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= 006943
(624 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 10/97 (10%)
Query: 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLI 197
E+E Q+ +P+ IIGK G IK+L SIK+ P + P M V+I
Sbjct: 1 EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRM-----VII 53
Query: 198 SGESEAVKKALFAISAIMYK---FSPREDIPLETTVR 231
+G EA KA I + + F P+E++ LET +R
Sbjct: 54 TGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIR 90
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 35/148 (23%), Positives = 59/148 (39%), Gaps = 24/148 (16%)
Query: 35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDP-FPGAKDRVVTIYSHXXXX 93
E + ++ P +G++IGK G+ I + + A +K+ P P +K R+V I
Sbjct: 1 EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVII------- 53
Query: 94 XXXXXXXXXXXXXPLCAAQDALLKVHXXXXXXXXXXTDNDKKRKEKEECQILVPSSQSAN 153
+A K K + K E I VP+S +
Sbjct: 54 ---------------TGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGR 98
Query: 154 IIGKAGATIKRLRSKTRTSIKVTPKDAS 181
+IGK G T+ L++ T + V P+D +
Sbjct: 99 VIGKGGKTVNELQNLTAAEV-VVPRDQT 125
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 299 LVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV--DDTKDNRDECVIT 356
G + +L + P + GRVIGKGG T+ ++ + A++ V D T D D+ ++
Sbjct: 76 FFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVK 135
Query: 357 V 357
+
Sbjct: 136 I 136
Score = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGD-RVALISGTPEQKRAAENLI 617
A AVG +IGK G ++ + + + A+I+++ ++ R+ +I+G PE + A+ I
Sbjct: 11 AQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRI 67
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 24 RINEKDEKGNEESVIY--RILCPDGVIGSVIGKSGKVINSIRQETRARVKVV-DPFPGAK 80
++ E++ G +E V I P G VIGK GK +N ++ T A V V D P
Sbjct: 70 KLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDEN 129
Query: 81 DRV-VTIYSH 89
D+V V I H
Sbjct: 130 DQVIVKIIGH 139
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 32/48 (66%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
+ + P+ +IG +IG+ G IN IRQ + A++K+ +P G+ DR VTI
Sbjct: 7 HELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTI 54
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 305 SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVT 358
S EL I P + IG +IG+ G I IRQ SGAQI + + + + +T+T
Sbjct: 6 SHELTI----PNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTIT 55
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 30/53 (56%)
Query: 565 VGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLI 617
+G +IG+ G+ + IR+ SGA I++++ DR I+G+ A+ LI
Sbjct: 16 IGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 68
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
++ P + GS+IGK G+ I IR E+ A +K+ +P G++DR++TI
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
+ +V P + G +IGKGG IK IR SGA I +D+ + ++ +IT+T + D I+
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ--DQIQ 71
Query: 368 SMAVEAVLLLQTKI 381
+ A LLQ +
Sbjct: 72 N----AQYLLQNSV 81
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 566 GKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ 618
G +IGK G + IR SGA+I++ + DR+ I+GT +Q + A+ L+Q
Sbjct: 26 GSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 78
Score = 36.6 bits (83), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKV-TPKDASEPTHSCAMEFDNFVLISGE 200
Q+ +P + +IIGK G IK++R ++ SIK+ P + SE D + I+G
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE---------DRIITITGT 66
Query: 201 SEAVKKALFAISAIMYKFSPR 221
+ ++ A + + + ++S +
Sbjct: 67 QDQIQNAQYLLQNSVKQYSGK 87
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 76/189 (40%), Gaps = 47/189 (24%)
Query: 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTIYSHXXXXX 94
++L P GS+IGK G+ I +++ET A +K+ D +PG +RV I
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI---- 62
Query: 95 XXXXXXXXXXXXPLCAAQDALLKVHXXXXXXXXXXTDNDKKRK--------------EKE 140
+AL VH N K +
Sbjct: 63 ------------------EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRAN 104
Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN-FVLISG 199
+ +I+VP+S + IIGK GAT+K + ++ ++++ K + N V +SG
Sbjct: 105 QVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD-------GINLQNRVVTVSG 157
Query: 200 ESEAVKKAL 208
E E +KA+
Sbjct: 158 EPEQNRKAV 166
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 564 AVGKVIGKAGSNLANIRKISGATIEMSDSK---SSRGDRVALISGTPEQKRAAENLIQAF 620
A G +IGK G + ++K +GATI++S SK +RV LI GT E A N + F
