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= psy16592
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 32/55 (58%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K+NAVALW+WD+ ++ CAICRNH+MD CI CQA A CTVAW
Sbjct: 30 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEE--CTVAWG 82
>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 98
Score = 70.1 bits (170), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/55 (58%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K+NAVALW+WD+ ++ CAICRNH+MD CI CQA A CTVAW
Sbjct: 11 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEE--CTVAWG 63
>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation.
pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 106
Score = 70.1 bits (170), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/55 (58%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K+NAVALW+WD+ ++ CAICRNH+MD CI CQA A CTVAW
Sbjct: 19 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEE--CTVAWG 71
>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
pdb|2HYE|D Chain D, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 108
Score = 70.1 bits (170), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/55 (58%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K+NAVALW+WD+ ++ CAICRNH+MD CI CQA Q CTVAW
Sbjct: 21 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQAN--QASATSEECTVAWG 73
>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 90
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 32/55 (58%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K+NAVALW+WD+ ++ CAICRNH+MD CI CQA Q CTVAW
Sbjct: 3 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQAN--QASATSEECTVAWG 55
>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 106
Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/55 (56%), Positives = 38/55 (69%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K+NAVALW+WD+ ++ CAICRNH+ D CI CQA A CTVAW
Sbjct: 19 RFEVKKWNAVALWAWDIVVDNCAICRNHIXDLCIECQANQASATSEE--CTVAWG 71
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 35/55 (63%), Gaps = 2/55 (3%)
Query: 69 RFTVRKFNAVALWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
RF V+K NA A +WD+ ++ CAICRNH+MD CI CQA A CTVAW
Sbjct: 13 RFEVKKSNASAQSAWDIVVDNCAICRNHIMDLCIECQANQA--SATSEECTVAWG 65
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 29/44 (65%), Gaps = 5/44 (11%)
Query: 80 LWSWDMDMETCAICRNHLMDECILCQARDAQDEPPPNGCTVAWA 123
+WSWD++ +TCAICR +MD C+ CQA + Q++ C V W
Sbjct: 8 MWSWDVECDTCAICRVQVMDACLRCQAENKQED-----CVVVWG 46
>pdb|3IR8|A Chain A, Red Fluorescent Protein Mkeima At Ph 7.0
pdb|3IR8|B Chain B, Red Fluorescent Protein Mkeima At Ph 7.0
Length = 221
Score = 30.8 bits (68), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 62 SEYP-DVPRFTVRKFNAVALWSWDMDMETCAICR----NHLMDECILCQARDAQDEPPPN 116
++YP D+P + + F W M+ E A+C + + C + + + + PPN
Sbjct: 69 TKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPN 128
Query: 117 G 117
G
Sbjct: 129 G 129
>pdb|2WHS|A Chain A, Fluorescent Protein Mkeima At Ph 3.8
pdb|2WHS|B Chain B, Fluorescent Protein Mkeima At Ph 3.8
pdb|2WHS|C Chain C, Fluorescent Protein Mkeima At Ph 3.8
pdb|2WHS|D Chain D, Fluorescent Protein Mkeima At Ph 3.8
pdb|2WHT|A Chain A, Fluorescent Protein Mkeima At Ph 5.6
pdb|2WHT|B Chain B, Fluorescent Protein Mkeima At Ph 5.6
pdb|2WHT|C Chain C, Fluorescent Protein Mkeima At Ph 5.6
pdb|2WHT|D Chain D, Fluorescent Protein Mkeima At Ph 5.6
pdb|2WHU|A Chain A, Fluorescent Protein Mkeima At Ph 8.0
pdb|2WHU|B Chain B, Fluorescent Protein Mkeima At Ph 8.0
pdb|2WHU|C Chain C, Fluorescent Protein Mkeima At Ph 8.0
pdb|2WHU|D Chain D, Fluorescent Protein Mkeima At Ph 8.0
Length = 240
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 62 SEYP-DVPRFTVRKFNAVALWSWDMDMETCAICR----NHLMDECILCQARDAQDEPPPN 116
++YP D+P + + F W M+ E A+C + + C + + + + PPN
Sbjct: 88 TKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPN 147
Query: 117 G 117
G
Sbjct: 148 G 148
>pdb|1X87|A Chain A, 2.4a X-Ray Structure Of Urocanase Protein Complexed With
Nad
pdb|1X87|B Chain B, 2.4a X-Ray Structure Of Urocanase Protein Complexed With
Nad
Length = 551
Score = 28.5 bits (62), Expect = 1.2, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 29 RKLQIQELINEELQKMKEDRELNRTYKKVLDLRSEYPDVPRFTVRKFNAVALW-SWD 84
R + E I + L +++ D L K + + +PD PR + N V W +WD
Sbjct: 55 RNWECYEAIVDTLLRLENDETLLIQSGKPVAVFRTHPDAPRVLIANSNLVPAWATWD 111
>pdb|1TA8|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
Length = 332
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 46 EDRELNRTYKKVLDLRSEYPDV 67
ED +R YK+++D+ +E+PD+
Sbjct: 38 EDYVYDRLYKELVDIETEFPDL 59
>pdb|1TAE|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|1TAE|B Chain B, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|1TAE|C Chain C, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|1TAE|D Chain D, Structural Rearrangement Accompanying Nad+ Synthesis
Within A Bacterial Dna Ligase Crystal
pdb|3BA8|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
pdb|3BA9|A Chain A, Structural Basis For Inhbition Of Nad-Dependent Ligase
pdb|3BAA|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
pdb|3BAB|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+
Dependent Dna Ligase
Length = 332
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 46 EDRELNRTYKKVLDLRSEYPDV 67
ED +R YK+++D+ +E+PD+
Sbjct: 38 EDYVYDRLYKELVDIETEFPDL 59
>pdb|2CU9|A Chain A, Crystal Structure Of Histone Chaperone Cia1
pdb|2DZE|A Chain A, Crystal Structure Of Histone Chaperone Asf1 In Complex
With A C-Terminus Of Histone H3
pdb|2DZE|B Chain B, Crystal Structure Of Histone Chaperone Asf1 In Complex
With A C-Terminus Of Histone H3
pdb|2Z34|A Chain A, Crystal Structure Of Spcia1ASF1 COMPLEX WITH HIP1
pdb|2Z34|B Chain B, Crystal Structure Of Spcia1ASF1 COMPLEX WITH HIP1
pdb|2Z3F|A Chain A, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|B Chain B, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|C Chain C, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|D Chain D, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|E Chain E, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|F Chain F, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|G Chain G, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
pdb|2Z3F|H Chain H, Crystal Structure Of Spcia1ASF1 COMPLEXED WITH CAC2
PEPTIDE
Length = 161
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 29/46 (63%), Gaps = 5/46 (10%)
Query: 28 MRKLQIQELINEELQKMKEDRELNRTYKKVLDLRSEYPDVPRFTVR 73
M L +QE+ + E++K+K D +++ ++ +L +E P V RF ++
Sbjct: 118 MEGLNLQEMDDAEIKKVKVD--ISKVWRSIL---AEKPRVTRFNIQ 158
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
0.319 0.131 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,032,580
Number of Sequences: 62578
Number of extensions: 144123
Number of successful extensions: 387
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 375
Number of HSP's gapped (non-prelim): 35
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)