Complet list of 1tmz hssp file
Complete list of 1tmz.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1TMZ
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 2014-05-10
HEADER TROPOMYOSIN 20-APR-98 1TMZ
COMPND MOL_ID: 1; MOLECULE: TMZIP; CHAIN: A, B; ENGINEERED: YES; OTHER_DETAIL
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: RATTUS RATTUS, SACCHAROMYCES CEREVISIA
AUTHOR N.J.GREENFIELD,G.T.MONTELIONE,S.E.HITCHCOCK-DEGREGORI, R.S.FARID
DBREF 1TMZ A 1 32 UNP P03069 GCN4_YEAST 250 281
DBREF 1TMZ B 1 32 UNP P03069 GCN4_YEAST 250 281
SEQLENGTH 32
NCHAIN 2 chain(s) in 1TMZ data set
KCHAIN 1 chain(s) used here ; chains(s) : A
NALIGN 19
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 : A6ZQT9_YEAS7 0.66 0.75 1 32 250 281 32 0 0 281 A6ZQT9 Transcriptional activator of amino acid biosynthetic genes OS=Saccharomyces cerevisiae (strain YJM789) GN=GCN4 PE=4 SV=1
2 : B3LS06_YEAS1 0.66 0.75 1 32 250 281 32 0 0 281 B3LS06 General control protein GCN4 OS=Saccharomyces cerevisiae (strain RM11-1a) GN=SCRG_04459 PE=4 SV=1
3 : B5VHC6_YEAS6 0.66 0.75 1 32 153 184 32 0 0 184 B5VHC6 YEL009Cp-like protein (Fragment) OS=Saccharomyces cerevisiae (strain AWRI1631) GN=AWRI1631_50610 PE=4 SV=1
4 : C7GKH1_YEAS2 0.66 0.75 1 32 250 281 32 0 0 281 C7GKH1 Gcn4p OS=Saccharomyces cerevisiae (strain JAY291) GN=GCN4 PE=4 SV=1
5 : E7KBL9_YEASA 0.66 0.75 1 32 237 268 32 0 0 268 E7KBL9 Gcn4p OS=Saccharomyces cerevisiae (strain AWRI796) GN=AWRI796_1274 PE=4 SV=1
6 : E7NGY6_YEASO 0.66 0.75 1 32 237 268 32 0 0 268 E7NGY6 Gcn4p OS=Saccharomyces cerevisiae (strain FostersO) GN=FOSTERSO_1235 PE=4 SV=1
7 : E7QDQ9_YEASZ 0.66 0.75 1 32 237 268 32 0 0 268 E7QDQ9 Gcn4p OS=Saccharomyces cerevisiae (strain Zymaflore VL3) GN=VL3_1263 PE=4 SV=1
8 : G2WCM2_YEASK 0.66 0.75 1 32 250 281 32 0 0 281 G2WCM2 K7_Gcn4p OS=Saccharomyces cerevisiae (strain Kyokai no. 7 / NBRC 101557) GN=K7_GCN4 PE=4 SV=1
9 : GCN4_YEAST 1LLM 0.66 0.75 1 32 250 281 32 0 0 281 P03069 General control protein GCN4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GCN4 PE=1 SV=1
10 : N1P3V4_YEASC 0.66 0.75 1 32 250 281 32 0 0 281 N1P3V4 Gcn4p OS=Saccharomyces cerevisiae (strain CEN.PK113-7D) GN=CENPK1137D_3647 PE=4 SV=1
11 : W7PUF5_YEASX 0.66 0.75 1 32 250 281 32 0 0 281 W7PUF5 Gcn4p OS=Saccharomyces cerevisiae R008 GN=Gcn4 PE=4 SV=1
12 : W7RC93_YEASX 0.66 0.75 1 32 250 281 32 0 0 281 W7RC93 Gcn4p OS=Saccharomyces cerevisiae P283 GN=Gcn4 PE=4 SV=1
13 : H0GTQ0_9SACH 0.65 0.74 1 31 238 268 31 0 0 269 H0GTQ0 Gcn4p OS=Saccharomyces cerevisiae x Saccharomyces kudriavzevii VIN7 GN=VIN7_6641 PE=4 SV=1
14 : J5PE00_SACK1 0.65 0.74 1 31 251 281 31 0 0 282 J5PE00 GCN4-like protein OS=Saccharomyces kudriavzevii (strain ATCC MYA-4449 / AS 2.2408 / CBS 8840 / NBRC 1802 / NCYC 2889) GN=YEL009C PE=4 SV=1
15 : C8Z6Z0_YEAS8 0.62 0.72 1 32 250 281 32 0 0 281 C8Z6Z0 Gcn4p OS=Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) GN=EC1118_1E8_0826g PE=4 SV=1
16 : E7KMI6_YEASL 0.62 0.72 1 32 237 268 32 0 0 268 E7KMI6 Gcn4p OS=Saccharomyces cerevisiae (strain Lalvin QA23) GN=QA23_1268 PE=4 SV=1
