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= 022221
(300 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
+++I LAG+IIGK G KQI +GA + I + R I + GT DQI+ A +
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYL 69
Query: 241 VR 242
++
Sbjct: 70 LQ 71
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
+++I LAG+IIGK G KQI +GA + I + R I + GT DQI+ A +
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYL 76
Query: 241 VR 242
++
Sbjct: 77 LQ 78
>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 = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELR 296
+KT+LC F + G+C +G++C FAHG ELR
Sbjct: 4 YKTELCRPFEESGTCKYGEKCQFAHGFHELR 34
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 106 VKSRLCNKYNSAEGCKFGDKCHFAHGEWEL 135
K+ LC + + CK+G+KC FAHG EL
Sbjct: 4 YKTELCRPFEESGTCKYGEKCQFAHGFHEL 33
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 267 FKTKLCENFAK-GSCTFGDRCHFAHGSEE 294
+KT+LC F G C +G RCHF H ++E
Sbjct: 42 YKTELCRTFHTIGFCPYGPRCHFIHNADE 70
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 34/92 (36%), Gaps = 30/92 (32%)
Query: 39 KSKPCTKFFSTSGCPFGEGCHFLHYVPGGFKAVSQMLNLGGTXXXXXXXXXXXXXXXXXX 98
K++ C F + C +GE C F H GF + +
Sbjct: 5 KTELCRPFEESGTCKYGEKCQFAH----GFHELRSL------------------------ 36
Query: 99 DGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAH 130
+ P K+ LC +++ C +G +CHF H
Sbjct: 37 --TRHPKYKTELCRTFHTIGFCPYGPRCHFIH 66
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 22 FKKSKQEMENFPTGIGSKSKPCTKFFSTSGCPFGEGCHFLH 62
F E+ + K++ C F + CP+G CHF+H
Sbjct: 26 FAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCHFIH 66
>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 = 35.4 bits (80), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 189 AGAIIGKNGVNSKQICRLTGAKLSIRDH---EVDPNLRNIELEGTFDQIKQASAMVRELI 245
G IIGK G K I + +GA++ ++ + DPN++ + GT QI A ++ E I
Sbjct: 115 TGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 24/33 (72%), Gaps = 1/33 (3%)
Query: 267 FKTKLCENFAK-GSCTFGDRCHFAHGSEELRKS 298
+KT+LC +++ G C +G +C FAHG ELR++
Sbjct: 10 YKTELCRTYSESGRCRYGAKCQFAHGLGELRQA 42
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 101 SSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWEL 135
++ K+ LC Y+ + C++G KC FAHG EL
Sbjct: 5 TTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGEL 39
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 267 FKTKLCENFA-KGSCTFGDRCHFAHGSEE 294
+KT+LC F +G C +G RCHF H E
Sbjct: 48 YKTELCHKFKLQGRCPYGSRCHFIHNPTE 76
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 104 PAVKSRLCNKYNSAEGCKFGDKCHFAHGEWE 134
P K+ LC+K+ C +G +CHF H E
Sbjct: 46 PKYKTELCHKFKLQGRCPYGSRCHFIHNPTE 76
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 39 KSKPCTKFFSTSGCPFGEGCHFLH 62
K++ C KF CP+G CHF+H
Sbjct: 49 KTELCHKFKLQGRCPYGSRCHFIH 72
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 35.0 bits (79), Expect = 0.051, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
+++I LA +IIGK G KQI +GA + I + R I + GT DQI+ A +
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYL 76
Query: 241 VR 242
++
Sbjct: 77 LQ 78
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 183 SIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDH---EVDPNLRNIELEGTFDQIKQASA 239
SI G +IG+ G N K I + TGA + I DPN + + G+ QI A
Sbjct: 12 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQ 71
Query: 240 MVRELI 245
++ E I
Sbjct: 72 LIEEKI 77
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNL---RNIELEGTFDQIKQA 237
++S+ + G IIG+ G + IC+ +GAK++ D E + L R I++ GT ++ A
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITC-DKESEGTLLLSRLIKISGTQKEVAAA 76
Query: 238 SAMVRELI 245
++ E +
Sbjct: 77 KHLILEKV 84
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEV-DPNLRNIELEG 229
++ I A+ GAIIGK G + KQ+ R A + I E D +R + + G
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITG 55
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 182 ISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNLRNI-ELEGTFDQIKQASA 239
I + A AG +IGK G ++ LT A++ + RD D N + I ++ G F + A
Sbjct: 89 IRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQR 148
Query: 240 MVRELIVNV 248
+R+++ V
Sbjct: 149 KIRDILAQV 157
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 33/61 (54%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
+++I L G IIG+ G N +I +++GA++ I + + R + + G+ I A +
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYL 68
Query: 241 V 241
+
Sbjct: 69 I 69
>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 = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
++ + K G+IIGK G + K+I +GA+++I E + R I L G + I +A AM
Sbjct: 6 RLLMHGKEVGSIIGKKGESVKRIREESGARINIS--EGNSPERIITLTGPTNAIFKAFAM 63
Query: 241 V 241
+
Sbjct: 64 I 64
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 271 LCENFAKGSCTFGDRCHFAHGSEELRK 297
+C+ + G+C G+ C FAHG+ EL +
Sbjct: 22 ICDRYMNGTCPEGNSCKFAHGNAELHE 48
>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 = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNLRN 224
+I++ L GAI+GK G + LTGA++ I + E P RN
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRN 50
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNLRN--IELEGTFDQIKQA 237
+I++ L GAI+GK G + LTG ++ I + E P RN + + GT + A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 238 SAMVRELI 245
++ + I
Sbjct: 66 QYLITQRI 73
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-----RDHEVDPNLRNIELEGTFDQIK 235
+I I A AG +IGK G KQ+ G K+ + ++ D LR + G +++
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR---ITGDPYKVQ 74
Query: 236 QASAMVRELI 245
QA MV ELI
Sbjct: 75 QAKEMVLELI 84
>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 = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-RDHEVDPNLRN 224
++++ L GAI+GK G + LTGA++ I + E P RN
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRN 50
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 28.1 bits (61), Expect = 5.9, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLS-IRDHEVDPNL-RNIELEGTFDQIKQAS 238
+I I A AG +IGK G KQ+ G K+ I+D + N+ + + + G +++QA
Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQAC 76
Query: 239 AMVRELI 245
MV +++
Sbjct: 77 EMVMDIL 83
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSI-----RDHEVDPNLRNIELEGTFDQIK 235
+I I A AG +IGK G KQ+ G K+ + ++ VD LR I G +++
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII---GDPYKVQ 61
Query: 236 QASAMVRELI 245
QA MV +++
Sbjct: 62 QACEMVMDIL 71
>pdb|2P2R|A Chain A, Crystal Structure Of The Third Kh Domain Of Human Poly(C)-
Binding Protein-2 In Complex With C-Rich Strand Of Human
Telomeric Dna
Length = 76
Score = 27.7 bits (60), Expect = 8.3, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 30/61 (49%)
Query: 181 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 240
+++I L G IIG+ G +I + +GA++ I + R + + G+ I A +
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYL 67
Query: 241 V 241
+
Sbjct: 68 I 68
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
0.317 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,655,572
Number of Sequences: 62578
Number of extensions: 255111
Number of successful extensions: 500
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 456
Number of HSP's gapped (non-prelim): 53
length of query: 300
length of database: 14,973,337
effective HSP length: 98
effective length of query: 202
effective length of database: 8,840,693
effective search space: 1785819986
effective search space used: 1785819986
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)