Protein alignment in HSSP format
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991
PDBID 1ppt
DATE file generated on 16-Aug-98
SEQBASE RELEASE 36.0 OF EMBL/SWISS-PROT WITH 74019 SEQUENCES
PARAMETER SMIN: -0.5 SMAX: 1.0
PARAMETER gap-open: 3.0 gap-elongation: 0.1
PARAMETER conservation weights: YES
PARAMETER InDels in secondary structure allowed: YES
PARAMETER alignments sorted according to :DISTANCE
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 e-mail (INTERNET) Schneider@EMBL-Heidelberg.DE or Sander@EMBL-Heidelberg.DE / fax +49-6221-387306
AVAILABLE Free academic use. Commercial users must apply for license.
AVAILABLE No inclusion in other databanks without permission.
HEADER PANCREATIC HORMONE
COMPND AVIAN PANCREATIC POLYPEPTIDE
SOURCE TURKEY (MELEAGRIS $GALLOPAVO) PANCREAS
AUTHOR T.L.BLUNDELL,J.E.PITTS,I.J.TICKLE,S.P.WOOD
SEQLENGTH 36
NCHAIN 1 chain(s) in 1ppt data set
NALIGN 31
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 : EMBL/SWISSPROT identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : paho_chick 1PPT 0.94 0.98 1 36 26 61 36 0 0 80 P01306 PANCREATIC HORMONE PRECURSOR (PANCREATIC
2 : paho_strca 0.94 0.98 1 36 1 36 36 0 0 36 P11967 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
3 : paho_larar 0.89 0.95 1 36 1 36 36 0 0 36 P41337 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
4 : paho_allmi 0.80 0.88 2 36 2 36 35 0 0 36 P06305 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
5 : paho_ansan 0.78 0.74 1 36 1 36 36 0 0 36 P06304 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
6 : neuy_sheep 0.60 0.75 2 36 2 36 35 0 0 36 P14765 NEUROPEPTIDE Y (NPY).
7 : neuy_pig 0.57 0.73 2 36 2 36 35 0 0 36 P01304 NEUROPEPTIDE Y (NPY).
8 : neuy_human 1RON 0.54 0.71 2 36 30 64 35 0 0 97 P01303 NEUROPEPTIDE Y PRECURSOR (NPY).
9 : neuy_rat 0.54 0.71 2 36 31 65 35 0 0 98 P07808 NEUROPEPTIDE Y PRECURSOR (NPY).
10 : pyy_pig 0.54 0.72 2 36 2 36 35 0 0 36 P01305 PEPTIDE YY (PYY).
11 : neuy_chick 0.54 0.72 2 36 30 64 35 0 0 97 P28673 NEUROPEPTIDE Y PRECURSOR (NPY).
12 : pyy_human 0.54 0.71 2 36 30 64 35 0 0 97 P10082 PEPTIDE YY PRECURSOR (PYY).
13 : neuy_rabit 0.54 0.71 2 36 2 36 35 0 0 36 P09640 NEUROPEPTIDE Y (NPY).
14 : pyy_rat 0.54 0.72 2 36 30 64 35 0 0 98 P10631 PEPTIDE YY PRECURSOR (PYY).
15 : neuy_torma 0.51 0.69 2 36 30 64 35 0 0 98 P28674 NEUROPEPTIDE Y PRECURSOR (NPY).
16 : pyy_amica 0.51 0.70 2 36 2 36 35 0 0 36 P29205 PEPTIDE YY-LIKE (PYY).
17 : neuy_xenla 0.51 0.70 2 36 30 64 35 0 0 97 P33689 NEUROPEPTIDE Y PRECURSOR.
18 : neuy_ranri 0.51 0.70 2 36 2 36 35 0 0 36 P29949 (NPY).
19 : npy_lamfl 0.49 0.68 2 36 36 70 35 0 0 104 P48097 NEUROPEPTIDE Y PRECURSOR (NPY).
20 : pyy_rajrh 0.49 0.69 2 36 2 36 35 0 0 36 P29206 PEPTIDE YY-LIKE (PYY).
21 : pyy_lepsp 0.49 0.69 2 36 2 36 35 0 0 36 P09473 PEPTIDE YY-LIKE (PYY) (NEUROPEPTIDE Y-REL
22 : neuy_oncmy 0.49 0.69 2 36 2 36 35 0 0 36 P29071 NEUROPEPTIDE Y (NPY).
