Complet list of 1vg5 hssp file
Complete list of 1vg5.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1VG5
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 2014-05-11
HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-APR-04 1VG5
COMPND MOL_ID: 1; MOLECULE: RHOMBOID FAMILY PROTEIN; CHAIN: A; FRAGMENT: UBA
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; ORGANISM_COMMON:
AUTHOR H.ONUKI,Y.DOI-KATAYAMA,F.HAYASHI,H.HIROTA,S.YOKOYAMA,RIKEN STRUCTURAL
DBREF 1VG5 A 8 67 UNP Q8LB17 Y3846_ARATH 342 401
SEQLENGTH 73
NCHAIN 1 chain(s) in 1VG5 data set
NALIGN 12
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 : F4J5V3_ARATH 0.95 0.98 7 69 364 426 63 0 0 426 F4J5V3 Rhomboid-like protein 15 OS=Arabidopsis thaliana GN=RBL15 PE=4 SV=1
2 : Y3846_ARATH 1VG5 0.95 0.98 7 69 341 403 63 0 0 403 Q8LB17 Uncharacterized protein At3g58460 OS=Arabidopsis thaliana GN=At3g58460 PE=1 SV=2
3 : R0FNT0_9BRAS 0.93 0.97 9 69 343 403 61 0 0 403 R0FNT0 Uncharacterized protein OS=Capsella rubella GN=CARUB_v10017375mg PE=4 SV=1
4 : D7LW43_ARALL 0.92 0.97 8 68 342 402 61 0 0 403 D7LW43 Rhomboid family protein OS=Arabidopsis lyrata subsp. lyrata GN=ARALYDRAFT_324326 PE=4 SV=1
5 : M4CT52_BRARP 0.89 0.94 7 68 345 406 62 0 0 417 M4CT52 Uncharacterized protein OS=Brassica rapa subsp. pekinensis GN=BRA007394 PE=4 SV=1
6 : V4LKH9_THESL 0.85 0.94 7 68 344 405 62 0 0 406 V4LKH9 Uncharacterized protein OS=Thellungiella salsuginea GN=EUTSA_v10006012mg PE=4 SV=1
7 : G8A188_MEDTR 0.64 0.77 14 69 348 403 56 0 0 403 G8A188 Putative uncharacterized protein OS=Medicago truncatula GN=MTR_118s0012 PE=4 SV=1
8 : I3T571_LOTJA 0.62 0.79 2 69 53 119 68 1 1 119 I3T571 Uncharacterized protein OS=Lotus japonicus PE=4 SV=1
9 : B9H9X7_POPTR 0.58 0.79 4 69 345 410 66 0 0 410 B9H9X7 Rhomboid family protein OS=Populus trichocarpa GN=POPTR_0006s21220g PE=4 SV=1
10 : V7CXV0_PHAVU 0.56 0.68 7 69 350 412 63 0 0 412 V7CXV0 Uncharacterized protein OS=Phaseolus vulgaris GN=PHAVU_001G199900g PE=4 SV=1
11 : V4SR96_9ROSI 0.52 0.68 3 67 339 403 65 0 0 404 V4SR96 Uncharacterized protein OS=Citrus clementina GN=CICLE_v10011870mg PE=4 SV=1
12 : V4T160_9ROSI 0.52 0.68 3 67 339 403 65 0 0 408 V4T160 Uncharacterized protein OS=Citrus clementina GN=CICLE_v10011870mg PE=4 SV=1
## ALIGNMENTS 1 - 12
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 141 1 0
2 2 A S - 0 0 119 2 73 P
3 3 A S - 0 0 124 4 0 S SS
4 4 A G + 0 0 52 5 45 EG DD
5 5 A S + 0 0 124 5 87 GR EE
6 6 A S + 0 0 134 5 45 RR RR
7 7 A G + 0 0 59 10 73 DD AA HSGQQ
8 8 A S + 0 0 129 11 79 SS SAA AVRPP
9 9 A R + 0 0 229 12 96 RRRRRR VVHAA
10 10 A Q + 0 0 202 12 83 QQQQQQ DDSLL
11 11 A A - 0 0 74 12 74 AAVVVV NNAGG
12 12 A P + 0 0 139 12 70 PPPPPP AADTT
13 13 A I + 0 0 141 12 76 IIIIII AVSAA
14 14 A A S S- 0 0 95 13 62 AAAAAAATGVVV
15 15 A N - 0 0 102 13 67 NNNNNNTAAAAA
16 16 A A - 0 0 80 13 63 AAAAAATATTVV
17 17 A A - 0 0 100 13 49 AAAAAAGAPADD
18 18 A V - 0 0 81 13 82 VVVVVVAGVTRR
19 19 A L - 0 0 135 13 81 LLLLLQAVHGVV
20 20 A P S S+ 0 0 108 13 32 PPPPPPVPPVPP
21 21 A Q S S+ 0 0 179 13 69 QQQQPQPHAPAA
22 22 A S S S+ 0 0 124 13 87 SSSTSPHHLPGG
23 23 A Q + 0 0 160 13 26 QQQQQQHQHHQQ
24 24 A G + 0 0 71 13 66 GGGGGGEAQQQQ
25 25 A R - 0 0 223 12 91 RRRRRRG.DGGG
26 26 A V S S+ 0 0 128 13 71 VVVVVVAASAAA
27 27 A A + 0 0 29 13 58 AAATAAVAAVVV
28 28 A A - 0 0 38 13 69 AAAAAGVVPVVV
29 29 A S > - 0 0 53 13 17 SSPPSSSSSSSS
30 30 A E H > S+ 0 0 129 13 13 EEEEEEEEEEDD
