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= 025001
(259 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 = 78.2 bits (191), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 41/106 (38%), Positives = 65/106 (61%), Gaps = 2/106 (1%)
Query: 148 GSPHRSIPRAKSHDEGKDSA--VHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITM 205
GS S+ + G +SA + G +RLRGLPF K++I+ FF + + I + +
Sbjct: 18 GSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPV 77
Query: 206 NSDGRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFPSSHEEM 251
+ +G+ TGEAFV+FA+ E ++ A+ K + +G RYIE+F SS EE+
Sbjct: 78 DPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEV 123
Score = 67.8 bits (164), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/78 (43%), Positives = 49/78 (62%), Gaps = 3/78 (3%)
Query: 59 VRLRGLPFDCTEVDVAEFFHGLDIVD---VLFVHKNNKFTGEAFCVLGYPLQVDFALQRN 115
VRLRGLPF CT+ ++ +FF GL+IV L V K TGEAF + AL ++
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKH 104
Query: 116 RQNMGRRYVEVFRSKRQE 133
++ +G RY+EVF+S ++E
Sbjct: 105 KERIGHRYIEVFKSSQEE 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 = 77.4 bits (189), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 35/86 (40%), Positives = 54/86 (62%), Gaps = 2/86 (2%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDS--IHITMNSDGRPTGEAFVEFANAEDSKAAM 229
+++LRGLP+S +D+ +F D + + + +H +GR +GEAFVE + +D K A+
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 230 AKDRMTLGSRYIELFPSSHEEMDEAL 255
KDR ++G RYIE+F S EMD L
Sbjct: 106 KKDRESMGHRYIEVFKSHRTEMDWVL 131
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 39/101 (38%), Positives = 55/101 (54%), Gaps = 13/101 (12%)
Query: 38 SFMYNPPPAYGYVSQPPPFPVVRLRGLPFDCTEVDVAEFFHGLDIVD----VLFVH-KNN 92
S M P G+V V+LRGLP+ C+ DV F I D V F++ +
Sbjct: 34 SMMLGPEGGEGFV--------VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG 85
Query: 93 KFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQE 133
+ +GEAF LG V AL+++R++MG RY+EVF+S R E
Sbjct: 86 RQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTE 126
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 35/86 (40%), Positives = 53/86 (61%), Gaps = 2/86 (2%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSED--SIHITMNSDGRPTGEAFVEFANAEDSKAAM 229
+++LRGLP+S +D+ +F D + + +H +GR +GEAFVE + +D K A+
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 230 AKDRMTLGSRYIELFPSSHEEMDEAL 255
KDR ++G RYIE+F S EMD L
Sbjct: 79 KKDRESMGHRYIEVFKSHRTEMDWVL 104
Score = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 56/107 (52%), Gaps = 13/107 (12%)
Query: 32 GTPPSSSFMYNPPPAYGYVSQPPPFPVVRLRGLPFDCTEVDVAEFFHGLDIVD-VLFVH- 89
G+ SS M P GYV V+LRGLP+ C+ DV F I D V VH
Sbjct: 1 GSSGSSGMMLGPEGGEGYV--------VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHF 52
Query: 90 ---KNNKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQE 133
+ + +GEAF L V AL+++R++MG RY+EVF+S R E
Sbjct: 53 IYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTE 99
>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 = 75.9 bits (185), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 35/86 (40%), Positives = 55/86 (63%), Gaps = 2/86 (2%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDS--IHITMNSDGRPTGEAFVEFANAEDSKAAM 229
++++RGLP+S D++ FF D + + I +GRP+GEAFVE + ++ K A+
Sbjct: 9 VVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL 68
Query: 230 AKDRMTLGSRYIELFPSSHEEMDEAL 255
KDR T+G RY+E+F S++ EMD L
Sbjct: 69 KKDRETMGHRYVEVFKSNNVEMDWVL 94
Score = 57.4 bits (137), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 5/81 (6%)
Query: 58 VVRLRGLPFDCTEVDVAEFFHGLDIVD----VLFVH-KNNKFTGEAFCVLGYPLQVDFAL 112
VV++RGLP+ C+ +V FF I + + F++ + + +GEAF L +V AL
Sbjct: 9 VVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL 68
Query: 113 QRNRQNMGRRYVEVFRSKRQE 133
+++R+ MG RYVEVF+S E
Sbjct: 69 KKDRETMGHRYVEVFKSNNVE 89
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 75.5 bits (184), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 52/81 (64%)
