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= 001894
(999 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 95.1 bits (235), Expect = 2e-19, Method: Composition-based stats.
Identities = 45/96 (46%), Positives = 69/96 (71%), Gaps = 2/96 (2%)
Query: 105 VRVIQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVY 164
VRV+Q+NLV++VGL L D ++L+R EYFG++GK+ KV ++ + + Q P + S Y
Sbjct: 10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP--SASAY 67
Query: 165 ITYSKEEEAVRCIQSVHGFVLEGKSLKACFGTTKYC 200
+TY + E+A+R IQ V+ V++G++LKA GTTKYC
Sbjct: 68 VTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 67.0 bits (162), Expect = 5e-11, Method: Composition-based stats.
Identities = 25/55 (45%), Positives = 34/55 (61%), Gaps = 5/55 (9%)
Query: 9 CPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKE 63
CPLC E +++ D PC CGY+IC +CWH I + + G CPACR PY ++
Sbjct: 3 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRI-----RTDENGLCPACRKPYPED 52
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 65.1 bits (157), Expect = 2e-10, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 35/58 (60%), Gaps = 5/58 (8%)
Query: 9 CPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPYDKEKIV 66
CPLC E +++ D PC CGY+IC +CWH I + + G CPACR PY ++ V
Sbjct: 14 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRI-----RTDENGLCPACRKPYPEDPAV 66
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 37.4 bits (85), Expect = 0.042, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 10/90 (11%)
Query: 109 QRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYS 168
Q +++ +P D DL R+ FGQ+GK+L V + G + ++T+
Sbjct: 28 QPKRLHVSNIPFRFRDPDL---RQMFGQFGKILDVEIIFNERG-------SKGFGFVTFE 77
Query: 169 KEEEAVRCIQSVHGFVLEGKSLKACFGTTK 198
+A R + +HG V+EG+ ++ T +
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 36.6 bits (83), Expect = 0.063, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 18/88 (20%)
Query: 110 RNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSM-----SRTAAGVIQQFPNNTCSVY 164
++ VY+ LP +L + DL + F +YGKV+KV++ +R + GV +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYR---IFSKYGKVVKVTIMKDKDTRKSKGV----------AF 62
Query: 165 ITYSKEEEAVRCIQSVHGFVLEGKSLKA 192
I + ++ A C ++++ L G+ +KA
Sbjct: 63 ILFLDKDSAQNCTRAINNKQLFGRVIKA 90
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 36.6 bits (83), Expect = 0.067, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 10/86 (11%)
Query: 113 VYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEE 172
+++ +P D DL R+ FGQ+GK+L V + G + ++T+ +
Sbjct: 18 LHVSNIPFRFRDPDL---RQMFGQFGKILDVEIIFNERG-------SKGFGFVTFENSAD 67
Query: 173 AVRCIQSVHGFVLEGKSLKACFGTTK 198
A R + +HG V+EG+ ++ T +
Sbjct: 68 ADRAREKLHGTVVEGRKIEVNNATAR 93
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 113 VYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEE 172
++I LP GD+DLLQ F +G V+ + + +Q + C +++Y
Sbjct: 28 LFIYHLPQEFGDQDLLQ---MFMPFGNVVSAKVF-----IDKQTNLSKCFGFVSYDNPVS 79
Query: 173 AVRCIQSVHGFVLEGKSLKA 192
A IQS++GF + K LK
Sbjct: 80 AQAAIQSMNGFQIGMKRLKV 99
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 33.9 bits (76), Expect = 0.47, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 6 EKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIMDMAEKEETEGRCPACRSPY 60
E TCP+C E + ++ C + C C + + +G CP CR PY
Sbjct: 19 EVTCPICLELL----KEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPY 69
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.1 bits (74), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 14/83 (16%)
Query: 113 VYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITYSKEEE 172
VY G+ L D+ + R+ F +G++++ I+ FP S ++ +S E
Sbjct: 28 VYCGGIASGLTDQLM---RQTFSPFGQIME----------IRVFPEKGYS-FVRFSTHES 73
Query: 173 AVRCIQSVHGFVLEGKSLKACFG 195
A I SV+G +EG +K +G