23 : pyy_oncki 0.49 0.69 2 36 2 36 35 0 0 36 P09474 PEPTIDE YY-LIKE (PYY).
24 : paho_didma 0.46 0.64 2 36 2 36 35 0 0 36 P18107 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
25 : pyy_bovin 0.46 0.65 2 36 30 64 35 0 0 97 P51694 PEPTIDE YY PRECURSOR (PYY).
26 : paho_canfa 0.46 0.64 2 36 31 65 35 0 0 93 P01299 PANCREATIC HORMONE PRECURSOR (PANCREATIC
27 : paho_rante 0.46 0.61 2 36 2 36 35 0 0 36 P31229 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
28 : paho_pig 0.46 0.64 2 36 2 36 35 0 0 36 P01300 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
29 : paho_rabit 0.46 0.65 2 36 2 36 35 0 0 36 P41336 PANCREATIC HORMONE (PANCREATIC POLYPEPTID
30 : neuy_gadmo 0.46 0.67 2 36 2 36 35 0 0 36 P80167 NEUROPEPTIDE Y (NPY).
31 : neuy_carau 0.46 0.66 2 36 30 64 35 0 0 96 P28672 NEUROPEPTIDE Y PRECURSOR (NPY).
## ALIGNMENTS 1 - 31
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 G 0 0 101 5 0 GGG G
2 2 P - 0 0 60 32 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
3 3 S - 0 0 106 32 43 SAVLSSSSSASISASPSSNPPVPQALSLPIT
4 4 Q - 0 0 139 32 30 QQQQQKKKKKKKKKKKKKKKKKKEKEEEEKK
5 5 P - 0 0 26 32 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
6 6 T - 0 0 126 32 43 TTTKTDDDDEDEDEDEDDDEEEEVQVHVVED
7 7 Y - 0 0 121 32 47 YYYYYNNNNASANANNNNSNNNNYAYHYYNN
8 8 P - 0 0 55 32 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
9 9 G > - 0 0 27 32 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
10 10 D T 3 S+ 0 0 128 32 14 DDDDNDEEEEEEEEEEEEEDEEEDEDDDDEE
11 11 D T 3 S+ 0 0 165 32 11 DDDGDDDDDDDDDDGDDDDDDDDDHDQDDDG
12 12 A S < S- 0 0 17 32 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13 13 P >> - 0 0 73 32 26 PPPPPPPPPSPSPSPPPPPAPPPTSTTTTPP
14 14 V H 3> S+ 0 0 108 32 38 VVVVVAAAAPAPAPAPAAAPPTPPPPQPPAA
15 15 E H 3> S+ 0 0 111 32 4 EEEEEEEEEEEEEEEEEEEEEEEEDEDEEDE
16 16 D H <> S+ 0 0 58 32 18 DDDDDDDDDEDEDEDEDDDEEEEQEQQQQEE
17 17 L H X S+ 0 0 62 32 3 LLLLLLLMMLMLMLLLMMLLLLLMLMLMMLL
18 18 I H X S+ 0 0 91 32 34 IVVIRAAAASANASAAAAAAAAAANAAAAAA
19 19 R H X S+ 0 0 142 32 30 RRRQFRRRRRRRRRKRKKRKKKKKRQQQEKK
20 20 F H X S+ 0 0 39 32 1 FFFFYYYYYYYYYYYYYYYYYYYYYYYYYYY
21 21 Y H X S+ 0 0 143 32 22 YYYYYYYYYYYYYYYYYYLYYYYAYAYAVYY
22 22 D H X S+ 0 0 79 32 37 NDNDDSSSSASASASTSSSSSTTATASAASS
23 23 N H X S+ 0 0 97 32 37 DNDDNAAAASASASAAAAAAAAAESEDEDAA
24 24 L H X S+ 0 0 58 32 2 LLLLLLLLLLLLLLLLLLVLLLLLLLLLLLL
25 25 Q H X S+ 0 0 90 32 25 QQQQQRRRRRRRRRRRRRRRRRRRRRYRRRR
26 26 Q H X S+ 0 0 112 32 24 QQQQQHHHHHHHHHHHHHHHHHHRHRQRRHH
27 27 Y H X S+ 0 0 56 32 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
28 28 L H X S+ 0 0 90 32 19 LLLLRIIIILILILIIIIIIIIIILIIIIII
29 29 N H <>S+ 0 0 33 32 10 NNNNLNNNNNNNNNNNNNNNNNNNNNTNNNN
30 30 V H ><5S+ 0 0 21 32 23 VVVVNLLLLLLLLLLLLLLLLLLRLMFMMLL
31 31 V H 3<5S+ 0 0 85 32 15 VVVVVIIIIVIVIVIIIIIIIIILVLVLLII
32 32 T T 3<5S- 0 0 91 32 6 TTTTFTTTTTTTTTTTTTTTTTTTTTTTTTT
33 33 R T < 5S+ 0 0 215 32 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
