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= 029263
(196 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 78.6 bits (192), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 41/106 (38%), Positives = 65/106 (61%), Gaps = 2/106 (1%)
Query: 85 GSPHRSIPRAKSHDEGKDSA--VHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITM 142
GS S+ + G +SA + G +RLRGLPF K++I+ FF + + I + +
Sbjct: 18 GSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPV 77
Query: 143 NSDGRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFPSSHEEM 188
+ +G+ TGEAFV+FA+ E ++ A+ K + +G RYIE+F SS EE+
Sbjct: 78 DPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEV 123
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 22 VLFVHKNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQE 70
L V K TGEAF + AL ++++ +G RY+EVF+S ++E
Sbjct: 74 TLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEE 122
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 76.3 bits (186), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/86 (40%), Positives = 54/86 (62%), Gaps = 2/86 (2%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSEDS--IHITMNSDGRPTGEAFVEFANAEDSKAAM 166
+++LRGLP+S +D+ +F D + + + +H +GR +GEAFVE + +D K A+
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 167 AKDRMTLGSRYIELFPSSHEEMDEAL 192
KDR ++G RYIE+F S EMD L
Sbjct: 106 KKDRESMGHRYIEVFKSHRTEMDWVL 131
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 38/62 (61%), Gaps = 4/62 (6%)
Query: 10 CTIHHQLMDIVDVLFVH-KNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKR 68
CTIH V F++ + + +GEAF LG V AL+++R++MG RY+EVF+S R
Sbjct: 68 CTIHD---GAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHR 124
Query: 69 QE 70
E
Sbjct: 125 TE 126
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 75.9 bits (185), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 52/81 (64%)
Query: 112 LRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKDRM 171
L+GLPF A ++DFFK + EDSI+I +G+ TGE FVEF N D KAA+ + +
Sbjct: 30 LKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQ 89
Query: 172 TLGSRYIELFPSSHEEMDEAL 192
+G+R+I++ P + + M E +
Sbjct: 90 YMGNRFIQVHPITKKGMLEKI 110
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 17 MDIV-DVLFVH--KNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEV 63
+DIV D +++ N K TGE F AL R++Q MG R+++V
Sbjct: 49 LDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQV 98
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 75.5 bits (184), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 35/86 (40%), Positives = 55/86 (63%), Gaps = 2/86 (2%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSEDS--IHITMNSDGRPTGEAFVEFANAEDSKAAM 166
++++RGLP+S D++ FF D + + I +GRP+GEAFVE + ++ K A+
Sbjct: 9 VVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL 68
Query: 167 AKDRMTLGSRYIELFPSSHEEMDEAL 192
KDR T+G RY+E+F S++ EMD L
Sbjct: 69 KKDRETMGHRYVEVFKSNNVEMDWVL 94
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/39 (48%), Positives = 26/39 (66%)
Query: 32 TGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQE 70
+GEAF L +V AL+++R+ MG RYVEVF+S E
Sbjct: 51 SGEAFVELESEDEVKLALKKDRETMGHRYVEVFKSNNVE 89
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 74.7 bits (182), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 35/86 (40%), Positives = 53/86 (61%), Gaps = 2/86 (2%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSED--SIHITMNSDGRPTGEAFVEFANAEDSKAAM 166
+++LRGLP+S +D+ +F D + + +H +GR +GEAFVE + +D K A+
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 167 AKDRMTLGSRYIELFPSSHEEMDEAL 192
KDR ++G RYIE+F S EMD L
Sbjct: 79 KKDRESMGHRYIEVFKSHRTEMDWVL 104
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 4/62 (6%)
