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= 006836
(629 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QGQ|A Chain A, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|B Chain B, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|C Chain C, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|D Chain D, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|E Chain E, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|F Chain F, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|G Chain G, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
pdb|2QGQ|H Chain H, Crystal Structure Of Tm_1862 From Thermotoga Maritima.
Northeast Structural Genomics Consortium Target Vr77
Length = 304
Score = 107 bits (266), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 80/281 (28%), Positives = 132/281 (46%), Gaps = 27/281 (9%)
Query: 196 LPINVGCLGACTYCKTKHARGHLGSYTVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDI 255
+ I+ GC CT+C +G L S ++E + V ++ +G KE+ L ++DT +YG D+
Sbjct: 8 VKISDGCDRGCTFCSIPSFKGSLRSRSIEDITREVEDLLKEGKKEIILVAQDTTSYGIDL 67
Query: 256 GVN--LPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQ 313
LP LL + + +G +R+ +P + E + I+ L V + VPVQ
Sbjct: 68 YRKQALPDLLRRLNS---LNGEFWIRVXYLHPDHLTEEI--ISAXLELDKVVKYFDVPVQ 122
Query: 314 SGSDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKE 373
GSD +L R + + + + ++ E P + T II GFPGET+EDF + ++E
Sbjct: 123 HGSDKILKLXGRTKSSEELKKXLSSIRERFPDAVLRTSIIVGFPGETEEDFEELKQFVEE 182
Query: 374 YKFPQVHISQFYPRPGTPAARMK-KVPSAVVKKRSREL--------TSVFEAFT----PY 420
+F ++ + GT A +K KV K+R EL S + F +
Sbjct: 183 IQFDKLGAFVYSDEEGTVAFNLKEKVDPEXAKRRQEELLLLQAEISNSRLDRFVGKKLKF 242
Query: 421 L--GMEGR--VERIWITEIAADGIHLV---GHTKGYVQVLV 454
L G EG+ V R W DG+ V G +++V++
Sbjct: 243 LVEGKEGKFLVGRTWTEAPEVDGVVFVRGKGKIGDFLEVVI 283
>pdb|3CIX|A Chain A, X-ray Structure Of The [fefe]-hydrogenase Maturase Hyde
From Thermotoga Maritima In Complex With Thiocyanate
Length = 348
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 59/202 (29%), Positives = 83/202 (41%), Gaps = 27/202 (13%)
Query: 202 CLGACTYCKTKHARGHLGSY--TVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNL 259
C C YC + +L Y T E +V R R + G K + L S + Y +
Sbjct: 63 CRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYY-------M 115
Query: 260 PILLNAIVAELPPDG-STMLRIGMTNPPFILEHLKEIAE---VLRHPCVYSFLHVPVQSG 315
P +++ IV E+ G + L +G P E KE +LRH LH ++
Sbjct: 116 PDVISDIVKEIKKMGVAVTLSLG-EWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPD 174
Query: 316 SDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYK 375
+ S NR L TL EL G + + G PG+T +D + +KE+
Sbjct: 175 T----SFENRLNXLL-------TLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHD 221
Query: 376 FPQVHISQFYPRPGTPAARMKK 397
F V I F P P TP A KK
Sbjct: 222 FDMVGIGPFIPHPDTPLANEKK 243
>pdb|3CIW|A Chain A, X-Ray Structure Of The [fefe]-Hydrogenase Maturase Hyde
From Thermotoga Maritima
pdb|3IIX|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From
T. Maritima In Complex With Methionine And
5'deoxyadenosine
Length = 348
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 83/202 (41%), Gaps = 27/202 (13%)
Query: 202 CLGACTYCKTKHARGHLGSY--TVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNL 259
C C YC + +L Y T E +V R R + G K + L S G D +
Sbjct: 63 CRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQS------GED-PYXM 115
Query: 260 PILLNAIVAELPPDG-STMLRIGMTNPPFILEHLKEIAE---VLRHPCVYSFLHVPVQSG 315
P +++ IV E+ G + L +G P E KE +LRH LH ++
Sbjct: 116 PDVISDIVKEIKKMGVAVTLSLG-EWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPD 174
Query: 316 SDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYK 375
+ S NR L TL EL G + + G PG+T +D + +KE+
Sbjct: 175 T----SFENRLNXLL-------TLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHD 221
Query: 376 FPQVHISQFYPRPGTPAARMKK 397
F V I F P P TP A KK
Sbjct: 222 FDMVGIGPFIPHPDTPLANEKK 243
>pdb|3IIZ|A Chain A, X-Ray Structure Of The Fefe-Hydrogenase Maturase Hyde From
T. Maritima In Complex With S-Adenosyl-L-Methionine
Length = 348
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 83/202 (41%), Gaps = 27/202 (13%)
Query: 202 CLGACTYCKTKHARGHLGSY--TVESLVGRVRTVIADGVKEVWLSSEDTGAYGRDIGVNL 259
C C YC + +L Y T E +V R R + G K + L S G D +
Sbjct: 63 CRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQS------GED-PYXM 115
Query: 260 PILLNAIVAELPPDG-STMLRIGMTNPPFILEHLKEIAE---VLRHPCVYSFLHVPVQSG 315
P +++ IV E+ G + L +G P E KE +LRH LH ++
Sbjct: 116 PDVISDIVKEIKKMGVAVTLSLG-EWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPD 174
Query: 316 SDAVLSAMNREYTLSDFRTVVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEYK 375
+ S NR L TL EL G + + G PG+T +D + +KE+
Sbjct: 175 T----SFENRLNXLL-------TLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHD 221
Query: 376 FPQVHISQFYPRPGTPAARMKK 397
F V I F P P TP A KK
Sbjct: 222 FDMVGIGPFIPHPDTPLANEKK 243
>pdb|4I6L|A Chain A, Crystal Structure Of Otub1 In Complex With Ubiquitin
Variant
Length = 229
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 11/94 (11%)
