Complet list of 1vfi hssp file
Complete list of 1vfi.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1VFI
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 METAL BINDING PROTEIN 13-APR-04 1VFI
COMPND MOL_ID: 1; MOLECULE: VANADIUM-BINDING PROTEIN 2; CHAIN: A; FRAGMENT: R
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: ASCIDIA SYDNEIENSIS SAMEA; ORGANISM_TA
AUTHOR T.HAMADA,H.HIROTA,M.ASANUMA,F.HAYASHI,N.KOBAYASHI,T.UEKI, H.MICHIBATA,
DBREF 1VFI A 5 95 UNP Q86BW2 Q86BW2_ASCSS 30 120
SEQLENGTH 95
NCHAIN 1 chain(s) in 1VFI 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 : VBP2_ASCSS 1VFI 0.99 1.00 4 95 29 120 92 0 0 120 Q86BW2 Vanadium-binding protein 2 OS=Ascidia sydneiensis samea GN=VANABIN2 PE=1 SV=1
2 : A7VMV6_ASCSS 0.47 0.65 9 94 39 124 86 0 0 125 A7VMV6 Vanadium-binding protein 4 OS=Ascidia sydneiensis samea GN=Vanabin4 PE=2 SV=1
3 : Q86BW3_ASCSS 0.38 0.51 17 94 43 119 80 2 5 120 Q86BW3 Vanadium-binding protein 1 OS=Ascidia sydneiensis samea GN=vanabin1 PE=2 SV=1
4 : A7VMU6_CIOIN 0.37 0.51 9 95 58 150 95 3 10 243 A7VMU6 Uncharacterized protein OS=Ciona intestinalis GN=CiVanabin1 PE=2 SV=1
5 : A7VMV0_CIOIN 0.37 0.59 9 95 34 125 93 3 7 130 A7VMV0 Uncharacterized protein OS=Ciona intestinalis GN=CiVanabin5 PE=2 SV=1
6 : A7VMU7_CIOIN 0.36 0.50 9 95 68 160 96 5 12 251 A7VMU7 Vanadium-binding protein 2 OS=Ciona intestinalis GN=Civanabin2 PE=2 SV=1
7 : F6T9H4_CIOIN 0.36 0.50 9 95 68 160 96 5 12 251 F6T9H4 Uncharacterized protein OS=Ciona intestinalis GN=vanabin2 PE=4 SV=2
8 : H2YD41_CIOSA 0.33 0.52 13 94 42 136 95 5 13 143 H2YD41 Uncharacterized protein OS=Ciona savignyi PE=4 SV=1
9 : A7VMU9_CIOIN 0.30 0.51 20 95 53 138 86 3 10 144 A7VMU9 Uncharacterized protein OS=Ciona intestinalis GN=CiVanabin4 PE=2 SV=1
10 : C5XFR1_SORBI 0.30 0.44 1 89 69 132 89 6 25 181 C5XFR1 Putative uncharacterized protein Sb03g009450 OS=Sorghum bicolor GN=Sb03g009450 PE=4 SV=1
11 : E4XE89_OIKDI 0.30 0.46 9 91 6 91 92 5 15 210 E4XE89 Whole genome shotgun assembly, reference scaffold set, scaffold scaffold_27 OS=Oikopleura dioica GN=GSOID_T00008493001 PE=4 SV=1
12 : E4YNL0_OIKDI 0.30 0.46 9 91 6 91 92 5 15 346 E4YNL0 Whole genome shotgun assembly, allelic scaffold set, scaffold scaffoldA_617 OS=Oikopleura dioica GN=GSOID_T00030125001 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 I 0 0 222 2 26 V
2 2 A S - 0 0 89 2 86 E
3 3 A E S S+ 0 0 177 2 33 D
4 4 A F + 0 0 170 3 148 Y D
