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= 008337
(569 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
Length = 119
Score = 77.4 bits (189), Expect = 2e-14, Method: Composition-based stats.
Identities = 43/106 (40%), Positives = 64/106 (60%), Gaps = 4/106 (3%)
Query: 211 VFLGFD-ADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLH 269
+F+G + A + N+ ++ GP Y+ HI ETGA V LRG+GSG E G E +P++
Sbjct: 16 LFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMY 75
Query: 270 LFLSSNNPKSLEEAKRLAENLLDTISAECGASRVSSCKVYNAVPPP 315
+++S P+ L AK+L ENLL T+ AE SR + ++ AVP P
Sbjct: 76 IYISHPKPEGLAAAKKLCENLLQTVHAE--YSRFVN-QINTAVPLP 118
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 47/93 (50%), Gaps = 10/93 (10%)
Query: 207 MSTSVFLGFDADASLNIAARIRGPNDQYINHIMNETGATVLLRGRGS------GNSEG-- 258
+S V + D +N + GP + +I E A +++RG+GS G +G
Sbjct: 7 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQM 66
Query: 259 LQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLL 291
L GE+ +PLH +++N +++++A N+L
Sbjct: 67 LPGED--EPLHALVTANTMENVKKAVEQIRNIL 97
>pdb|1WZM|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-amylase Ii (tva Ii)
Mutatnt R469k
pdb|1WZM|B Chain B, Thermoactinomyces Vulgaris R-47 Alpha-amylase Ii (tva Ii)
Mutatnt R469k
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1WZL|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
Mutatnt R469l
pdb|1WZL|B Chain B, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
Mutatnt R469l
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1JF5|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2 Mutant F286a
pdb|1JF5|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2 Mutant F286a
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1G1Y|A Chain A, Crystal Structure Of Alpha-Amylase Ii (Tvaii) From
Thermoactinomyces Vulgaris R-47 And Beta-Cyclodextrin
Complex
pdb|1G1Y|B Chain B, Crystal Structure Of Alpha-Amylase Ii (Tvaii) From
Thermoactinomyces Vulgaris R-47 And Beta-Cyclodextrin
Complex
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1VFM|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2ALPHA-Cyclodextrin Complex
pdb|1VFM|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2ALPHA-Cyclodextrin Complex
pdb|1VFO|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2BETA-Cyclodextrin Complex
pdb|1VFO|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2BETA-Cyclodextrin Complex
pdb|1VFU|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Amylase 2GAMMA-Cyclodextrin Complex
pdb|1VFU|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Amylase 2GAMMA-Cyclodextrin Complex
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1WZK|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
Mutatnt D465n
pdb|1WZK|B Chain B, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
Mutatnt D465n
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1BVZ|A Chain A, Alpha-Amylase Ii (Tvaii) From Thermoactinomyces Vulgaris
R- 47
pdb|1BVZ|B Chain B, Alpha-Amylase Ii (Tvaii) From Thermoactinomyces Vulgaris
R- 47
pdb|1JI2|A Chain A, Improved X-Ray Structure Of Thermoactinomyces Vulgaris
R-47 Alpha-Amylase 2
pdb|1JI2|B Chain B, Improved X-Ray Structure Of Thermoactinomyces Vulgaris
R-47 Alpha-Amylase 2
pdb|3A6O|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2ACARBOSE COMPLEX
pdb|3A6O|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 2ACARBOSE COMPLEX
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1JL8|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Beta-Cyclodextrin
Based On A Co- Crystallization With Methyl
Beta-Cyclodextrin
pdb|1JL8|B Chain B, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Beta-Cyclodextrin
Based On A Co- Crystallization With Methyl
Beta-Cyclodextrin
pdb|1JIB|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Maltotetraose Based
On A Crystal Soaked With Maltohexaose.
pdb|1JIB|B Chain B, Complex Of Alpha-Amylase Ii (Tva Ii) From
Thermoactinomyces Vulgaris R-47 With Maltotetraose Based
On A Crystal Soaked With Maltohexaose.
pdb|1VB9|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase Ii (Tva Ii) Complexed With
Transglycosylated Product
pdb|1VB9|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase Ii (Tva Ii) Complexed With
Transglycosylated Product
pdb|2D2O|A Chain A, Structure Of A Complex Of Thermoactinomyces Vulgaris R-47
Alpha-Amylase 2 With Maltohexaose Demonstrates The
Important Role Of Aromatic Residues At The Reducing End
Of The Substrate Binding Cleft
pdb|2D2O|B Chain B, Structure Of A Complex Of Thermoactinomyces Vulgaris R-47
Alpha-Amylase 2 With Maltohexaose Demonstrates The
Important Role Of Aromatic Residues At The Reducing End
Of The Substrate Binding Cleft
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1JF6|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase Mutant F286y
pdb|1JF6|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase Mutant F286y
Length = 585
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 215 FDADASLNIAARIRGPNDQYINHIMNETGA--TVLLRGRGSGNS---EGLQGEEVH 265
+ AD N+ A +R DQ++ ++N G TVLL+ SG + L GEEVH
Sbjct: 508 WHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVH 563
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 256 SEGLQGEEVHQPLHLFLSSNNP-KSLEEAK-----RLAENLLDTISAECGASRVSSCKVY 309
S ++G E P +LF+ + NP KS+ E K A+N L + G +R +
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61
Query: 310 NAVPPPQQLL--TGIQGFGNEQKL 331
+ ++ L TG++ FGNE KL
Sbjct: 62 ESAEDLEKALELTGLKVFGNEIKL 85
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 30.0 bits (66), Expect = 3.4, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 259 LQGEEVHQPLHLFLSSNNP-KSLEEAK-----RLAENLLDTISAECGASRVSSCKVYNAV 312
++G E P +LF+ + NP KS+ E K A+N L + G +R + +
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68
Query: 313 PPPQQLL--TGIQGFGNEQKL 331
++ L TG++ FGNE KL
Sbjct: 69 EDLEKALELTGLKVFGNEIKL 89
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
Star-Gsg Quaking Protein
Length = 140
Score = 29.3 bits (64), Expect = 6.1, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 221 LNIAARIRGPNDQYINHIMNETGATVLLRGRGS--------GNSEGLQGEEVHQPLHLFL 272
N RI GP + ETG +++RG+GS N E +++ LH+ +
Sbjct: 16 FNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLI 75
Query: 273 SSNNPKSLEEAK 284
+ + ++ E K
Sbjct: 76 TVEDAQNRAELK 87
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
0.311 0.129 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,821,310
Number of Sequences: 62578
Number of extensions: 495709
Number of successful extensions: 957
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 953
Number of HSP's gapped (non-prelim): 18
length of query: 569
length of database: 14,973,337
effective HSP length: 104
effective length of query: 465
effective length of database: 8,465,225
effective search space: 3936329625
effective search space used: 3936329625
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)