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= psy11278
(238 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+++++ + H H+IG+ G I ++ ++ V P ++EKSN + I G G+++
Sbjct: 7 VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIP-----PDSEKSNLIRIEGDPQGVQQ 61
Query: 61 ARYRVRELT 69
A+ + EL
Sbjct: 62 AKRELLELA 70
>pdb|2CTK|A Chain A, Solution Structure Of The 12th Kh Type I Domain From
Human Vigilin
Length = 104
Score = 33.9 bits (76), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 9/72 (12%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++++V + H ++IG+ G I+K+M+E ++H P +S+ ++I G L+R
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLAANLDR 73
Query: 61 ARY----RVREL 68
A+ RV+EL
Sbjct: 74 AKAGLLERVKEL 85
>pdb|2CTJ|A Chain A, Solution Structure Of The 8th Kh Type I Domain From
Human Vigilin
Length = 95
Score = 33.9 bits (76), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 10 HSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
H+ +IG G I+ +MEE G H+HFP V S+ V I G +E+A+ ++ L
Sbjct: 28 HNSLIGTKGRLIRSIMEECGGVHIHFP-----VEGSGSDTVVIRGPSSDVEKAKKQLLHL 82
Query: 69 T 69
Sbjct: 83 A 83
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVN 42
+K+ V + IIG+GG T+K +ME++G V +N
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGIN 147
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 32.3 bits (72), Expect = 0.26, Method: Composition-based stats.
Identities = 14/55 (25%), Positives = 29/55 (52%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRE 67
I+G+GG T+ + E TGC + + ++ +V+I G+ + A+Y + +
Sbjct: 17 ILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQYLITQ 71
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 13 IIGRGGLTIKKVMEETGCHVHF-PDSN 38
IIGRGG I K+ +++GC V PDS
Sbjct: 30 IIGRGGEQINKIQQDSGCKVQISPDSG 56
>pdb|2CTE|A Chain A, Solution Structure Of The 1st Kh Type I Domain From
Human Vigilin
Length = 94
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV 65
H +IG+ G ++ + +T + P + + SNQ+ I G+ G+E+AR+ V
Sbjct: 28 HRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEKARHEV 78
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
QT + I +HH + G N L+ + +T +I P +DP + + ++G
Sbjct: 14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------SNQIKITGT 67
Query: 205 IDSVYLAR 212
+ + AR
Sbjct: 68 KEGIEKAR 75
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein
1
Length = 92
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 13 IIGRGGLTIKKVMEETGCHVHF-PDSN 38
IIGRGG I ++ +E+GC + PDS
Sbjct: 29 IIGRGGEQISRIQQESGCKIQIAPDSG 55
>pdb|1FI4|A Chain A, The X-Ray Crystal Structure Of Mevalonate 5-Diphosphate
Decarboxylase At 2.3 Angstrom Resolution
Length = 416
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 63 YRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEK 122
Y + E +F F Y L GS P + F EA+N Q N + L + +K
Sbjct: 330 YYLAENESKLFAFIYKLFGSVPGWDKKFTTEQLEAFNHQFESSNFTARELDLEL----QK 385
Query: 123 DVERV 127
DV RV
Sbjct: 386 DVARV 390
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVN 42
+K+ V + IIG+GG T+K + E++G V +N
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGIN 147
>pdb|2CTL|A Chain A, Solution Structure Of The 13th Kh Type I Domain From
Human Vigilin
Length = 97
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERAR 62
H IIGR G I ++ E ++ FPD + + +Q++I G E AR
Sbjct: 28 HPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKNTEAAR 78
>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
pdb|1EC6|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
Length = 87
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARY 63
I+G+GG T+ + E TG + + ++ +V+I GS + A+Y
Sbjct: 17 ILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQY 67
>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 = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARY 63
I+G+GG T+ + E TG + + ++ +V+I GS + A+Y
