQQQ
20 20 A E H <> S+ 0 0 107 43 22 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEGEEGKESDD
21 21 A S H 3X S+ 0 0 45 43 33 SSSSSSSSSSSSSSSSSSSSTSSSTSTSSSHSSSSSSSSHTT
22 22 A L H S+ 0 0 92 43 50 TTTAAAAAAATAAAAAAAAAASTSAAATAAANSESAETSATT
32 32 A A H X S+ 0 0 58 43 32 AAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAVAAVTAKTT
33 33 A A H X S+ 0 0 57 43 6 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVAA
34 34 A Q H X S+ 0 0 125 43 44 QQQQQQQQQQQSSQSSQQQQQQQQQQQQQHGQEKEQKEQQRR
35 35 A N H X S+ 0 0 65 42 59 NNNNKKKKKK.KNGSSDKDEGGDEGKGDDKEDDDDDDGGEEE
36 36 A L H < S+ 0 0 105 42 0 LLLLLLLLLL.LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
37 37 A Y H >X S+ 0 0 151 42 0 YYYYYYYYYY.YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
38 38 A E H >X S+ 0 0 82 42 54 EEEEEEQEEE.QQEQQQKQQNEKEEKNMRKQMKQKKQQEEEE
39 39 A K H 3< S+ 0 0 97 42 16 KKKKKKKKKK.KKKKKKKKKNKKKKKNKKKKMKKKKKKKNKK
40 40 A T H <4 S+ 0 0 87 42 22 TTTTTTTTTT.TTTTTTTTTTTTTTTTTTTTTATATTTTVAA
41 41 A Y H << S+ 0 0 170 42 39 YYYYYYYYYY.YYYYYYYYYYYSYCYYYYYYYYYYYYAYHKK
42 42 A L S < S- 0 0 98 42 42 LLLLLLLLLL.LLLLLLLLLLLLLLLLLLLLLPPPLPLLINN
43 43 A P >> + 0 0 95 42 54 PPPPPPPPPP.PPNHPPPPTPNTTPPPPPPTPTITTIPNPTT
44 44 A A H 3> + 0 0 27 42 58 AAAAAAAAAA.TTDTAAAASAGTATAASTTSSTSTTSTGRGG
45 45 A V H 3> S+ 0 0 75 42 29 VVVVVVVVVV.VVMVVVVVVVMVMVVVMVVVMMMMVMVMMLL
46 46 A D H <> S+ 0 0 118 42 10 DDDDDDDDDD.DDDDDDDDDDDDDDDDDDDDDDDDDDNDDNN
47 47 A E H X S+ 0 0 102 42 9 EEEEEEEEEE.EEEEEEEEEEEEEREEEEEEKEEEEEEEEEE
48 48 A K H X S+ 0 0 137 42 19 KKKKKKKKKK.KKKKKKKRKTKKKKKTNKKKKKKKKKKKNKK
49 49 A L H X S+ 0 0 99 43 30 LLLLLLLLLLNLLILLIIILIIIIIIIFIILIILIILIILII
50 50 A R H X S+ 0 0 152 43 13 RRRRRRRRRRLRRRRRRRRRRRRRRRRRRRRRRRRRRGRRRR
51 51 A D H X S+ 0 0 94 43 12 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDEDDDDDDSHDD
52 52 A L H X S+ 0 0 124 43 41 LLLLLLLLLLLMMLMMMIMMIMMLMIIMMIMVIMIMMMAIAA
53 53 A Y H X S+ 0 0 144 43 5 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYLYYY
54 54 A S H >X S+ 0 0 63 43 20 SSSSSSSSSSSSSSSSSSSSSSSTSTSISSSSSSSSSTSGSS
55 55 A K H >X S+ 0 0 166 43 15 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKEKKKTKKLKKK
56 56 A S H 3X S+ 0 0 23 43 26 SSSSSSSSSSSSSGSSSSSSGSSSSSGNSSSSSSSSSCLGSS
57 57 A T H << S+ 0 0 101 43 34 TTTTTTTTTTTTTSTTTTTSSTTTSTSTTTSTTSTTSTASTT
58 58 A A H << S+ 0 0 73 43 17 AAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASTEAA
59 59 A A H >X S+ 0 0 46 43 5 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVAAA
60 60 A M H 3X S+ 0 0 107 43 39 MMMMMMMMMMMMMMVVVVVMIVVVIVIVVVMVVMVVMAVMMM
61 61 A S H 3> S+ 0 0 84 43 46 SSSSSSSSSSSSSSSSTTTSSSSSRTSTTTTSSSSRSTTTTT
62 62 A T H <> S+ 0 0 80 43 13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTITTTTTTITTSTTT
63 63 A Y H X S+ 0 0 159 42 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY YYY
64 64 A T H X S+ 0 0 72 42 45 TTTTTTTTTTTAAAAAAAAATAAATATAAAAAAAATAL TTT
65 65 A G H X S+ 0 0 38 42 6 GGGGGGGGGGGGGGGGGGGGGEEGGGGGGGGGGGGGGG GGG
66 66 A I H >X S+ 0 0 94 42 0 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII III
67 67 A F H 3X S+ 0 0 151 42 15 FFFFFFFFFFFLLFLFFIFFLFLFFILFFIFFFFFLFL LLL
68 68 A T H 3X S+ 0 0 56 42 3 TTTTTTTTTTTTTTTTTTTTTTTSTTTTTTTTTTTTTT TTT
69 69 A D H X S+ 0 0 67 42 29 VVVVVVVVVVVVVLLVLVLLILFLIVIVVVLVLLLILI III
72 72 A L H >X S+ 0 0 105 42 20 LLLLLLLLLLLLLLLLFFFFLLLLLFLLLFLLLLLLLV IYY
73 73 A S H >X S+ 0 0 46 42 52 SSSSSSSSSSSSSTSSSSSTTSSSTSTSSSTHSTSSTS HHH
74 74 A V H