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= 018129
(360 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 = 184/262 (70%), Positives = 204/262 (77%), Gaps = 11/262 (4%)
Query: 3 SSIAQKTWELENNIVSMETPPTNSTADTSASDAIFFYDEGAQTKFQQEKPWVNDPHYFKR 62
S AQKTWEL NN + + D I+ YD+ Q + KPW D HYFK
Sbjct: 6 SGXAQKTWELANN-----------XQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKY 54
Query: 63 VKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAY 122
KISALALLK V HARSGG +EV GL GK DG+ I+ D+FALPVEGTETRVNAQA AY
Sbjct: 55 CKISALALLKXVXHARSGGNLEVXGLXLGKVDGETXIIXDSFALPVEGTETRVNAQAAAY 114
Query: 123 EYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTR 182
EY Y + KQ GRLENA+GWYHSHPGYGCWLSGIDVSTQ LNQQFQEPF+AVVIDPTR
Sbjct: 115 EYXAAYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQXLNQQFQEPFVAVVIDPTR 174
Query: 183 TVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIEDFGVHCKQYYSLDITYFKSSLD 242
T+SAGKV +GAFRTYP+GYKPPDE SEYQTIPLNKIEDFGVHCKQYY+L+++YFKSSLD
Sbjct: 175 TISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLD 234
Query: 243 CHLLDLLWNKYWVNTLSSSPLL 264
LL+LLWNKYWVNTLSSS LL
Sbjct: 235 RKLLELLWNKYWVNTLSSSSLL 256
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 306
Score = 132 bits (333), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 82/200 (41%), Positives = 114/200 (57%), Gaps = 13/200 (6%)
Query: 63 VKISALALLKMVVHARSGGTIEVMGLMQGK-TDGDAIIVMDAFALPVEGTETRVNAQADA 121
V IS++ALLKM+ H R+G +EVMGLM G+ D + V+D FA+P GT V A D
Sbjct: 27 VYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDV 86
Query: 122 YEY-MVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDP 180
++ M+D KQ GR + VGWYHSHPG+GCWLS +DV+TQ +Q +AVV+DP
Sbjct: 87 FQAKMMDML---KQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDP 143
Query: 181 TRTVSAGKVEIGAFRTYPEGY----KPPDEPISEYQTIPLNKIEDFGVHC--KQYYSLDI 234
++V GKV I AFR G P + S + I+ +H + YYSL+I
Sbjct: 144 IQSVK-GKVVIDAFRLIDTGALINNLEPRQTTSNTGLLNKANIQAL-IHGLNRHYYSLNI 201
Query: 235 TYFKSSLDCHLLDLLWNKYW 254
Y K++ + +L L + W
Sbjct: 202 DYHKTAKETKMLMNLHKEQW 221
>pdb|4B4T|U Chain U, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 338
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 57/122 (46%), Gaps = 9/122 (7%)
Query: 61 KRVKISALALLKMVVHARSGGTIE---VMGLMQGKTDGDAIIVMDAFALPVEGTETRVNA 117
++V I+ L LL + H T E +G++ G + I V ++FALP E E +
Sbjct: 6 EKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDV 65
Query: 118 QADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQE--PFLA 175
+ Y+ + ++ K+ E +GWYHS P L D+ L +++ + P L
Sbjct: 66 WFLDHNYIENMNEMCKKINAKEKLIGWYHSGPK----LRASDLKINELFKKYTQNNPLLL 121
Query: 176 VV 177
+V
Sbjct: 122 IV 123
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/123 (23%), Positives = 57/123 (46%), Gaps = 8/123 (6%)
Query: 61 KRVKISALALLKMVVH----ARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVN 116
++V + L LL +V H + G V+G++ G + V ++FA+P + + +
Sbjct: 8 QKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDS 67
Query: 117 AQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAV 176
++Y+ + K+ E VGWYH+ P L D++ L +++ + V
Sbjct: 68 VWFLDHDYLENMYGMFKKVNARERIVGWYHTGPK----LHKNDIAINELMKRYCPNSVLV 123
Query: 177 VID 179
+ID
Sbjct: 124 IID 126
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/123 (23%), Positives = 57/123 (46%), Gaps = 8/123 (6%)
Query: 61 KRVKISALALLKMVVH----ARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVN 116
++V + L LL +V H + G V+G++ G + V ++FA+P + + +
Sbjct: 8 QKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDS 67
Query: 117 AQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAV 176
++Y+ + K+ E VGWYH+ P L D++ L +++ + V
Sbjct: 68 VWFLDHDYLENMYGMFKKVNARERIVGWYHTGPK----LHKNDIAINELMKRYCPNSVLV 123
Query: 177 VID 179
+ID
Sbjct: 124 IID 126
>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 = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 142 VGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPT-------RTVSAGKVEIGAF 194
+GW H+HP +LS +D+ T Q +A+V P R +AG +E+ A
Sbjct: 85 LGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSAC 144
Query: 195 RTYPEGYKP 203
+ +G+ P
Sbjct: 145 KK--KGFHP 151
>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp
Length = 178
