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= 027432
(223 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J4W|A Chain A, Complex Of The Kh3 And Kh4 Domains Of Fbp With A
Single_stranded 29mer Dna Oligonucleotide From The Fuse
Element Of The C-Myc Oncogene
Length = 174
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 109 AGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELI 165
G IIGKGG K I +Q+GA++ ++ + ADPN++ + G+ +QI A ++ E I
Sbjct: 115 TGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQAS 158
S+ G +IG+GG N K I +QTGA + I DPN + + GS +QI A
Sbjct: 11 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAK 70
Query: 159 AMVRELI 165
++ E I
Sbjct: 71 QLIEEKI 77
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T ++++ LAG+IIGKGG KQI ++GA + I + R I + G+ +QI+ A
Sbjct: 15 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 159 AMVR 162
+++
Sbjct: 75 YLLQ 78
>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp
K In Complex With Ssdna
pdb|1ZZI|B Chain B, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp
K In Complex With Ssdna
pdb|1ZZJ|A Chain A, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZJ|B Chain B, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZJ|C Chain C, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZK|A Chain A, Crystal Structure Of The Third Kh Domain Of Hnrnp K At
0.95a Resolution
Length = 82
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T ++++ LAG+IIGKGG KQI ++GA + I + R I + G+ +QI+ A
Sbjct: 8 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 67
Query: 159 AMVR 162
+++
Sbjct: 68 YLLQ 71
>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 = 0.001, Method: Composition-based stats.
Identities = 17/34 (50%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 187 SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELR 219
S+ +KT+LC F + G+C +G++C FAHG ELR
Sbjct: 1 STRYKTELCRPFEESGTCKYGEKCQFAHGFHELR 34
Score = 34.3 bits (77), Expect = 0.053, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 26 TVVKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
T K+ +C + CK+G+KC FAHG EL
Sbjct: 2 TRYKTELCRPFEESGTCKYGEKCQFAHGFHEL 33
Score = 33.9 bits (76), Expect = 0.067, Method: Composition-based stats.
Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 184 HPLSSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAE 217
HP +KT+LC F G C +G RCHF H A E
Sbjct: 39 HP---KYKTELCRTFHTIGFCPYGPRCHFIHNADE 70
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 187 SSNFKTKLCGNFAK-GSCTFGDRCHFAHGAAELRK 220
SS +KT+LC +++ G C +G +C FAHG ELR+
Sbjct: 7 SSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ 41
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 190 FKTKLCGNFA-KGSCTFGDRCHFAHGAAE 217
+KT+LC F +G C +G RCHF H E
Sbjct: 48 YKTELCHKFKLQGRCPYGSRCHFIHNPTE 76
Score = 30.0 bits (66), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 28 VKSRMCNRLNSAEGCKFGDKCHFAHGEWEL 57
K+ +C + + C++G KC FAHG EL
Sbjct: 10 YKTELCRTYSESGRCRYGAKCQFAHGLGEL 39
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T ++++ LA +IIGKGG KQI ++GA + I + R I + G+ +QI+ A
Sbjct: 15 TTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQ 74
Query: 159 AMVR 162
+++
Sbjct: 75 YLLQ 78
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRN--IELEGSFEQIKQA 157
KI V S AG IIGKGG K I Q+GA + + NL+N + + G EQ ++A
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKA 165
Query: 158 SAMVRELI 165
++ + I
Sbjct: 166 VELIIQKI 173
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSI---RDHEADPNLRNIELEGSFEQIKQA 157
K+ + + AG+IIGKGG Q+ ++TGA + + +D R ++G+ E +
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 158 SAMVRELI 165
+ E I
Sbjct: 69 HGFIAEKI 76
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 8/70 (11%)
Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-----RDHEADPNLRNIELEGSFEQIK 155
+I + AS AG +IGKGG KQ+ + G K+ + ++ AD LR + G +++
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR---ITGDPYKVQ 74
Query: 156 QASAMVRELI 165
QA MV ELI
Sbjct: 75 QAKEMVLELI 84
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRN--IELEGSFEQIKQA 157
KI V S AG IIGKGG K I Q+GA + + NL+N + + G EQ ++A
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKA 165
Query: 158 SAMVRELI 165
++ + I
Sbjct: 166 VELIIQKI 173
