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= 003969
(783 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BH2|A Chain A, Crystal Structure Of E. Coli 5-Methyluridine
Methyltransferase Ruma In Complex With Ribosomal Rna
Substrate And S-Adenosylhomocysteine.
pdb|2BH2|B Chain B, Crystal Structure Of E. Coli 5-Methyluridine
Methyltransferase Ruma In Complex With Ribosomal Rna
Substrate And S-Adenosylhomocysteine
Length = 433
Score = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 1/91 (1%)
Query: 563 HDSISNLRFCISPTAFFQVNTLAAEKLYSLGGDWADLGPDTLLFDVCCGTGTIGLTLAHR 622
+DS + LR SP F QVN +K+ + +W D+ P+ + D+ CG G L LA +
Sbjct: 249 YDS-NGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQ 307
Query: 623 VGMVIGIEMNASAVSDAHRNAEINGIKNCRF 653
V+G+E + V +NA +NG++N F
Sbjct: 308 AASVVGVEGVPALVEKGQQNARLNGLQNVTF 338
>pdb|1UWV|A Chain A, Crystal Structure Of Ruma, The Iron-Sulfur Cluster
Containing E. Coli 23s Ribosomal Rna 5-Methyluridine
Methyltransferase
Length = 433
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 48/91 (52%), Gaps = 1/91 (1%)
Query: 563 HDSISNLRFCISPTAFFQVNTLAAEKLYSLGGDWADLGPDTLLFDVCCGTGTIGLTLAHR 622
+DS + LR SP F QVN +K + +W D+ P+ + D+ CG G L LA +
Sbjct: 249 YDS-NGLRLTFSPRDFIQVNAGVNQKXVARALEWLDVQPEDRVLDLFCGXGNFTLPLATQ 307
Query: 623 VGMVIGIEMNASAVSDAHRNAEINGIKNCRF 653
V+G+E + V +NA +NG++N F
Sbjct: 308 AASVVGVEGVPALVEKGQQNARLNGLQNVTF 338
>pdb|2VS1|A Chain A, The Crystal Structure Of Pyrococcus Abyssi Trna
(Uracil-54, C5)-Methyltransferase In Complex With
S-Adenosyl-L- Homocysteine
Length = 425
Score = 49.3 bits (116), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 3/87 (3%)
Query: 562 IHDSISNLRFCISPTAFFQVNTLAAEKLYSLGGDWADLGPDTLLFDVCCGTGTIGLTLAH 621
I + + ++ + I P +FFQ N+ A L ++L + D+ G GT G+ LA
Sbjct: 254 IRERLDDVDYLIHPNSFFQTNSYQAVNLVR---KVSELVEGEKILDMYSGVGTFGIYLAK 310
Query: 622 RVGMVIGIEMNASAVSDAHRNAEINGI 648
R V G + N A+ A RN EIN +
Sbjct: 311 RGFNVKGFDSNEFAIEMARRNVEINNV 337
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/150 (23%), Positives = 63/150 (42%), Gaps = 41/150 (27%)
Query: 307 LAHMSYSVQLEHKKNSIAQMLKKLTRNARKACPNGVSLPEWIMKSREIGGLPCKLEGILG 366
L H++Y QLE K+ + ++L G + ++
Sbjct: 92 LQHLNYDYQLEFKRKKLKRIL----------------------------GFEVE---VVP 120
Query: 367 SPLVNGYRNKCEFSVGYSLQAKPTVGFM-LGNFREGVTAVEEPVDCPNVSEIACKYASIF 425
SP + G+RN+ + ++ K +GF G + + V E PV E +
Sbjct: 121 SPKIFGHRNRIDLAI-----TKDGIGFRERGKWWKIVDIDEXPVFGKTSREAIER----L 171
Query: 426 QEFLQQSDLPVWNRFKNSGFWRQLTVREGR 455
+EF+++ + VWN K+ GF R + +REG+
Sbjct: 172 KEFIEEEKISVWNIKKDEGFLRYMVLREGK 201
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 753 AIVDPPRGGLHPTVIKIL 770
IVDPPR GLHP ++K L
Sbjct: 357 VIVDPPRAGLHPRLVKRL 374
>pdb|2JJQ|A Chain A, The Crystal Structure Of Pyrococcus Abyssi Trna
(Uracil-54, C5)-Methyltransferase In Complex With
S-Adenosyl-L- Homocysteine
Length = 425
Score = 49.3 bits (116), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 3/87 (3%)
Query: 562 IHDSISNLRFCISPTAFFQVNTLAAEKLYSLGGDWADLGPDTLLFDVCCGTGTIGLTLAH 621
I + + ++ + I P +FFQ N+ A L ++L + D+ G GT G+ LA
Sbjct: 254 IRERLDDVDYLIHPNSFFQTNSYQAVNLVR---KVSELVEGEKILDMYSGVGTFGIYLAK 310
Query: 622 RVGMVIGIEMNASAVSDAHRNAEINGI 648
R V G + N A+ A RN EIN +
Sbjct: 311 RGFNVKGFDSNEFAIEMARRNVEINNV 337
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 33/149 (22%), Positives = 63/149 (42%), Gaps = 39/149 (26%)
Query: 307 LAHMSYSVQLEHKKNSIAQMLKKLTRNARKACPNGVSLPEWIMKSREIGGLPCKLEGILG 366
L H++Y QLE K+ + ++L E+ +P
Sbjct: 92 LQHLNYDYQLEFKRKKLKRIL-----------------------GFEVEVVP-------- 120
