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= 041233
(240 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 154 bits (388), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 85/191 (44%), Positives = 122/191 (63%), Gaps = 12/191 (6%)
Query: 53 SNTE--PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLII 110
SN+E P++ L+ V + +L FL+LA NT + +ETCG+L L F +T ++I
Sbjct: 6 SNSESIPTIDG-LRHVVVPGRLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVLI 64
Query: 111 PKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170
PKQ + S C NEE++F IQ+++ L +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE
Sbjct: 65 PKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPE 124
Query: 171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTN 229
+ AIV +P + G F+LT+ G+ + C++ GFHPH K+P P++ CSHV T
Sbjct: 125 SVAIVCSP--KFQETGFFKLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TV 176
Query: 230 SNLRFEIFDLR 240
+ I DLR
Sbjct: 177 VDRAVTITDLR 187
>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic
Domain Of Amsh
Length = 211
Score = 152 bits (384), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 84/191 (43%), Positives = 121/191 (63%), Gaps = 12/191 (6%)
Query: 53 SNTE--PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLII 110
SN+E P++ L+ V + +L FL+LA NT + + TCG+L L F +T ++I
Sbjct: 30 SNSESIPTIDG-LRHVVVPGRLCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLI 88
Query: 111 PKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170
PKQ + S C NEE++F IQ+++ L +GWIHTHP+Q+ F+SSVDLHTH SYQMM+PE
Sbjct: 89 PKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPE 148
Query: 171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTN 229
+ AIV +P + G F+LT+ G+ + C++ GFHPH K+P P++ CSHV T
Sbjct: 149 SVAIVCSP--KFQETGFFKLTD-HGLEEISSCRQKGFHPHSKDP----PLFCSCSHV-TV 200
Query: 230 SNLRFEIFDLR 240
+ I DLR
Sbjct: 201 VDRAVTITDLR 211
>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp
Length = 178
Score = 149 bits (377), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 77/179 (43%), Positives = 113/179 (63%), Gaps = 9/179 (5%)
Query: 63 LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
L+ V + L FL+LA+ NT + +ETCG+L L + F +T +I+PKQ + C
Sbjct: 8 LRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDM 67
Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
N E++F +Q++ L +GWIHTHP+Q+ F+SSVDLHTH SYQ+M+PEA AIV +P
Sbjct: 68 ENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSP--KH 125
Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
+ GIF+LT +GM + C++ GFHPH KEP ++ C HV +++ + DLR
Sbjct: 126 KDTGIFRLTN-AGMLEVSACKKKGFHPHTKEPR----LFSICKHVLVK-DIKIIVLDLR 178
>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 = 147 bits (371), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 76/179 (42%), Positives = 112/179 (62%), Gaps = 9/179 (5%)
Query: 63 LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQA 122
L+ V + L FL+LA+ NT + + TCG+L L + F +T +I+PKQ + C
Sbjct: 8 LRCVVLPEDLCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHVIVPKQSAGPDYCDM 67
Query: 123 LNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS 182
N E++F +Q++ L +GWIHTHP+Q+ F+SSVDLHTH SYQ+M+PEA AIV +P
Sbjct: 68 ENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSP--KH 125
Query: 183 RSYGIFQLTEPSGMSVLKECQETGFHPH-KEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240
+ GIF+LT +GM + C++ GFHPH KEP ++ C HV +++ + DLR
Sbjct: 126 KDTGIFRLTN-AGMLEVSACKKKGFHPHTKEPR----LFSICKHVLVK-DIKIIVLDLR 178
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 306
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 10/105 (9%)
Query: 88 LETCGV-LGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAI-------QNERSLFP 139
+E G+ LG F+++ T V + Q T S +A+ +DVF Q R
Sbjct: 47 MEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAV--DDVFQAKMMDMLKQTGRDQMV 104
Query: 140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS 184
+GW H+HP C++SSVD++T S++ + A A+V+ P S +
Sbjct: 105 VGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKG 149
>pdb|4F7O|A Chain A, Crystal Structure Of Csn5
pdb|4F7O|B Chain B, Crystal Structure Of Csn5
Length = 257
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPT 179
+GW H+HP C++S +D+ T Q A+V+ PT
Sbjct: 134 IGWYHSHPGYGCWLSGIDVSTQXLNQQFQEPFVAVVIDPT 173
>pdb|4I43|B Chain B, Crystal Structure Of Prp8:aar2 Complex
Length = 1564
Score = 33.9 bits (76), Expect = 0.079, Method: Composition-based stats.