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSI---RDHEADPNLRNIELEGSFEQIKQA 157
K+ + + AG+IIGKGG Q+ ++TGA + + +D R ++G+ E +
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 158 SAMVRELI 165
+ E I
Sbjct: 69 HGFIAEKI 76
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T + V + G IIG+GG +I + +G K+ I R++ L G+ E +++A
Sbjct: 17 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAK 76
Query: 159 AMVRELIVR 167
M+ +++ R
Sbjct: 77 MMLDDIVSR 85
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 35.0 bits (79), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 102 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNI-ELEGSFEQIKQASA 159
I V AS AG +IGKGG ++ T A++ + RD D N + I ++ G F + A
Sbjct: 89 IRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQR 148
Query: 160 MVRELIVRIGPAHAK 174
+R+++ ++ H K
Sbjct: 149 KIRDILAQVKQQHQK 163
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-DPNLRNIELEG 149
++ + A GAIIGK G + KQ+ R A + I E D +R + + G
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITG 55
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 34.3 bits (77), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNL---RNIELEGSFEQIKQA 157
++SV G IIG+GG + IC+ +GAK++ D E++ L R I++ G+ +++ A
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITC-DKESEGTLLLSRLIKISGTQKEVAAA 76
Query: 158 SAMVRELI 165
++ E +
Sbjct: 77 KHLILEKV 84
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLS-IRDHEADPNL-RNIELEGSFEQIKQ 156
+I + A AG +IGKGG KQ+ + G K+ I+D + N+ + + + G +++Q
Sbjct: 3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62
Query: 157 ASAMVRELI 165
A MV +++
Sbjct: 63 ACEMVMDIL 71
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLS-IRDHEADPNL-RNIELEGSFEQIKQ 156
+I + A AG +IGKGG KQ+ + G K+ I+D + N+ + + + G +++Q
Sbjct: 15 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 74
Query: 157 ASAMVRELI 165
A MV +++
Sbjct: 75 ACEMVMDIL 83
>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
pdb|1EC6|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
Length = 87
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRN--IELEGSFEQIKQ 156
+I+V +L GAI+GKGG + TGA++ I + E P RN + + GS +
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 157 ASAMVRELIVRIGPAHAKNP 176
A ++ + + A NP
Sbjct: 65 AQYLISQRVTYEQGVRASNP 84
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR-DHEADPNLRNIELEG----SFEQ 153
T ++ V AS G++IGKGG K+I TGA++ + D + R I + G E
Sbjct: 90 TLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIEC 149
Query: 154 IKQASAMVRE 163
+KQ ++ E
Sbjct: 150 VKQICVVMLE 159
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 34/63 (53%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T ++++ +L G IIG+ G N +I + +GA++ I + + R + + GS I A
Sbjct: 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQ 66
Query: 159 AMV 161
++
Sbjct: 67 YLI 69
>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 = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 194 LCGNFAKGSCTFGDRCHFAHGAAELRK 220
+C + G+C G+ C FAHG AEL +
Sbjct: 22 ICDRYMNGTCPEGNSCKFAHGNAELHE 48
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T + V + G IIG+GG +I +++G K+ I R+ L G+ E ++ A
Sbjct: 16 TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAK 75
Query: 159 AMVRELIV--RIGPA 171
++ +++ R GP+
Sbjct: 76 RLLDQIVEKGRSGPS 90
>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|C Chain C, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|D Chain D, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
Length = 76
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 100 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRN 144
+++V +L GAI+GKGG + TGA++ I + E P RN
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRN 50
>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|B Chain B, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|C Chain C, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|D Chain D, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
Length = 76
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T ++ + G+IIGK G + K+I ++GA+++I E + R I L G I +A
Sbjct: 4 TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNSPERIITLTGPTNAIFKAF 61
Query: 159 AMV 161
AM+
Sbjct: 62 AMI 64
>pdb|2F7L|A Chain A, Crystal Structure Of Sulfolobus Tokodaii
