Complet list of 1dme hssp file
Complete list of 1dme.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1DME
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 2014-04-12
HEADER METALLOTHIONEIN 22-NOV-94 1DME
COMPND MOL_ID: 1; MOLECULE: CD6 METALLOTHIONEIN-1; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CALLINECTES SAPIDUS; ORGANISM_COMMON:
AUTHOR S.S.NARULA,M.BROUWER,Y.HUA,I.M.ARMITAGE
DBREF 1DME A 1 28 UNP P55949 MT1_CALSI 2 29
SEQLENGTH 28
NCHAIN 1 chain(s) in 1DME data set
NALIGN 39
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 : MT1_CALSI 1DMC 1.00 1.00 1 28 2 29 28 0 0 59 P55949 Metallothionein-1B OS=Callinectes sapidus PE=1 SV=1
2 : Q548Y3_CALSI 1.00 1.00 1 28 2 29 28 0 0 59 Q548Y3 Cadmium-inducible metallothionein CdMT-I OS=Callinectes sapidus PE=4 SV=1
3 : A2I5Y4_PORPE 0.96 1.00 1 27 2 28 27 0 0 59 A2I5Y4 Metallothionein OS=Portunus pelagicus GN=METAL2 PE=4 SV=1
4 : T2BQT3_PORTR 0.96 1.00 1 28 2 29 28 0 0 59 T2BQT3 Metallothionein 2 OS=Portunus trituberculatus GN=MT2 PE=4 SV=1
5 : MT1_SCYSE 0.93 0.96 1 28 1 28 28 0 0 58 P02805 Metallothionein-1 OS=Scylla serrata PE=1 SV=1
6 : A7DY27_MAJSQ 0.82 0.96 1 28 2 29 28 0 0 58 A7DY27 Metallothionein OS=Maja squinado GN=Mt PE=4 SV=1
7 : A7DY25_9EUCA 0.79 0.93 1 28 2 29 28 0 0 58 A7DY25 Metallothionein OS=Segonzacia mesatlantica GN=Mt PE=4 SV=1
8 : A7DY28_NECPU 0.79 0.96 1 28 2 29 28 0 0 58 A7DY28 Metallothionein OS=Necora puber GN=Mt PE=4 SV=1
9 : A7DY31_PACMR 0.79 0.90 1 28 2 30 29 1 1 59 A7DY31 Metallothionein OS=Pachygrapsus marmoratus GN=Mt PE=4 SV=1
10 : A7DY33_9EUCA 0.79 0.96 1 28 2 29 28 0 0 58 A7DY33 Metallothionein OS=Cyanagraea praedator GN=Mt PE=4 SV=1
11 : A7DY34_9EUCA 0.79 0.93 1 28 2 29 28 0 0 58 A7DY34 Metallothionein OS=Segonzacia mesatlantica GN=Mt PE=4 SV=1
12 : E9K8X5_ERISI 0.79 0.86 1 28 2 30 29 1 1 59 E9K8X5 Metallothionein-1 OS=Eriocheir sinensis GN=MT-1 PE=4 SV=1
13 : I3NLQ1_CHAJP 0.79 0.93 1 28 2 29 28 0 0 57 I3NLQ1 Metallothionein OS=Charybdis japonica PE=4 SV=1
14 : MT1_HOMAM 1J5L 0.79 0.93 1 28 1 28 28 0 0 58 P29499 Metallothionein-1 OS=Homarus americanus PE=1 SV=2
15 : MT_ASTAS 0.79 0.82 1 28 2 29 28 0 0 58 P55951 Metallothionein OS=Astacus astacus PE=1 SV=1
16 : MT_CARMA 0.79 0.93 1 28 2 29 28 0 0 58 P55948 Metallothionein OS=Carcinus maenas PE=1 SV=1
17 : Q86M28_CARMA 0.79 0.93 1 28 2 29 28 0 0 58 Q86M28 Metallothionein Ib OS=Carcinus maenas GN=MTIb PE=4 SV=1
18 : Q95P38_HOMAM 0.79 0.93 1 28 2 29 28 0 0 58 Q95P38 Metallothionein OS=Homarus americanus GN=mth PE=4 SV=1
19 : E5KXY4_PENMO 0.78 0.81 1 27 2 28 27 0 0 58 E5KXY4 Metallothionein OS=Penaeus monodon PE=4 SV=1
20 : Q9U623_PACLE 0.78 0.85 1 27 2 28 27 0 0 58 Q9U623 Metallothionein OS=Pacifastacus leniusculus PE=4 SV=1
21 : A7DY24_BYTTH 0.75 0.96 1 28 2 29 28 0 0 58 A7DY24 Metallothionein OS=Bythograea thermydron GN=Mt PE=4 SV=1
