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= psy10054
(910 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DT7|B Chain B, Solution Structure Of The Second Surp Domain Of Human
Splicing Factor Sf3a120 In Complex With A Fragment Of
Human Splicing Factor Sf3a60
Length = 85
Score = 145 bits (365), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 68/76 (89%), Positives = 71/76 (93%)
Query: 120 VPKDPPKEFEFIADPPSISALDLDIVKLTAQFVARNGRGFLTSLMQKEQRNYQFDFLRPQ 179
VPK+PP EFEFIADPPSISA DLD+VKLTAQFVARNGR FLT LMQKEQRNYQFDFLRPQ
Sbjct: 10 VPKEPPPEFEFIADPPSISAFDLDVVKLTAQFVARNGRQFLTQLMQKEQRNYQFDFLRPQ 69
Query: 180 HSLFQYFTKLLEQYTK 195
HSLF YFTKL+EQYTK
Sbjct: 70 HSLFNYFTKLVEQYTK 85
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 27 PPEVR----NIVDKTANFVARNGPEFESRIRQNEIGNPKFNFLSPGDPYHAYYQHRVK 80
PP + ++V TA FVARNG +F +++ Q E N +F+FL P Y+ V+
Sbjct: 24 PPSISAFDLDVVKLTAQFVARNGRQFLTQLMQKEQRNYQFDFLRPQHSLFNYFTKLVE 81
>pdb|2DT6|A Chain A, Solution Structure Of The First Surp Domain Of Human
Splicing Factor Sf3a120
Length = 64
Score = 108 bits (269), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/61 (78%), Positives = 56/61 (91%)
Query: 29 EVRNIVDKTANFVARNGPEFESRIRQNEIGNPKFNFLSPGDPYHAYYQHRVKDIREGKVK 88
EVRNIVDKTA+FVARNGPEFE+RIRQNEI NPKFNFL+P DPYHAYY+H+V + +EGK +
Sbjct: 2 EVRNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEFKEGKAQ 61
Query: 89 E 89
E
Sbjct: 62 E 62
Score = 38.1 bits (87), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%)
Query: 143 DIVKLTAQFVARNGRGFLTSLMQKEQRNYQFDFLRPQHSLFQYFTKLLEQY 193
+IV TA FVARNG F + Q E N +F+FL P Y+ + ++
Sbjct: 5 NIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEF 55
>pdb|1ZKH|A Chain A, Solution Structure Of A Human Ubiquitin-Like Domain In
Sf3a1
Length = 86
Score = 49.7 bits (117), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 21/32 (65%), Positives = 24/32 (75%)
Query: 839 QETGLFFKDSNSLAYYNITPGTKVHLQLKERG 870
Q G+F KDSNSLAYYN+ G +HL LKERG
Sbjct: 55 QYEGIFIKDSNSLAYYNMANGAVIHLALKERG 86
>pdb|1WE7|A Chain A, Solution Structure Of Ubiquitin-Like Domain In Sf3a120
Length = 115
Score = 49.3 bits (116), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/33 (63%), Positives = 24/33 (72%)
Query: 839 QETGLFFKDSNSLAYYNITPGTKVHLQLKERGG 871
Q G+F KDSNSLAYYN+ G +HL LKER G
Sbjct: 79 QYEGIFIKDSNSLAYYNMASGAVIHLALKERSG 111
>pdb|2E5Z|A Chain A, Solution Structure Of The Surp2 Domain In Splicing
Factor, ArginineSERINE-Rich 8
Length = 90
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 2/50 (4%)
Query: 29 EVRNIVDKTANFVARNGPEFESRIRQNEIGNPKFNFLSPGDPYHAYYQHR 78
+V+ ++DK A +VARNG +FE+ +R + +F FL P Y+AYY+ +
Sbjct: 23 DVQPVIDKLAEYVARNGLKFETSVRAK--NDQRFEFLQPWHQYNAYYEFK 70
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 144 IVKLTAQFVARNGRGFLTSLMQKEQRNYQFDFLRPQHSLFQYF 186
++ A++VARNG F TS+ K + +F+FL+P H Y+
Sbjct: 27 VIDKLAEYVARNGLKFETSVRAKNDQ--RFEFLQPWHQYNAYY 67
