BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy2728
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J3T|C Chain C, The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 Complex
Length = 145
Score = 96.7 bits (239), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 45/73 (61%), Positives = 58/73 (79%)
Query: 67 EGKLMYGMLFSLKSFVSKISPLDSKTGFLSYKTTKYALHLYETPTGLKFVLNTDVQAQDV 126
E KLMYGMLFS++SFVSK+SPLD K GFLS++T++Y LH YETPTG+K V+NTD+ +
Sbjct: 34 EYKLMYGMLFSIRSFVSKMSPLDMKDGFLSFQTSRYKLHYYETPTGIKVVMNTDLGVGPI 93
Query: 127 RKFLASVYSKVYV 139
R L +YS +YV
Sbjct: 94 RDVLHHIYSALYV 106
>pdb|3CUE|C Chain C, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|I Chain I, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|O Chain O, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|U Chain U, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
Length = 159
Score = 60.1 bits (144), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 31/73 (42%), Positives = 43/73 (58%)
Query: 67 EGKLMYGMLFSLKSFVSKISPLDSKTGFLSYKTTKYALHLYETPTGLKFVLNTDVQAQDV 126
+ KL+YGM+FSL+S K+S K S T KY +H Y T +GL FVL +D + Q
Sbjct: 40 DAKLLYGMIFSLRSITQKLSKGSVKNDIRSISTGKYRVHTYCTASGLWFVLLSDFKQQSY 99
Query: 127 RKFLASVYSKVYV 139
+ L +YS +YV
Sbjct: 100 TQVLQYIYSHIYV 112
>pdb|2ZMV|A Chain A, Crystal Structure Of Synbindin
pdb|2ZMV|B Chain B, Crystal Structure Of Synbindin
Length = 227
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 69 KLMYGMLF-SLKSFVSKISPLDSKTGFLSYKTTKYALHLYETPTGLKFVLNTDVQAQDVR 127
KLM +F SL + S++SP +G +T + LH Y+T TG+KFV+ D + +
Sbjct: 108 KLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGID 167
Query: 128 KFLASVY 134
L +Y
Sbjct: 168 SLLRKIY 174
>pdb|2J3T|D Chain D, The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 Complex
Length = 219
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 69 KLMYGMLF-SLKSFVSKISPLDSKTGFLSYKTTKYALHLYETPTGLKFVLNTDVQAQDVR 127
KLM +F SL + S++SP +G +T + LH Y+T TG+KFV+ D + +
Sbjct: 108 KLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGID 167
Query: 128 KFLASVY 134
L +Y
Sbjct: 168 SLLRKIY 174
>pdb|2J5L|A Chain A, Structure Of A Plasmodium Falciparum Apical Membrane
Antigen 1-Fab F8.12.19 Complex
Length = 581
Score = 30.0 bits (66), Expect = 0.49, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 8 EHRPHPQEYHHPKQEYHPKQE 28
EHR HP+EY +P + H Q+
Sbjct: 11 EHREHPKEYEYPLHQEHTYQQ 31
>pdb|3HO7|A Chain A, Crystal Structure Of Oxyr From Porphyromonas Gingivalis
pdb|3HO7|B Chain B, Crystal Structure Of Oxyr From Porphyromonas Gingivalis
Length = 232
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 20 KQEYHPKQEYPKPLIGYDRSATPADVYRLILGQSVDH 56
+Q+Y +++ + LIG RSA P+D+++L GQ + H
Sbjct: 194 RQDY-SRRKLREQLIGLLRSAVPSDMHKLQTGQHLAH 229
>pdb|3CUE|A Chain A, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|G Chain G, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|M Chain M, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
pdb|3CUE|S Chain S, Crystal Structure Of A Trapp Subassembly Activating The
Rab Ypt1p
Length = 219
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 90 SKTGFLSYKTTKYALHLYETPTGLKFV 116
+K+G T ++ + +Y+T TGLKFV
Sbjct: 115 NKSGLRQLCTDQFTMFIYQTLTGLKFV 141
>pdb|3ISM|A Chain A, Crystal Structure Of The EndogENDOGI COMPLEX: MECHANISM OF
ENDOG Inhibition
pdb|3ISM|B Chain B, Crystal Structure Of The EndogENDOGI COMPLEX: MECHANISM OF
ENDOG Inhibition
Length = 267
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 33 LIGYDRSATPADVYRLILGQSVDH 56
+IG + A P Y++I+G+S DH
Sbjct: 178 VIGANTVAVPTHFYKVIVGESADH 201
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 7 PEHRPHPQEYHHPKQEYHPK 26
P H PHP EY QEY P+
Sbjct: 50 PSHYPHPYEYEIDHQEYSPE 69
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.134 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,263,393
Number of Sequences: 62578
Number of extensions: 156440
Number of successful extensions: 339
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 328
Number of HSP's gapped (non-prelim): 11
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)