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 9/70 (12%)
Query: 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPT-------RTVSAGKVEIGA 193
+GW H+HP +LS +D+ T Q +A+V P R +AG +E+ A
Sbjct: 84 TLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSA 143
Query: 194 FRTYPEGYKP 203
+ +G+ P
Sbjct: 144 CKK--KGFHP 151
>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 = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 28/138 (20%), Positives = 50/138 (36%), Gaps = 17/138 (12%)
Query: 77 ARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAG 136
A + +E G++ GK + + N + + +++ Q G
Sbjct: 36 ANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLI-----QDQQG 90
Query: 137 RLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPT-------RTVSAGKV 189
+ +GW H+HP +LS +D+ T Q +A+V P + G
Sbjct: 91 LI--TLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLTDHGLE 148
Query: 190 EIGAFRT---YPEGYKPP 204
EI + R +P PP
Sbjct: 149 EISSCRQKGFHPHSKDPP 166
>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic
Domain Of Amsh
Length = 211
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 142 VGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPT-------RTVSAGKVEIGAF 194
+GW H+HP +LS +D+ T Q +A+V P + G EI +
Sbjct: 118 LGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQETGFFKLTDHGLEEISSC 177
Query: 195 RT---YPEGYKPP 204
R +P PP
Sbjct: 178 RQKGFHPHSKDPP 190
>pdb|3UOV|A Chain A, Crystal Structure Of Otemo (Fad Bound Form 1)
pdb|3UOV|B Chain B, Crystal Structure Of Otemo (Fad Bound Form 1)
pdb|3UOX|A Chain A, Crystal Structure Of Otemo (Fad Bound Form 2)
pdb|3UOX|B Chain B, Crystal Structure Of Otemo (Fad Bound Form 2)
pdb|3UOY|A Chain A, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
1)
pdb|3UOY|B Chain B, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
1)
pdb|3UOZ|A Chain A, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
2)
pdb|3UOZ|B Chain B, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
2)
pdb|3UP4|A Chain A, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
3)
pdb|3UP4|B Chain B, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
3)
pdb|3UP5|A Chain A, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
4)
pdb|3UP5|B Chain B, Crystal Structure Of Otemo Complex With Fad And Nadp (Form
4)
Length = 545
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/113 (20%), Positives = 44/113 (38%), Gaps = 16/113 (14%)
Query: 146 HSHPGYGCWLSGI--------------DVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEI 191
+ PGYG WLSG D + + Q+ ++P +A + P + G +
Sbjct: 280 YRQPGYGIWLSGFRDLLLNKESNKFLADFVAKKIRQRVKDPVVAEKLIP-KDHPFGAKRV 338
Query: 192 GAFRTYPEGYKPPDEPISEYQTIPLNKIEDFGVH-CKQYYSLDITYFKSSLDC 243
Y E Y + + + + P+ ++ G+ Y LD+ + + D
Sbjct: 339 PMETNYYETYNRDNVHLVDIREAPIQEVTPEGIKTADAAYDLDVIIYATGFDA 391
>pdb|3V97|A Chain A, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sah Binding
pdb|3V97|B Chain B, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sah Binding
Length = 703
Score = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 14/77 (18%)
Query: 259 SSSPLLGNGDYVAGQISDLAEKLEQAENQLSHSRYGPLIAPPPRRKEEDSQLAKITRDSA 318
+++ L G G+ + ++ D+A Q N L YG +++ PP + DS+ A I
Sbjct: 274 TNARLAGIGELITFEVKDVA----QLTNPLPKGPYGTVLSNPPYGERLDSEPALIA---- 325
Query: 319 KITVEQVHGLMSQVIKD 335
+H L+ +++K+
Sbjct: 326 ------LHSLLGRIMKN 336
>pdb|3V8V|A Chain A, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sam Binding
pdb|3V8V|B Chain B, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sam Binding
Length = 702
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 14/77 (18%)
Query: 259 SSSPLLGNGDYVAGQISDLAEKLEQAENQLSHSRYGPLIAPPPRRKEEDSQLAKITRDSA 318
+++ L G G+ + ++ D+A Q N L YG +++ PP + DS+ A I
Sbjct: 273 TNARLAGIGELITFEVKDVA----QLTNPLPKGPYGTVLSNPPYGERLDSEPALIA---- 324
Query: 319 KITVEQVHGLMSQVIKD 335
+H L+ +++K+
Sbjct: 325 ------LHSLLGRIMKN 335
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
0.314 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,026,278
Number of Sequences: 62578
Number of extensions: 454845
Number of successful extensions: 786
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 773
Number of HSP's gapped (non-prelim): 16
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)