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= psy9085
(394 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F7O|A Chain A, Crystal Structure Of Csn5
pdb|4F7O|B Chain B, Crystal Structure Of Csn5
Length = 257
Score = 365 bits (937), Expect = e-101, Method: Compositional matrix adjust.
Identities = 178/239 (74%), Positives = 198/239 (82%)
Query: 64 KTWIMENNIETLSATDEIFKYDRKRQQDMIAAKPWEKDPHFFKDIKISALALLKMVMHAR 123
KTW + NN + + DEI+KYD+K+QQ+++AAKPW KD H+FK KISALALLK V HAR
Sbjct: 11 KTWELANNXQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKXVXHAR 70
Query: 124 SGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRL 183
SGG LEV GL LGK+D + I+ D+FALPVEGTETRVNAQA AYEY AYIE AK+VGRL
Sbjct: 71 SGGNLEVXGLXLGKVDGETXIIXDSFALPVEGTETRVNAQAAAYEYXAAYIENAKQVGRL 130
Query: 184 ENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYP 243
ENAIGWYHSHPGYGCWLSGIDVSTQ LNQ FQEPFVA+VIDP RTISAGKV LG+FRTYP
Sbjct: 131 ENAIGWYHSHPGYGCWLSGIDVSTQXLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYP 190
Query: 244 KGYKPANEEPSEYQTIPLNKIEDFGVHCKQYYSLDVSYFKXXXXXXXXXXXWNKYWVNT 302
KGYKP +E PSEYQTIPLNKIEDFGVHCKQYY+L+VSYFK WNKYWVNT
Sbjct: 191 KGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNT 249
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 306
Score = 132 bits (331), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 73/183 (39%), Positives = 111/183 (60%), Gaps = 11/183 (6%)
Query: 108 IKISALALLKMVMHARSGGTLEVMGLLLGK-IDANSMIVMDAFALPVEGTETRVNAQAQA 166
+ IS++ALLKM+ H R+G +EVMGL+LG+ +D ++ V+D FA+P GT V A
Sbjct: 27 VYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDV 86
Query: 167 YEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPV 226
++ ++ K+ GR + +GWYHSHPG+GCWLS +DV+TQ + VA+V+DP+
Sbjct: 87 FQ--AKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPI 144
Query: 227 RTISAGKVCLGSFRTYPKGYKPANEEPSEY--QTIPLNK--IEDFGVHC--KQYYSLDVS 280
+++ GKV + +FR G N EP + T LNK I+ +H + YYSL++
Sbjct: 145 QSVK-GKVVIDAFRLIDTGALINNLEPRQTTSNTGLLNKANIQAL-IHGLNRHYYSLNID 202
Query: 281 YFK 283
Y K
Sbjct: 203 YHK 205
>pdb|4B4T|U Chain U, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 338
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 108 IKISALALLKMVMHARSGGTLE---VMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQA 164
+ I+ L LL + H T E +G++LG +++++ V ++FALP E E +
Sbjct: 8 VTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWF 67
Query: 165 QAYEYMTAYIEAAKEVGRLENAIGWYHSHP 194
+ Y+ E K++ E IGWYHS P
Sbjct: 68 LDHNYIENMNEMCKKINAKEKLIGWYHSGP 97
>pdb|2O95|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-186)
pdb|2O95|B Chain B, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-186)
Length = 187
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 55/121 (45%), Gaps = 8/121 (6%)
Query: 108 IKISALALLKMVMH----ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQ 163
+ + L LL +V H + G V+G+LLG + V ++FA+P + + +
Sbjct: 10 VVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVW 69
Query: 164 AQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVI 223
++Y+ K+V E +GWYH+ P L D++ L + + V ++I
Sbjct: 70 FLDHDYLENMYGMFKKVNARERIVGWYHTGPK----LHKNDIAINELMKRYCPNSVLVII 125
Query: 224 D 224
D
Sbjct: 126 D 126
>pdb|2O96|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-177)
pdb|2O96|B Chain B, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-177)
Length = 178
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 55/121 (45%), Gaps = 8/121 (6%)
Query: 108 IKISALALLKMVMH----ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQ 163
+ + L LL +V H + G V+G+LLG + V ++FA+P + + +
Sbjct: 10 VVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVW 69
Query: 164 AQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVI 223
++Y+ K+V E +GWYH+ P L D++ L + + V ++I
Sbjct: 70 FLDHDYLENMYGMFKKVNARERIVGWYHTGPK----LHKNDIAINELMKRYCPNSVLVII 125
Query: 224 D 224
D
Sbjct: 126 D 126
>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp
Length = 178
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/141 (24%), Positives = 60/141 (42%), Gaps = 26/141 (18%)
Query: 128 LEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLEN-- 185