Sbjct: 16 AAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE----ALNAVHGF 71
Query: 621 I 621
I
Sbjct: 72 I 72
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD--NRDECVITVTA 359
++++ P + G +IGKGG T+K+I + SGA + + D N V+TV+
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSG 157
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 566 GKVIGKAGSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLI 617
G +IGK G+ + I + SGA +++S + +RV +SG PEQ R A LI
Sbjct: 116 GLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELI 169
Score = 37.0 bits (84), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 48/104 (46%), Gaps = 19/104 (18%)
Query: 307 ELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-----NRDECVI--TVTA 359
+ ++VL P G +IGKGG TI +++ +GA I + +KD C+I T+ A
Sbjct: 5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64
Query: 360 I------------ESPDDIKSMAVEAVLLLQTKINDEDDDTVTI 391
+ E P ++ ++L QT +N + + V I
Sbjct: 65 LNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKI 108
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 47/189 (24%), Positives = 77/189 (40%), Gaps = 47/189 (24%)
Query: 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTIYSHXXXXX 94
++L P GS+IGK G+ I +++ET A +K+ D +PG +RV I
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI---- 62
Query: 95 XXXXXXXXXXXXPLCAAQDALLKVHXXXXXXXXXXTDNDKKRK--------------EKE 140
+AL VH N K +
Sbjct: 63 ------------------EALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRAN 104
Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN-FVLISG 199
+ +I+VP+S + IIGK GAT+K + ++ ++++ K + N V +SG
Sbjct: 105 QVKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPD-------GINLQNRVVTVSG 157
Query: 200 ESEAVKKAL 208
E E +KA+
Sbjct: 158 EPEQNRKAV 166
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 564 AVGKVIGKAGSNLANIRKISGATIEMSDSK---SSRGDRVALISGTPEQKRAAENLIQAF 620
A G +IGK G + ++K +GATI++S SK +RV LI GT E A N + F
Sbjct: 16 AAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE----ALNAVHGF 71
Query: 621 I 621
I
Sbjct: 72 I 72
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD--NRDECVITVTA 359
++++ P + G +IGKGG T+K+I + SGA + + D N V+TV+
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSG 157
Score = 37.0 bits (84), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 48/104 (46%), Gaps = 19/104 (18%)
Query: 307 ELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-----NRDECVI--TVTA 359
+ ++VL P G +IGKGG TI +++ +GA I + +KD C+I T+ A
Sbjct: 5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64
Query: 360 I------------ESPDDIKSMAVEAVLLLQTKINDEDDDTVTI 391
+ E P ++ ++L QT +N + + V I
Sbjct: 65 LNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKI 108
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 566 GKVIGKAGSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLI 617
G +IGK G+ + I + SGA +++S + +RV +SG PEQ R A LI
Sbjct: 116 GLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELI 169
>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 = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
++ P + GS+IGK G+ I IR E+ A +K+ +P G++DR++TI
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 56
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
+ +V P + G +IGKGG IK IR SGA I +D+ + ++ +IT+T + D I+
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ--DQIQ 64
Query: 368 SMAVEAVLLLQTKI 381
+ A LLQ +
Sbjct: 65 N----AQYLLQNSV 74
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 566 GKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ 618
G +IGK G + IR SGA+I++ + DR+ I+GT +Q + A+ L+Q
Sbjct: 19 GSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 71
Score = 36.2 bits (82), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKV-TPKDASEPTHSCAMEFDNFVLISGE 200
Q+ +P + +IIGK G IK++R ++ SIK+ P + SE D + I+G
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE---------DRIITITGT 59
Query: 201 SEAVKKALFAISAIMYKFSPR 221
+ ++ A + + + ++S +
Sbjct: 60 QDQIQNAQYLLQNSVKQYSGK 80
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc
Binding Protein
Length = 82
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
+ + P+ +IG +IG+ G IN IRQ + A++K+ +P G+ R VTI
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 300 VGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTA 359
+G+ + EL I P N IG +IG+ G I IRQ SGAQI + + + +T+T
Sbjct: 2 LGSQTTHELTI----PNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG 57
Query: 360 IESPDDIKSMAVEAVL 375
+ + + A L
Sbjct: 58 SAASISLAQYLINARL 73