Query: 10 CTIHHQLMDIVDVLFVH-KNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKR 68
CTIH + V F++ + + +GEAF L V AL+++R++MG RY+EVF+S R
Sbjct: 41 CTIHD---GVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHR 97
Query: 69 QE 70
E
Sbjct: 98 TE 99
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 73.6 bits (179), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 53/81 (65%)
Query: 108 GILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA 167
G +RLRGLPF K++I+ FF + + + + ++ GR TGEAFV+FA+ E ++ A+
Sbjct: 16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75
Query: 168 KDRMTLGSRYIELFPSSHEEM 188
K + +G RYIE+F SS E+
Sbjct: 76 KHKERIGHRYIEIFKSSRAEV 96
Score = 35.0 bits (79), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 32 TGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQE 70
TGEAF + AL+++++ +G RY+E+F+S R E
Sbjct: 57 TGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE 95
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 37/75 (49%), Positives = 51/75 (68%), Gaps = 2/75 (2%)
Query: 110 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKD 169
+ +RGLP+ A ++DI +FF L+ +HI + DGR TGEA VEFA ED+ AAMAKD
Sbjct: 18 VHMRGLPYRATENDIYNFFSP--LNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75
Query: 170 RMTLGSRYIELFPSS 184
+ + RY+ELF +S
Sbjct: 76 KANMQHRYVELFLNS 90
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 37/89 (41%), Positives = 55/89 (61%), Gaps = 3/89 (3%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKD---FVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAA 165
I+R+RGLPF+A ++++ FF ++ I DGRPTG+AFV FA E ++ A
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA 84
Query: 166 MAKDRMTLGSRYIELFPSSHEEMDEALSR 194
+ K + LG RYIELF S+ E+ + L+R
Sbjct: 85 LRKHKDLLGKRYIELFRSTAAEVQQVLNR 113
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 22 VLFV-HKNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQEYYKAIANEVS 80
+LFV + + + TG+AF + AL++++ +G+RY+E+FRS E + + N S
Sbjct: 57 ILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAE-VQQVLNRFS 115
Query: 81 DVRGGS 86
G S
Sbjct: 116 SASGPS 121
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 37/75 (49%), Positives = 51/75 (68%), Gaps = 2/75 (2%)
Query: 110 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKD 169
+ +RGLP+ A ++DI +FF L+ +HI + DGR TGEA VEFA E++ AAM+KD
Sbjct: 49 VHMRGLPYKATENDIYNFFSP--LNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKD 106
Query: 170 RMTLGSRYIELFPSS 184
R + RYIELF +S
Sbjct: 107 RANMQHRYIELFLNS 121
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 55/83 (66%), Gaps = 2/83 (2%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVL--SEDSIHITMNSDGRPTGEAFVEFANAEDSKAAM 166
++R +GLP+S +D+++FF D + E+ IH +N DG+ G+A +E + +D + A+
Sbjct: 13 LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 167 AKDRMTLGSRYIELFPSSHEEMD 189
K RM +G RY+E++ ++E++D
Sbjct: 73 EKHRMYMGQRYVEVYEINNEDVD 95
Score = 30.0 bits (66), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 23 LFVHKNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVF 64
++++ K G+A + V AL+++R MG+RYVEV+
Sbjct: 46 FLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY 87
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 4/79 (5%)
Query: 103 SAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDS 162
+ HT ++LRG PF+ + ++M+F L +I I N+ G TG FV+F+N E+
Sbjct: 8 TTCHT--VKLRGAPFNVTEKNVMEFLAP--LKPVAIRIVRNAHGNKTGYIFVDFSNEEEV 63
Query: 163 KAAMAKDRMTLGSRYIELF 181
K A+ +R +G RYIE+F
Sbjct: 64 KQALKCNREYMGGRYIEVF 82
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 21/36 (58%)
Query: 32 TGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSK 67
TG F +V AL+ NR+ MG RY+EVFR K
Sbjct: 50 TGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK 85
