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= psy7604
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The
P1 Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The
C2 Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The
C2 Space Group
Length = 118
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 28 PSTSSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
P SK +C IC + + T C HRFC C
Sbjct: 13 PPLESKYECPICLMALREAVQTP--CGHRFCKAC 44
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 28 PSTSSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
P SK +C IC + + T C HRFC C
Sbjct: 20 PPLESKYECPICLMALREAVQT--PCGHRFCKAC 51
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 28.5 bits (62), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 29 STSSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
S S+ C IC + +T MT EC HRFC C
Sbjct: 50 SLHSELMCPICLDMLKNT-MTTKECLHRFCADC 81
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 28.5 bits (62), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 26 SQPSTSSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
S S S+ C IC + +T MT EC HRFC C
Sbjct: 27 SPRSLHSELMCPICLDMLKNT-MTTKECLHRFCADC 61
>pdb|1NYT|A Chain A, Shikimate Dehydrogenase Aroe Complexed With Nadp+
pdb|1NYT|B Chain B, Shikimate Dehydrogenase Aroe Complexed With Nadp+
pdb|1NYT|C Chain C, Shikimate Dehydrogenase Aroe Complexed With Nadp+
pdb|1NYT|D Chain D, Shikimate Dehydrogenase Aroe Complexed With Nadp+
Length = 271
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 29 STSSKSKCEICFTNMPSTLM-TGLECSHRFCTQ------CWCEYLTTKIIQEGMGQTIAC 81
+TSS +I +PS+L+ G+ C F + WCE +K +G+G +A
Sbjct: 187 ATSSGISGDI--PAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQ 244
Query: 82 AAH 84
AAH
Sbjct: 245 AAH 247
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 28 PSTSSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
P SK +C IC + + T C HRFC C
Sbjct: 13 PPLESKYECPICLMALREAVQTP--CGHRFCKAC 44
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 29 STSSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
S S+ C IC + +T MT EC HRFC C
Sbjct: 49 SLHSELMCPICLDMLKNT-MTTKECLHRFCADC 80
>pdb|3QDG|D Chain D, The Complex Between Tcr Dmf5 And Human Class I Mhc Hla-A2
With The Bound Mart-1(26-35)(A27l) Peptide
pdb|3QDJ|D Chain D, The Complex Between Tcr Dmf5 And Human Class I Mhc Hla-A2
With The Bound Mart-1(27-35) Nonameric Peptide
Length = 199
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 4 YYDGDQE------QLFAEARVINPLVKNSQPSTSSKSKCEICFTNMPSTLMTGLECS 54
Y +GD+E QL ++ ++ L+++SQPS S+ C + F G E S
Sbjct: 50 YSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELS 106
>pdb|3QEU|A Chain A, The Crystal Structure Of Tcr Dmf5
pdb|3QEU|D Chain D, The Crystal Structure Of Tcr Dmf5
Length = 202
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 4 YYDGDQE------QLFAEARVINPLVKNSQPSTSSKSKCEICFTNMPSTLMTGLECS 54
Y +GD+E QL ++ ++ L+++SQPS S+ C + F G E S
Sbjct: 51 YSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELS 107
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 31 SSKSKCEICFTNMPSTLMTGLECSHRFCTQC 61
SK +C IC + + T C HRFC C
Sbjct: 4 GSKYECPICLMALREAVQT--PCGHRFCKAC 32
>pdb|3MAW|A Chain A, Structure Of The Newcastle Disease Virus F Protein In The
Po Conformation
pdb|3MAW|B Chain B, Structure Of The Newcastle Disease Virus F Protein In The
Po Conformation
Length = 483
Score = 26.2 bits (56), Expect = 5.4, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 25 NSQPSTSSKSKCEICFTNMPSTLMTGLECSHRFCTQCWCEYLTTKIIQEGMGQTIACA-A 83
N S SK E T P + G ++ T C C II + G+ ++
Sbjct: 333 NGNTSACMYSKTEGALTT-PYMTLKGSVIANCKMTTCRCAD-PPGIISQNYGEAVSLIDR 390
Query: 84 HGCNILVDDGTVMRL 98
H CN+L DG +RL
Sbjct: 391 HSCNVLSLDGITLRL 405
>pdb|2ECY|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger)" Domain Of Tnf Receptor-Associated Factor 3
Length = 66
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 33 KSKCEICFTNMPSTLMTGLECSHRFCTQCWCEYLTT 68
K KCE C + S T EC HRFC C L++
Sbjct: 15 KYKCEKCHLVLCSPKQT--ECGHRFCESCMAALLSS 48
>pdb|3QH3|A Chain A, The Crystal Structure Of Tcr A6
pdb|3QH3|C Chain C, The Crystal Structure Of Tcr A6
Length = 194
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 1 MERYYDGDQE------QLFAEARVINPLVKNSQPSTSSKSKCEI 38
M Y +GD+E QL ++ ++ L+++SQPS S+ C +
Sbjct: 47 MSIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAV 90
>pdb|1QSE|D Chain D, Structure Of Human A6-Tcr Bound To Hla-A2 Complexed With
Altered Htlv-1 Tax Peptide V7r
pdb|1QSF|D Chain D, Structure Of A6-Tcr Bound To Hla-A2 Complexed With
Altered Htlv-1 Tax Peptide Y8a
pdb|2GJ6|D Chain D, The Complex Between Tcr A6 And Human Class I Mhc Hla-a2
With The Modified Htlv-1 Tax (y5k-4-[3-indolyl]-butyric
Acid) Peptide
pdb|3D39|D Chain D, The Complex Between Tcr A6 And Human Class I Mhc Hla-A2
With The Modified Htlv-1 Tax
(Y5(4-Fluorophenylalanine)) Peptide
pdb|3D3V|D Chain D, The Complex Between Tcr A6 And Human Class I Mhc Hla-A2
With The Modified Htlv-1 Tax
(Y5(3,4-Difluorophenylalanine)) Peptide
pdb|3H9S|D Chain D, The Complex Between Tcr A6 And Human Class I Mhc Hla-A2
With The Bound Tel1p Peptide
pdb|3PWP|D Chain D, The Complex Between Tcr A6 And Human Class I Mhc Hla-A2
With The Bound Hud Peptide
pdb|3QFJ|D Chain D, The Complex Between Tcr A6 And Human Class I Mhc Hla-A2
With The Modified Tax (Y5f) Peptide
Length = 200
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 1 MERYYDGDQE------QLFAEARVINPLVKNSQPSTSSKSKCEI 38
M Y +GD+E QL ++ ++ L+++SQPS S+ C +
Sbjct: 47 MSIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAV 90
>pdb|1QRN|D Chain D, Crystal Structure Of Human A6 Tcr Complexed With Hla-A2
Bound To Altered Htlv-1 Tax Peptide P6a
Length = 200
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 1 MERYYDGDQE------QLFAEARVINPLVKNSQPSTSSKSKCEI 38
M Y +GD+E QL ++ ++ L+++SQPS S+ C +
Sbjct: 47 MSIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAV 90
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
0.322 0.134 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,430,819
Number of Sequences: 62578
Number of extensions: 117247
Number of successful extensions: 271
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 260
Number of HSP's gapped (non-prelim): 37
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)