Score = 36.2 bits (82), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
N +G +IG+ G+N+ IR++SGA I++++ R I+G+ A+ LI A
Sbjct: 15 NLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 71
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV-DDTKDNRDECVITVTAIESPDDI 366
+ +R++ P ++ G +IGKGG IK IR+++GAQ+ V D N E IT+ I P I
Sbjct: 89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGI--PQSI 146
Query: 367 KSMAVE-AVLLLQT 379
+ V++L+T
Sbjct: 147 IECVKQICVVMLET 160
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 62/141 (43%), Gaps = 21/141 (14%)
Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHXXXXXX 95
++ R+L +GS+IGK G+ + +R+E+ AR+ + + +R++T+
Sbjct: 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAG------- 54
Query: 96 XXXXXXXXXXXPLCAAQDAL-LKVHXXXXXXXXXXTDNDKKRKEKEECQILVPSSQSANI 154
P A A + + T++ + +++VP+SQ ++
Sbjct: 55 -----------PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSL 103
Query: 155 IGKAGATIKRLRSKTRTSIKV 175
IGK G IK +R T ++V
Sbjct: 104 IGKGGCKIKEIRESTGAQVQV 124
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV-DPFPGAKDRVVTI 86
V R++ P GS+IGK G I IR+ T A+V+V D P + +R +TI
Sbjct: 89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITI 139
Score = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 63/129 (48%), Gaps = 14/129 (10%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
L IR+L ++G +IGK G ++K +R+ SGA+I++ + N E +IT+ P +
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAG---PTNAI 59
Query: 368 SMAVEAVL-LLQTKINDEDDDT-------VTIRLLVXXXXXXXXXXXXXXXXNEIRKRTK 419
A ++ L+ I+ ++ VT+RL+V EIR+ T
Sbjct: 60 FKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119
Query: 420 ADVRISKGD 428
A V+++ GD
Sbjct: 120 AQVQVA-GD 127
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
++ P + S+IGK G+ I IR E+ A +K+ +P G++DR++TI
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
+ +V P + +IGKGG IK IR SGA I +D+ + ++ +IT+T + D I+
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ--DQIQ 71
Query: 368 SMAVEAVLLLQTKI 381
+ A LLQ +
Sbjct: 72 N----AQYLLQNSV 81
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%)
Query: 568 VIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ 618
+IGK G + IR SGA+I++ + DR+ I+GT +Q + A+ L+Q
Sbjct: 28 IIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 78
Score = 35.8 bits (81), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 10/79 (12%)
Query: 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKV-TPKDASEPTHSCAMEFDNFVLISGE 200
Q+ +P + +IIGK G IK++R ++ SIK+ P + SE D + I+G
Sbjct: 16 TQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSE---------DRIITITGT 66
Query: 201 SEAVKKALFAISAIMYKFS 219
+ ++ A + + + ++S
Sbjct: 67 QDQIQNAQYLLQNSVKQYS 85
>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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTA 359
L IR+L ++G +IGK G ++K IR+ SGA+I++ + N E +IT+T
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNSPERIITLTG 52
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
R+L +GS+IGK G+ + IR+E+ AR+ + + + +R++T+
Sbjct: 6 RLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNSPERIITL 50
>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 = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTA 359
L IR+L ++G +IGK G ++K IR+ SGA+I++ + N E +IT+T
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTG 52
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
R+L +GS+IGK G+ + IR+E+ AR+ + + +R++T+
Sbjct: 6 RLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITL 50
>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 = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 312 VLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVD-DTKDNRDECVITVTAIESPDDI 366
+ P K G +IGKGG TIKSI Q SGA+I++ + N D + T +P I
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQI 163
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 566 GKVIGKAGSNLANIRKISGATIEMSDSKSSRGD---RVALISGTPEQKRAAENLIQ 618
G +IGK G + +I + SGA IE+ + D ++ I GTP+Q A LI+
Sbjct: 116 GLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIE 171
Score = 33.1 bits (74), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%)
Query: 564 AVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLI 617
AVG VIG+ G + I+ +G I+ + +R+A I+G P++ + A +I
Sbjct: 13 AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEII 66
Score = 32.7 bits (73), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV-DPFPGA 79
+ + P G G +IGK G+ I SI Q++ AR+++ +P P A