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 49/82 (59%), Gaps = 2/82 (2%)
Query: 110 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKD 169
+ + G+PFSA ++D+ DFF L D++H+ + GR G V+F + +D+ A+ ++
Sbjct: 19 VSVHGMPFSAMENDVRDFFHG--LRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 170 RMTLGSRYIELFPSSHEEMDEA 191
RM + RY+E+ P++ + A
Sbjct: 77 RMLMIQRYVEVSPATERQWVAA 98
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA- 167
I++++ +PF+ D+I+DFF + + S+ + N G PTGEA V F + +++ AA+
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 168 -KDRMTLGSRYIEL 180
DR +GSR ++L
Sbjct: 77 LNDR-PIGSRKVKL 89
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 49/79 (62%), Gaps = 4/79 (5%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA- 167
+++++ +PF+ D+I+DFF + + S+ + N G PTGEA V F + +++ AA+
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 168 -KDRMTLGSRYIELF-PSS 184
DR +GSR ++L PSS
Sbjct: 77 LNDR-PIGSRKVKLSGPSS 94
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 4/79 (5%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA- 167
+++++ PF+ D+I+DFF + + S+ + N G PTGEA V F + +++ AA+
Sbjct: 17 VIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVID 76
Query: 168 -KDRMTLGSRYIELF-PSS 184
DR +GSR ++L PSS
Sbjct: 77 LNDR-PIGSRKVKLSGPSS 94
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 45/79 (56%)
Query: 112 LRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKDRM 171
+ +PFS K D++ F + + E+++H+ ++++G+ G+A V+F N +D++ + R
Sbjct: 20 ITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRK 79
Query: 172 TLGSRYIELFPSSHEEMDE 190
L R + + E+M E
Sbjct: 80 KLNGREAFVHVVTLEDMRE 98
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 110 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFAN-AEDSKAAMAK 168
L + GLPFS K+++ + K +D + + N G+P G A+VE+ N ++ S+A M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKD-LRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 169 DRMTLGSRYIEL 180
D MT+ I++
Sbjct: 79 DGMTIKENIIKV 90
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 5/89 (5%)
Query: 104 AVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSK 163
A H+ L +R LP + + + F F E ++ + ++ GRP+G+ VEF+ ++
Sbjct: 93 ACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAV-VIVDDRGRPSGKGIVEFSGKPAAR 151
Query: 164 AAMAKDRMTLGSRYIELFPS--SHEEMDE 190
A+ DR + GS + FP + E MD+
Sbjct: 152 KAL--DRCSEGSFLLTTFPRPVTVEPMDQ 178
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 109 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAM 166
L L L +SA ++ + + F+ I + N +G+ G AF+EFA+ ED+K A+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 13/77 (16%)
Query: 6 VQVLCTIHH-QLMDIVDVL--FVHKNNKFT---GEAFCVLGYPLQVDFALQRNR---QNM 56
+VLC + + ++ D+L FV+K+ F G++FC + LQVDF ++NR Q++
Sbjct: 404 TKVLCVLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDL 463
Query: 57 GRRYVEVFRSKRQEYYK 73
R+ V F Q YY+
Sbjct: 464 HRKMVTQF----QRYYQ 476
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 13/77 (16%)
Query: 6 VQVLCTIHH-QLMDIVDVL--FVHKNNKFT---GEAFCVLGYPLQVDFALQRNR---QNM 56
+VLC + + ++ D+L FV+K+ F G++FC + LQVDF ++NR Q++
Sbjct: 397 TKVLCVLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDL 456
Query: 57 GRRYVEVFRSKRQEYYK 73
R+ V F Q YY+
Sbjct: 457 HRKMVTQF----QRYYQ 469
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 107 TGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMN-SDGRPTGEAFVEFANAEDSKAA 165
+ I+ LR LP +A +DDI + + + + N S G+ G AFVEF++ +D+
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW 60
Query: 166 MAKDRMTL 173
M ++ +L
Sbjct: 61 MEANQHSL 68
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 33/138 (23%), Positives = 63/138 (45%), Gaps = 12/138 (8%)
