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= psy4929
(633 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NO8|A Chain A, Crystal Structure Of The Phr Domain From Human Btbd2
Protein
pdb|3NO8|B Chain B, Crystal Structure Of The Phr Domain From Human Btbd2
Protein
Length = 176
Score = 172 bits (436), Expect = 5e-43, Method: Composition-based stats.
Identities = 74/109 (67%), Positives = 90/109 (82%)
Query: 77 RCSMTGKEQVVHRFQHIESRWGYSGTSDRIRFSVDRRIFVVGFGLYGCIHGPTEYDVQMQ 136
RC + GKE ++RFQ +ESRWGYSGTSDRIRFSV++RIFVVGFGLYG IHGPT+Y V +Q
Sbjct: 7 RCCLRGKECSINRFQQVESRWGYSGTSDRIRFSVNKRIFVVGFGLYGSIHGPTDYQVNIQ 66
Query: 137 LVRTANGKVIAGNRTSFACDGSTFTSRVMFKEPVEVMPNISYTACATLK 185
++ T + V+ N T F+CDGS T RVMFKEPVEV+PN++YTACATLK
Sbjct: 67 IIHTDSNTVLGQNDTGFSCDGSASTFRVMFKEPVEVLPNVNYTACATLK 115
Score = 60.8 bits (146), Expect = 2e-09, Method: Composition-based stats.
Identities = 24/35 (68%), Positives = 28/35 (80%)
Query: 574 FDGPRCSMTGKEQVVHRFQHIESRWGYSGTSDRIR 608
D PRC + GKE ++RFQ +ESRWGYSGTSDRIR
Sbjct: 3 LDRPRCCLRGKECSINRFQQVESRWGYSGTSDRIR 37
>pdb|2VKP|A Chain A, Crystal Structure Of Btb Domain From Btbd6
pdb|2VKP|B Chain B, Crystal Structure Of Btb Domain From Btbd6
Length = 109
Score = 82.4 bits (202), Expect = 7e-16, Method: Composition-based stats.
Identities = 38/66 (57%), Positives = 47/66 (71%)
Query: 12 FNNEILCDVHFIVGRETELQRIPAHRFVLSVGSVVFDAMFNGTLATRSDEIELPDVEPAA 71
FNNE+ DVHF+VG + +PAH++VL+VGS VF A F G LA EI +PDVEPAA
Sbjct: 3 FNNELXADVHFVVGPPGATRTVPAHKYVLAVGSSVFYAXFYGDLAEVKSEIHIPDVEPAA 62
Query: 72 FLALLR 77
FL LL+
Sbjct: 63 FLILLK 68
>pdb|3IZS|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|W Chain W, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 155
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 5/75 (6%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVDPSFEFAKRRN-VPLKYDREF 243
KIFRF SK LFK++KNPR+ AWT +RK K + + E AK+R+ +K R
Sbjct: 27 KIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHKKGI----TEEVAKKRSRKTVKAQRPI 82
Query: 244 WNKTVEAIKKVEHIK 258
+++ IK+ +K
Sbjct: 83 TGASLDLIKERRSLK 97
>pdb|1S1I|S Chain S, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h.