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA 147
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 140 EECQILVPSSQSANIIGKAGATIKRL--RSKTRTSIKVTPKDASEP 183
+E +VP+ ++ IIGK G TIK + +S R ++ P ++P
Sbjct: 104 QEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADP 149
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 315 PFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAV 374
P +GR+IG+GG TI+SI +ASGA+I D + ++ I+ K +A
Sbjct: 22 PQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKH 78
Query: 375 LLLQTKINDED 385
L+L+ DE+
Sbjct: 79 LILEKVSEDEE 89
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 6/58 (10%)
Query: 564 AVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG----DRVALISGTPEQKRAAENLI 617
+VG++IG+ G + +I K SGA I + K S G R+ ISGT ++ AA++LI
Sbjct: 25 SVGRIIGRGGETIRSICKASGAKI--TCDKESEGTLLLSRLIKISGTQKEVAAAKHLI 80
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 36.6 bits (83), Expect = 0.039, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 566 GKVIGKAGSNLANIRKISGATIEMSDSKSSRGD---RVALISGTPEQKRAAENLIQAFI 621
G VIG+ G N+ I + +GA +E+S GD ++ +I G+P+Q A+ LI+ I
Sbjct: 19 GLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKI 77
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 315 PFNKIGRVIGKGGGTIKSIRQASGAQIDV 343
P +K G VIG+GG +K+I Q +GA +++
Sbjct: 14 PTHKCGLVIGRGGENVKAINQQTGAFVEI 42
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 36.6 bits (83), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 34/57 (59%)
Query: 565 VGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI 621
VG +IG+ G ++ I++ SG I+++ +R +++GTPE ++A+ L+ +
Sbjct: 26 VGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIV 82
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
Y++ PDG++G +IG+ G+ I+ I+QE+ ++++ G +R +
Sbjct: 19 YKV--PDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML 64
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 146 VPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVK 205
VP IIG+ G I R++ ++ I++ P P SC +++G E+V+
Sbjct: 21 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC--------MLTGTPESVQ 72
Query: 206 KALFAISAIMYK 217
A + I+ K
Sbjct: 73 SAKRLLDQIVEK 84
Score = 28.9 bits (63), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 315 PFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDE--CVITVTAIESPDDIKS 368
P +G +IG+GG I I+Q SG +I + E C++T T P+ ++S
Sbjct: 22 PDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT----PESVQS 73
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 32/48 (66%), Gaps = 2/48 (4%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
YR+ PDG++G +IG+ G+ IN I+Q++ +V++ G +R V++
Sbjct: 20 YRV--PDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSL 65
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 30/57 (52%)
Query: 565 VGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI 621
VG +IG+ G + I++ SG +++S +R ++G PE + A+ ++ +
Sbjct: 27 VGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 83
Score = 28.9 bits (63), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 146 VPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVK 205
VP IIG+ G I +++ + ++++P P S V ++G E+V+
Sbjct: 22 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERS--------VSLTGAPESVQ 73
Query: 206 KALFAISAIMYK 217
KA + I+ +
Sbjct: 74 KAKMMLDDIVSR 85
>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 = 35.8 bits (81), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMSDS----KSSRGDRVALISGTPEQKRAAENLI 617
N VG ++GK G L ++++GA I++S +R RV I+G+P +AA+ LI
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVT-ITGSPAATQAAQYLI 69
Score = 35.4 bits (80), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 41 ILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTI 86
I P+ ++G+++GK GK + ++ T AR+++ + PG ++R VTI
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVD 344
++ + P N +G ++GKGG T+ ++ +GA+I +
Sbjct: 4 LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQIS 39
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMSDS----KSSRGDRVALISGTPEQKRAAENLI 617
N VG ++GK G L ++++GA I++S +R RV I+G+P +AA+ LI
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVT-ITGSPAATQAAQYLI 69
Score = 33.1 bits (74), Expect = 0.46, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 44 PDGVIGSVIGKSGKVINSIRQETRARVKVVDP---FPGAKDRVVTI 86
P+ ++G+++GK GK + ++ T AR+++ PG ++R VTI
Sbjct: 10 PENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55
Score = 28.9 bits (63), Expect = 9.8, Method: Composition-based stats.