PhosphomannomutasePHOSPHOGLUCOMUTASE
pdb|2F7L|B Chain B, Crystal Structure Of Sulfolobus Tokodaii
PhosphomannomutasePHOSPHOGLUCOMUTASE
Length = 455
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 116 GGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAH 172
G +++ + R G K+ + DP + E +F+ +K+ + +V+ L V +G AH
Sbjct: 184 GALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGVAH 240
>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
Length = 72
Score = 28.9 bits (63), Expect = 2.5, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 191 KTKLCGNFAKGSCTFGDRCHFAH 213
KT +C ++ +G C GD+C F H
Sbjct: 15 KTVVCKHWLRGLCKKGDQCEFLH 37
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 28.5 bits (62), Expect = 3.2, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRN--IELEGSFEQIKQA 157
+I+V +L GAI+GKGG + TG ++ I + E P RN + + G+ + A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 158 SAMVRELI 165
++ + I
Sbjct: 66 QYLITQRI 73
>pdb|4II1|A Chain A, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|B Chain B, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|C Chain C, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|D Chain D, Crystal Structure Of The Zinc Finger Of Zgpat
Length = 167
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 150 SFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAHPLSSNFKTKLCGNFAKGSCTFGDRC 209
S+ ++ +AMV +G A++ + + ++ K C F +G C F + C
Sbjct: 40 SWGTLEYHNAMV------VGTEEAEDGSAGVRVLYLYPTHKSLKPCPFFLEGKCRFKENC 93
Query: 210 HFAHGAA----ELR 219
F+HG ELR
Sbjct: 94 RFSHGQVVSLDELR 107
>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|B Chain B, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|C Chain C, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|D Chain D, Human Alpha Polyc Binding Protein Kh1
Length = 74
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQAS 158
T ++ + G+IIGK G + K+I ++GA+++I E + R I L G I +A
Sbjct: 4 TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLTGPTNAIFKAF 61
Query: 159 AMV 161
AM+
Sbjct: 62 AMI 64
>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In
Cleavage And Polyadenylation Specificity Factor
Length = 77
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 187 SSNFKTKLCGNFAKGSCTFGDRCHFAH 213
SS KT +C ++ +G C GD+C F H
Sbjct: 5 SSGEKTVVCKHWLRGLCKKGDQCEFLH 31
>pdb|1VIG|A Chain A, Nmr Study Of Vigilin, Repeat 6, 40 Structures
pdb|1VIH|A Chain A, Nmr Study Of Vigilin, Repeat 6, Minimized Average
Structure
Length = 71
Score = 27.3 bits (59), Expect = 6.2, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 101 KISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAM 160
+I++D +IGK G N +I Q + I NL I +EG + ++QA
Sbjct: 8 EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNL--IRIEGDPQGVQQAKRE 65
Query: 161 VREL 164
+ EL
Sbjct: 66 LLEL 69
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 26.9 bits (58), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 99 TAKISVDASLAGAIIGKGGVNSKQICRQTG 128
T ++ ++A G +IGK G S++I + TG
Sbjct: 99 TCEVIIEARKPGLVIGKYGSTSREIVKNTG 128
>pdb|3TXS|A Chain A, Crystal Structure Of Phage 44rr Small Terminase Gp16
pdb|3TXS|B Chain B, Crystal Structure Of Phage 44rr Small Terminase Gp16
pdb|3TXS|C Chain C, Crystal Structure Of Phage 44rr Small Terminase Gp16
pdb|3TXS|D Chain D, Crystal Structure Of Phage 44rr Small Terminase Gp16
Length = 94
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 29/59 (49%)
Query: 126 QTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPATAGSAAH 184
Q A L +RD ++PN R I+ + +E +++ ++++ + +N A S H
Sbjct: 1 QVYAPLVLRDPVSNPNNRKIDQDDDYELVRRNMHYQSQMLLDMAKIALENAKNADSPRH 59
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
Star-Gsg Quaking Protein
Length = 140
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 105 DASLAGAIIGKGGVNSKQICRQTGAKLSIR 134
D + G I+G G+ +KQ+ +TG K+ +R
Sbjct: 15 DFNFVGRILGPRGLTAKQLEAETGCKIMVR 44
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
0.318 0.133 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,209,484
Number of Sequences: 62578
Number of extensions: 218150
Number of successful extensions: 511
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 462
Number of HSP's gapped (non-prelim): 54
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)