Complet list of 1prb hssp file
Complete list of 1prb.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1PRB
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 2014-05-05
HEADER ALBUMIN-BINDING PROTEIN 15-JAN-97 1PRB
COMPND MOL_ID: 1; MOLECULE: PROTEIN PAB; CHAIN: A; FRAGMENT: ALBUMIN-BINDING
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: FINEGOLDIA MAGNA ATCC 29328; ORGANISM_
AUTHOR M.U.JOHANSSON,M.DE CHATEAU,M.WIKSTROM,S.FORSEN,T.DRAKENBERG, L.BJORCK
DBREF 1PRB A 1 53 UNP Q51911 PAB_PEPMA 213 265
SEQLENGTH 53
NCHAIN 1 chain(s) in 1PRB data set
NALIGN 22
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 : PAB_FINMA 2VDB 1.00 1.00 1 53 213 265 53 0 0 387 Q51911 Peptostreptococcal albumin-binding protein OS=Finegoldia magna GN=pab PE=1 SV=1
2 : Q51918_FINMA1YMH 0.85 0.94 1 53 727 779 53 0 0 992 Q51918 Protein L (Precursor) OS=Finegoldia magna PE=1 SV=1
3 : E1KY41_FINMA 0.79 0.91 1 53 511 563 53 0 0 954 E1KY41 LPXTG-motif cell wall anchor domain protein OS=Finegoldia magna BVS033A4 GN=pab PE=4 SV=1
4 : B0S3H9_FINM2 0.70 0.87 7 52 389 434 46 0 0 2230 B0S3H9 Putative albumin-binding protein homolog-1 OS=Finegoldia magna (strain ATCC 29328) GN=FMG_1501 PE=4 SV=1
5 : D6S921_FINMA 0.70 0.85 7 52 382 427 46 0 0 1814 D6S921 GA module OS=Finegoldia magna ATCC 53516 GN=HMPREF0391_10957 PE=4 SV=1
6 : D9PRS5_FINMA 0.70 0.87 7 52 399 444 46 0 0 1842 D9PRS5 Putative phage tail component domain protein OS=Finegoldia magna ACS-171-V-Col3 GN=HMPREF9261_1352 PE=4 SV=1
7 : E1KY24_FINMA 0.70 0.87 7 52 369 414 46 0 0 1988 E1KY24 Leucine Rich Repeat protein OS=Finegoldia magna BVS033A4 GN=HMPREF9289_1939 PE=4 SV=1
8 : B0S4H6_FINM2 0.63 0.85 7 52 179 224 46 0 0 509 B0S4H6 Albumin-binding protein homolog-4 OS=Finegoldia magna (strain ATCC 29328) GN=FMG_P0118 PE=4 SV=1
9 : K9EPZ2_9LACT 0.56 0.79 10 52 45 87 43 0 0 411 K9EPZ2 Uncharacterized protein OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_01331 PE=4 SV=1
10 : F3LZY8_9LACO 0.55 0.69 11 52 232 273 42 0 0 445 F3LZY8 Gram-positive signal peptide protein, YSIRK family OS=Lactobacillus iners SPIN 1401G GN=HMPREF9210_1187 PE=4 SV=1
11 : F0GRB1_9LACO 0.53 0.74 10 52 451 493 43 0 0 665 F0GRB1 Gram-positive signal peptide protein, YSIRK family OS=Lactobacillus iners UPII 60-B GN=HMPREF0523_0860 PE=4 SV=1
12 : K9EAV4_9LACT 0.52 0.74 10 51 152 193 42 0 0 513 K9EAV4 YSIRK family Gram-positive signal peptide OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_01330 PE=4 SV=1
13 : K9EXL1_9LACT 0.52 0.71 10 51 51 92 42 0 0 531 K9EXL1 Uncharacterized protein (Fragment) OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_00510 PE=4 SV=1