31 31 A E H > S+ 0 0 128 13 0 EEEEEEEEEEEE
32 32 A Q H > S+ 0 0 22 13 45 QQQQQQEEQGEE
33 33 A I H X S+ 0 0 4 13 0 IIIIIIIIIIII
34 34 A Q H X S+ 0 0 86 13 42 QQQQQQKKQTQQ
35 35 A K H < S+ 0 0 111 13 0 KKKKKKKKKKKK
36 36 A L H X>S+ 0 0 2 13 0 LLLLLLLLLLLL
37 37 A V H <5S+ 0 0 49 13 22 VVVVVVIVVAVV
38 38 A A T <5S+ 0 0 84 13 46 AAAAAAAASSSS
39 39 A M T 45S- 0 0 122 13 0 MMMMMMMMMMMM
40 40 A G T <5S+ 0 0 66 13 0 GGGGGGGGGGGG
41 41 A F < - 0 0 34 13 0 FFFFFFFFFFFF
42 42 A D > - 0 0 100 13 4 DDDDEDDDDDDD
43 43 A R H > S+ 0 0 126 13 24 RRRRRRRRKRKK
44 44 A T H > S+ 0 0 85 13 0 TTTTTTTTTTTT
45 45 A Q H > S+ 0 0 65 13 0 QQQQQQQQQQQQ
46 46 A V H X S+ 0 0 0 13 0 VVVVVVVVVVVV
47 47 A E H X S+ 0 0 67 13 0 EEEEEEEEEEEE
48 48 A V H X S+ 0 0 85 13 0 VVVVVVVVVVVV
49 49 A A H X S+ 0 0 1 13 0 AAAAAAAAAAAA
50 50 A L H X>S+ 0 0 1 13 9 LLLLLLLLILLL
51 51 A A H ><5S+ 0 0 67 13 14 AAAAAAAASAAA
52 52 A A H 3<5S+ 0 0 40 13 0 AAAAAAAAAAAA
53 53 A A H 3<5S- 0 0 6 13 7 AAAAAGAAAAAA
54 54 A D T <<5S- 0 0 115 13 0 DDDDDDDDDDDD
55 55 A D S - 0 0 77 13 10 DDDDDDDDDNDD
57 57 A L H > S+ 0 0 31 13 0 LLLLLLLLLLLL
58 58 A T H > S+ 0 0 113 13 49 TTTTNNNNNNNN
59 59 A V H > S+ 0 0 51 13 0 VVVVVVVVVVVV
60 60 A A H >X S+ 0 0 0 13 0 AAAAAAAAAAAA
61 61 A V H 3X S+ 0 0 25 13 0 VVVVVVVVVVVV
62 62 A E H 3X S+ 0 0 118 13 0 EEEEEEEEEEEE
63 63 A I H << S+ 0 0 17 13 0 IIIIIIIIIIII
64 64 A L H >< S+ 0 0 9 13 0 LLLLLLLLLLLL
65 65 A M H 3< S+ 0 0 134 13 47 MMMMMMMMMMSS
66 66 A S T 3< S+ 0 0 89 13 41 SSSSSSSSSSQQ
67 67 A Q < + 0 0 55 13 0 QQQQQQQQQQQQ
68 68 A S S S+ 0 0 116 11 15 QQQQQQQQQQ
69 69 A G - 0 0 41 8 44 AAA GGGS
70 70 A P S S+ 0 0 149 1 0
71 71 A S S S- 0 0 107 1 0
72 72 A S 0 0 137 1 0
73 73 A G 0 0 118 1 0
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 50 50 0 0 0 0 0 0 0 0 0 2 0 0 0.693 23 0.27
3 3 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 0 0 20 0 40 5 0 0 1.055 35 0.54
5 5 A 0 0 0 0 0 0 0 20 0 0 20 0 0 0 20 0 0 40 0 0 5 0 0 1.332 44 0.13
6 6 A 0 0 0 0 0 0 0 0 0 0 20 0 0 0 80 0 0 0 0 0 5 0 0 0.500 16 0.54
7 7 A 0 0 0 0 0 0 0 20 20 0 10 0 0 10 0 0 20 0 0 20 10 0 0 1.748 58 0.26
8 8 A 9 0 0 0 0 0 0 0 27 18 36 0 0 0 9 0 0 0 0 0 11 0 0 1.468 49 0.20
9 9 A 17 0 0 0 0 0 0 0 17 0 0 0 0 8 58 0 0 0 0 0 12 0 0 1.119 37 0.04
10 10 A 0 17 0 0 0 0 0 0 0 0 8 0 0 0 0 0 58 0 0 17 12 0 0 1.119 37 0.16
11 11 A 33 0 0 0 0 0 0 17 33 0 0 0 0 0 0 0 0 0 17 0 12 0 0 1.330 44 0.25
12 12 A 0 0 0 0 0 0 0 0 17 58 0 17 0 0 0 0 0 0 0 8 12 0 0 1.119 37 0.30
13 13 A 8 0 58 0 0 0 0 0 25 0 8 0 0 0 0 0 0 0 0 0 12 0 0 1.075 35 0.24
14 14 A 23 0 0 0 0 0 0 8 62 0 0 8 0 0 0 0 0 0 0 0 13 0 0 1.032 34 0.37
15 15 A 0 0 0 0 0 0 0 0 38 0 0 8 0 0 0 0 0 0 54 0 13 0 0 0.898 29 0.33
16 16 A 15 0 0 0 0 0 0 0 62 0 0 23 0 0 0 0 0 0 0 0 13 0 0 0.925 30 0.37
17 17 A 0 0 0 0 0 0 0 8 69 8 0 0 0 0 0 0 0 0 0 15 13 0 0 0.937 31 0.51
18 18 A 62 0 0 0 0 0 0 8 8 0 0 8 0 0 15 0 0 0 0 0 13 0 0 1.179 39 0.18
19 19 A 23 46 0 0 0 0 0 8 8 0 0 0 0 8 0 0 8 0 0 0 13 0 0 1.484 49 0.19
20 20 A 15 0 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.67
21 21 A 0 0 0 0 0 0 0 0 23 23 0 0 0 8 0 0 46 0 0 0 13 0 0 1.231 41 0.30
22 22 A 0 8 0 0 0 0 0 15 0 15 38 8 0 15 0 0 0 0 0 0 13 0 0 1.626 54 0.13
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 77 0 0 0 13 0 0 0.540 18 0.74
24 24 A 0 0 0 0 0 0 0 54 8 0 0 0 0 0 0 0 31 8 0 0 13 1 0 1.091 36 0.34
25 25 A 0 0 0 0 0 0 0 33 0 0 0 0 0 0 58 0 0 0 0 8 12 0 0 0.888 29 0.08
26 26 A 54 0 0 0 0 0 0 0 38 0 8 0 0 0 0 0 0 0 0 0 13 0 0 0.898 29 0.29
