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= 033681
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OXW|A Chain A, The Crystal Structure Of Semet Patatin
pdb|1OXW|B Chain B, The Crystal Structure Of Semet Patatin
pdb|1OXW|C Chain C, The Crystal Structure Of Semet Patatin
Length = 373
Score = 64.7 bits (156), Expect = 1e-11, Method: Composition-based stats.
Identities = 36/94 (38%), Positives = 52/94 (55%), Gaps = 1/94 (1%)
Query: 12 DGDYQHNKIMEMLVVKFLHQTLTDVIIPTFDIRLLQPISFSTLKAKRNASKVSWLSDNCI 71
DG Y + E L +HQ LT+V+I +FDI+ +P+ F+ + + D
Sbjct: 113 DGKYLXQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKXYDISY 172
Query: 72 GTSAAPYYMPPYYFEMHASTGTK-KFNLVDGVVA 104
T+AAP Y PP+YF + S G + +FNLVDG VA
Sbjct: 173 STAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVA 206
>pdb|1KKO|A Chain A, Crystal Structure Of Citrobacter Amalonaticus
Methylaspartate Ammonia Lyase
pdb|1KKO|B Chain B, Crystal Structure Of Citrobacter Amalonaticus
Methylaspartate Ammonia Lyase
pdb|1KKR|A Chain A, Crystal Structure Of Citrobacter Amalonaticus
Methylaspartate Ammonia Lyase Containing
(2s,3s)-3-Methylaspartic Acid
pdb|1KKR|B Chain B, Crystal Structure Of Citrobacter Amalonaticus
Methylaspartate Ammonia Lyase Containing
(2s,3s)-3-Methylaspartic Acid
Length = 413
Score = 28.1 bits (61), Expect = 1.3, Method: Composition-based stats.
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 54 LKAKRNASKVSWLSDNCIGTSAAPYYMPPYYFEMHASTG 92
K ++ V WLSD + ++P Y P + +++ + G
Sbjct: 206 FKGEKLREYVRWLSDRILSLRSSPRYHPTLHIDVYGTIG 244
>pdb|2I7K|A Chain A, Solution Structure Of The Bromodomain Of Human Brd7
Protein
Length = 117
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 18 NKIMEMLVVK----FLHQTLTDVIIPTFDIRLLQPISFSTLKAK---RNASKVSWLSDN- 69
N++M L K F +TD I P + + + P+ FST+K K + + L DN
Sbjct: 14 NQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNF 73
Query: 70 -CIGTSAAPYYMP 81
+ T+A Y P
Sbjct: 74 KLMCTNAMIYNKP 86
>pdb|3P5T|A Chain A, Cfim25-Cfim68 Complex
pdb|3P5T|B Chain B, Cfim25-Cfim68 Complex
pdb|3P5T|C Chain C, Cfim25-Cfim68 Complex
pdb|3P5T|D Chain D, Cfim25-Cfim68 Complex
pdb|3P5T|E Chain E, Cfim25-Cfim68 Complex
pdb|3P5T|F Chain F, Cfim25-Cfim68 Complex
pdb|3P6Y|A Chain A, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|B Chain B, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|E Chain E, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|F Chain F, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|I Chain I, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|J Chain J, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|M Chain M, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|N Chain N, Cf Im25-Cf Im68-Uguaa Complex
Length = 202
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 97 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 125
>pdb|2CL3|A Chain A, Crystal Structure Of Human Cleavage And Polyadenylation
Specificity Factor 5 (Cpsf5)
pdb|3N9U|A Chain A, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|B Chain B, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 230
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 133 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 161
>pdb|2J8Q|A Chain A, Crystal Structure Of Human Cleavage And Polyadenylation
Specificity Factor 5 (Cpsf5) In Complex With A Sulphate
Ion.
pdb|2J8Q|B Chain B, Crystal Structure Of Human Cleavage And Polyadenylation
Specificity Factor 5 (Cpsf5) In Complex With A Sulphate
Ion
Length = 227
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 130 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 158
>pdb|3BHO|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im With Ap4a
Length = 208
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 111 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 139
>pdb|3Q2S|A Chain A, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|B Chain B, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|A Chain A, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|B Chain B, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 207
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 110 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 138
>pdb|3MDG|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uuguau
pdb|3MDG|B Chain B, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uuguau
pdb|3MDI|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uguaaa
pdb|3MDI|B Chain B, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uguaaa
Length = 227
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 130 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 158
>pdb|3BAP|A Chain A, Crystal Structure Of The 25 Kda Subunit Of Human Cleavage
Factor Im
Length = 227
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 56 AKRNASKVSWLSDNCIGTSAAPYYMPPYY 84
+++ W+ D+CIG P + PP Y
Sbjct: 130 GRQDGVLQDWVIDDCIGNWWRPNFEPPQY 158
>pdb|2DZS|A Chain A, Structure Of Mutant Tryptophan Synthase Alpha-Subunit
(E103a) From A Hyperthermophile, Pyrococcus Furiosus
pdb|2DZS|B Chain B, Structure Of Mutant Tryptophan Synthase Alpha-Subunit
(E103a) From A Hyperthermophile, Pyrococcus Furiosus
Length = 248
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 5/76 (6%)
Query: 39 PTFDIRLLQPISFSTLKAKRNASKVSWLSDNCIGTSAAP-----YYMPPYYFEMHASTGT 93
P D + +Q + LK + W+ S+ P YY P Y +
Sbjct: 44 PIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAA 103
Query: 94 KKFNLVDGVVAANIPV 109
K + VDG++ ++PV
Sbjct: 104 AKASGVDGILVVDLPV 119
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 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,171,999
Number of Sequences: 62578
Number of extensions: 101603
Number of successful extensions: 210
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 197
Number of HSP's gapped (non-prelim): 13
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)