14 : E1NUT2_9LACO 0.50 0.69 11 52 348 389 42 0 0 561 E1NUT2 GA module OS=Lactobacillus iners LactinV 01V1-a GN=HMPREF9211_0601 PE=4 SV=1
15 : E3BZQ1_9LACO 0.50 0.69 11 52 505 546 42 0 0 718 E3BZQ1 Gram-positive signal peptide protein, YSIRK family OS=Lactobacillus iners LEAF 2062A-h1 GN=HMPREF9218_0753 PE=4 SV=1
16 : E3BRG6_9LACO 0.48 0.67 11 52 486 527 42 0 0 699 E3BRG6 Putative immunoglobulin G-binding protein G OS=Lactobacillus iners LEAF 2053A-b GN=HMPREF9216_0952 PE=4 SV=1
17 : E6LV42_9LACO 0.48 0.67 11 52 524 565 42 0 0 737 E6LV42 Gram-positive signal peptide protein, YSIRK family OS=Lactobacillus iners ATCC 55195 GN=HMPREF9223_0874 PE=4 SV=1
18 : K9E8M0_9LACT 0.48 0.67 7 52 251 296 46 0 0 598 K9E8M0 YSIRK family Gram-positive signal peptide (Fragment) OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_01324 PE=4 SV=1
19 : E3BXE5_9LACO 0.47 0.67 7 51 255 299 45 0 0 611 E3BXE5 Gram-positive signal peptide protein, YSIRK family (Fragment) OS=Lactobacillus iners LEAF 2052A-d GN=HMPREF9217_0973 PE=4 SV=1
20 : K9E8I0_9LACT 0.41 0.65 7 52 209 254 46 0 0 665 K9E8I0 YSIRK family Gram-positive signal peptide OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_01026 PE=4 SV=1
21 : K9EAV1_9LACT 0.41 0.61 12 52 302 342 41 0 0 444 K9EAV1 Uncharacterized protein (Fragment) OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_01325 PE=4 SV=1
22 : I0SHA6_STRAP 0.39 0.67 3 51 110 157 49 1 1 234 I0SHA6 Gram-positive signal peptide protein, YSIRK family (Fragment) OS=Streptococcus anginosus subsp. whileyi CCUG 39159 GN=HMPREF1043_0296 PE=4 SV=1
## ALIGNMENTS 1 - 22
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A T 0 0 156 4 0 TTT
2 2 A I > + 0 0 84 4 0 III
3 3 A D T 3 + 0 0 123 5 0 DDD D
4 4 A Q T >> + 0 0 138 5 72 QEE A
5 5 A W G X4 + 0 0 126 5 0 WWW W
6 6 A L G 34 S- 0 0 98 5 87 LLL E
7 7 A L G <4 S+ 0 0 3 13 0 LLLLLLLL LLL L
8 8 A K << + 0 0 146 13 51 KKKKKKKK QEE E
9 9 A N S > S+ 0 0 75 13 70 NNNEEEEK AAQ A
10 10 A A H >>S+ 0 0 7 17 12 AAAAAAAAA AAA AAE A
11 11 A K H >5S+ 0 0 60 22 9 KKKKKKKKKKKKKKKKKKKQ K
12 12 A E H >5S+ 0 0 153 23 47 EEEEEEEEAENEEKKKKEKEDD
13 13 A D H <5S+ 0 0 127 23 80 DDDKKKKQEDVSAAAVVSSSSA
14 14 A A H >X5S+ 0 0 9 23 0 AAAAAAAAAAAAAAAAAAAAAA
15 15 A I H >XS+ 0 0 15 23 18 LLLLLLLLLLFVVFFFFLLLLL
19 19 A K T 3<5S+ 0 0 150 23 62 KKKKKKKKTNTKQTTTTQKQKN
20 20 A K T 345S+ 0 0 192 23 74 KEENENNAADKATKKKKAKGSQ
21 21 A A T <45S- 0 0 69 23 64 AAANNNNNDAAAAAAAAAAILY
22 22 A G T <5S+ 0 0 55 23 0 GGGGGGGGGGGGGGGGGGGGGG
23 23 A I < + 0 0 21 23 25 IIIIIIIIVIIFFIIIIAIIIV
24 24 A T + 0 0 100 22 23 TSKTTTTTTTTTTTTTTTTET.