27 27 A 31 0 0 0 0 0 0 0 62 0 0 8 0 0 0 0 0 0 0 0 13 0 0 0.859 28 0.42
28 28 A 38 0 0 0 0 0 0 8 46 8 0 0 0 0 0 0 0 0 0 0 13 0 0 1.119 37 0.30
29 29 A 0 0 0 0 0 0 0 0 0 15 85 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.82
30 30 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 0 15 13 0 0 0.429 14 0.87
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 13 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 62 31 0 0 13 0 0 0.859 28 0.55
33 33 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
34 34 A 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 15 77 0 0 0 13 0 0 0.687 22 0.57
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 13 0 0 0.000 0 1.00
36 36 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
37 37 A 85 0 8 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.536 17 0.78
38 38 A 0 0 0 0 0 0 0 0 69 0 31 0 0 0 0 0 0 0 0 0 13 0 0 0.617 20 0.53
39 39 A 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
40 40 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
41 41 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
42 42 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 92 13 0 0 0.271 9 0.96
43 43 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 77 23 0 0 0 0 13 0 0 0.540 18 0.75
44 44 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
45 45 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 13 0 0 0.000 0 1.00
46 46 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
47 47 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 13 0 0 0.000 0 1.00
48 48 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
49 49 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
50 50 A 0 92 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.91
51 51 A 0 0 0 0 0 0 0 0 92 0 8 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.85
52 52 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
53 53 A 0 0 0 0 0 0 0 8 92 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.271 9 0.93
54 54 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 13 0 0 0.000 0 1.00
55 55 A 0 0 0 0 0 0 0 46 0 0 0 0 0 0 0 0 0 0 0 54 13 0 0 0.690 23 0.61
56 56 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 92 13 0 0 0.271 9 0.89
57 57 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
58 58 A 0 0 0 0 0 0 0 0 0 0 0 38 0 0 0 0 0 0 62 0 13 0 0 0.666 22 0.50
59 59 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
60 60 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
61 61 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
62 62 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 13 0 0 0.000 0 1.00
63 63 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
64 64 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
65 65 A 0 0 0 85 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 13 0 0 0.429 14 0.53
66 66 A 0 0 0 0 0 0 0 0 0 0 85 0 0 0 0 0 15 0 0 0 13 0 0 0.429 14 0.58
67 67 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 13 0 0 0.000 0 1.00
68 68 A 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 91 0 0 0 11 0 0 0.305 10 0.85
69 69 A 0 0 0 0 0 0 0 50 38 0 13 0 0 0 0 0 0 0 0 0 8 0 0 0.974 32 0.56
70 70 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
71 71 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
72 72 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
73 73 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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