22 : A7DY26_9EUCA 0.75 0.96 1 28 2 29 28 0 0 58 A7DY26 Metallothionein OS=Cyanagraea praedator GN=Mt PE=4 SV=1
23 : A7DY30_CANPG 0.75 0.93 1 28 2 29 28 0 0 58 A7DY30 Metallothionein OS=Cancer pagurus GN=Mt PE=4 SV=1
24 : A7DY32_BYTTH 0.75 0.96 1 28 2 29 28 0 0 58 A7DY32 Metallothionein OS=Bythograea thermydron GN=Mt PE=4 SV=1
25 : D3VN22_9EUCA 0.75 0.96 1 28 2 29 28 0 0 58 D3VN22 Metallothionein OS=Allograea tomentosa GN=mt PE=4 SV=1
26 : D3VN23_9EUCA 0.75 0.96 1 28 2 29 28 0 0 58 D3VN23 Metallothionein OS=Gandalfus puia GN=mt PE=4 SV=1
27 : D3VN24_AUSRO 0.75 0.96 1 28 2 29 28 0 0 58 D3VN24 Metallothionein OS=Austinograea rodriguezensis GN=mt PE=4 SV=1
28 : MT2_SCYSE 0.75 0.93 1 28 1 28 28 0 0 57 P02806 Metallothionein-2 OS=Scylla serrata PE=1 SV=1
29 : Q7YW25_PANAR 0.75 0.79 1 28 2 29 28 0 0 59 Q7YW25 Metallothionein OS=Panulirus argus PE=4 SV=1
30 : Q95U92_ERISI 0.75 0.89 1 28 2 29 28 0 0 58 Q95U92 Metallothionein OS=Eriocheir sinensis PE=4 SV=1
31 : MT2_CALSI 0.71 0.89 1 28 2 29 28 0 0 58 P55950 Metallothionein-2B OS=Callinectes sapidus PE=1 SV=1
32 : Q548Y2_CALSI 0.71 0.89 1 28 2 29 28 0 0 58 Q548Y2 Cadmium-inducible metallothionein CdMT-II OS=Callinectes sapidus PE=4 SV=1
33 : Q95U91_SCYSE 0.71 0.89 1 28 2 29 28 0 0 58 Q95U91 Metallothionein OS=Scylla serrata PE=4 SV=1
34 : Q95U93_PORPE 0.71 0.86 1 28 2 29 28 0 0 58 Q95U93 Metallothionein OS=Portunus pelagicus PE=4 SV=1
35 : A7DY29_CARMA 0.70 0.87 1 28 2 31 30 1 2 60 A7DY29 Metallothionein OS=Carcinus maenas GN=Mt PE=4 SV=1
36 : A7DY35_9EUCA 0.70 0.78 1 27 2 28 27 0 0 58 A7DY35 Metallothionein OS=Dromia personata GN=Mt PE=4 SV=1
37 : A7DY36_9EUCA 0.70 0.78 1 27 2 28 27 0 0 58 A7DY36 Metallothionein OS=Dromia personata GN=Mt PE=4 SV=1
38 : MT_POTPO 0.69 0.83 1 28 1 29 29 1 1 58 P55952 Metallothionein OS=Potamon potamios PE=1 SV=1
39 : F8UU34_9EUCA 0.66 0.79 1 28 2 30 29 1 1 59 F8UU34 Metallothionein OS=Sinopotamon honanense GN=Mt PE=4 SV=1
## ALIGNMENTS 1 - 39
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A P 0 0 183 40 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
2 2 A G - 0 0 63 40 29 GGGGGDDDDDDGDGGDDGGGDDDDDDDDGDDDDDDDDDD
3 3 A P - 0 0 52 40 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
4 4 A C S > S+ 0 0 7 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5 5 A C T 3 + 0 0 9 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6 6 A N T 3 S- 0 0 102 40 72 NNNNNNKNNKKKNKNIIKINKKKKKKKNINNNIIITTAT
7 7 A D S < S+ 0 0 146 40 8 DDDDDDDDdDDdDDDDDDDDDDDDDDDDDDDDDDDEEee
8 8 A K - 0 0 122 40 22 KKKKKKKKkKKkKKVKKKKQKKKKKKKKKKKKKKKKKtt
9 9 A C + 0 0 65 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCC
10 10 A V > + 0 0 15 40 47 VVVVVEEEVEEVEEEEEEEEEEEEEEEDEEEEDEeEEEE
11 11 A C T 5 + 0 0 42 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 12 A Q T 5S+ 0 0 183 40 64 QQQQKKKKAKKAKAAKKAAAKKKKKKKKAKKKKKKAAEA
13 13 A E T 5S- 0 0 127 40 12 EEEEEEEEEEEEEEAEEEEAEEEEDEEEEEEEEEDEEEE