Identities = 11/35 (31%), Positives = 23/35 (65%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV 343
++ + P N +G ++GKGG T+ ++ +GA+I +
Sbjct: 4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQI 38
>pdb|3RGW|L Chain L, Crystal Structure At 1.5 A Resolution Of An H2-Reduced,
O2-Tolerant Hydrogenase From Ralstonia Eutropha Unmasks
A Novel Iron-Sulfur Cluster
Length = 603
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 325 KGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSM--AVEAVLLLQTKIN 382
KG GT+ + R A G I + D + +CV+ T SP D K A EA L+ +N
Sbjct: 521 KGVGTVAAPRGALGHWIRIKDGRIENYQCVVPTTWNGSPRDYKGQIGAFEASLMNTPMVN 580
Query: 383 DE 384
E
Sbjct: 581 PE 582
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMS---DSKSSRGDRVALISGTPEQKRAAENLI 617
N VG ++GK G L ++++G I++S + +R I+GTP +AA+ LI
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQYLI 69
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTI 86
+ I P+ ++G+++GK GK + ++ T R+++ + PG ++R VTI
Sbjct: 4 VVEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTI 55
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVD 344
V+ + P N +G ++GKGG T+ ++ +G +I +
Sbjct: 4 VVEIAVPENLVGAILGKGGKTLVEYQELTGCRIQIS 39
>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 = 0.23, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITV 357
L IR+L ++G +IGK G ++K R+ SGA+I++ + N E +IT+
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREESGARINISE--GNCPERIITL 52
Score = 28.9 bits (63), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
++ R+L +GS+IGK G+ + R+E+ AR+ + + +R++T+
Sbjct: 4 TLTIRLLXHGKEVGSIIGKKGESVKKXREESGARINISE--GNCPERIITL 52
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN 193
Q+ VP ++G GATIKR++ +T T I VTP EP + +N
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYI-VTPGRDKEPVFAVTGMPEN 62
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 307 ELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDI 366
+ I+V P+ +G V+G G TIK I+Q + I V +D E V VT + D
Sbjct: 9 QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYI-VTPGRDK--EPVFAVTGMPENVDR 65
Query: 367 KSMAVEAVLLLQT 379
+EA + L++
Sbjct: 66 AREEIEAHITLRS 78
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 314 CPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
P +KI VIG GG I+ I +GA++D++D
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDIND 607
>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 = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 314 CPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
P +KI VIG GG I+ I +GA++D++D
Sbjct: 567 IPTDKIREVIGSGGKVIREIVATTGAKVDIND 598
>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 = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 314 CPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
P +KI VIG GG I+ I +GA++D++D
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDIND 607
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 10/55 (18%)
Query: 153 NIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKA 207
++IGK+GA I R++ + + S+++ P E N + I G+ + V++A
Sbjct: 18 HLIGKSGANINRIKDQYKVSVRIPPDS----------EKSNLIRIEGDPQGVQQA 62
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
+I V P +KIG VIG I I++ +GA+I ++D
Sbjct: 599 IITVKIPVDKIGEVIGPKRQXINQIQEDTGAEITIED 635
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQI 341
V ++ P +K G VIGKGG TIK +++ +G ++
Sbjct: 16 VQEIMIPASKAGLVIGKGGETIKQLQERAGVKM 48
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 6/65 (9%)
Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
+I++P+S++ +IGK G TIK+L+ + + V +D + T + D + I+G+
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAGVKM-VMIQDGPQNTGA-----DKPLRITGDPY 71
Query: 203 AVKKA 207
V++A
Sbjct: 72 KVQQA 76
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
+I++P+ ++ +IGK G TIK+L+ + + + +D S+ T+ D + I G+
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKM-ILIQDGSQNTN-----VDKPLRIIGDPY 58
Query: 203 AVKKALFAISAIM 215
V++A + I+
Sbjct: 59 KVQQACEMVMDIL 71
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQI 341
V ++ P K G VIGKGG TIK +++ +G ++
Sbjct: 3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKM 35
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 32/61 (52%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM 622
++VG VIG++G + I+ +G I+ + +++A I G P++ A +I +
Sbjct: 100 HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ 159
Query: 623 A 623
+
Sbjct: 160 S 160
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
+I V P +KIG VIG I I++ +GA+I ++D
Sbjct: 599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED 635
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
+I++P+ ++ +IGK G TIK+L+ + + + +D S+ T+ D + I G+
Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQERAGVKM-ILIQDGSQNTN-----VDKPLRIIGDPY 70
Query: 203 AVKKALFAISAIM 215
V++A + I+
Sbjct: 71 KVQQACEMVMDIL 83
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQI 341
V ++ P K G VIGKGG TIK +++ +G ++
Sbjct: 15 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKM 47
Score = 28.9 bits (63), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV 73
G + + I+ P G G VIGK G+ I +++ RA VK++
Sbjct: 9 GGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQE--RAGVKMI 48