+E G+L GK+ N + T V Q+ +Y +E +E+ +++
Sbjct: 33 IETCGILCGKLTHNEFTI----------THVIVPKQSAGPDYCD--MENVEELFNVQDQH 80
Query: 186 ---AIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP-------VRTISAGKVC 235
+GW H+HP +LS +D+ T Q +AIV P R +AG +
Sbjct: 81 DLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLE 140
Query: 236 LGSFRTYPKGYKPANEEPSEY 256
+ + + KG+ P +EP +
Sbjct: 141 VSACKK--KGFHPHTKEPRLF 159
>pdb|2ZNV|A Chain A, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
With Lys63-Linked Ubiquitin Dimer
pdb|2ZNV|D Chain D, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
With Lys63-Linked Ubiquitin Dimer
Length = 178
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/137 (24%), Positives = 58/137 (42%), Gaps = 26/137 (18%)
Query: 132 GLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLEN-----A 186
G+L GK+ N + T V Q+ +Y +E +E+ +++
Sbjct: 37 GILCGKLTHNEFTI----------THVIVPKQSAGPDYCD--MENVEELFNVQDQHDLLT 84
Query: 187 IGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP-------VRTISAGKVCLGSF 239
+GW H+HP +LS +D+ T Q +AIV P R +AG + + +
Sbjct: 85 LGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSAC 144
Query: 240 RTYPKGYKPANEEPSEY 256
+ KG+ P +EP +
Sbjct: 145 KK--KGFHPHTKEPRLF 159
>pdb|3RZU|A Chain A, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|B Chain B, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|C Chain C, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|D Chain D, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|E Chain E, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|F Chain F, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|G Chain G, The Crystal Structure Of The Catalytic Domain Of Amsh
Length = 187
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 34/147 (23%), Positives = 59/147 (40%), Gaps = 26/147 (17%)
Query: 122 ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVG 181
A + +E G+L GK+ N + T + Q+ +Y E +E+
Sbjct: 36 ANTARGVETCGILCGKLMRNEFTI----------THVLIPKQSAGSDYCNT--ENEEELF 83
Query: 182 RLEN-----AIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP-------VRTI 229
+++ +GW H+HP +LS +D+ T Q VAIV P +
Sbjct: 84 LIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLT 143
Query: 230 SAGKVCLGSFRTYPKGYKPANEEPSEY 256
G + S R KG+ P +++P +
Sbjct: 144 DHGLEEISSCRQ--KGFHPHSKDPPLF 168
>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic
Domain Of Amsh
Length = 211
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 33/147 (22%), Positives = 58/147 (39%), Gaps = 26/147 (17%)
Query: 122 ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVG 181
A + + G+L GK+ N + T + Q+ +Y E +E+
Sbjct: 60 ANTARGVATCGILCGKLMRNEFTI----------THVLIPKQSAGSDYCNT--ENEEELF 107
Query: 182 RLEN-----AIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP-------VRTI 229
+++ +GW H+HP +LS +D+ T Q VAIV P +
Sbjct: 108 LIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLT 167
Query: 230 SAGKVCLGSFRTYPKGYKPANEEPSEY 256
G + S R KG+ P +++P +
Sbjct: 168 DHGLEEISSCRQ--KGFHPHSKDPPLF 192
>pdb|2FM8|A Chain A, Crystal Structure Of The Salmonella Secretion Chaperone
Invb In Complex With Sipa
pdb|2FM8|B Chain B, Crystal Structure Of The Salmonella Secretion Chaperone
Invb In Complex With Sipa
Length = 135
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 18/68 (26%)
Query: 127 TLEVMGL---LLGKIDANSMIVMDAFALPV---------------EGTETRVNAQAQAYE 168
LEV G L+G ID++S IV+D FALP G ++ V Q +AYE
Sbjct: 13 ALEVSGCDPSLIGGIDSHSTIVLDLFALPSICISVKDDDVWIWAQLGADSMVVLQQRAYE 72
Query: 169 YMTAYIEA 176
+ +E
Sbjct: 73 ILMTIMEG 80
>pdb|2P8R|A Chain A, Crystal Structure Of The C-Terminal Domain Of C. Elegans
Pre-Mrna Splicing Factor Prp8 Carrying R2303k Mutant
Length = 273
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 44/102 (43%), Gaps = 18/102 (17%)
Query: 151 LPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVST--Q 208
+P G+ +VN Q ++ E+ R +GW H+ P LS DV+T +
Sbjct: 85 VPQTGSHQQVNLPTQLPDH---------ELLRDFEPLGWMHTQPNELPQLSPQDVTTHAK 135
Query: 209 MLNQNFQ---EPFVAIVIDPVRTISAGKVCLGSFRTYPKGYK 247
+L N E V I + + G V L +++ P GY+
Sbjct: 136 LLTDNISWDGEKTVMITC----SFTPGSVSLTAYKLTPSGYE 173
>pdb|2P87|A Chain A, Crystal Structure Of The C-Terminal Domain Of C. Elegans