Query: 367 SPLVNGYRNKCEFSVGYSLQAKPTVGFMLGNFREGVTAVEEPVDCPNVSEIACKYASIFQ 426
SP + G+RN+ + ++ K +GF + ++E CP + + + +
Sbjct: 121 SPKIFGHRNRIDLAI-----TKDGIGFRERGKWWKIVDIDE---CPVFGKTSREAIERLK 172
Query: 427 EFLQQSDLPVWNRFKNSGFWRQLTVREGR 455
EF+++ + VWN K+ GF R + +REG+
Sbjct: 173 EFIEEEKISVWNIKKDEGFLRYMVLREGK 201
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 753 AIVDPPRGGLHPTVIKIL 770
IVDPPR GLHP ++K L
Sbjct: 357 VIVDPPRAGLHPRLVKRL 374
>pdb|2YXD|A Chain A, Crystal Structure Of Cobalamin Biosynthesis Precorrin 8w
Decarboxylase (Cbit)
pdb|2YXD|B Chain B, Crystal Structure Of Cobalamin Biosynthesis Precorrin 8w
Decarboxylase (Cbit)
Length = 183
Score = 42.7 bits (99), Expect = 9e-04, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 35/68 (51%)
Query: 598 DLGPDTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGIKNCRFVCAK 657
+L D ++ DV CG+G + +A R V I+ A+ +N IKNC+ + +
Sbjct: 32 NLNKDDVVVDVGCGSGGXTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGR 91
Query: 658 AEDVMGSL 665
AEDV+ L
Sbjct: 92 AEDVLDKL 99
>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
Rich Element By The Tandem Zinc Finger Domain Of Tis11d
Length = 70
Score = 40.0 bits (92), Expect = 0.006, Method: Composition-based stats.
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 82 KTSLCSYFRKVGTCCHGSTCRYAHGEEELR 111
KT LC F + GTC +G C++AHG ELR
Sbjct: 5 KTELCRPFEESGTCKYGEKCQFAHGFHELR 34
Score = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 82 KTSLCSYFRKVGTCCHGSTCRYAHGEEE 109
KT LC F +G C +G C + H +E
Sbjct: 43 KTELCRTFHTIGFCPYGPRCHFIHNADE 70
>pdb|1KXZ|A Chain A, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|B Chain B, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|C Chain C, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|D Chain D, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|E Chain E, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|F Chain F, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|G Chain G, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1KXZ|H Chain H, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, P1 Spacegroup
pdb|1L3B|A Chain A, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|B Chain B, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|C Chain C, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|D Chain D, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|E Chain E, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|F Chain F, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|G Chain G, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3B|H Chain H, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup W LONG CELL
pdb|1L3C|A Chain A, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup With Short
Cell
pdb|1L3C|B Chain B, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup With Short
Cell
pdb|1L3C|C Chain C, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup With Short
Cell
pdb|1L3C|D Chain D, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, C2 Spacegroup With Short
Cell
pdb|1L3I|A Chain A, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, Adohcy Binary Complex
pdb|1L3I|B Chain B, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, Adohcy Binary Complex
pdb|1L3I|C Chain C, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, Adohcy Binary Complex
pdb|1L3I|D Chain D, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, Adohcy Binary Complex
pdb|1L3I|E Chain E, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, Adohcy Binary Complex
