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= 010611
(506 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 65.5 bits (158), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 46/148 (31%), Positives = 81/148 (54%), Gaps = 11/148 (7%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
++ R+L +VG++IGK G ++ ++ E+GA I++ + C ER+IT+ GP +
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI--SEGNCPERIITLA---GPTNAI 59
Query: 246 SPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRK 305
KA ++ +L E S + ++ V RLVV ++Q G L+GKGG I E+R+
Sbjct: 60 F---KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRE 116
Query: 306 VTGTSIRIISDQLLKCISENDRVVQISG 333
TG +++ D L + +R + I+G
Sbjct: 117 STGAQVQVAGDMLP---NSTERAITIAG 141
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 45/92 (48%), Gaps = 7/92 (7%)
Query: 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333
K + + RL++ +VG ++GK G + +MR+ +G I I +R++ ++G
Sbjct: 1 KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC------PERIITLAG 54
Query: 334 EFSKVKDAVYNVTGRLRDNHFSGTLN-TARTR 364
+ + A + +L ++ S N TA +R
Sbjct: 55 PTNAIFKAFAMIIDKLEEDISSSMTNSTAASR 86
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 45.8 bits (107), Expect = 6e-05, Method: Composition-based stats.
Identities = 40/141 (28%), Positives = 70/141 (49%), Gaps = 16/141 (11%)
Query: 197 VGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTASEGPESRYSPAQKAVVLV 255
VGA+IGK G I+ L A A I + P+ R++ +T PE+++ KA +
Sbjct: 14 VGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP--PEAQF----KAQGRI 67
Query: 256 FSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315
+ +L E F + + + + V ++ G ++GKGG ++E++ +T + +
Sbjct: 68 YGKLKEENF-----FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
Query: 316 DQLLKCISENDRV-VQISGEF 335
DQ END+V V+I G F
Sbjct: 123 DQ---TPDENDQVIVKIIGHF 140
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 38/181 (20%), Positives = 81/181 (44%), Gaps = 28/181 (15%)
Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESR 244
++L + G++IGKGG I LQ E GA I + + P ER+ + +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI----- 62
Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLV-------------NARLVVASNQVGC 291
+A+ V + E E + + + + + +++V ++ G
Sbjct: 63 -----EALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGL 117
Query: 292 LLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
++GKGG + + + +G +++ Q I+ +RVV +SGE + + AV + ++++
Sbjct: 118 IIGKGGATVKAIXEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175
Query: 352 N 352
+
Sbjct: 176 D 176
Score = 37.0 bits (84), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 47/101 (46%), Gaps = 8/101 (7%)
Query: 161 VSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS 220
V+ P+S+ + R Q +I+ N G +IGKGG ++A+ ++GA++
Sbjct: 83 VAKTEPVSILQPQTTVNPDRANQ----VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQ 138
Query: 221 VGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261
+ + + VT S PE +KAV L+ ++ E
Sbjct: 139 LSQKPDGINLQNRVVTVSGEPEQN----RKAVELIIQKIQE 175
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 38/181 (20%), Positives = 81/181 (44%), Gaps = 28/181 (15%)
Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESR 244
++L + G++IGKGG I LQ E GA I + + P ER+ + +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI----- 62
Query: 245 YSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLV-------------NARLVVASNQVGC 291
+A+ V + E E + + + + + +++V ++ G
Sbjct: 63 -----EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGL 117
Query: 292 LLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351
++GKGG + + + +G +++ Q I+ +RVV +SGE + + AV + ++++
Sbjct: 118 IIGKGGATVKAIMEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175
Query: 352 N 352
+
Sbjct: 176 D 176
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 47/101 (46%), Gaps = 8/101 (7%)
Query: 161 VSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS 220
V+ P+S+ + R Q +I+ N G +IGKGG ++A+ ++GA++
Sbjct: 83 VAKTEPVSILQPQTTVNPDRANQ----VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQ 138
Query: 221 VGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261
+ + + VT S PE +KAV L+ ++ E
Sbjct: 139 LSQKPDGINLQNRVVTVSGEPEQN----RKAVELIIQKIQE 175
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 34/54 (62%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
++ ++ D G++IGKGG I+ ++ E+GA I + + ++R+IT+T ++
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
G ++ ++ + + G ++GKGG I ++R +G SI+I D+ L+ DR++ I+G
Sbjct: 11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLE--GSEDRIITITGT 66
Query: 335 FSKVKDAVY 343
++++A Y
Sbjct: 67 QDQIQNAQY 75
>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 = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 34/54 (62%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
++ ++ D G++IGKGG I+ ++ E+GA I + + ++R+IT+T ++
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
G ++ ++ + + G ++GKGG I ++R +G SI+I D+ L+ DR++ I+G
Sbjct: 4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLE--GSEDRIITITGT 59
Query: 335 FSKVKDAVY 343
++++A Y
