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= 041141
(575 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2L2N|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
The First Dsrbd Of Protein Hyl1
Length = 103
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
++K++LQE AQ+ P Y ++EGP H F++ V +G + S P F + + AE +
Sbjct: 18 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNR-KAAEQS 76
Query: 60 AAEVALDVLSKKGPSKVLAARVLDETG 86
AAEVAL L+K ++ + ETG
Sbjct: 77 AAEVALRELAKSSELSQCVSQPVHETG 103
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 87 VYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEP 134
V+K+ LQE + + L PVY V+ GP H +F TV L GV + P
Sbjct: 18 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLP 65
>pdb|3ADG|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
pdb|3ADI|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
pdb|3ADI|B Chain B, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
pdb|3ADI|C Chain C, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
Length = 73
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 1 MYKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAVNFNGETFES-PTFCSTLRQAEHA 59
++K++LQE AQ+ P Y ++EGP H F++ V +G + S P F + + AE +
Sbjct: 4 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNR-KAAEQS 62
Query: 60 AAEVALDVLSK 70
AAEVAL L+K
Sbjct: 63 AAEVALRELAK 73
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 87 VYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSFTGEP 134
V+K+ LQE + + L PVY V+ GP H +F TV L GV + P
Sbjct: 4 VFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLP 51
>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease
Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni
pdb|3N3W|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of Nuclease
Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni
Length = 248
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 2 YKNQLQELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAA 60
YK +LQE+ Q P Y +R GPDH +F+ A+ +G+ + + ++A+ A
Sbjct: 179 YKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKEL-ARAIAGSKKEAQQMA 237
Query: 61 AEVALDVL 68
A++AL+ L
Sbjct: 238 AKIALEKL 245
>pdb|2L2M|A Chain A, Solution Structure Of The Second Dsrbd Of Hyl1
Length = 77
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 82 LDETGVYKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTG 132
+ ETG+ KNLLQE + + +P+Y + G F+CTVE+ G+ +TG
Sbjct: 3 MHETGLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTG 54
>pdb|3ADJ|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
Length = 76
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 86 GVYKNLLQETSHRAGLKLPVYTTVR-SGPGHGPVFSCTVELAGVSFTG 132
G+ KNLLQE + + +P+Y + G F+CTVE+ G+ +TG
Sbjct: 4 GLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTG 51
>pdb|2LRS|A Chain A, The Second Dsrbd Domain From A. Thaliana Dicer-like 1
Length = 71
Score = 33.5 bits (75), Expect = 0.32, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 8 ELAQRSCFNLPSYSCIRE-GPDHAPRFKAAVNFNGETFESPTFC-----STLRQAEHAAA 61
++ R + +PSY C++E GP HA RF V N C ++++A+ +AA
Sbjct: 2 DICLRKNWPMPSYRCVKEGGPAHAKRFTFGVRVNTSDRGWTDECIGEPMPSVKKAKDSAA 61
Query: 62 EVALDVLSK 70
+ L++L+K
Sbjct: 62 VLLLELLNK 70
>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii
From Mycobacterium Tuberculosis
Length = 242
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 16/36 (44%)
Query: 2 YKNQLQELAQRSCFNLPSYSCIREGPDHAPRFKAAV 37
+K LQEL PSY GPDH F A V
Sbjct: 164 WKTSLQELTAARGLGAPSYLVTSTGPDHDKEFTAVV 199
>pdb|2L3J|A Chain A, The Solution Structure Of The Adar2 Dsrbm-Rna Complex
Reveals A Sequence-Specific Read Out Of The Minor
Groove
Length = 236
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 24 REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVAL 65
+ GP HAP F +V NG+ FE T ++A+ AAE AL
Sbjct: 27 QTGPVHAPLFVMSVEVNGQVFEGS--GPTKKKAKLHAAEKAL 66
>pdb|2DMY|A Chain A, Solution Structure Of Dsrm Domain In Spermatid Perinuclear
Rna-Bind Protein
Length = 97
Score = 28.9 bits (63), Expect = 7.1, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 75 KVLAARVLDETGVYKNLLQETSHRAGLKLPVYTTVRSGPGHGPVFSCTVELAGVSF 130
K+L ++ +D + L++ R GL+ + + +SGP H PVF+ +V++ G ++
Sbjct: 9 KILDSKAID---LMNALMRLNQIRPGLQYKLLS--QSGPVHAPVFTMSVDVDGTTY 59
>pdb|2B7T|A Chain A, Structure Of Adar2 Dsrbm1
Length = 73
Score = 28.9 bits (63), Expect = 8.0, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 24 REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVAL 65
+ GP HAP F +V NG+ FE T ++A+ AAE AL
Sbjct: 27 QTGPVHAPLFVMSVEVNGQVFEGSG--PTKKKAKLHAAEKAL 66
>pdb|2L3C|A Chain A, Solution Structure Of Adar2 Dsrbm1 Bound To Lsl Rna
Length = 74
Score = 28.9 bits (63), Expect = 8.2, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 24 REGPDHAPRFKAAVNFNGETFESPTFCSTLRQAEHAAAEVAL 65
+ GP HAP F +V NG+ FE T ++A+ AAE AL
Sbjct: 27 QTGPVHAPLFVMSVEVNGQVFEGSG--PTKKKAKLHAAEKAL 66
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
0.316 0.131 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,285,000
Number of Sequences: 62578
Number of extensions: 566861
Number of successful extensions: 1095
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1081
Number of HSP's gapped (non-prelim): 23
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)