Complet list of 1x9b hssp file
Complete list of 1x9b.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1X9B
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 2014-05-12
HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-AUG-04 1X9B
COMPND MOL_ID: 1; MOLECULE: HYPOTHETICAL MEMBRANE PROTEIN TA0354_69_121; CHAI
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM; ORGANISM_TAX
AUTHOR B.WU,A.YEE,Y.J.HUANG,T.A.RAMELOT,A.SEMESI,A.LEMAK,A.EDWARD, M.KENNEDY,
DBREF 1X9B A 1 53 UNP Q9HL76 Q9HL76_THEAC 69 121
SEQLENGTH 53
NCHAIN 1 chain(s) in 1X9B data set
NALIGN 10
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 : Q9HL76_THEAC1X9B 1.00 1.00 1 53 69 121 53 0 0 121 Q9HL76 Hypothetical membrane protein OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) GN=Ta0354 PE=1 SV=1
2 : Q97BN8_THEVO 0.73 0.90 2 53 70 121 52 0 0 121 Q97BN8 TVG0404408 protein OS=Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) GN=TV0417 PE=4 SV=1
3 : T0LTH0_9EURY 0.52 0.74 8 53 79 124 46 0 0 124 T0LTH0 Uncharacterized protein OS=Thermoplasmatales archaeon A-plasma GN=AMDU1_APLC00043G0018 PE=4 SV=1
4 : L0HIR5_ACIS0 0.51 0.71 3 53 78 128 51 0 0 128 L0HIR5 Uncharacterized protein (Precursor) OS=Aciduliprofundum sp. (strain MAR08-339) GN=AciM339_0757 PE=4 SV=1
5 : B5IDP6_ACIB4 0.49 0.65 3 53 78 128 51 0 0 128 B5IDP6 Uncharacterized protein OS=Aciduliprofundum boonei (strain DSM 19572 / T469) GN=Aboo_0307 PE=4 SV=1
6 : T0LQA9_9EURY 0.48 0.72 8 53 79 124 46 0 0 124 T0LQA9 Uncharacterized protein OS=Thermoplasmatales archaeon E-plasma GN=AMDU2_EPLC00006G0431 PE=4 SV=1
7 : S0ASR1_FERAC 0.43 0.67 3 53 70 120 51 0 0 121 S0ASR1 Uncharacterized protein OS=Ferroplasma acidarmanus fer1 GN=FACI_IFERC00001G1104 PE=4 SV=1
8 : T0LU07_9EURY 0.42 0.62 9 53 80 124 45 0 0 125 T0LU07 Uncharacterized protein OS=Thermoplasmatales archaeon Gpl GN=AMDU5_GPLC00019G0080 PE=4 SV=1
9 : Q6L1F3_PICTO 0.41 0.67 3 53 72 122 51 0 0 125 Q6L1F3 Hypothetical membrane associated protein OS=Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) GN=PTO0614 PE=4 SV=1
10 : T0N898_9EURY 0.41 0.71 3 53 70 120 51 0 0 121 T0N898 Uncharacterized protein OS=Ferroplasma sp. Type II GN=AMDU4_FER2C00184G0009 PE=4 SV=1
## ALIGNMENTS 1 - 10
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A R 0 0 281 2 0 R
2 2 A N + 0 0 159 3 0 NN
3 3 A L + 0 0 137 8 13 LL LL L IL
4 4 A S > + 0 0 55 8 74 SR RR N KN
5 5 A D H > S+ 0 0 14 8 38 DD KK D DD
6 6 A R H > S+ 0 0 137 8 81 RT RR I TM
7 7 A A H > S+ 0 0 55 8 94 AS LL Y IS
8 8 A K H X S+ 0 0 68 10 48 KRRKKKT DK
9 9 A F H X S+ 0 0 3 11 0 FFFFFFFFFF
10 10 A E H X S+ 0 0 118 11 70 EEEEEIKMNK
11 11 A S H X S+ 0 0 76 11 70 SSDEESKKRK
12 12 A M H < S+ 0 0 23 11 63 MLLYYMLNYL
13 13 A I H < S+ 0 0 47 11 32 IIIIITLIIL
14 14 A N H < S- 0 0 115 11 62 NNSDNSKNGK