Query: 272 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 330
PDG++ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 45 PDGNSFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 94
Query: 331 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 364
DF LIE V D++ F ++ D+
Sbjct: 95 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 128
>pdb|3VON|A Chain A, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|H Chain H, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|O Chain O, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|V Chain V, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|CC Chain c, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|JJ Chain j, Crystalstructure Of The Ubiquitin Protease
Length = 228
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 11/94 (11%)
Query: 272 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 330
PDG+ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 44 PDGNCFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 93
Query: 331 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 364
DF LIE V D++ F ++ D+
Sbjct: 94 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 127
>pdb|2ZFY|A Chain A, Crystal Structure Of Human Otubain 1
Length = 234
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 11/94 (11%)
Query: 272 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 330
PDG+ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 50 PDGNCFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 99
Query: 331 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 364
DF LIE V D++ F ++ D+
Sbjct: 100 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 133
>pdb|4DDG|A Chain A, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|B Chain B, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|C Chain C, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|J Chain J, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|K Chain K, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|L Chain L, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|A Chain A, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|B Chain B, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|C Chain C, Crystal Structure Of Human Otub1UBCH5B~UBUB
Length = 399
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 11/94 (11%)
Query: 272 PDGSTMLR-IGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLS 330
PDG++ R G ++ +L+ KE+ F V +S D V E+T+
Sbjct: 215 PDGNSFYRAFGFSHLEALLDDSKELQR---------FKAVSAKSKEDLVSQGFT-EFTIE 264
Query: 331 DFRTVVDTLIELVPGMQIATDIICGFPGETDEDF 364
DF LIE V D++ F ++ D+
Sbjct: 265 DFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDY 298
>pdb|3K1Q|D Chain D, Backbone Model Of An Aquareovirus Virion By Cryo-Electron
Microscopy And Bioinformatics
pdb|3K1Q|E Chain E, Backbone Model Of An Aquareovirus Virion By Cryo-Electron
Microscopy And Bioinformatics
pdb|3IYL|U Chain U, Atomic Cryoem Structure Of A Nonenveloped Virus Suggests
How Penetration Protein Is Primed For Cell Entry
pdb|3IYL|V Chain V, Atomic Cryoem Structure Of A Nonenveloped Virus Suggests
How Penetration Protein Is Primed For Cell Entry
Length = 412
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 274 GSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYSFLHVPVQSGSDAVLSAMNREYTLSDFR 333
G T G P F L L+E+A P F H+ + +GS V SA R +++
Sbjct: 8 GLTYNFYGQPAPLFDLNDLQELAGCYARPWTSRFSHLAISTGSLPVWSA--RYPSVASRN 65
Query: 334 TVVDTLI 340
VV+TL+
Sbjct: 66 IVVNTLL 72
>pdb|1UX8|A Chain A, X-Ray Structure Of Truncated Oxygen-Avid Haemoglobin From
Bacillus Subtilis
Length = 132
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 8/115 (6%)
Query: 335 VVDTLIELVPGMQIATDIICGFPGETDEDFNQTVNLIKEY-KFPQVHISQFYPRPGTPAA 393
+VDT E V + I FP + E + + +Y P ++ + G P
Sbjct: 20 LVDTFYERVASHPLLKPI---FPSDLTETARKQKQFLTQYLGGPPLYTEEH----GHPML 72
Query: 394 RMKKVPSAVVKKRSRELTSVFEAFTPYLGMEGRVERIWITEIAADGIHLVGHTKG 448
R + +P + +R+ S + ++G+EG + + H+V T+
Sbjct: 73 RARHLPFPITNERADAWLSCMKDAMDHVGLEGEIREFLFGRLELTARHMVNQTEA 127
>pdb|1UJO|A Chain A, Solution Structure Of The Ch Domain From Mouse Trangelin
Length = 144
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/63 (20%), Positives = 32/63 (50%)
Query: 247 DTGAYGRDIGVNLPILLNAIVAELPPDGSTMLRIGMTNPPFILEHLKEIAEVLRHPCVYS 306
D G G + + ++L+ +V L P+GS +++ P + + ++++A+ L+ Y
Sbjct: 30 DRGRLGFQVWLKNGVILSKLVNSLYPEGSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYG 89
Query: 307 FLH 309
+
Sbjct: 90 VIK 92
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 0.136 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,127,116
Number of Sequences: 62578
Number of extensions: 745744
Number of successful extensions: 1648
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1642
Number of HSP's gapped (non-prelim): 14
length of query: 629
length of database: 14,973,337
effective HSP length: 105
effective length of query: 524
effective length of database: 8,402,647
effective search space: 4402987028
effective search space used: 4402987028
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)