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= 020975
(319 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 45/161 (27%), Positives = 67/161 (41%), Gaps = 26/161 (16%)
Query: 58 GVDLCRH------GSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCK 111
VDL H G C+MQ++ +++D ++ + +L I KV H
Sbjct: 133 AVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMY-ILNESLTDPAIVKVFHGAD 191
Query: 112 RDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEK 171
D E L FG+ + N+ DT A L+ GR S D + YC + ++
Sbjct: 192 SDIEWLQKDFGLYVVNMFDTHQAARLL--NLGR-HSLDHLLKL--------YCNVDSNKQ 240
Query: 172 EEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212
++ W RPL E M+ AA DD +L YIY M
Sbjct: 241 YQLAD--------WRIRPLPEEMLSAARDDTHYLLYIYDKM 273
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 63/263 (23%), Positives = 105/263 (39%), Gaps = 34/263 (12%)
Query: 19 GKPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDL-CRHGSLCIMQLAFPDA 77
K D VPI + T +++L + + + ++ I D E D +G +C+MQ++ +
Sbjct: 79 SKSWDDSVPIWVDT-STELESMLEDLKNTKE--IAVDLEHHDYRSYYGIVCLMQISTRER 135
Query: 78 IYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSL 137
YLVD ++ E + + I KV H D L G+ + + DT A
Sbjct: 136 DYLVDTLKLREN-LHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKA 194
Query: 138 IEEQEGRKRSPDDYI--SFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMV 195
I G R Y+ +F +Y W RPL++ M
Sbjct: 195 I----GLPRHSLAYLLENFANFKTSKKYQLAD-----------------WRIRPLSKPMT 233
Query: 196 RAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALY-CRCFCINENDYVDWPPLPPVPD- 253
AA D FL IY + KL + + + G LY R +Y + PL P +
Sbjct: 234 AAARADTHFLLNIYDQLRNKLIESN----KLAGVLYESRNVAKRRFEYSKYRPLTPSSEV 289
Query: 254 YLIVEGDVPEEEILSILDVPPGK 276
Y +E + P + ++ ++PP +
Sbjct: 290 YSPIEKESPWKILMYQYNIPPER 312
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 62/148 (41%), Gaps = 20/148 (13%)
Query: 65 GSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIK 124
G C+MQ++ +++D ++ + +L I KV H D E L FG+
Sbjct: 146 GLTCLMQISTRTEDFIIDTLELRSDMY-ILNESLTDPAIVKVFHGADSDIEWLQKDFGLY 204
Query: 125 LHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQF 184
+ N+ DT A L+ GR S D + YC + ++ ++
Sbjct: 205 VVNMFDTHQAARLL--NLGR-HSLDHLLKL--------YCNVDSNKQYQLAD-------- 245
Query: 185 WTYRPLTELMVRAAADDVRFLPYIYHNM 212
W RPL E M+ A DD +L YIY M
Sbjct: 246 WRIRPLPEEMLSYARDDTHYLLYIYDKM 273
>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An
Exoribonuclease Involved In Structured Rna Processing
Length = 375
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 68/268 (25%), Positives = 96/268 (35%), Gaps = 53/268 (19%)
Query: 51 VIGFDCEGVDL-CRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHD 109
I D E V + L ++QL + + L+D + G T K L ITK +H
Sbjct: 24 AIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPL--GITDWSPLKAILRDPSITKFLHA 81
Query: 110 CKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQ 169
D E FG ++DTQI + GR S F ++ + Y G++
Sbjct: 82 GSEDLEVFLNVFGELPQPLIDTQILAAFC----GRPMS----WGFASMVEE--YSGVTLD 131
Query: 170 EKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGA 229
+ E R D W RPLTE AA DV +L I +M + + S W A
Sbjct: 132 KSES-----RTD---WLARPLTERQCEYAAADVWYLLPITAKLMVE-TEASGWLPAALDE 182
Query: 230 LYCRCFCINENDYV---------------------------DWPPLPPVPDYLIVEGDVP 262
CR + + V DW L V V
Sbjct: 183 --CRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240
Query: 263 EEEILSILDVPPGKMGRI--IGRRGSSI 288
EE + S+ PG +G + +G GS I
Sbjct: 241 EEHLWSVARYMPGSLGELDSLGLSGSEI 268
>pdb|3CSL|A Chain A, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa And Heme
pdb|3CSL|B Chain B, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa And Heme
pdb|3CSN|A Chain A, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa
pdb|3CSN|B Chain B, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr In Complex With Its Hemophore Hasa
Length = 865
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 32 TNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPD 76
++++Q P FL+P R +GF+ + DL G + ++A+ D
Sbjct: 604 SSSTQYPNPFLQPERSRAWEVGFNVQQPDLWFEGDRLVAKVAYFD 648
>pdb|3DDR|A Chain A, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr-Ile671gly Mutant In Complex With Its Hemophore Hasa
And Heme
pdb|3DDR|B Chain B, Structure Of The Serratia Marcescens Hemophore Receptor
Hasr-Ile671gly Mutant In Complex With Its Hemophore Hasa
And Heme
Length = 865
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 32 TNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPD 76
++++Q P FL+P R +GF+ + DL G + ++A+ D
Sbjct: 604 SSSTQYPNPFLQPERSRAWEVGFNVQQPDLWFEGDRLVAKVAYFD 648
>pdb|3BD9|A Chain A, Human 3-O-Sulfotransferase Isoform 5 With Bound Pap