15 15 A S S < S+ 0 0 99 11 0 SSSSSSSSSS
16 16 A P - 0 0 9 11 63 PSDEEESDES
17 17 A S > - 0 0 70 11 0 SSSSSSSSSS
18 18 A K H > S+ 0 0 144 11 0 KKKKKKKKKK
19 19 A S H > S+ 0 0 90 11 80 SSYRRQKSKK
20 20 A V H > S+ 0 0 56 11 82 VVTEETTHMT
21 21 A F H X S+ 0 0 3 11 0 FFFFFFFFFF
22 22 A V H X S+ 0 0 86 11 34 VVVVVMIMMI
23 23 A R H < S+ 0 0 140 11 67 RRKNNKDKEE
24 24 A N H X S+ 0 0 21 11 13 NNNNNNNNHN
25 25 A L H X S+ 0 0 14 11 20 LLILLLMMLI
26 26 A N H X S+ 0 0 102 11 76 NDKRRKPKTP
27 27 A E H > S+ 0 0 92 11 46 EEEEESSKED
28 28 A L H X S+ 0 0 0 11 0 LLLLLLLLLL
29 29 A E H X S+ 0 0 70 11 10 EEQEEEEEEE
30 30 A A H X S+ 0 0 50 11 70 ARKEEKRKRR
31 31 A L H X S+ 0 0 8 11 24 LLLIIIIIII
32 32 A A H X S+ 0 0 0 11 43 AAASSASASS
33 33 A V H < S+ 0 0 78 11 86 VKRYYRKRKK
34 34 A R H < S+ 0 0 151 11 50 RKDKKKRERR
35 35 A L H < S- 0 0 49 11 43 LLLLLHLHFL
36 36 A G < - 0 0 25 11 10 GGGGGGGGDG
37 37 A K S > S+ 0 0 172 11 71 KKPKESKSGT
38 38 A S H > S+ 0 0 73 11 87 SGRKKRNLSH
39 39 A Y H > S+ 0 0 50 11 1 YYYYYFYYYY
40 40 A R H > S+ 0 0 106 11 71 RLGQQQDQEH
41 41 A I H X S+ 0 0 100 11 80 IIQENSEQED
42 42 A Q H X S+ 0 0 75 11 76 QQQRRMLMRL
43 43 A L H X S+ 0 0 5 11 0 LLLLLLLLLL
44 44 A D H X S+ 0 0 95 11 59 DENEENKQET
45 45 A Q H X S+ 0 0 119 11 43 QNQEEEQNEQ
46 46 A A H X S+ 0 0 9 11 44 AAATKAAKAA
47 47 A K H X S+ 0 0 37 11 16 KKMKKKKKKK
48 48 A E H < S+ 0 0 104 11 71 EEERREHSKH
49 49 A K H < S+ 0 0 132 11 42 KKKKEKKFKK
50 50 A W H < S- 0 0 97 11 0 WWWWWWWWWW
51 51 A K < + 0 0 110 11 52 KKKRRKGKKG
52 52 A V 0 0 61 11 22 VVIVVVIILI
53 53 A K 0 0 230 11 21 KKRKKRKKKR
## 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 0 0 0 0 0 100 0 0 0 0 0 2 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 0 0 0 100 0 3 0 0 0.000 0 1.00
3 3 A 0 88 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.377 12 0.86
4 4 A 0 0 0 0 0 0 0 0 0 0 25 0 0 0 38 13 0 0 25 0 8 0 0 1.321 44 0.26
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 75 8 0 0 0.562 18 0.62
6 6 A 0 0 13 13 0 0 0 0 0 0 0 25 0 0 50 0 0 0 0 0 8 0 0 1.213 40 0.18
7 7 A 0 25 13 0 0 0 13 0 25 0 25 0 0 0 0 0 0 0 0 0 8 0 0 1.560 52 0.05
8 8 A 0 0 0 0 0 0 0 0 0 0 0 10 0 0 20 60 0 0 0 10 10 0 0 1.089 36 0.52
9 9 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
10 10 A 0 0 9 9 0 0 0 0 0 0 0 0 0 0 0 18 0 55 9 0 11 0 0 1.295 43 0.29
11 11 A 0 0 0 0 0 0 0 0 0 0 36 0 0 0 9 27 0 18 0 9 11 0 0 1.468 49 0.29
12 12 A 0 36 0 27 0 0 27 0 0 0 0 0 0 0 0 0 0 0 9 0 11 0 0 1.295 43 0.36
13 13 A 0 18 73 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 11 0 0 0.760 25 0.68
14 14 A 0 0 0 0 0 0 0 9 0 0 18 0 0 0 0 18 0 0 45 9 11 0 0 1.414 47 0.37
15 15 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 18 27 0 0 0 0 0 0 36 0 18 11 0 0 1.342 44 0.36
17 17 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 11 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 9 0 0 0 36 0 0 0 18 27 9 0 0 0 11 0 0 1.468 49 0.19