pdb|2X7N|D Chain D, Mechanism Of Eif6s Anti-Association Activity
Length = 56
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKAYR 214
KIFRF SK LFK++KNPR+ AWT +R
Sbjct: 27 KIFRFQNSKSASLFKQRKNPRRIAWTVLFR 56
>pdb|3ZF7|Y Chain Y, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 125
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%)
Query: 176 ISYTACATLKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGK 219
+ + +T + F R KC ++ RKKNPR AWT+ YR++ K
Sbjct: 22 VPFAFLSTKPVLTFARPKCFAMYMRKKNPRFIAWTRTYRRIHRK 65
>pdb|3J21|V Chain V, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 66
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVR 217
++ FC KC + + +NPRK WTKAY++ R
Sbjct: 28 RVLFFCSRKCERYYFMGRNPRKLKWTKAYQEAR 60
>pdb|3JYW|S Chain S, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 45
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 17/26 (65%), Positives = 20/26 (76%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWT 210
KIFRF SK LFK++KNPR+ AWT
Sbjct: 20 KIFRFQNSKSASLFKQRKNPRRIAWT 45
>pdb|3IZR|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 162
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 182 ATLKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVDPSFEFAKRRNVPLKYDR 241
A ++F F SKC + F + P K WT YRK KD+ + + +RR Y R
Sbjct: 26 ADSQVFLFANSKCKRYFHNRLKPAKLTWTAMYRKQHKKDIHAEAVKK--RRRTTKKPYSR 83
Query: 242 EFWNKTVEAIKK 253
T+E I+K
Sbjct: 84 SIVGATLEVIQK 95
>pdb|4EOZ|A Chain A, Crystal Structure Of The Spop Btb Domain Complexed With
The Cul3 N- Terminal Domain
pdb|4EOZ|C Chain C, Crystal Structure Of The Spop Btb Domain Complexed With
The Cul3 N- Terminal Domain
Length = 145
Score = 36.6 bits (83), Expect = 0.043, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 31 QRIPAHRFVLSVGSVVFDAMFNGTL-ATRSDEIELPDVEPAAFLALLRCSMTGK 83
Q AH+ +L+ S VF AMF + ++ + +E+ DVEP F ++ TGK
Sbjct: 35 QEFQAHKAILAARSPVFSAMFEHEMEESKKNRVEINDVEPEVFKEMMCFIYTGK 88
>pdb|3HQI|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HQI|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HU6|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HU6|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
Length = 312
Score = 36.6 bits (83), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 31 QRIPAHRFVLSVGSVVFDAMFNGTL-ATRSDEIELPDVEPAAFLALLRCSMTGK 83
Q AH+ +L+ S VF AMF + ++ + +E+ DVEP F ++ TGK
Sbjct: 184 QEFQAHKAILAARSPVFSAMFEHEMEESKKNRVEINDVEPEVFKEMMCFIYTGK 237
>pdb|3GA1|A Chain A, Crystal Structure Of The Human Nac1 Poz Domain
pdb|3GA1|B Chain B, Crystal Structure Of The Human Nac1 Poz Domain
Length = 129
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 16 ILCDVHFIVGRETELQRIPAHRFVLSVGSVVFDAMFNGTLATRSDEIELP-DVEPAAFLA 74
+ CDV +V + AHR VL+ S F +FN +RS +ELP V+P +F
Sbjct: 32 LYCDVSVVV----KGHAFKAHRAVLAASSSYFRDLFNN---SRSAVVELPAAVQPQSFQQ 84
Query: 75 LLRCSMTGK 83
+L TG+
Sbjct: 85 ILSFCYTGR 93
>pdb|2ZKR|UU Chain u, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 157
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKAYRK 215
K+F+F +KC F K+NPR+ WT YR+
Sbjct: 27 KVFQFLNAKCESAFLSKRNPRQINWTVLYRR 57
>pdb|1KXQ|E Chain E, Camelid Vhh Domain In Complex With Porcine Pancreatic
Alpha- Amylase
pdb|1KXQ|F Chain F, Camelid Vhh Domain In Complex With Porcine Pancreatic
Alpha- Amylase
pdb|1KXQ|G Chain G, Camelid Vhh Domain In Complex With Porcine Pancreatic
Alpha- Amylase
pdb|1KXQ|H Chain H, Camelid Vhh Domain In Complex With Porcine Pancreatic
Alpha- Amylase
Length = 120
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 134 QMQLVRTANGKVIAGNRTSFACDGSTFTSRV 164