17 : E7LTN5_YEASV 0.62 0.72 1 32 237 268 32 0 0 268 E7LTN5 Gcn4p OS=Saccharomyces cerevisiae (strain VIN 13) GN=VIN13_1264 PE=4 SV=1
18 : E7Q385_YEASB 0.62 0.72 1 32 237 268 32 0 0 268 E7Q385 Gcn4p OS=Saccharomyces cerevisiae (strain FostersB) GN=FOSTERSB_1252 PE=4 SV=1
19 : H0GEY2_9SACH 0.62 0.72 1 32 237 268 32 0 0 268 H0GEY2 Gcn4p OS=Saccharomyces cerevisiae x Saccharomyces kudriavzevii VIN7 GN=VIN7_1280 PE=4 SV=1
## ALIGNMENTS 1 - 19
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A M >> 0 0 117 20 0 MMMMMMMMMMMMMMMMMMM
2 2 A D T 34 + 0 0 135 20 58 KKKKKKKKKKKKKKKKKKK
3 3 A A T 3> S+ 0 0 75 20 62 QQQQQQQQQQQQQQQQQQQ
4 4 A I H <> S+ 0 0 41 20 33 LLLLLLLLLLLLLLLLLLL
5 5 A K H < S+ 0 0 119 20 58 EEEEEEEEEEEEEEEEEEE
6 6 A K H > S+ 0 0 88 20 58 DDDDDDDDDDDDDDDDDDD
7 7 A K H >X S+ 0 0 84 17 10 KKKKKKKKKKKKKKEXXKX
8 8 A M H 3X S+ 0 0 50 20 43 VVVVVVVVVVVVVVVVVVV
9 9 A Q H 3> S+ 0 0 93 20 38 EEEEEEEEEEEEEEEEEEE
10 10 A M H X S+ 0 0 16 20 0 LLLLLLLLLLLLLLLLLLL
26 26 A K H 3< S+ 0 0 95 19 0 KKKKKKKKKKKKKKKKKXK
27 27 A K T 3< S+ 0 0 135 20 0 KKKKKKKKKKKKKKKKKKK
28 28 A L T <4 S+ 0 0 105 20 0 LLLLLLLLLLLLLLLLLLL
29 29 A V S < S+ 0 0 44 20 0 VVVVVVVVVVVVVVVVVVV
30 30 A G S S+ 0 0 38 20 0 GGGGGGGGGGGGGGGGGGG
31 31 A E 0 0 107 20 0 EEEEEEEEEEEEEEEEEEE
32 32 A R 0 0 225 18 0 RRRRRRRRRRRR RRRRR
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 0 0 0 5 20 0 0 0.199 6 0.42
3 3 A 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 95 0 0 0 20 0 0 0.199 6 0.37
4 4 A 0 95 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.199 6 0.66
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 95 0 0 20 0 0 0.199 6 0.42
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 95 20 0 0 0.199 6 0.42
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 0 6 0 0 17 0 0 0.224 7 0.89
8 8 A 95 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.199 6 0.56
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 95 0 0 20 0 0 0.199 6 0.61
10 10 A 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 95 0 0 20 0 0 0.199 6 0.18
11 11 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
12 12 A 0 95 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 20 0 0 0.199 6 0.13
13 13 A 0 5 0 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 0 0 20 0 0 0.199 6 0.08
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 0 0 0 5 20 0 0 0.199 6 0.42
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 20 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 20 0 0 0.000 0 1.00
18 18 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 20 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 20 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 20 0 0 0.000 0 1.00
22 22 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 20 0 0 0.000 0 1.00
25 25 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 19 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 20 0 0 0.000 0 1.00
28 28 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
29 29 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 20 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 18 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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