Length = 280
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 46/101 (45%), Gaps = 8/101 (7%)
Query: 142 EGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW-TYRPLTELMV----R 196
EG++R Y F L DP C ++ + K + + + W Y P+ + V R
Sbjct: 132 EGKERKNKTYYKFEKLAIDPNTCEVNTKYKAVRTSIYTKHLERWLKYFPIEQFHVVDGDR 191
Query: 197 AAADDVRFLPYI--YHNMMKKLNQQSLWYLAVRGALYCRCF 235
+ + L + + N+ +++Q +L++ A RG YC F
Sbjct: 192 LITEPLPELQLVEKFLNLPPRISQYNLYFNATRG-FYCLRF 231
>pdb|2JFB|A Chain A, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|B Chain B, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|C Chain C, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|D Chain D, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|E Chain E, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|F Chain F, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|G Chain G, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|H Chain H, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|I Chain I, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|J Chain J, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|K Chain K, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|L Chain L, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|M Chain M, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|N Chain N, 3d Structure Of Lumazine Synthase From Candida Albicans
pdb|2JFB|O Chain O, 3d Structure Of Lumazine Synthase From Candida Albicans
Length = 164
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 22/33 (66%)
Query: 19 GKPIDSVVPIHIVTNASQLPAEFLEPSSERQLV 51
GKP+D+++PI ++ S + E++ S+ QL+
Sbjct: 79 GKPLDAIIPIGVLIKGSTMHFEYICDSTTHQLM 111
>pdb|2BA0|A Chain A, Archaeal Exosome Core
pdb|2BA0|B Chain B, Archaeal Exosome Core
pdb|2BA0|C Chain C, Archaeal Exosome Core
Length = 229
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 269 ILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGG-----AKGPPDKVSLQKLKIY 319
I+ + P ++ R+IG++GS I +K + +I++G G KVS+ + IY
Sbjct: 139 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRRKVSIAEEAIY 194
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 266 ILSILDVPPGKMGRIIGRRGSSILAIKESCNAEI 299
+ L VP +GRIIGR G +I +I ++ A+I
Sbjct: 15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKI 48
>pdb|2Y1H|A Chain A, Crystal Structure Of The Human Tatd-Domain Protein 3
(Tatdn3)
pdb|2Y1H|B Chain B, Crystal Structure Of The Human Tatd-Domain Protein 3
(Tatdn3)
Length = 272
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 130 DTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQ 180
D +A +IE + R + I VGL PR+ G Q++E+ +VL+RQ
Sbjct: 85 DLDVALPIIENYKDRLLA----IGEVGLDFSPRFAGTGEQKEEQRQVLIRQ 131
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 277 MGRIIGRRGSSILAIKESCNAEILIGG 303
+G +IG RG+++ I++ CNA+I+I G
Sbjct: 24 VGLLIGPRGNTLKNIEKECNAKIMIRG 50
>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 = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 276 KMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVSL 313
++G IIG++G S+ I+E A I I P ++L
Sbjct: 13 EVGSIIGKKGESVKRIREESGARINISEGNSPERIITL 50
>pdb|1EJB|A Chain A, Lumazine Synthase From Saccharomyces Cerevisiae
pdb|1EJB|B Chain B, Lumazine Synthase From Saccharomyces Cerevisiae
pdb|1EJB|C Chain C, Lumazine Synthase From Saccharomyces Cerevisiae
pdb|1EJB|D Chain D, Lumazine Synthase From Saccharomyces Cerevisiae
pdb|1EJB|E Chain E, Lumazine Synthase From Saccharomyces Cerevisiae
Length = 168
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 19 GKPIDSVVPIHIVTNASQLPAEFLEPSSERQLV 51
GKP+D V+PI ++ S + E++ S+ L+
Sbjct: 78 GKPLDVVIPIGVLIKGSTMHFEYISDSTTHALM 110
>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 = 28.5 bits (62), Expect = 5.0, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 266 ILSILDVPPGK-MGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVSL 313
IL+I + GK +G IIG++G S+ I+E A I I P ++L
Sbjct: 2 ILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITL 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 = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 272 VPPGKMGRIIGRRGSSILAIKESCNAEI 299
VP GK G IIG+ G +I +I + A I
Sbjct: 110 VPTGKTGLIIGKGGETIKSISQQSGARI 137
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 0.140 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,896,585
Number of Sequences: 62578
Number of extensions: 405948
Number of successful extensions: 926
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 909
Number of HSP's gapped (non-prelim): 22
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
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: 51 (24.3 bits)