Sbjct: 17 ILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQY 67
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG 53
++L V + +IG+GG IK++ E TG V + E++ ++IAG
Sbjct: 91 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERA--ITIAG 141
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 12 HIIGRGGLTIKKVMEETGCHVHFPDSN 38
IIG+ G ++KK+ EE+G ++ + N
Sbjct: 18 SIIGKKGESVKKMREESGARINISEGN 44
>pdb|2CTM|A Chain A, Solution Structure Of The 14th Kh Type I Domain From
Human Vigilin
Length = 95
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG 53
H+ IIG G I+K+M+E + FP S A N V++ G
Sbjct: 28 HARIIGARGKAIRKIMDEFKVDIRFPQS----GAPDPNCVTVTG 67
>pdb|2X0O|A Chain A, Apo Structure Of The Alcaligin Biosynthesis Protein C
(Alcc) From Bordetella Bronchiseptica
pdb|2X0P|A Chain A, Co-Complex Structure Of Alcaligin Biosynthetase Protein C
(Alcc) With Adenosine From Bordetella Bronchiseptica
pdb|2X0Q|A Chain A, Co-Complex Structure Of Alcaligin Biosynthesis Protein C
(Alcc) With Atp From Bordetella Bronchiseptica
Length = 618
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 25/117 (21%), Positives = 51/117 (43%), Gaps = 8/117 (6%)
Query: 49 VSIAGSLLGLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRP 108
+ +G G RY LTPLI CF + P+ + + +IQ+ V+ ++
Sbjct: 413 IQASGLDAGTWLERYVDAYLTPLIHCFYAHDLVFMPHGEN-VILVIQDGVPVRAFMKDIA 471
Query: 109 K----LQPTLVMVKGCEK---DVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQH 158
+ L P + + + ++ DV + T ++ G + T +++ E+ P+H
Sbjct: 472 EESSILNPQVRLPQAAQRLAADVPEAYKLLTIFVDVFEGYFRHLTQILVETELMPEH 528
>pdb|2GAI|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Triclinic Crystal Form
pdb|2GAI|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Triclinic Crystal Form
pdb|2GAJ|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Monoclinic Crystal Form
pdb|2GAJ|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Monoclinic Crystal Form
Length = 633
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 55/121 (45%), Gaps = 20/121 (16%)
Query: 110 LQPTLVMVKGCEKDVERVKEATTK---LI--------EHMCGSLANQTSV------IMMM 152
+P ++KG EK VE++K+ K LI E + +A T+ I+
Sbjct: 53 FEPEFAVIKGKEKVVEKLKDLAKKGELLIASDMDREGEAIAWHIARVTNTLGRKNRIVFS 112
Query: 153 EISPQH-HPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS--SVTVSGNIDSVY 209
EI+P+ ++ P I++K + AQ +I+ + PVL ++ S +G + S
Sbjct: 113 EITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSAT 172
Query: 210 L 210
L
Sbjct: 173 L 173
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 13 IIGRGGLTIKKVMEETGCH-VHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
+IG+GG TIK++ E G V D ++ A+K + I G +++A+ V EL
Sbjct: 29 VIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKP--LRITGDPYKVQQAKEMVLEL 83
>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 = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQV-SIAGSLLGLERARYRVRE 67
IIG+GG TIK + +++G + N NA+ + ++ +I G+ ++ AR + E
Sbjct: 118 IIGKGGETIKSISQQSGARIEL-QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEE 172
>pdb|2FI1|A Chain A, The Crystal Structure Of A Hydrolase From Streptococcus
Pneumoniae Tigr4
Length = 190
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 115 VMVKGCEKDVERVKEA----TTKLIEHMCGSLANQTSVIMMMEISPQHHPIM-EGPNAIN 169
+ + G +D + V +A T IE +L N E HPI+ EG + +
Sbjct: 32 LALYGITQDHDSVYQALKVSTPFAIETFAPNLENFLEKYKENEARELEHPILFEGVSDL- 90
Query: 170 LKTIMAQTGAQIVFPEANDPIIPVLKKSSV 199
L+ I Q G + ND ++ +L+K+S+
Sbjct: 91 LEDISNQGGRHFLVSHRNDQVLEILEKTSI 120
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
0.319 0.133 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,177,129
Number of Sequences: 62578
Number of extensions: 217195
Number of successful extensions: 440
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 418
Number of HSP's gapped (non-prelim): 42
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
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)