20 20 A 27 0 0 9 0 0 0 0 0 0 0 36 0 9 0 0 0 18 0 0 11 0 0 1.468 49 0.18
21 21 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
22 22 A 55 0 18 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.995 33 0.65
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 0 18 18 9 11 0 0 1.547 51 0.32
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 91 0 11 0 0 0.305 10 0.86
25 25 A 0 64 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.908 30 0.79
26 26 A 0 0 0 0 0 0 0 0 0 18 0 9 0 0 18 27 0 0 18 9 11 0 0 1.720 57 0.23
27 27 A 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 9 0 64 0 9 11 0 0 1.034 34 0.53
28 28 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 91 0 0 11 0 0 0.305 10 0.90
30 30 A 0 0 0 0 0 0 0 0 18 0 0 0 0 0 36 27 0 18 0 0 11 0 0 1.342 44 0.30
31 31 A 0 36 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.655 21 0.75
32 32 A 0 0 0 0 0 0 0 0 55 0 45 0 0 0 0 0 0 0 0 0 11 0 0 0.689 22 0.56
33 33 A 18 0 0 0 0 0 18 0 0 0 0 0 0 0 27 36 0 0 0 0 11 0 0 1.342 44 0.13
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 36 0 9 0 9 11 0 0 1.162 38 0.50
35 35 A 0 73 0 0 9 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 11 0 0 0.760 25 0.57
36 36 A 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 0 0 9 11 0 0 0.305 10 0.89
37 37 A 0 0 0 0 0 0 0 9 0 9 18 9 0 0 0 45 0 9 0 0 11 0 0 1.540 51 0.28
38 38 A 0 9 0 0 0 0 0 9 0 0 27 0 0 9 18 18 0 0 9 0 11 0 0 1.846 61 0.12
39 39 A 0 0 0 0 9 0 91 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.305 10 0.99
40 40 A 0 9 0 0 0 0 0 9 0 0 0 0 0 9 18 0 36 9 0 9 11 0 0 1.768 59 0.28
41 41 A 0 0 27 0 0 0 0 0 0 0 9 0 0 0 0 0 18 27 9 9 11 0 0 1.673 55 0.19
42 42 A 0 18 0 18 0 0 0 0 0 0 0 0 0 0 27 0 36 0 0 0 11 0 0 1.342 44 0.24
43 43 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
44 44 A 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 9 9 36 18 18 11 0 0 1.642 54 0.41
45 45 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 36 18 0 11 0 0 1.036 34 0.56
46 46 A 0 0 0 0 0 0 0 0 73 0 0 9 0 0 0 18 0 0 0 0 11 0 0 0.760 25 0.55
47 47 A 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 11 0 0 0.305 10 0.83
48 48 A 0 0 0 0 0 0 0 0 0 0 9 0 0 18 18 9 0 45 0 0 11 0 0 1.414 47 0.29
49 49 A 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 82 0 9 0 0 11 0 0 0.600 20 0.58
50 50 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.000 0 1.00
51 51 A 0 0 0 0 0 0 0 18 0 0 0 0 0 0 18 64 0 0 0 0 11 0 0 0.908 30 0.47
52 52 A 55 9 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0.916 30 0.78
53 53 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 73 0 0 0 0 11 0 0 0.586 19 0.79
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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