Query: 46 DFALQRNRQNMGRRYVEVFRSKRQEYYKAIANEVSDVRGGSPHRSIPRAKSHDEGKDSAV 105
D A+ R M R++ V ++ KA+ E++ ++ + + K D K+
Sbjct: 36 DLAVVDVRIGMTRKFGYVDFESAEDLEKAL--ELTGLKVFGNEIKLEKPKGKDSKKERDA 93
Query: 106 HTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNS-DGRPTGEAFVEFANAEDSKA 164
T L + LP+ +D++ + F ED+ I + S DG+ G A++EF D++
Sbjct: 94 RT--LLAKNLPYKVTQDELKEVF------EDAAEIRLVSKDGKSKGIAYIEFKTEADAEK 145
Query: 165 AMAKDRMT-LGSRYIELF 181
+ + T + R I L+
Sbjct: 146 TFEEKQGTEIDGRSISLY 163
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 30.8 bits (68), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 146 GRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFP 182
G P G A++EFA AA+A D R I++ P
Sbjct: 75 GHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 8/65 (12%)
Query: 110 LRLRGLPFSAGKDDIMDFFKDFVL-------SEDSIHITMNSD-GRPTGEAFVEFANAED 161
+ ++GL S DD+ DFFK + + IHI ++ + G+P G+A V + +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 162 SKAAM 166
+KAA+
Sbjct: 78 AKAAV 82
>pdb|3UBH|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-4
Length = 419
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 39/68 (57%), Gaps = 6/68 (8%)
Query: 79 VSDVRGGSPHRSIPRAKSHDEGKDSAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSI 138
V+DV +P +P ++H+ +D + T ILR++ + +G + + ++++S+D
Sbjct: 314 VTDVNDNAPKFELPDYQAHNVDEDIPLGTSILRVKAMDSDSGSNAEI----EYLVSDD-- 367
Query: 139 HITMNSDG 146
H ++S+G
Sbjct: 368 HFAVDSNG 375
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 30.4 bits (67), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 8/99 (8%)
Query: 101 KDSAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSD---GRPTGEAFVEFA 157
K + T L + GLP+ + D+ ++F F + + + + D G G FV F
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTF---GEVLMVQVKKDLKTGHSKGFGFVRFT 65
Query: 158 NAEDSKAAMAKDRMTLGSRYIEL-FPSSHEEMDEALSRG 195
E M++ M G R+ + P+S + D S G
Sbjct: 66 EYETQVKVMSQRHMIDG-RWCDCKLPNSKQSQDSGPSSG 103
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 29.6 bits (65), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 146 GRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFP 182
G P G A++EF++ E + ++A D R I++ P
Sbjct: 44 GHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIP 80
>pdb|3M9U|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367
pdb|3M9U|B Chain B, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367
pdb|3M9U|C Chain C, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367
pdb|3M9U|D Chain D, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367
pdb|3PDE|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367 Complexed With
Isoprenyl Diphosphate And Magnesium
pdb|3PDE|B Chain B, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367 Complexed With
Isoprenyl Diphosphate And Magnesium
pdb|3PDE|C Chain C, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367 Complexed With
Isoprenyl Diphosphate And Magnesium
pdb|3PDE|D Chain D, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase
From Lactobacillus Brevis Atcc 367 Complexed With
Isoprenyl Diphosphate And Magnesium
Length = 309
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 105 VHTGILRLRGLPFSAGKDDIMDFFKDF 131
+H+G L+GLP S +DD+ FF F
Sbjct: 269 IHSGQAALQGLPTSTQRDDLAAFFSYF 295
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 146 GRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFP 182
G P G A++EF++ E + ++A D R I++ P
Sbjct: 45 GHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIP 81
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 107 TGILRLRGLPFSAGKDDIMDFFKDFV-LSEDSIHITMNSDGRPTGEAFVEFANAEDSKAA 165
T + +R +PF A + +I + F F L + M G G FV+F +D+K A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 166 M 166