Sbjct: 60 QDQIQNAQY 68
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYS 246
I + DK+ VIGKGG++IRAL E G I + D+ + + A++G +++++
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTIEI------EDDGTVKIAATDGEKAKHA 614
Score = 28.5 bits (62), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKC 321
+++ ++GKGG++I + + TGT+I I D +K
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKI 603
>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 = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTA 237
++ R+L +VG++IGK G ++ ++ E+GA I++ + C ER+IT+T
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNCPERIITLTG 52
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
L + +N +GC++G+ G I+E+R+++G I+I + + R V I+G + + A
Sbjct: 10 LTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP----VEGSSGRQVTITGSAASISLA 65
Query: 342 VYNVTGRL 349
Y + RL
Sbjct: 66 QYLINARL 73
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQVS 498
+ TT E+ +P N+IG + G G+N+ +RQ+S
Sbjct: 4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMS 35
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 9/78 (11%)
Query: 194 NDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVV 253
N+ +G +IG+ G I ++ +GA I + + R +T+T G + S AQ
Sbjct: 14 NNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT---GSAASISLAQ---Y 67
Query: 254 LVFSRLIEGTSEKGLDFS 271
L+ +RL +SEKG+ S
Sbjct: 68 LINARL---SSEKGMGCS 82
>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 = 35.8 bits (81), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
L + ++ +GC++G+ G I+E+R+ +G I+I + DR V I+G + + A
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIAN----PVEGSTDRQVTITGSAASISLA 64
Query: 342 VYNVTGRL 349
Y + RL
Sbjct: 65 QYLINVRL 72
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238
Q S + ND +G +IG+ G I ++ +GA I + + +R +T+T S
Sbjct: 3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGS 57
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 35.4 bits (80), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 33/54 (61%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239
++ ++ D ++IGKGG I+ ++ E+GA I + + ++R+IT+T ++
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334
G ++ ++ + + ++GKGG I ++R +G SI+I D+ L+ DR++ I+G
Sbjct: 11 GPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI--DEPLE--GSEDRIITITGT 66
Query: 335 FSKVKDAVY 343
++++A Y
Sbjct: 67 QDQIQNAQY 75
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 33/130 (25%), Positives = 57/130 (43%), Gaps = 9/130 (6%)
Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAGA---FISVGATMPECDERLITVTASEGPESRYS 246
I+ K G VIGKGG I+ LQ AG I G+ D+ L + G +
Sbjct: 6 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII----GDPYKVQ 61
Query: 247 PAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKV 306
A + V+ + +G ++ S G ++ + V + VG ++G+ G +I +++
Sbjct: 62 QACEMVMDILRERDQGGFGDRNEYGSRIGGGID--VPVPRHSVGVVIGRSGEMIKKIQND 119
Query: 307 TGTSIRIISD 316
G I+ D
Sbjct: 120 AGVRIQFKQD 129
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
+ V N VG +LGKGG + E +++TG I+ IS + +R V I+G + + A
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGCRIQ-ISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 342 VYNVTGRL 349
Y +T R+
Sbjct: 66 QYLITQRI 73
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 471 VEIIVPENVIGSVYGENGSNLLRLRQVS 498
VEI VPEN++G++ G+ G L+ ++++
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELT 32
>pdb|2AXY|A Chain A, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|B Chain B, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|C Chain C, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|D Chain D, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2PQU|A Chain A, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|B Chain B, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|C Chain C, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|D Chain D, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PY9|A Chain A, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|B Chain B, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|C Chain C, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|D Chain D, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
Length = 73
Score = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 12/80 (15%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRY 245
++ R+L +VG++IGK G ++ + E+GA I++ + C ER+IT+ GP +
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREESGARINI--SEGNCPERIITLA---GPTN-- 57
Query: 246 SPAQKAVVLVFSRLIEGTSE 265
A+ F+ +I+ E
Sbjct: 58 -----AIFKAFAXIIDKLEE 72
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP 226
E++F I K G VIG+GG ++A+ + GAF+ + +P
Sbjct: 8 EMTFSI--PTHKCGLVIGRGGENVKAINQQTGAFVEISRQLP 47
>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 = 33.5 bits (75), Expect = 0.27, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
+ V N VG +LGKGG + E +++TG I+I + N RV I+G + + A
Sbjct: 7 MAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVT-ITGSPAATQAA 65
Query: 342 VYNVTGRL 349
Y ++ R+
Sbjct: 66 QYLISQRV 73