pdb|1L3I|F Chain F, Mt0146, The Precorrin-6y Methyltransferase (Cbit) Homolog
From M. Thermoautotrophicum, Adohcy Binary Complex
pdb|1F38|A Chain A, X-Ray Crystallographic Structure Of Precorrin 8w
Decarboxylase, The Product Of Gene Mt0146 In The
Methanobacterium Thermoautotrophicum Genome
pdb|1F38|B Chain B, X-Ray Crystallographic Structure Of Precorrin 8w
Decarboxylase, The Product Of Gene Mt0146 In The
Methanobacterium Thermoautotrophicum Genome
pdb|1F38|C Chain C, X-Ray Crystallographic Structure Of Precorrin 8w
Decarboxylase, The Product Of Gene Mt0146 In The
Methanobacterium Thermoautotrophicum Genome
pdb|1F38|D Chain D, X-Ray Crystallographic Structure Of Precorrin 8w
Decarboxylase, The Product Of Gene Mt0146 In The
Methanobacterium Thermoautotrophicum Genome
Length = 192
Score = 37.4 bits (85), Expect = 0.032, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 597 ADLGPDTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGI 648
A+ G + + DV CGTG + L LA RV V I+ N A+S N + +G+
Sbjct: 29 AEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEXNLQRHGL 80
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 35.8 bits (81), Expect = 0.092, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 82 KTSLCSYFRKVGTCCHGSTCRYAHGEEELR 111
KT LC + + G C +G+ C++AHG ELR
Sbjct: 11 KTELCRTYSESGRCRYGAKCQFAHGLGELR 40
Score = 30.0 bits (66), Expect = 4.8, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 82 KTSLCSYFRKVGTCCHGSTCRYAHGEEE 109
KT LC F+ G C +GS C + H E
Sbjct: 49 KTELCHKFKLQGRCPYGSRCHFIHNPTE 76
>pdb|1DL5|A Chain A, Protein-L-Isoaspartate O-Methyltransferase
pdb|1DL5|B Chain B, Protein-L-Isoaspartate O-Methyltransferase
Length = 317
Score = 35.4 bits (80), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 580 QVNTLAAEKLYSLGGDWADLGPDTLLFDVCCGTGTIGLTLAHRVG---MVIGIEMNASAV 636
+ +T + L +L +W L + ++ GTG ++ VG +V+ +E +
Sbjct: 54 EYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKIC 113
Query: 637 SDAHRNAEINGIKNCRFVCA 656
A RN E GI+N FVC
Sbjct: 114 EIAKRNVERLGIENVIFVCG 133
>pdb|3SM3|A Chain A, Crystal Structure Of Sam-Dependent Methyltransferases
Q8puk2_metma From Methanosarcina Mazei. Northeast
Structural Genomics Consortium Target Mar262
Length = 235
Score = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%)
Query: 599 LGPDTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGI 648
L D + D+ CG+G I L LA + V GI++N+ A+ A A G+
Sbjct: 28 LQEDDEILDIGCGSGKISLELASKGYSVTGIDINSEAIRLAETAARSPGL 77
>pdb|1DUS|A Chain A, Mj0882-A Hypothetical Protein From M. Jannaschii
Length = 194
Score = 33.5 bits (75), Expect = 0.46, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 25/49 (51%)
Query: 602 DTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGIKN 650
D + D+ CG G IG+ LA V ++N A+ A N ++N + N
Sbjct: 53 DDDILDLGCGYGVIGIALADEVKSTTXADINRRAIKLAKENIKLNNLDN 101
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 188 DHGILYKSAKKKKGMTVGFVKFESVEQLKNAVEELEGISIGNKTLKVANVVPR 240
D+ +L K + + GF+ F E + A+E+L G + + ++V +V R
Sbjct: 33 DNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTER 85
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 205 GFVKFESVEQLKNAVEELEGISIGNKTLKVA 235
GFVKF+S + A+ L G +I NK LKVA
Sbjct: 87 GFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 205 GFVKFESVEQLKNAVEELEGISIGNKTLKVANVVPRS 241
GF+ F E K A+E+L G + + +KV +V R+
Sbjct: 71 GFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107
>pdb|4AZS|A Chain A, High Resolution (2.2 A) Crystal Structure Of Wbdd.
pdb|4AZT|A Chain A, Co-Crystal Structure Of Wbdd And Kinase Inhibitor
Ly294002.