Query: 175 LRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKDRM 234
L+GLPF A ++DFFK + EDSI+I +G+ TGE FVEF N D KAA+ + +
Sbjct: 30 LKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQ 89
Query: 235 TLGSRYIELFPSSHEEMDEAL 255
+G+R+I++ P + + M E +
Sbjct: 90 YMGNRFIQVHPITKKGMLEKI 110
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 58 VVRLRGLPFDCTEVDVAEFFHGLDIV-DVLFVH--KNNKFTGEAFCVLGYPLQVDFALQR 114
V L+GLPF+ V +FF LDIV D +++ N K TGE F AL R
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86
Query: 115 NRQNMGRRYVEV 126
++Q MG R+++V
Sbjct: 87 HKQYMGNRFIQV 98
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 53/81 (65%)
Query: 171 GILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA 230
G +RLRGLPF K++I+ FF + + + + ++ GR TGEAFV+FA+ E ++ A+
Sbjct: 16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75
Query: 231 KDRMTLGSRYIELFPSSHEEM 251
K + +G RYIE+F SS E+
Sbjct: 76 KHKERIGHRYIEIFKSSRAEV 96
Score = 64.3 bits (155), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 32/78 (41%), Positives = 49/78 (62%), Gaps = 3/78 (3%)
Query: 59 VRLRGLPFDCTEVDVAEFFHGLDIVD---VLFVHKNNKFTGEAFCVLGYPLQVDFALQRN 115
VRLRGLPF C++ ++ +FF GL+IV L V + TGEAF + AL+++
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 116 RQNMGRRYVEVFRSKRQE 133
++ +G RY+E+F+S R E
Sbjct: 78 KERIGHRYIEIFKSSRAE 95
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 72.0 bits (175), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 37/76 (48%), Positives = 51/76 (67%), Gaps = 2/76 (2%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAK 231
+ +RGLP+ A ++DI +FF L+ +HI + DGR TGEA VEFA ED+ AAMAK
Sbjct: 17 CVHMRGLPYRATENDIYNFFSP--LNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 74
Query: 232 DRMTLGSRYIELFPSS 247
D+ + RY+ELF +S
Sbjct: 75 DKANMQHRYVELFLNS 90
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 58 VVRLRGLPFDCTEVDVAEFFHGLDIVDV-LFVHKNNKFTGEAFCVLGYPLQVDFALQRNR 116
V +RGLP+ TE D+ FF L+ + V + + + + TGEA A+ +++
Sbjct: 17 CVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDK 76
Query: 117 QNMGRRYVEVF 127
NM RYVE+F
Sbjct: 77 ANMQHRYVELF 87
>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 = 5e-13, Method: Compositional matrix adjust.
Identities = 37/76 (48%), Positives = 51/76 (67%), Gaps = 2/76 (2%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAK 231
+ +RGLP+ A ++DI +FF L+ +HI + DGR TGEA VEFA E++ AAM+K
Sbjct: 48 CVHMRGLPYKATENDIYNFFSP--LNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK 105
Query: 232 DRMTLGSRYIELFPSS 247
DR + RYIELF +S
Sbjct: 106 DRANMQHRYIELFLNS 121
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 49 YVSQPPPFPVVRLRGLPFDCTEVDVAEFFHGLDIVDV-LFVHKNNKFTGEAFCVLGYPLQ 107
+ Q V +RGLP+ TE D+ FF L+ V V + + + + TGEA +
Sbjct: 39 FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEE 98
Query: 108 VDFALQRNRQNMGRRYVEVF 127
A+ ++R NM RY+E+F
Sbjct: 99 AVAAMSKDRANMQHRYIELF 118
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 70.9 bits (172), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 37/89 (41%), Positives = 55/89 (61%), Gaps = 3/89 (3%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKD---FVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAA 228
I+R+RGLPF+A ++++ FF ++ I DGRPTG+AFV FA E ++ A
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA 84
Query: 229 MAKDRMTLGSRYIELFPSSHEEMDEALSR 257
+ K + LG RYIELF S+ E+ + L+R
Sbjct: 85 LRKHKDLLGKRYIELFRSTAAEVQQVLNR 113
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 52/98 (53%), Gaps = 7/98 (7%)
Query: 58 VVRLRGLPFDCTEVDVAEFFHGLDIVD-----VLFV-HKNNKFTGEAFCVLGYPLQVDFA 111
+VR+RGLPF T +V FF + +LFV + + + TG+AF + A
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA 84
Query: 112 LQRNRQNMGRRYVEVFRSKRQEYYKAIANEVSDVRGGS 149
L++++ +G+RY+E+FRS E + + N S G S
Sbjct: 85 LRKHKDLLGKRYIELFRSTAAE-VQQVLNRFSSASGPS 121
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 70.1 bits (170), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 55/83 (66%), Gaps = 2/83 (2%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVL--SEDSIHITMNSDGRPTGEAFVEFANAEDSKAAM 229