Score = 30.0 bits (66), Expect = 3.1, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 197 VGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTAS 238
VGA++GKGG + Q GA I + G +P R +T+T S
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
>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 = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 55/132 (41%), Gaps = 21/132 (15%)
Query: 197 VGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLV- 255
VG VIG+ G +I+ +Q++AG I ER+ +T GP R AQ A ++
Sbjct: 14 VGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQIT---GPPDR---AQHAAEIIT 67
Query: 256 -FSRLIEGTSEKGLDFSSNK-------------GLLVNARLVVASNQVGCLLGKGGTIIS 301
R ++ + G G L +V + + G ++GKGG I
Sbjct: 68 DLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIK 127
Query: 302 EMRKVTGTSIRI 313
+ + +G I +
Sbjct: 128 SISQQSGARIEL 139
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP---ECDERLITVTAS 238
F + K G +IGKGG I+++ ++GA I + P + + +L T+ +
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT 159
>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 = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTA 237
++ R+L +VG++IGK G ++ ++ E+GA I++ + ER+IT+T
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI--SEGNSPERIITLTG 52
>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 = 33.1 bits (74), Expect = 0.39, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
+ V N VG +LGKGG + E +++TG I+I + N RV I+G + + A
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVT-ITGSPAATQAA 65
Query: 342 VYNVTGRL 349
Y ++ R+
Sbjct: 66 QYLISQRV 73
Score = 29.6 bits (65), Expect = 3.8, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 197 VGAVIGKGGTIIRALQSEAGAFISV---GATMPECDERLITVTAS 238
VGA++GKGG + Q GA I + G +P R +T+T S
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
Score = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 471 VEIIVPENVIGSVYGENGSNLLRLRQVS 498
VEI VPEN++G++ G+ G L+ ++++
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELT 32
>pdb|2IUJ|A Chain A, Crystal Structure Of Soybean Lipoxygenase-B
Length = 853
Score = 32.0 bits (71), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 213 SEAG---AFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGL 268
S+AG AF G + E +++LI E +RY PA+ L++ EG + +G+
Sbjct: 789 SDAGPLEAFKRFGKNLEEIEKKLIEKNNDETLRNRYGPAKMPYTLLYPSSEEGLTFRGI 847
>pdb|3DMK|A Chain A, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
pdb|3DMK|B Chain B, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
pdb|3DMK|C Chain C, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
Length = 816
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 13/76 (17%)
Query: 325 NDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPAS 384
NDRV Q+SG +KDAV +G+ + N+ S +VLT T+P S DP +
Sbjct: 298 NDRVKQVSGTLI-IKDAVVEDSGK----YLCVVNNSVGGESVETVLTVTAPLSAKIDPPT 352
Query: 385 FGVHSSVAVSHDFSQP 400
V DF +P
Sbjct: 353 QTV--------DFGRP 360
>pdb|2V5M|A Chain A, Structural Basis For Dscam Isoform Specificity
Length = 388
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 13/76 (17%)
Query: 325 NDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPAS 384
NDRV Q+SG +KDAV +G+ + N+ S +VLT T+P S DP +
Sbjct: 262 NDRVKQVSGTLI-IKDAVVEDSGK----YLCVVNNSVGGESVETVLTVTAPLSAKIDPPT 316
Query: 385 FGVHSSVAVSHDFSQP 400
V DF +P
Sbjct: 317 QTV--------DFGRP 324
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISEN---DRVVQISGEFSKV 338
+++ + + G ++GKGG I ++++ G + +I D S+N D+ ++I G+ KV
Sbjct: 18 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-----SQNTNVDKPLRIIGDPYKV 72
Query: 339 KDAVYNVTGRLRD 351
+ A V LR+
Sbjct: 73 QQACEMVMDILRE 85
Score = 30.0 bits (66), Expect = 3.5, Method: Composition-based stats.
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAG 216
I+ K G VIGKGG I+ LQ AG
Sbjct: 18 IMIPAGKAGLVIGKGGETIKQLQERAG 44
>pdb|2V5S|A Chain A, Structural Basis For Dscam Isoform Specificity
pdb|2V5S|B Chain B, Structural Basis For Dscam Isoform Specificity
Length = 394
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 13/76 (17%)
Query: 325 NDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPAS 384
NDRV Q+SG +KDAV +G+ + N+ S +VLT T+P S DP +
Sbjct: 268 NDRVKQVSGTLI-IKDAVVEDSGK----YLCVVNNSVGGESVETVLTVTAPLSAKIDPPT 322
Query: 385 FGVHSSVAVSHDFSQP 400
V DF +P
Sbjct: 323 QTV--------DFGRP 330
>pdb|2V5R|A Chain A, Structural Basis For Dscam Isoform Specificity
pdb|2V5R|B Chain B, Structural Basis For Dscam Isoform Specificity
Length = 391
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 13/76 (17%)
Query: 325 NDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPAS 384
NDRV Q+SG +KDAV +G+ + N+ S +VLT T+P S DP +
Sbjct: 265 NDRVKQVSGTLI-IKDAVVEDSGK----YLCVVNNSVGGESVETVLTVTAPLSAKIDPPT 319
Query: 385 FGVHSSVAVSHDFSQP 400
V DF +P
Sbjct: 320 QTV--------DFGRP 327
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341
+++ +++ G ++GKGG I ++++ G + +I D + D+ ++I+G+ KV+ A
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN--TGADKPLRITGDPYKVQQA 76
Query: 342 VYNVTGRLRD 351
V +RD
Sbjct: 77 KEMVLELIRD 86
Score = 29.3 bits (64), Expect = 5.4, Method: Composition-based stats.