pdb|4AZV|A Chain A, Co-crystal Structure Of Wbdd And Kinase Inhibitor
Gw435821x
Length = 569
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%)
Query: 599 LGPDTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGIKNCRFVCAKA 658
LG + D+ C G L+LA + ++GI+ ++ AE N F +
Sbjct: 64 LGRPLNVLDLGCAQGFFSLSLASKGATIVGIDFQQENINVCRALAEENPDFAAEFRVGRI 123
Query: 659 EDVMGSL 665
E+V+ +L
Sbjct: 124 EEVIAAL 130
>pdb|4AX8|A Chain A, Medium Resolution Structure Of The Bifunctional Kinase-
Methyltransferase Wbdd
Length = 569
Score = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%)
Query: 599 LGPDTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGIKNCRFVCAKA 658
LG + D+ C G L+LA + ++GI+ ++ AE N F +
Sbjct: 64 LGRPLNVLDLGCAQGFFSLSLASKGATIVGIDFQQENINVCRALAEENPDFAAEFRVGRI 123
Query: 659 EDVMGSL 665
E+V+ +L
Sbjct: 124 EEVIAAL 130
>pdb|1WZN|A Chain A, Crystal Structure Of The Sam-Dependent Methyltransferase
From Pyrococcus Horikoshii Ot3
pdb|1WZN|B Chain B, Crystal Structure Of The Sam-Dependent Methyltransferase
From Pyrococcus Horikoshii Ot3
pdb|1WZN|C Chain C, Crystal Structure Of The Sam-Dependent Methyltransferase
From Pyrococcus Horikoshii Ot3
Length = 252
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 605 LFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGIK 649
+ D+ CGTG L LA R V+G++++ + A R A+ +K
Sbjct: 45 VLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLK 89
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 173 LPRKWHSDNLKKFLADHG----ILYKSAKKKKGMTVGFVKFESVEQLKNAVEELEGISIG 228
L R+ + LK HG +L + K F+ FE+ KNA +++ G S+
Sbjct: 15 LNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLH 74
Query: 229 NKTLKVANVVPRSF 242
K +KV SF
Sbjct: 75 GKAIKVEQAKKPSF 88
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 172 HLPRKWHSDNLKKFLADHGILYKSAK----KKKGMTVG--FVKFESVEQLKNAVEELEGI 225
+LP+ D L+ + G + +SAK K G ++G FV + + + + A+ L G+
Sbjct: 9 YLPQNMTQDELRSLFSSIGEV-ESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL 67
Query: 226 SIGNKTLKVANVVPRS 241
+ +KT+KV+ P S
Sbjct: 68 RLQSKTIKVSYARPSS 83
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 172 HLPRKWHSDNLKKFLADHGILYKSAK----KKKGMTVG--FVKFESVEQLKNAVEELEGI 225
+LP+ D L+ + G + +SAK K G ++G FV + + + + A+ L G+
Sbjct: 9 YLPQNMTQDELRSLFSSIGEV-ESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL 67
Query: 226 SIGNKTLKVANVVPRS 241
+ +KT+KV+ P S
Sbjct: 68 RLQSKTIKVSYARPSS 83
>pdb|4AZW|A Chain A, Crystal Structure Of Monomeric Wbdd
Length = 471
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%)
Query: 599 LGPDTLLFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRNAEINGIKNCRFVCAKA 658
LG + D+ C G L+LA + ++GI+ ++ AE N F +
Sbjct: 64 LGRPLNVLDLGCAQGFFSLSLASKGATIVGIDFQQENINVCRALAEENPDFAAEFRVGRI 123
Query: 659 EDVMGSL 665
E+V+ +L
Sbjct: 124 EEVIAAL 130
>pdb|3MGG|A Chain A, Crystal Structure Of Methyl Transferase From
Methanosarcina Mazei
pdb|3MGG|B Chain B, Crystal Structure Of Methyl Transferase From
Methanosarcina Mazei
Length = 276
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 601 PDTLLFDVCCGTGTIGLTLAHRV--GMVIGIEMNASAVSDAHRNAEINGIKNCRFVCA 656
P + + CG G + LA + I+++ ++ A N E NGIKN +F+ A
Sbjct: 37 PGAKVLEAGCGIGAQTVILAKNNPDAEITSIDISPESLEKARENTEKNGIKNVKFLQA 94
>pdb|2D9M|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 3 In
Zinc Finger Ccch-Type Domain Containing 7a
Length = 69
Score = 30.0 bits (66), Expect = 4.9, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 84 SLCSYFRKVGTCCHGSTCRYAHGEEEL 110
S+C + GTC G++C++AHG EL
Sbjct: 21 SICDRYMN-GTCPEGNSCKFAHGNAEL 46
>pdb|3PFG|A Chain A, X-Ray Crystal Structure The N,N-Dimethyltransferase Tylm1
From Streptomyces Fradiae In Complex With Sam And
Dtdp-Phenol
pdb|3PFH|A Chain A, X-Ray Crystal Structure The N,N-Dimethyltransferase Tylm1
From Streptomyces Fradiae In Complex With Sah And
Dtdp-Quip3n
pdb|3PFH|D Chain D, X-Ray Crystal Structure The N,N-Dimethyltransferase Tylm1