++R +GLP+S +D+++FF D + E+ IH +N DG+ G+A +E + +D + A+
Sbjct: 13 LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 230 AKDRMTLGSRYIELFPSSHEEMD 252
K RM +G RY+E++ ++E++D
Sbjct: 73 EKHRMYMGQRYVEVYEINNEDVD 95
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 58 VVRLRGLPFDCTEVDVAEFFHGLDIVD-----VLFVHKNNKFTGEAFCVLGYPLQVDFAL 112
++R +GLP+ CT DV FF I + ++++ K G+A + V AL
Sbjct: 13 LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 113 QRNRQNMGRRYVEVF 127
+++R MG+RYVEV+
Sbjct: 73 EKHRMYMGQRYVEVY 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 = 3e-09, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 4/79 (5%)
Query: 166 SAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDS 225
+ HT ++LRG PF+ + ++M+F L +I I N+ G TG FV+F+N E+
Sbjct: 8 TTCHT--VKLRGAPFNVTEKNVMEFLAP--LKPVAIRIVRNAHGNKTGYIFVDFSNEEEV 63
Query: 226 KAAMAKDRMTLGSRYIELF 244
K A+ +R +G RYIE+F
Sbjct: 64 KQALKCNREYMGGRYIEVF 82
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 58 VVRLRGLPFDCTEVDVAEFFHGLDIVDVLFV---HKNNKFTGEAFCVLGYPLQVDFALQR 114
V+LRG PF+ TE +V EF L V + V H N TG F +V AL+
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNK--TGYIFVDFSNEEEVKQALKC 69
Query: 115 NRQNMGRRYVEVFRSK 130
NR+ MG RY+EVFR K
Sbjct: 70 NREYMGGRYIEVFREK 85
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 49/82 (59%), Gaps = 2/82 (2%)
Query: 173 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKD 232
+ + G+PFSA ++D+ DFF L D++H+ + GR G V+F + +D+ A+ ++
Sbjct: 19 VSVHGMPFSAMENDVRDFFHG--LRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 233 RMTLGSRYIELFPSSHEEMDEA 254
RM + RY+E+ P++ + A
Sbjct: 77 RMLMIQRYVEVSPATERQWVAA 98
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 46/93 (49%), Gaps = 13/93 (13%)
Query: 55 PFPV------VRLRGLPFDCTEVDVAEFFHGL--DIVDVL--FVHKNNKFTGEAFCVLGY 104
P P+ V + G+PF E DV +FFHGL D V +L V +NN G
Sbjct: 9 PLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNN---GNGLVKFLS 65
Query: 105 PLQVDFALQRNRQNMGRRYVEVFRSKRQEYYKA 137
P AL+RNR M +RYVEV + +++ A
Sbjct: 66 PQDTFEALKRNRMLMIQRYVEVSPATERQWVAA 98
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA- 230
I++++ +PF+ D+I+DFF + + S+ + N G PTGEA V F + +++ AA+
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 231 -KDRMTLGSRYIEL 243
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 = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 3/74 (4%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA- 230
+++++ +PF+ D+I+DFF + + S+ + N G PTGEA V F + +++ AA+
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 231 -KDRMTLGSRYIEL 243
DR +GSR ++L
Sbjct: 77 LNDR-PIGSRKVKL 89
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 3/74 (4%)
Query: 172 ILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMA- 230
+++++ PF+ D+I+DFF + + S+ + N G PTGEA V F + +++ AA+
Sbjct: 17 VIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVID 76
Query: 231 -KDRMTLGSRYIEL 243
DR +GSR ++L
Sbjct: 77 LNDR-PIGSRKVKL 89
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 45/79 (56%)
Query: 175 LRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAMAKDRM 234
+ +PFS K D++ F + + E+++H+ ++++G+ G+A V+F N +D++ + R
Sbjct: 20 ITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRK 79
Query: 235 TLGSRYIELFPSSHEEMDE 253
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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 173 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFAN-AEDSKAAMAK 231
L + GLPFS K+++ + K +D + + N G+P G A+VE+ N ++ S+A M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKD-LRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 232 DRMTLGSRYIELFPSS 247
D MT+ I++ S+
Sbjct: 79 DGMTIKENIIKVAISN 94
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 169 HTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAA 228
+ L L L +SA ++ + + F+ I + N +G+ G AF+EFA+ ED+K A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 229 M 229
+
Sbjct: 70 L 70