34 34 H < + 0 0 101 32 28 HHHPHQQQQQQQQQQQQQQQQQQPQPPPPQQ
35 35 R 0 0 180 32 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
36 36 Y 0 0 224 32 1 YYYFYYYYYYYYYYYYYYYYYYYYFYFYYYY
## 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 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.000 0 1.22
2 2 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.30
3 3 6 9 6 0 0 0 0 0 13 16 41 3 0 0 0 0 3 0 3 0 32 0 0 1.809 60 0.42
4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 19 16 0 0 32 0 0 0.880 29 0.79
5 5 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.30
6 6 13 0 0 0 0 0 0 0 0 0 0 16 0 3 0 3 3 28 0 34 32 0 0 1.599 53 0.52
7 7 0 0 0 0 0 0 31 0 13 0 6 0 0 3 0 0 0 0 47 0 32 0 0 1.260 42 0.41
8 8 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.30
9 9 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.30
10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 59 3 38 32 0 0 0.786 26 1.08
11 11 0 0 0 0 0 0 0 9 0 0 0 0 0 3 0 0 3 0 0 84 32 0 0 0.582 19 1.05
12 12 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.30
13 13 0 0 0 0 0 0 0 0 3 69 13 16 0 0 0 0 0 0 0 0 32 0 0 0.916 31 0.72
14 14 19 0 0 0 0 0 0 0 38 38 0 3 0 0 0 0 3 0 0 0 32 0 0 1.266 42 0.67
15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 0 9 32 0 0 0.311 10 1.21
16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 50 32 0 0 1.004 34 0.93
17 17 0 69 0 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.621 21 1.23
18 18 6 0 9 0 0 0 0 0 69 0 6 0 0 0 3 0 0 0 6 0 32 0 0 1.108 37 0.81
19 19 0 0 0 0 3 0 0 0 0 0 0 0 0 0 50 31 13 3 0 0 32 0 0 1.187 40 0.77
20 20 0 0 0 0 16 0 84 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.433 14 1.28
21 21 3 3 0 0 0 0 84 0 9 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.582 19 0.80
22 22 0 0 0 0 0 0 0 0 22 0 47 13 0 0 0 0 0 0 6 13 32 0 0 1.381 46 0.65
23 23 0 0 0 0 0 0 0 0 53 0 13 0 0 0 0 0 0 9 9 16 32 0 0 1.330 44 0.61
24 24 3 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.139 5 1.26
25 25 0 0 0 0 0 0 3 0 0 0 0 0 0 0 78 0 19 0 0 0 32 0 0 0.615 21 0.96
26 26 0 0 0 0 0 0 0 0 0 0 0 0 0 66 13 0 22 0 0 0 32 0 0 0.869 29 0.88
27 27 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.30
28 28 0 28 69 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 32 0 0 0.723 24 1.06
29 29 0 3 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 94 0 32 0 0 0.277 9 1.18
30 30 16 66 0 9 3 0 0 0 0 0 0 0 0 0 3 0 0 0 3 0 32 0 0 1.113 37 0.99
31 31 34 13 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.963 32 1.00
32 32 0 0 0 0 3 0 0 0 0 0 0 97 0 0 0 0 0 0 0 0 32 0 0 0.139 5 1.28
33 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 32 0 0 0.000 0 1.30
34 34 0 0 0 0 0 0 0 0 0 19 0 0 0 16 0 0 66 0 0 0 32 0 0 0.880 29 0.80
35 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 32 0 0 0.000 0 1.30
36 36 0 0 0 0 9 0 91 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.311 10 1.28
//