From Streptomyces Fradiae In Complex With Sah And
Dtdp-Quip3n
Length = 263
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 605 LFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRN 642
L DV CGTG LA G V G+E++A ++ A R
Sbjct: 54 LLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRR 91
>pdb|3PX3|A Chain A, Structure Of Tylm1 From Streptomyces Fradiae H123a Mutant
In Complex With Sah And Dtdp-Quip3n
pdb|3PX3|D Chain D, Structure Of Tylm1 From Streptomyces Fradiae H123a Mutant
In Complex With Sah And Dtdp-Quip3n
Length = 263
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 605 LFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRN 642
L DV CGTG LA G V G+E++A ++ A R
Sbjct: 54 LLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRR 91
>pdb|2AS0|A Chain A, Crystal Structure Of Ph1915 (Apc 5817): A Hypothetical Rna
Methyltransferase
pdb|2AS0|B Chain B, Crystal Structure Of Ph1915 (Apc 5817): A Hypothetical Rna
Methyltransferase
Length = 396
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 14/88 (15%)
Query: 576 TAFF---QVNTLAAEKLYSLGGDWADLGPDTLLFDVCCGTGTIGLTLA-HRVGMVIGIEM 631
T FF + N LA EK W P + DV TG + A VIGI+
Sbjct: 198 TGFFLDQRENRLALEK-------WVQ--PGDRVLDVFTYTGGFAIHAAIAGADEVIGIDK 248
Query: 632 NASAVSDAHRNAEINGIKN-CRFVCAKA 658
+ A+ A NA++NG+++ +F+ A
Sbjct: 249 SPRAIETAKENAKLNGVEDRXKFIVGSA 276
>pdb|3PX2|A Chain A, Structure Of Tylm1 From Streptomyces Fradiae H123n Mutant
In Complex With Sah And Dtdp-Quip3n
pdb|3PX2|D Chain D, Structure Of Tylm1 From Streptomyces Fradiae H123n Mutant
In Complex With Sah And Dtdp-Quip3n
Length = 262
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 605 LFDVCCGTGTIGLTLAHRVGMVIGIEMNASAVSDAHRN 642
L DV CGTG LA G V G+E++A ++ A R
Sbjct: 54 LLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRR 91
>pdb|4DCM|A Chain A, Crystal Structure Of Methyltransferase Rlmg Modifying
G1835 Of 23s Rrna In Escherichia Coli
Length = 375
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 605 LFDVCCGTGTIGLTLAHR--VGMVIGIEMNASAVSDAHRNAEIN---GIKNCRFVCAKA 658
+ D+ CG G IGLTL + V+ ++ + AV+ + N E N + C F A
Sbjct: 226 IVDLGCGNGVIGLTLLDKNPQAKVVFVDESPXAVASSRLNVETNXPEALDRCEFXINNA 284
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 29.6 bits (65), Expect = 7.1, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 172 HLPRKWHSDNLKKFLADHGILYKSAK----KKKGMTVG--FVKFESVEQLKNAVEELEGI 225
+LP+ D L+ + G + +SAK K G ++G FV + + + + A+ L G+
Sbjct: 11 YLPQNMTQDELRSLFSSIGEV-ESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL 69
Query: 226 SIGNKTLKVANVVP 239
+ +KT+KV+ P
Sbjct: 70 RLQSKTIKVSYARP 83
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 29.6 bits (65), Expect = 7.4, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 205 GFVKFESVEQLKNAVEELEGISIGNKTLKV 234
FV+FE E A+EE+ G S N+ L+V
Sbjct: 68 AFVEFEEAESAAKAIEEVHGKSFANQPLEV 97
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 29.6 bits (65), Expect = 7.5, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 172 HLPRKWHSDNLKKFLADHGILYKSAK----KKKGMTVG--FVKFESVEQLKNAVEELEGI 225
+LP+ D L+ + G + +SAK K G ++G FV + + + + A+ L G+
Sbjct: 26 YLPQNXTQDELRSLFSSIGEV-ESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL 84
Query: 226 SIGNKTLKVANVVP 239
+ +KT+KV+ P
Sbjct: 85 RLQSKTIKVSYARP 98
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
0.313 0.131 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,275,985
Number of Sequences: 62578
Number of extensions: 825961
Number of successful extensions: 1522
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1483
Number of HSP's gapped (non-prelim): 47
length of query: 783
length of database: 14,973,337
effective HSP length: 106
effective length of query: 677
effective length of database: 8,340,069
effective search space: 5646226713
effective search space used: 5646226713
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)