25 25 A S > - 0 0 61 23 47 SSSSSSSSSGGDDGGGGSGNSS
26 26 A D H >>S+ 0 0 112 23 54 DDQEEEEKDDKQEKKKKPDDED
27 27 A F H 45S+ 0 0 133 23 85 FIFKKKKFLIIKKIIIIKITRY
28 28 A Y H 45S+ 0 0 14 23 19 YYFYYYYFWFFYYFFFFLFLLY
29 29 A F H X5S+ 0 0 36 23 91 FFFIIIIVFHHVAHHHHAHFFK
30 30 A N H >X5S+ 0 0 103 23 46 NDNEDEDDEKDDGDDDDEKGDK
31 31 A A H 3>4 S+ 0 0 0 23 2 IIIIIIIIIIIIIIIIIIIIIV
33 33 A N H << S+ 0 0 63 23 45 NNNNNNNNNDDNNDDDDDDRRN
34 34 A K H 3< S+ 0 0 171 23 70 KKNKKKKAKAAAAAAAASADES
35 35 A A S << S- 0 0 16 23 21 AAAAAAAGAAAQQAAAAAAAAA
36 36 A K S S- 0 0 148 23 43 KKKKKKKKNKKEEKKKKDKDTK
37 37 A T S >> S- 0 0 54 23 24 TTTTTTTTTTTTTTTTTSTSST
38 38 A V H 3> S+ 0 0 52 23 6 VVVVVVVVIVVVVVVVVVLVVV
39 39 A E H 3> S+ 0 0 158 23 24 EEEEEEEEEAEQQEEEEEEEEA
40 40 A E H <> S+ 0 0 88 23 32 EGGGGGGGGGGDDGGGGEGEEG
41 41 A V H X S+ 0 0 0 23 21 VVVVVVVVVVLVVLLLLVLVVV
42 42 A N H X S+ 0 0 65 23 59 NEENNNNKGNQNNQQKQDKKEK
43 43 A A H X S+ 0 0 39 23 55 AASAAAAASAAGAAAAARARQK
44 44 A L H >X S+ 0 0 24 23 53 LLLLLLLLLYYVVYYYYLYVLL
45 45 A K H 3X S+ 0 0 14 23 70 KKKKKKKKKVVKKVVVVKVKAQ
46 46 A N H 3< S+ 0 0 117 23 75 NNNDDDDENAARRAAAANASTA
47 47 A E H XX S+ 0 0 116 23 24 EEEEEEEEDEEEEEEEEDEDSQ
48 48 A I H 3X>S+ 0 0 0 23 55 IIIIIIILITTIITTTTFTIIV
49 49 A L H 3<5S+ 0 0 116 23 23 LLLIIIIILLLLLLLLLLLILV
50 50 A K H <45S+ 0 0 186 23 66 KKKKKKKKNAKTTKKAAEADEE
51 51 A A H <5S+ 0 0 41 23 54 AAAAASASAAATTAAAAVPVTS
52 52 A H T <5 0 0 85 19 31 HHHHHHHHRHH HHHHR RR
53 53 A A < 0 0 100 4 0 AAA
## 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 0 100 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
2 2 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 5 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 40 40 0 0 5 0 0 1.055 35 0.27
5 5 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.000 0 1.00
6 6 A 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 5 0 0 0.500 16 0.12
7 7 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 69 8 23 0 0 13 0 0 0.790 26 0.49
9 9 A 0 0 0 0 0 0 0 0 23 0 0 0 0 0 0 8 8 31 31 0 13 0 0 1.458 48 0.29
10 10 A 0 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 0 6 0 0 17 0 0 0.224 7 0.87
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 95 5 0 0 0 22 0 0 0.185 6 0.91
12 12 A 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 22 0 61 4 9 23 0 0 1.119 37 0.53
13 13 A 13 0 0 0 0 0 0 0 17 0 22 0 0 0 0 17 4 4 0 22 23 0 0 1.810 60 0.20
14 14 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.000 0 1.00
15 15 A 13 9 43 0 0 0 0 0 0 0 0 0 0 30 0 4 0 0 0 0 23 0 0 1.339 44 0.22
16 16 A 0 0 0 0 0 0 0 0 35 0 0 0 0 0 0 17 0 48 0 0 23 0 0 1.024 34 0.43
17 17 A 0 0 0 0 0 0 0 0 9 0 0 4 0 0 0 0 0 87 0 0 23 0 0 0.470 15 0.78
18 18 A 9 70 0 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.797 26 0.82
