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= 040106
(324 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 90.1 bits (222), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 40/104 (38%), Positives = 64/104 (61%), Gaps = 1/104 (0%)
Query: 101 SPTLLLSNMYQRPDMITPGVDAQGQPIDPRKIQEHFEDFYEDIFEELS-KFGEIECLNVC 159
S T+ L N+Y+ P + D + ++QEH+++F+E++F E+ K+GE+E +NVC
Sbjct: 1 SQTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC 60
Query: 160 DNLADHMIGNVYVQFRXXXXXXXXXXXXXGRFYSGRPIIVEFSP 203
DNL DH++GNVYV+FR R+++G+PI E SP
Sbjct: 61 DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 141 EDIFEELSKFGEIECLNVCDNLADHMIGNVYVQFRXXXXXXXXXXXXXGRFYSGRPIIVE 200
ED+ E SKFG+I L + D H G V FR GR++ GR I +
Sbjct: 41 EDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 97
Query: 201 -FSPVTDFREA 210
+ TD++
Sbjct: 98 AWDGTTDYQSG 108
>pdb|1WPW|A Chain A, Crystal Structure Of Ipmdh From Sulfolobus Tokodaii
pdb|1WPW|B Chain B, Crystal Structure Of Ipmdh From Sulfolobus Tokodaii
Length = 336
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 106 LSNMYQ--RPDMITPGVDAQGQPIDPRKIQEHFEDFYEDIFEELSKFGEIECLNVCDNLA 163
+ +MY RP PG+D + +D ++E+ ED Y+ FE + G + + A
Sbjct: 87 IYDMYANIRPAKSIPGIDTKYGNVDILIVRENTEDLYKG-FEHIVSDGVAVGMKIITRFA 145
Query: 164 DHMIGNVYVQF 174
I V + F
Sbjct: 146 SERIAKVGLNF 156
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 127 IDPRKIQEHFEDFYEDIFEELSKFGEIECLNV-----CDNLADHMIGNVYVQFRXXXXXX 181
+DP+ I + E ++ EE KFG + + + + +I ++V+F
Sbjct: 133 VDPKDIDDDLEG---EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETH 189
Query: 182 XXXXXXXGRFYSGRPIIVE 200
GR+++GR ++ E
Sbjct: 190 KAIQALNGRWFAGRKVVAE 208
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 127 IDPRKIQEHFEDFYEDIFEELSKFGEIECLNV-----CDNLADHMIGNVYVQFRXXXXXX 181
+DP+ I + E ++ EE KFG + + + + +I ++V+F
Sbjct: 24 VDPKDIDDDLEG---EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETH 80
Query: 182 XXXXXXXGRFYSGRPIIVE 200
GR+++GR ++ E
Sbjct: 81 KAIQALNGRWFAGRKVVAE 99
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 127 IDPRKIQEHFEDFYEDIFEELSKFGEIECLNV-----CDNLADHMIGNVYVQFRXXXXXX 181
+DP+ I + E ++ EE KFG + + + + +I ++V+F
Sbjct: 29 VDPKDIDDDLEG---EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETH 85
Query: 182 XXXXXXXGRFYSGRPIIVE 200
GR+++GR ++ E
Sbjct: 86 KAIQALNGRWFAGRKVVAE 104
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
0.323 0.140 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,580,136
Number of Sequences: 62578
Number of extensions: 268139
Number of successful extensions: 642
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 640
Number of HSP's gapped (non-prelim): 11
length of query: 324
length of database: 14,973,337
effective HSP length: 99
effective length of query: 225
effective length of database: 8,778,115
effective search space: 1975075875
effective search space used: 1975075875
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)