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 167 AVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSK 226
A H+ L +R LP + + + F F E ++ + ++ GRP+G+ VEF+ ++
Sbjct: 93 ACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAV-VIVDDRGRPSGKGIVEFSGKPAAR 151
Query: 227 AAMAKDRMTLGSRYIELFP 245
A+ DR + GS + FP
Sbjct: 152 KAL--DRCSEGSFLLTTFP 168
>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 = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 170 TGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMN-SDGRPTGEAFVEFANAEDSKAA 228
+ I+ LR LP +A +DDI + + + + N S G+ G AFVEF++ +D+
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW 60
Query: 229 MAKDRMTLG 237
M ++ +L
Sbjct: 61 MEANQHSLN 69
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 34.7 bits (78), Expect = 0.058, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 12/64 (18%)
Query: 81 DIVDVL--FVHKNNKF---TGEAFCVLGYPLQVDFALQRNR---QNMGRRYVEVFRSKRQ 132
++ D+L FV+K+ F G++FC + LQVDF ++NR Q++ R+ V F Q
Sbjct: 417 EVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQF----Q 472
Query: 133 EYYK 136
YY+
Sbjct: 473 RYYQ 476
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 34.7 bits (78), Expect = 0.058, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 12/64 (18%)
Query: 81 DIVDVL--FVHKNNKF---TGEAFCVLGYPLQVDFALQRNR---QNMGRRYVEVFRSKRQ 132
++ D+L FV+K+ F G++FC + LQVDF ++NR Q++ R+ V F Q
Sbjct: 410 EVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQF----Q 465
Query: 133 EYYK 136
YY+
Sbjct: 466 RYYQ 469
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 33/138 (23%), Positives = 60/138 (43%), Gaps = 12/138 (8%)
Query: 109 DFALQRNRQNMGRRYVEVFRSKRQEYYKAIANEVSDVRGGSPHRSIPRAKSHDEGKDSAV 168
D A+ R M R++ V ++ KA+ V G P+ K + +D+
Sbjct: 36 DLAVVDVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDART 95
Query: 169 HTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNS-DGRPTGEAFVEFANAEDSKA 227
L + LP+ +D++ + F ED+ I + S DG+ G A++EF D++
Sbjct: 96 ----LLAKNLPYKVTQDELKEVF------EDAAEIRLVSKDGKSKGIAYIEFKTEADAEK 145
Query: 228 AMAKDRMT-LGSRYIELF 244
+ + T + R I L+
Sbjct: 146 TFEEKQGTEIDGRSISLY 163
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 54 PPFPVVRLRGLPFDCTEVDVAEFFHGLDIVDV 85
PP+ L LP+D TE + EFF GL+I V
Sbjct: 18 PPYTAF-LGNLPYDVTEESIKEFFRGLNISAV 48
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 54 PPFPVVRLRGLPFDCTEVDVAEFFHGLDIVDV 85
PP+ L LP+D TE + EFF GL+I V
Sbjct: 14 PPYTAF-LGNLPYDVTEESIKEFFRGLNISAV 44
>pdb|3UBH|A Chain A, Crystal Structure Of Drosophila N-Cadherin Ec1-4
Length = 419
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 142 VSDVRGGSPHRSIPRAKSHDEGKDSAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSI 201
V+DV +P +P ++H+ +D + T ILR++ + +G + +++ +S+D
Sbjct: 314 VTDVNDNAPKFELPDYQAHNVDEDIPLGTSILRVKAMDSDSGSNAEIEYL----VSDD-- 367
Query: 202 HITMNSDG 209
H ++S+G
Sbjct: 368 HFAVDSNG 375
>pdb|1VZA|A Chain A, Thymidylate Synthase E60d Mutant Binary Complex With 2'-
Deoxyuridine 5'-Monophosphate (Dump)
Length = 316
Score = 30.4 bits (67), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 56 FPVVRLRGLPFDCTEVDVAEFFHGLDIVDVLFVHKNNKFTGEAF 99
FP++ + +PF + D+ F HG + L H+N+ + AF
Sbjct: 44 FPLLTTKKVPFGLIKSDLLWFLHGDTNIRFLLQHRNHIWDEWAF 87
>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 = 1.0, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 8/65 (12%)
Query: 173 LRLRGLPFSAGKDDIMDFFKDFVL-------SEDSIHITMNSD-GRPTGEAFVEFANAED 224
+ ++GL S DD+ DFFK + + IHI ++ + G+P G+A V + +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 225 SKAAM 229
+KAA+
Sbjct: 78 AKAAV 82
>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 = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 209 GRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFP 245
G P G A++EFA AA+A D R I++ P
Sbjct: 75 GHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111
>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 = 1.1, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 8/99 (8%)
Query: 164 KDSAVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSD---GRPTGEAFVEFA 220