14 14 A G T 5S+ 0 0 72 40 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
15 15 A G < + 0 0 35 40 40 GGGGGGGGGGGGGGGGGGGGGGGGGGGEKKEEEKGGGKK
16 16 A C - 0 0 22 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
17 17 A K - 0 0 142 40 8 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKEKKKEKKKKK
18 18 A A S S+ 0 0 115 40 57 AAAAEAAATTAKATTAATTTTTATATTTSATTTAAQQAS
19 19 A G + 0 0 30 40 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
20 20 A C + 0 0 32 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
21 21 A Q + 0 0 132 40 65 QQQQQKTKVKTTKKVKKKVVKKKKKKKKQKKKKKKVVKK
22 22 A C > - 0 0 18 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
23 23 A T T 3 + 0 0 130 40 32 TTTTTTTSTTTTKTTTTTKTTTTTTTTTKTKKTTTKKTT
24 24 A S T 3 S+ 0 0 102 40 12 SSAASSSSSSSSSSSSSSSSSSASSSSSSSSSSSSSSSS
25 25 A C S < S- 0 0 28 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
26 26 A R + 0 0 198 40 13 RRRRRRRRRRRRRRRRRRRRRRCRRRRRTRRRRRRRRRR
27 27 A C 0 0 55 40 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
28 28 A S 0 0 147 35 59 SS SSPTATSTTPASTTA PPSPPPPPSPPPPPT SS
## 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 0 0 100 0 0 0 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 32 0 0 0 0 0 0 0 0 0 0 0 68 40 0 0 0.631 21 0.71
3 3 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
6 6 A 0 0 17 0 0 0 0 0 3 0 0 8 0 0 0 32 0 0 40 0 40 0 0 1.323 44 0.28
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 90 40 0 4 0.325 10 0.92
8 8 A 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 90 3 0 0 0 40 0 0 0.429 14 0.78
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 1 0.000 0 1.00
10 10 A 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 0 5 40 0 0 0.687 22 0.52
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 28 0 0 0 0 0 0 57 13 3 0 0 40 0 0 1.025 34 0.36
13 13 A 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 90 0 5 40 0 0 0.394 13 0.87
14 14 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 13 0 10 0 0 40 0 0 0.688 22 0.60
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 0 5 0 0 40 0 0 0.199 6 0.92
18 18 A 0 0 0 0 0 0 0 0 45 0 5 40 0 0 0 3 5 3 0 0 40 0 0 1.210 40 0.43
19 19 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
21 21 A 15 0 0 0 0 0 0 0 0 0 0 8 0 0 0 60 17 0 0 0 40 0 0 1.090 36 0.34
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 3 80 0 0 0 17 0 0 0 0 40 0 0 0.576 19 0.68
24 24 A 0 0 0 0 0 0 0 0 8 0 93 0 0 0 0 0 0 0 0 0 40 0 0 0.266 8 0.88
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 0 3 3 0 95 0 0 0 0 0 40 0 0 0.233 7 0.86
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 40 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 0 9 40 31 20 0 0 0 0 0 0 0 0 35 0 0 1.263 42 0.41
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
9 8 9 1 dGk
12 8 9 1 dGk
35 10 11 2 cESe
38 8 8 1 eGt
39 8 9 1 eGt
//