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 190 ILCSNDKVGAVIGKGGTIIRALQSEAG 216
I+ K G VIGKGG I+ LQ AG
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQERAG 45
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
DK+ VIG GG +IR + + GA + + D+ ++ V+AS+G
Sbjct: 579 DKIREVIGSGGKVIREIVATTGAKVDI------NDDGVVKVSASDG 618
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
DK+ VIG GG +IR + + GA + + D+ ++ V+AS+G
Sbjct: 579 DKIREVIGSGGKVIREIVATTGAKVDI------NDDGVVKVSASDG 618
>pdb|3HR8|A Chain A, Crystal Structure Of Thermotoga Maritima Reca
Length = 356
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 48/107 (44%), Gaps = 1/107 (0%)
Query: 42 PVDTIPHETIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILR- 100
P + + + L I + S+ + +T +PVE +P L + +G R
Sbjct: 2 PEEKQKKSVLEKALKRIEENFGKGSIMILGDETQVQPVEVIPTGSLAIDIATGVGGYPRG 61
Query: 101 RPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRN 147
R +E+F ESS +++ AL + + G V+ I + +D + +N
Sbjct: 62 RIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKN 108
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240
DK+ VIG GG +IR + + GA + + D+ ++ V+AS+G
Sbjct: 570 DKIREVIGSGGKVIREIVATTGAKVDI------NDDGVVKVSASDG 609
>pdb|1VSN|A Chain A, Crystal Structure Of A Potent Small Molecule Inhibitor
Bound To Cathepsin K
Length = 215
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 297 GTIISEMRKVTGTSIRIISDQLLKCISEND 326
G + +++K TG + + L+ C+SEND
Sbjct: 32 GALEGQLKKATGALLNLAPQNLVDCVSEND 61
>pdb|2CDF|B Chain B, Structure And Binding Kinetics Of Three Different Human
Cd1d-Alpha-Galactosylceramide-Specific T Cell Receptors
(Tcr 5e)
Length = 244
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 348 RLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQ--PP 401
R+R HF TL +AR TS L +S + + FG + ++V D ++ PP
Sbjct: 68 RIRTEHFPLTLESARPSHTSQYLCASSEFRDGNEKLFFGSGTQLSVLEDLNKVFPP 123
>pdb|1ITQ|A Chain A, Human Renal Dipeptidase
pdb|1ITQ|B Chain B, Human Renal Dipeptidase
pdb|1ITU|A Chain A, Human Renal Dipeptidase Complexed With Cilastatin
pdb|1ITU|B Chain B, Human Renal Dipeptidase Complexed With Cilastatin
Length = 369
Score = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/51 (25%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 50 TIHRPLDTISHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQEILR 100
+++ P DT + + +RR+LE + D + R P+ L+ + +G ++ R
Sbjct: 66 SVYTPCDTQNKDAVRRTLEQM--DVVHRMCRMYPETFLYVTSSAGIRQAFR 114
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 28.5 bits (62), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 197 VGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLV 255
VG +IG+GG I +Q ++G + + ER +++T + PES QKA +++
Sbjct: 27 VGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGA--PES----VQKAKMML 79
>pdb|1L2F|A Chain A, Crystal Structure Of Nusa From Thermotoga Maritima: A
Structure-Based Role Of The N-Terminal Domain
Length = 369
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 49/119 (41%), Gaps = 25/119 (21%)
Query: 195 DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVL 254
D +GA IG+GG+ I A+ E E+L + S+ P+ + A +
Sbjct: 270 DPIGACIGEGGSRIAAILKELKG------------EKLDVLKWSDDPKQLIANALAPATV 317
Query: 255 VFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313
+ +++ NK AR++V Q+ +GKGG K+TG I I
Sbjct: 318 IEVEILD---------KENKA----ARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDI 363
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
0.316 0.131 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,250,261
Number of Sequences: 62578
Number of extensions: 497075
Number of successful extensions: 1329
Number of sequences better than 100.0: 53
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1251
Number of HSP's gapped (non-prelim): 90
length of query: 506
length of database: 14,973,337
effective HSP length: 103
effective length of query: 403
effective length of database: 8,527,803
effective search space: 3436704609
effective search space used: 3436704609
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: 54 (25.4 bits)