K + T L + GLP+ + D+ ++F F + + + + D G G FV F
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTF---GEVLMVQVKKDLKTGHSKGFGFVRFT 65
Query: 221 NAEDSKAAMAKDRMTLGSRYIEL-FPSSHEEMDEALSRG 258
E M++ M G R+ + P+S + D S G
Sbjct: 66 EYETQVKVMSQRHMIDG-RWCDCKLPNSKQSQDSGPSSG 103
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 57/122 (46%), Gaps = 11/122 (9%)
Query: 109 DFALQRNRQNMGRRYVEVFRSKRQEYYKAIANEVSDVRGGSPHRSIPRAKSHDEGKDSAV 168
D A+ R R++ V ++ KA+ E++ ++ + + K D K A
Sbjct: 42 DLAVVDVRTGTNRKFGYVDFESAEDLEKAL--ELTGLKVFGNEIKLEKPKGRDSKKVRAA 99
Query: 169 HTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNS-DGRPTGEAFVEFANAEDSKA 227
T L + L F+ +D++ + F ED++ I + S DG+ G A++EF + D++
Sbjct: 100 RT--LLAKNLSFNITEDELKEVF------EDALEIRLVSQDGKSKGIAYIEFKSEADAEK 151
Query: 228 AM 229
+
Sbjct: 152 NL 153
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 178 LPFSAGKDDIMDFFKDFVLSEDSIHITMNSDG-RPTGEAFVEFANAEDSKAAMAKDRMTL 236
LPF+ + DI FKD LS S+ + + D + G +VEF + K A+ D L
Sbjct: 23 LPFNTVQGDIDAIFKD--LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALL 80
Query: 237 GSRYIELFPSSHEEMDEA 254
G R + + + + D++
Sbjct: 81 GDRSLRVDIAEGRKQDKS 98
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 170 TGILRLRGLPFSAGKDDIMDFFKDF-VLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAA 228
T + +R +PF A + +I + F F L + M G G FV+F +D+K A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
>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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 209 GRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFP 245
G P G A++EF++ E + ++A D R I++ P
Sbjct: 44 GHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIP 80
>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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 209 GRPTGEAFVEFANAEDSKAAMAKDRMTLGSRYIELFP 245
G P G A++EF++ E + ++A D R I++ P
Sbjct: 45 GHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIP 81
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 177 GLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSKAAM 229
G+P + G+ ++ ++FK F + + + I RP G F+ F + + A+
Sbjct: 17 GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 168 VHTGILRLRGLPFSAGKDDIMDFFKDF 194
+H+G L+GLP S +DD+ FF F
Sbjct: 269 IHSGQAALQGLPTSTQRDDLAAFFSYF 295
>pdb|1EMS|A Chain A, Crystal Structure Of The C. Elegans Nitfhit Protein
pdb|1EMS|B Chain B, Crystal Structure Of The C. Elegans Nitfhit Protein
Length = 440
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 5/72 (6%)
Query: 30 FYGTPPSSSFMYNPPPAYGYVSQPPPFPVVRLRGLPFDCTEVDVAEFFHGLDIVDVLFVH 89
FY TP S F+ P G+V P V RL D T+ + A+ F V + +
Sbjct: 312 FYSTPHSFVFVNLKPVTDGHVLVSPKRVVPRLT----DLTDAETADLFIVAKKVQAM-LE 366
Query: 90 KNNKFTGEAFCV 101
K++ T CV
Sbjct: 367 KHHNVTSTTICV 378
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 167 AVHTGILRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNSDGRPTGEAFVEFANAEDSK 226
A H L ++ L + + F F E ++ + ++ GR TG+ FVEFA ++
Sbjct: 93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV-VVVDDRGRATGKGFVEFAAKPPAR 151
Query: 227 AAMAK 231
A+ +
Sbjct: 152 KALER 156
>pdb|3ZF7|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 164
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 92 NKFTGEAFCVLGYPLQVDFALQRNRQNMGRRYVEVFRSKRQEYYKAI 138
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 = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 173 LRLRGLPFSAGKDDIMDFFKDFVLSEDSIHITMNS-DGRPTGEAFVEFANAEDSKAAM 229
L + L F+ +D++ + F ED++ I + S DG+ G A++EF + D++ +
Sbjct: 19 LLAKNLSFNITEDELKEVF------EDALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70
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 0.138 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,433,957
Number of Sequences: 62578
Number of extensions: 370443
Number of successful extensions: 800
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 721
Number of HSP's gapped (non-prelim): 76
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)