Q+QLV + G V AG S +C ST+T V
Sbjct: 1 QVQLVESGGGSVQAGGSLSLSCAASTYTDTV 31
>pdb|3SJQ|C Chain C, Crystal Structure Of A Small Conductance Potassium Channel
Splice Variant Complexed With Calcium-Calmodulin
pdb|3SJQ|D Chain D, Crystal Structure Of A Small Conductance Potassium Channel
Splice Variant Complexed With Calcium-Calmodulin
Length = 87
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 9/84 (10%)
Query: 228 EFAKR-RNVPLKYDREFW--NKTVEAIKKVEHIKTKRHNLYLAQRLRKAREVETARDIKA 284
+ KR +N RE W K + +KK++H K ++H Q + +AR++ R +K
Sbjct: 4 QLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRKFLQAIHQARKL---RSVKM 60
Query: 285 VQRDIAILNDPTEVIRAKKKKMVE 308
QR LND + K +E
Sbjct: 61 EQRK---LNDQANTLVDLAKTQLE 81
>pdb|3V7I|A Chain A, Germicidin Synthase (Gcs) From Streptomyces Coelicolor, A
Type Iii Polyketide Synthase
Length = 413
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 32/103 (31%), Positives = 44/103 (42%), Gaps = 16/103 (15%)
Query: 380 GRKPSAPDSRCRSRLSANPGIEPSAWQANLTYHCAPARLFDEPQLAALCLDTIDKNTPDA 439
GR P AP + ++A+ GIE W L AP D L A +A
Sbjct: 52 GRHPHAPWAPRIDGIAASTGIESRGWMLPLEAAVAPGGGGD---LGA---------AREA 99
Query: 440 LAADGFTDVDRD----TLCAVLERDTLRIREAKLFQAVIRWSE 478
L DGFT+ D + L AV T++ R A ++AV + E
Sbjct: 100 LVRDGFTEQDANRAIAALKAVPASQTVQERTAPAWEAVQAYGE 142
>pdb|1HN0|A Chain A, Crystal Structure Of Chondroitin Abc Lyase I From Proteus
Vulgaris At 1.9 Angstroms Resolution
Length = 1021
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 15/96 (15%)
Query: 470 FQAVIRWSEAEC----TRQSLPITPENQRAVLGPSLTLVRFPLMSVEEFAAGPAQSGLLE 525
+Q R SE E + LP+TPEN A+ L+R L + EF G ++ L
Sbjct: 227 YQVKTRLSEPEIQFHNVKPQLPVTPENLAAI-----DLIRQRL--INEFVGGEKETNLAL 279
Query: 526 DSQLVRL---FLYFHVEEFAAGPAQS-GLLEDSQLV 557
+ + +L F ++ A G Q L+ D Q++
Sbjct: 280 EENISKLKSDFDALNIHTLANGGTQGRHLITDKQII 315
>pdb|3HTM|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopbtb3-Box
pdb|3HTM|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopbtb3-Box
pdb|3HTM|C Chain C, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopbtb3-Box
pdb|3HTM|D Chain D, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopbtb3-Box
Length = 172
Score = 29.3 bits (64), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 31 QRIPAHRFVLSVGSVVFDAMFNGTLA-TRSDEIELPDVEPAAF 72
Q AH+ +L+ S VF A F ++ + +E+ DVEP F
Sbjct: 44 QEFQAHKAILAARSPVFSAXFEHEXEESKKNRVEINDVEPEVF 86
>pdb|1G4Y|B Chain B, 1.60 A Crystal Structure Of The Gating Domain From Small
Conductance Potassium Channel Complexed With
Calcium-Calmodulin
Length = 101
Score = 28.9 bits (63), Expect = 8.6, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 205 RKTAWTKAYRKVRGKDLAVDPSFEFAKR-RNVPLKYDREFW--NKTVEAIKKVEHIKTKR 261
RK TKA + V + +D + KR +N RE W K + +KK++H K ++
Sbjct: 3 RKLELTKAEKHVH--NFMMDT--QLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRK 58
Query: 262 HNLYLAQRLRKAREVE 277
H Q + + R V+
Sbjct: 59 HQRKFLQAIHQLRSVK 74
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
0.323 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,207,775
Number of Sequences: 62578
Number of extensions: 742461
Number of successful extensions: 1449
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1431
Number of HSP's gapped (non-prelim): 23
length of query: 633
length of database: 14,973,337
effective HSP length: 105
effective length of query: 528
effective length of database: 8,402,647
effective search space: 4436597616
effective search space used: 4436597616
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)