5 5 A A S S- 0 0 76 3 99 A K
6 6 A P - 0 0 71 3 0 P P
7 7 A V - 0 0 59 3 112 V K
8 8 A D - 0 0 103 3 33 D E
9 9 A a S S+ 0 0 25 10 30 CC CCCC KCC
10 10 A K S S+ 0 0 178 10 71 KK RGRR KGG
11 11 A G S S+ 0 0 54 10 60 GT SATT DGG
12 12 A Q S S+ 0 0 143 10 64 QN QEQQ PAA
13 13 A b + 0 0 8 11 0 CC CCCCC CCC
14 14 A T S S+ 0 0 95 11 66 TS NQTTK KTT
15 15 A T S > S+ 0 0 114 11 77 TT ETNNT EMM
16 16 A P T 3 S+ 0 0 26 11 69 PE TETTE APP
17 17 A c T 3> S+ 0 0 7 12 0 CCCCCCCC CCC
18 18 A E H <> S+ 0 0 123 12 77 ELGAGVVA EDD
19 19 A P H > S+ 0 0 56 12 59 PPEPAPPP KEE
20 20 A L H >> S+ 0 0 7 13 37 LLVAIVVLLLLL
21 21 A T H 3X S+ 0 0 74 12 95 TKKHIGGAA.LL
22 22 A A H 3X S+ 0 0 53 12 73 ANKQTAATT.PP
23 23 A d H < S+ 0 0 105 12 75 EEREVGGRA.GG
30 30 A S H 3< S+ 0 0 103 12 66 SHSSTKKTT.SS
31 31 A f T >< S+ 0 0 6 13 20 CCCCCCCCRCCC
32 32 A E T < S- 0 0 105 13 71 EENIAGGREDGG
33 33 A T T 3 S+ 0 0 130 13 63 TGGAGSSTAKTT
34 34 A S X - 0 0 51 13 86 SLDAAttnAIcc
35 35 A A T 3 S- 0 0 85 11 82 AS.RAiiaE.gg
36 36 A D T 3> S- 0 0 117 11 55 DD.DAPPgg.gg
37 37 A K H <> S+ 0 0 68 9 77 KK.PK..na.hh
38 38 A K H > S+ 0 0 126 12 56 KKRQRKKKN.EE
39 39 A T H > S+ 0 0 77 13 94 TADLPLLHRTKK
40 40 A f H X S+ 0 0 37 13 0 CCCCCCCCCCCC
41 41 A R H X S+ 0 0 67 13 90 RHTKISSMMCSS
42 42 A R H < S+ 0 0 118 13 56 RQKRRKKMIKRR
43 43 A N H >X S+ 0 0 116 13 61 NNDNNNNKREAA
44 44 A e H 3X S+ 0 0 33 13 0 CCCCCCCCCCCC
45 45 A K H 3X S+ 0 0 46 12 96 KRAFKIIVG.gg
46 46 A K H <4 S+ 0 0 130 13 87 KKKVLMMFLKgg
47 47 A A H < S- 0 0 75 13 79 AVANNNNKTDHH
48 48 A D H < S+ 0 0 110 13 82 DTKGTEETQKII
49 49 A d X + 0 0 0 13 0 CCCCCCCCCCCC
50 50 A E H > S+ 0 0 96 13 89 EKgEMPPLLEnn
51 51 A P H > S+ 0 0 71 8 41 PAp....NP.pp
52 52 A Q H > S+ 0 0 44 9 89 QEN.Q..QR.CC
53 53 A D H X S+ 0 0 51 12 94 DDAVNIITF.HH
54 54 A K H X S+ 0 0 128 12 76 KGGSTSSPP.EE
55 55 A V H X S+ 0 0 72 12 78 VQDDEVVAS.VV
56 56 A c H >X S+ 0 0 6 12 0 CCCCCCCCC.CC
57 57 A D H 3X S+ 0 0 105 13 92 DRGLEIIKKKPP
58 58 A A H 3X S+ 0 0 42 13 74 AAHGTQQTAEPP
59 59 A b H X S+ 0 0 120 13 54 KKSSAKKPRKKK
63 63 A a H 3X S+ 0 0 21 13 0 CCCCCCCCCCCC
64 64 A H H 3X S+ 0 0 117 13 100 HKEFFFFMAESS
65 65 A K H - 0 0 27 10 86 SSAFNLLSL...
84 84 A D H > S+ 0 0 138 12 89 DPPFKPPVS.EE
85 85 A T H > S+ 0 0 63 12 86 TAGFRAAPG.EE
86 86 A i H >> S+ 0 0 7 13 0 CCCCCCCCCCCC
87 87 A R H 3X S+ 0 0 175 13 77 RKLRKRRRVSVV
88 88 A A H 3X S+ 0 0 53 13 80 ASDATKKTRRPP
89 89 A h H