>pdb|2E60|A Chain A, Solution Structure Of The Surp1 Domain In Splicing
Factor, ArginineSERINE-Rich 8
Length = 101
Score = 43.1 bits (100), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 36/61 (59%)
Query: 26 PPPEVRNIVDKTANFVARNGPEFESRIRQNEIGNPKFNFLSPGDPYHAYYQHRVKDIREG 85
P ++ I+++TA+FV R G +FE ++ + N +F+FL + YY+ K ++EG
Sbjct: 23 PTAKMHAIIERTASFVCRQGAQFEIMLKAKQARNSQFDFLRFDHYLNPYYKFIQKAMKEG 82
Query: 86 K 86
+
Sbjct: 83 R 83
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/43 (48%), Positives = 25/43 (58%)
Query: 144 IVKLTAQFVARNGRGFLTSLMQKEQRNYQFDFLRPQHSLFQYF 186
I++ TA FV R G F L K+ RN QFDFLR H L Y+
Sbjct: 30 IIERTASFVCRQGAQFEIMLKAKQARNSQFDFLRFDHYLNPYY 72
>pdb|1UG0|A Chain A, Solution Structure Of Surp Domain In Bab30904
Length = 88
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 24 IYPP--PEVRNIVDKTANFVARNGPEFESRIRQNEIGNPKFNFLSPGDPYH-AYYQHRVK 80
+ PP E R +++K A FVA GPE E ++ NP F FL + YY+ +V
Sbjct: 19 VSPPEGAETRRVIEKLARFVAEGGPELEKVAMEDYKDNPAFTFLHDKNSREFLYYRRKVA 78
Query: 81 DIR 83
+IR
Sbjct: 79 EIR 81
>pdb|4DGW|B Chain B, Crystal Structure Of The Sf3a Splicing Factor Complex Of
U2 Snrnp
Length = 152
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 59/124 (47%), Gaps = 8/124 (6%)
Query: 137 ISALDLDIVKLTAQFVARNGRGFLTSLMQKEQRNYQFDFLRPQHSLFQYFTKLLEQYTKI 196
IS D +++KLTA++ A++ + + + K+ + +F H L + FT + QY ++
Sbjct: 3 ISRRDXEVIKLTARYYAKD-KSIVEQXISKDGEA-RLNFXNSSHPLHKTFTDFVAQYKRV 60
Query: 197 LIPPKDMMFRLKDESSSMAAILDEVKYRADYIRYQEAQRKQEEARVEKDRVAYAQIDWHD 256
F ++ S ILD R Y +++ + ++ + VE ++ +A I W
Sbjct: 61 ------YSFTGQEIKKSKRTILDNCFERTQYWEFEKDKDREHDKLVELCKIQFAAIPWDK 114
Query: 257 FVVV 260
F V
Sbjct: 115 FTQV 118
>pdb|1X4O|A Chain A, Solution Structure Of Surp Domain In Splicing Factor 4
Length = 78
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 29 EVRNIVDKTANFVARNGPEFESRIRQNEIGNPKFNFL-SPGDPYHAYYQHRVKDIR 83
E +N+ +K A F+A GPE E+ QN N F+FL P + YY+ ++ + R
Sbjct: 16 EAKNLAEKLARFIADGGPEVETIALQNNRENQAFSFLYDPNSQGYRYYRQKLDEFR 71
>pdb|1WE6|A Chain A, Solution Structure Of Ubiquitin-Like Domain In Splicing
Factor Aal91182
Length = 111
Score = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 835 EKINQETGLFFKDSNSLAYYNITPGTKVHLQLKERGG 871
+K++ + G F KD+ SLA+YN+ G + L L+ER G
Sbjct: 72 QKLSGKAG-FLKDNMSLAHYNVGAGEILTLSLRERSG 107
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
0.314 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,115,596
Number of Sequences: 62578
Number of extensions: 825303
Number of successful extensions: 1491
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1474
Number of HSP's gapped (non-prelim): 19
length of query: 910
length of database: 14,973,337
effective HSP length: 108
effective length of query: 802
effective length of database: 8,214,913
effective search space: 6588360226
effective search space used: 6588360226
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)