Sbjct: 74 AAHAIVSVNGTTIEGHVVKCYWG 96
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 6 EKTCPLCAEEMDLTDQQLKPCKCGYEICVWCW--HHIMDMAEKEETEGRCPACRSPYDKE 63
E TCP+C ++L Q L CG+ C C +H M +K E+ CP CR Y E
Sbjct: 19 EVTCPIC---LELLTQPLSL-DCGHSFCQACLTANHKKSMLDKGESS--CPVCRISYQPE 72
Query: 64 KI 65
I
Sbjct: 73 NI 74
>pdb|1X4W|A Chain A, Solution Structure Of The Zf-An1 Domain From Human
Hypothetical Protein Flj13222
Length = 67
Score = 31.2 bits (69), Expect = 3.3, Method: Composition-based stats.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 4 EGEKTCPLCAEEMDLTDQQLKPCKCGYEICV 34
+ + C C +++L Q+L C+CGY C+
Sbjct: 13 KSRRRCFQCQTKLELVQQELGSCRCGYVFCM 43
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.8 bits (68), Expect = 3.8, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 108 IQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITY 167
I+ +Y+ LP + D+ L FG+YG +++ ++ R + P ++ Y
Sbjct: 87 IKDTNLYVTNLPRTITDDQL---DTIFGKYGSIVQKNILRDK---LTGRPRGV--AFVRY 138
Query: 168 SKEEEAVRCIQSVHGFVLEGKS 189
+K EEA I +++ + EG S
Sbjct: 139 NKREEAQEAISALNNVIPEGGS 160
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 30.0 bits (66), Expect = 5.9, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 108 IQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITY 167
I+ +Y+ LP + D+ L FG+YG +++ ++ R + P ++ Y
Sbjct: 98 IKDTNLYVTNLPRTITDDQL---DTIFGKYGSIVQKNILRDK---LTGRPRGV--AFVRY 149
Query: 168 SKEEEAVRCIQSVHGFVLEGKS 189
+K EEA I +++ + EG S
Sbjct: 150 NKREEAQEAISALNNVIPEGGS 171
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.0 bits (66), Expect = 6.4, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 111 NLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSM 145
N +++ G+P N G+ +L REYF ++G V +V M
Sbjct: 11 NKIFVGGIPHNCGETEL---REYFKKFGVVTEVVM 42
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 30.0 bits (66), Expect = 7.2, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 108 IQRNLVYIVGLPLNLGDEDLLQRREYFGQYGKVLKVSMSRTAAGVIQQFPNNTCSVYITY 167
I+ +Y+ LP + D+ L FG+YG +++ ++ R + P ++ Y
Sbjct: 11 IKDTNLYVTNLPRTITDDQL---DTIFGKYGSIVQKNILRDK---LTGRPRGV--AFVRY 62
Query: 168 SKEEEAVRCIQSVHGFVLEGKS 189
+K EEA I +++ + EG S
Sbjct: 63 NKREEAQEAISALNNVIPEGGS 84
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 29.6 bits (65), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 9 CPLCAEEMDLTDQQLKP--CKCGYEICVWCWHHIMDMAEKEETEG-RCPAC 56
CP+C E T++QL+P CG+ IC C ++ G RCP C
Sbjct: 18 CPICME--SFTEEQLRPKLLHCGHTICRQCLEKLL----ASSINGVRCPFC 62
>pdb|3EKS|A Chain A, Crystal Structure Of Monomeric Actin Bound To Cytochalasin
D
pdb|3EKU|A Chain A, Crystal Structure Of Monomeric Actin Bound To Cytochalasin
D
pdb|3EL2|A Chain A, Crystal Structure Of Monomeric Actin Bound To Ca-Atp
Length = 375
Score = 29.6 bits (65), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 20/92 (21%), Positives = 44/92 (47%), Gaps = 13/92 (14%)
Query: 512 ETGKSITSKNDAFVSRE--------PFDWRTDPTQAATDASPQEEED-----VLSFDNQR 558
E G S T+ + + R+ D+ + AA+ +S ++ + V++ N+R
Sbjct: 195 ERGYSFTTTEEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELKDGQVITIGNER 254
Query: 559 LKDPEVVCRSNYLPKSANSLHVTNHSSSLKSN 590
+ PE + + ++L A +H T ++S +K +
Sbjct: 255 FRCPEALFQPSFLGMEACGIHETTYNSIMKCD 286
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
0.313 0.129 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,288,687
Number of Sequences: 62578
Number of extensions: 1178589
Number of successful extensions: 1815
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1802
Number of HSP's gapped (non-prelim): 22
length of query: 999
length of database: 14,973,337
effective HSP length: 108
effective length of query: 891
effective length of database: 8,214,913
effective search space: 7319487483
effective search space used: 7319487483
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)