>pdb|1FFK|T Chain T, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|V Chain V, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|V Chain V, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|X Chain X, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|X Chain X, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|X Chain X, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|X Chain X, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|X Chain X, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|X Chain X, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|X Chain X, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|X Chain X, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|X Chain X, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|X Chain X, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|X Chain X, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|X Chain X, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|X Chain X, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|V Chain V, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|V Chain V, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|W Chain W, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|V Chain V, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|W Chain W, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|W Chain W, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|W Chain W, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|W Chain W, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|W Chain W, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|W Chain W, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|W Chain W, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|W Chain W, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|W Chain W, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|W Chain W, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|W Chain W, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|W Chain W, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|W Chain W, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|W Chain W, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|W Chain W, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|W Chain W, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|W Chain W, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|W Chain W, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|W Chain W, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|W Chain W, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|W Chain W, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|W Chain W, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|W Chain W, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|W Chain W, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|W Chain W, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|W Chain W, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|V Chain V, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|W Chain W, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|W Chain W, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|W Chain W, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|V Chain V, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3G4S|W Chain W, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|W Chain W, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|W Chain W, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|W Chain W, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|W Chain W, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|W Chain W, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
pdb|3OW2|V Chain V, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 154
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 24/52 (46%)
Query: 260 PSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIR 311
PS+ + A R L+G AD + W T +SGL A SEE +R
Sbjct: 57 PSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFALLSEETTLR 108
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 317 NKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
+KI VIGKGG I+++ + +G I+++D
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIED 597
>pdb|1A5Z|A Chain A, Lactate Dehydrogenase From Thermotoga Maritima (tmldh)
Length = 319
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 569 IGKAGSNLANIRKISGATIEMS----DSKSSRGDRVALISGTPEQKRA 612
+G+ GS+ A + G EM D K + GD + LI GTP +RA
Sbjct: 8 LGRVGSSTAFALLMKGFAREMVLIDVDKKRAEGDALDLIHGTPFTRRA 55
>pdb|4B8T|A Chain A, Rna Binding Protein Solution Structure Of The Third Kh
Domain Of Ksrp In Complex With The G-rich Target
Sequence
Length = 106
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 32/61 (52%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM 622
++VG VIG++G + I+ +G I+ + +++A I G P++ A +I +
Sbjct: 20 HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ 79
Query: 623 A 623
+
Sbjct: 80 S 80
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 32/61 (52%)
Query: 563 NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM 622
++VG VIG++G + I+ +G I+ + +++A I G P++ A +I +
Sbjct: 20 HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ 79
Query: 623 A 623
+
Sbjct: 80 S 80
>pdb|2CXC|A Chain A, Crystal Structure Of Archaeal Transcription Termination
Factor Nusa
pdb|2CY1|A Chain A, Crystal Structure Of Ape1850
Length = 144
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 320 GRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECV 354
GR IG+GG IK +R+A G I+V + + + V
Sbjct: 48 GRAIGRGGRLIKLLREALGKNIEVVEYSSDLERIV 82
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
0.314 0.132 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,220,036
Number of Sequences: 62578
Number of extensions: 451332
Number of successful extensions: 759
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 609
Number of HSP's gapped (non-prelim): 151
length of query: 624
length of database: 14,973,337
effective HSP length: 105
effective length of query: 519
effective length of database: 8,402,647
effective search space: 4360973793
effective search space used: 4360973793
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: 54 (25.4 bits)