Pre-Mrna Splicing Factor Prp8
Length = 273
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 44/102 (43%), Gaps = 18/102 (17%)
Query: 151 LPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVST--Q 208
+P G+ +VN Q ++ E+ R +GW H+ P LS DV+T +
Sbjct: 85 VPQTGSHQQVNLPTQLPDH---------ELLRDFEPLGWMHTQPNELPQLSPQDVTTHAK 135
Query: 209 MLNQNFQ---EPFVAIVIDPVRTISAGKVCLGSFRTYPKGYK 247
+L N E V I + + G V L +++ P GY+
Sbjct: 136 LLTDNISWDGEKTVMITC----SFTPGSVSLTAYKLTPSGYE 173
>pdb|2YGL|A Chain A, The X-Ray Crystal Structure Of Tandem Cbm51 Modules Of
Sp3gh98, The Family 98 Glycoside Hydrolase From
Streptococcus Pneumoniae Sp3-Bs71
pdb|2YGL|B Chain B, The X-Ray Crystal Structure Of Tandem Cbm51 Modules Of
Sp3gh98, The Family 98 Glycoside Hydrolase From
Streptococcus Pneumoniae Sp3-Bs71
pdb|2YGM|A Chain A, The X-Ray Crystal Structure Of Tandem Cbm51 Modules Of
Sp3gh98, The Family 98 Glycoside Hydrolase From
Streptococcus Pneumoniae Sp3-Bs71, In Complex With The
Blood Group B Antigen
pdb|2YGM|B Chain B, The X-Ray Crystal Structure Of Tandem Cbm51 Modules Of
Sp3gh98, The Family 98 Glycoside Hydrolase From
Streptococcus Pneumoniae Sp3-Bs71, In Complex With The
Blood Group B Antigen
Length = 354
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 13/67 (19%)
Query: 202 GIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPAN-------EEPS 254
GID S LN ++ + I ++ GKV S YPKG K E P
Sbjct: 270 GIDRSANHLNSDYAD------IQKFEVVADGKVIYSSDSKYPKGIKYDTSAFLVDVEIPK 323
Query: 255 EYQTIPL 261
+ QTI L
Sbjct: 324 DTQTIEL 330
>pdb|1G0S|A Chain A, The Crystal Structure Of The E.Coli Adp-Ribose
Pyrophosphatase
pdb|1G0S|B Chain B, The Crystal Structure Of The E.Coli Adp-Ribose
Pyrophosphatase
pdb|1G9Q|A Chain A, Complex Structure Of The Adpr-Ase And Its Substrate Adp-
Ribose
pdb|1G9Q|B Chain B, Complex Structure Of The Adpr-Ase And Its Substrate Adp-
Ribose
pdb|1GA7|A Chain A, Crystal Structure Of The Adp-Ribose Pyrophosphatase In
Complex With Gd+3
pdb|1GA7|B Chain B, Crystal Structure Of The Adp-Ribose Pyrophosphatase In
Complex With Gd+3
pdb|1KHZ|A Chain A, Structure Of The Adpr-Ase In Complex With Ampcpr And Mg
pdb|1KHZ|B Chain B, Structure Of The Adpr-Ase In Complex With Ampcpr And Mg
Length = 209
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 122 ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVG 181
A GGT E +++G++DA + + A E V ++ QAY+++ E G
Sbjct: 132 ASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWV--------EEG 183
Query: 182 RLENA 186
+++NA
Sbjct: 184 KIDNA 188
>pdb|1VIQ|A Chain A, Crystal Structure Of Putative Adp Ribose Pyrophosphatase
pdb|1VIQ|B Chain B, Crystal Structure Of Putative Adp Ribose Pyrophosphatase
pdb|1VIQ|C Chain C, Crystal Structure Of Putative Adp Ribose Pyrophosphatase
Length = 220
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 122 ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVG 181
A GGT E +++G++DA + + A E V ++ QAY+++ E G
Sbjct: 133 ASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWV--------EEG 184
Query: 182 RLENA 186
+++NA
Sbjct: 185 KIDNA 189
>pdb|3TEB|A Chain A, EndonucleaseEXONUCLEASEPHOSPHATASE FAMILY PROTEIN FROM
LEPTOTRICHIA Buccalis C-1013-B
pdb|3TEB|B Chain B, EndonucleaseEXONUCLEASEPHOSPHATASE FAMILY PROTEIN FROM
LEPTOTRICHIA Buccalis C-1013-B
Length = 266
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 189 WYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVC 235
W +SH G+G + G+ V T+ + ++ F VRTISA ++
Sbjct: 81 WSNSHIGFGKYNEGVAVITRHKIK-AEDEFYCTFAQSVRTISARRIV 126
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 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,724,150
Number of Sequences: 62578
Number of extensions: 411225
Number of successful extensions: 966
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 953
Number of HSP's gapped (non-prelim): 19
length of query: 394
length of database: 14,973,337
effective HSP length: 101
effective length of query: 293
effective length of database: 8,652,959
effective search space: 2535316987
effective search space used: 2535316987
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: 52 (24.6 bits)