Sbjct: 75 F 75
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 57/122 (46%), Gaps = 11/122 (9%)
Query: 46 DFALQRNRQNMGRRYVEVFRSKRQEYYKAIANEVSDVRGGSPHRSIPRAKSHDEGKDSAV 105
D A+ R R++ V ++ KA+ E++ ++ + + K D K A
Sbjct: 42 DLAVVDVRTGTNRKFGYVDFESAEDLEKAL--ELTGLKVFGNEIKLEKPKGRDSKKVRAA 99
Query: 106 HTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNS-DGRPTGEAFVEFANAEDSKA 164
T L + L F+ +D++ + F ED++ I + S DG+ G A++EF + D++
Sbjct: 100 RT--LLAKNLSFNITEDELKEVF------EDALEIRLVSQDGKSKGIAYIEFKSEADAEK 151
Query: 165 AM 166
+
Sbjct: 152 NL 153
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 114 GLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAM 166
G+P + G+ ++ ++FK F + + + I RP G F+ F + + A+
Sbjct: 17 GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 104 AVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSK 163
A H L ++ L + + F F E ++ + ++ GR TG+ FVEFA ++
Sbjct: 93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV-VVVDDRGRATGKGFVEFAAKPPAR 151
Query: 164 AAMAK 168
A+ +
Sbjct: 152 KALER 156
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 115 LPFSAGKDDIMDFFKDFVLSEDSIHITMNSDG-RPTGEAFVEFANAEDSKAAMAKDRMTL 173
LPF+ + DI FKD LS S+ + + D + G +VEF + K A+ D L
Sbjct: 23 LPFNTVQGDIDAIFKD--LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALL 80
Query: 174 GSRYIEL 180
G R + +
Sbjct: 81 GDRSLRV 87
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 89 RSIPRAKSHDEGKDSAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDS-IHITMNSDGR 147
R IP S++ G+ + V L L+ L + D++ F F + I M + GR
Sbjct: 11 RKIPMFSSYNPGEPNKV----LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT-GR 65
Query: 148 PTGEAFVEFANAEDSKAAM 166
G+AF+ F N E + A+
Sbjct: 66 MRGQAFITFPNKEIAWQAL 84
>pdb|3ZF7|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 164
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 29 NKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQEYYKAI 75
NK+ +AF ++ YPL D A+++ +N ++ R+ + E KAI
Sbjct: 77 NKW--DAFRIIRYPLTTDKAMKKIEENNTLTFIVDSRANKTEIKKAI 121
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 110 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNS-DGRPTGEAFVEFANAEDSK 163
L + L F+ +D++ + F ED++ I + S DG+ G A++EF + D++
Sbjct: 19 LLAKNLSFNITEDELKEVF------EDALEIRLVSQDGKSKGIAYIEFKSEADAE 67
>pdb|3EE4|A Chain A, R2-Like Ligand Binding MnFE OXIDASE FROM M. TUBERCULOSIS
pdb|4AC8|A Chain A, R2-Like Ligand Binding Mn-Fe Oxidase From M. Tuberculosis
With An Organized C-Terminal Helix
pdb|4AC8|B Chain B, R2-Like Ligand Binding Mn-Fe Oxidase From M. Tuberculosis
With An Organized C-Terminal Helix
pdb|4AC8|C Chain C, R2-Like Ligand Binding Mn-Fe Oxidase From M. Tuberculosis
With An Organized C-Terminal Helix
pdb|4AC8|D Chain D, R2-Like Ligand Binding Mn-Fe Oxidase From M. Tuberculosis
With An Organized C-Terminal Helix
Length = 323
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 116 PFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKDRMTLGS 175
PF KDD + + D + N+ GRP E V+++ A+ +DR TL +
Sbjct: 263 PFDLSKDDFLQYSTDKGMRR--FGTISNARGRPVAEIDVDYSPAQLEDTFADEDRRTLAA 320
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
0.321 0.136 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,954,216
Number of Sequences: 62578
Number of extensions: 244775
Number of successful extensions: 549
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 493
Number of HSP's gapped (non-prelim): 60
length of query: 196
length of database: 14,973,337
effective HSP length: 94
effective length of query: 102
effective length of database: 9,091,005
effective search space: 927282510
effective search space used: 927282510
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)