Identities = 49/213 (23%), Positives = 89/213 (41%), Gaps = 40/213 (18%)
Query: 37 QGALVTHVSVADSDKQSNT------EPSVSNVL-----QDVHISAQLMEDFLE------L 79
QG + V+ AD + Q+ + + +++N L +++++SA +DF+E L
Sbjct: 1280 QGEEIVVVASADYESQTFSSKNEWRKSAIANTLLYLRLKNIYVSA---DDFVEEQNVYVL 1336
Query: 80 AKENTDKDLETCGV---LGAFLENGTFY-------VTTLIIPKQDSTSSSCQALNEEDVF 129
K K +E V + AF+ + + T+++ Q S Q N D+
Sbjct: 1337 PKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIG 1396
Query: 130 AIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYS-YQMMVPEAFAIVLAPTDSSRSYGIF 188
+ + L +GWIHT + FM++ ++ TH + + I + T S S +
Sbjct: 1397 DLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAY 1456
Query: 189 QLTEPSG---------MSVLKECQETGFHPHKE 212
LT+ M+VL E E F H +
Sbjct: 1457 NLTDEGYQWGEENKDIMNVLSEGFEPTFSTHAQ 1489
>pdb|4DJ3|A Chain A, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ3|B Chain B, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
Length = 317
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 48/99 (48%), Gaps = 6/99 (6%)
Query: 57 PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDST 116
P L+DV + + +ED LA E+T K+ +T + +FL +++ +S
Sbjct: 6 PEFPGRLEDVTVYS--LEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSK 63
Query: 117 SSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSS 155
++++ D+ A Q+ R+ + HT P+Q F ++
Sbjct: 64 RGFLKSVHFVDLLAPQDVRAFY----AHTAPTQLPFWNN 98
>pdb|3ZEF|B Chain B, Crystal Structure Of Prp8:aar2 Complex: Second Crystal Form
At 3.1 Angstrom Resolution
pdb|3ZEF|E Chain E, Crystal Structure Of Prp8:aar2 Complex: Second Crystal Form
At 3.1 Angstrom Resolution
Length = 1531
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 67/152 (44%), Gaps = 30/152 (19%)
Query: 37 QGALVTHVSVAD------SDKQSNTEPSVSNVL-----QDVHISAQLMEDFLE------L 79
QG + V+ AD S K + +++N L +++++SA +DF+E L
Sbjct: 1247 QGEEIVVVASADYESQTFSSKNEWRKSAIANTLLYLRLKNIYVSA---DDFVEEQNVYVL 1303
Query: 80 AKENTDKDLETCGV---LGAFLENGTFY-------VTTLIIPKQDSTSSSCQALNEEDVF 129
K K +E V + AF+ + + T+++ Q S Q N D+
Sbjct: 1304 PKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIG 1363
Query: 130 AIQNERSLFPMGWIHTHPSQSCFMSSVDLHTH 161
+ + L +GWIHT + FM++ ++ TH
Sbjct: 1364 DLPDTEGLELLGWIHTQTEELKFMAASEVATH 1395
>pdb|2OG4|A Chain A, Structure Of An Expanded Jab1-mpn-like Domain Of Splicing
Factor Prp8p From Yeast
Length = 254
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 105 VTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTH 161
+ T+++ Q S Q N D+ + + L +GWIHT + FM++ ++ TH
Sbjct: 78 IKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATH 134
>pdb|3SBG|A Chain A, Crystal Structure Of A Prp8 C-Terminal Fragment
Length = 565
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 67/152 (44%), Gaps = 30/152 (19%)
Query: 37 QGALVTHVSVAD------SDKQSNTEPSVSNVL-----QDVHISAQLMEDFLE------L 79
QG + V+ AD S K + +++N L +++++SA +DF+E L
Sbjct: 297 QGEEIVVVASADYESQTFSSKNEWRKSAIANTLLYLRLKNIYVSA---DDFVEEQNVYVL 353
Query: 80 AKENTDKDLETCGV---LGAFLENGTFY-------VTTLIIPKQDSTSSSCQALNEEDVF 129
K K +E V + AF+ + + T+++ Q S Q N D+
Sbjct: 354 PKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIG 413
Query: 130 AIQNERSLFPMGWIHTHPSQSCFMSSVDLHTH 161
+ + L +GWIHT + FM++ ++ TH
Sbjct: 414 DLPDTEGLELLGWIHTQTEELKFMAASEVATH 445
>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 = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 135 RSLFPMGWIHTHPSQSCFMSSVDLHTH 161
R P+GW+HT P++ +S D+ TH
Sbjct: 107 RDFEPLGWMHTQPNELPQLSPQDVTTH 133
>pdb|2P87|A Chain A, Crystal Structure Of The C-Terminal Domain Of C. Elegans
Pre-Mrna Splicing Factor Prp8
Length = 273
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 135 RSLFPMGWIHTHPSQSCFMSSVDLHTH 161
R P+GW+HT P++ +S D+ TH
Sbjct: 107 RDFEPLGWMHTQPNELPQLSPQDVTTH 133
>pdb|2NO4|A Chain A, Crystal Structure Analysis Of A Dehalogenase
pdb|2NO4|B Chain B, Crystal Structure Analysis Of A Dehalogenase
Length = 240
Score = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 68 ISAQLMEDFLEL-----AKENTDKDLETCGVLGAFLENGT--FYVTTLIIPKQDSTSSSC 120
+ +LM + EL A E +K L++ G + A L NG L K D SC
Sbjct: 93 LKDRLMSAYKELSAYPDAAETLEK-LKSAGYIVAILSNGNDEMLQAALKASKLDRVLDSC 151
Query: 121 QALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSS 155
+ ++ ++ F + +P++ CF+SS
Sbjct: 152 LSADDLKIYKPDPRIYQFACDRLGVNPNEVCFVSS 186
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
0.317 0.129 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,092,215
Number of Sequences: 62578
Number of extensions: 276500
Number of successful extensions: 545
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 526
Number of HSP's gapped (non-prelim): 17
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)