19 19 A 0 0 0 0 0 0 0 0 0 0 0 26 0 0 0 52 13 0 9 0 23 0 0 1.168 38 0.37
20 20 A 0 0 0 0 0 0 0 4 17 0 4 4 0 0 0 35 4 13 13 4 23 0 0 1.885 62 0.26
21 21 A 0 4 4 0 0 0 4 0 61 0 0 0 0 0 0 0 0 0 22 4 23 0 0 1.179 39 0.35
22 22 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.000 0 1.00
23 23 A 9 0 78 0 9 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 23 1 0 0.753 25 0.74
24 24 A 0 0 0 0 0 0 0 0 0 0 5 86 0 0 0 5 0 5 0 0 22 0 0 0.548 18 0.77
25 25 A 0 0 0 0 0 0 0 30 0 0 57 0 0 0 0 0 0 0 4 9 23 0 0 1.033 34 0.53
26 26 A 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 26 9 26 0 35 23 0 0 1.417 47 0.46
27 27 A 0 4 35 0 17 0 4 0 0 0 0 4 0 0 4 30 0 0 0 0 23 0 0 1.579 52 0.15
28 28 A 0 13 0 0 39 4 43 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 1.131 37 0.80
29 29 A 9 0 17 0 30 0 0 0 9 0 0 0 0 30 0 4 0 0 0 0 23 0 0 1.589 53 0.09
30 30 A 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 13 0 17 13 48 23 0 0 1.401 46 0.54
31 31 A 0 17 0 0 0 9 4 0 43 0 0 0 0 0 4 0 17 4 0 0 23 0 0 1.592 53 0.09
32 32 A 4 0 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.179 5 0.97
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 57 35 23 0 0 0.902 30 0.54
34 34 A 0 0 0 0 0 0 0 0 43 0 9 0 0 0 0 35 0 4 4 4 23 0 0 1.351 45 0.30
35 35 A 0 0 0 0 0 0 0 4 87 0 0 0 0 0 0 0 9 0 0 0 23 0 0 0.470 15 0.79
36 36 A 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 74 0 9 4 9 23 0 0 0.921 30 0.56
37 37 A 0 0 0 0 0 0 0 0 0 0 13 87 0 0 0 0 0 0 0 0 23 0 0 0.387 12 0.75
38 38 A 91 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.356 11 0.93
39 39 A 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 9 83 0 0 23 0 0 0.583 19 0.75
40 40 A 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 0 0 22 0 9 23 0 0 0.797 26 0.67
41 41 A 74 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.574 19 0.78
42 42 A 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 22 17 13 39 4 23 0 0 1.541 51 0.41
43 43 A 0 0 0 0 0 0 0 4 70 0 9 0 0 0 9 4 4 0 0 0 23 0 0 1.086 36 0.44
44 44 A 13 57 0 0 0 0 30 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.950 31 0.47
45 45 A 30 0 0 0 0 0 0 0 4 0 0 0 0 0 0 61 4 0 0 0 23 0 0 0.937 31 0.29
46 46 A 0 0 0 0 0 0 0 0 35 0 4 4 0 0 9 0 0 4 26 17 23 0 0 1.643 54 0.25
47 47 A 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 4 78 0 13 23 0 0 0.730 24 0.76
48 48 A 4 4 57 0 4 0 0 0 0 0 0 30 0 0 0 0 0 0 0 0 23 0 0 1.094 36 0.45
49 49 A 4 70 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0 0 0.739 24 0.77
50 50 A 0 0 0 0 0 0 0 0 17 0 0 9 0 0 0 52 0 13 4 4 23 0 0 1.394 46 0.34
51 51 A 9 0 0 0 0 0 0 0 61 4 13 13 0 0 0 0 0 0 0 0 23 0 0 1.182 39 0.46
52 52 A 0 0 0 0 0 0 0 0 0 0 0 0 0 79 21 0 0 0 0 0 19 0 0 0.515 17 0.69
53 53 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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