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= 030016
(184 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TMP|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|C Chain C, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|E Chain E, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
pdb|3TMP|G Chain G, The Catalytic Domain Of Human Deubiquitinase Duba In
Complex With Ubiquitin Aldehyde
Length = 184
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/102 (22%), Positives = 45/102 (44%), Gaps = 8/102 (7%)
Query: 3 VQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRH---- 58
+ Y++KN + F ++ +D F Y + H+E+QA + + + + ++++
Sbjct: 81 MDYLMKNADYFSNYVTED--FTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGT 138
Query: 59 --MSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIG 98
+ P +E I +SYH HYN V + IG
Sbjct: 139 SAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKATIG 180
>pdb|3TMO|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba
Length = 184
Score = 30.0 bits (66), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 8/100 (8%)
Query: 5 YIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRH------ 58
Y+ KN + F ++ +D F Y + H+E QA + + + ++++
Sbjct: 83 YLXKNADYFSNYVTED--FTTYINRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTGTSA 140
Query: 59 MSPRWYIRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIG 98
+ P +E I +SYH HYN V + IG
Sbjct: 141 VEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKATIG 180
>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
Length = 185
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 3/86 (3%)
Query: 5 YIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS-PRW 63
Y+ KN + F ++ +D F Y + H+E QA + + + ++++ + P
Sbjct: 96 YLXKNADYFSNYVTED--FTTYINRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTEPIN 153
Query: 64 YIRNFDYHEARMIHLSYHDGEHYNGV 89
+E I +SYH HYN V
Sbjct: 154 TFHGIHQNEDEPIRVSYHRNIHYNSV 179
>pdb|4DHZ|A Chain A, The Structure Of HCEOTUB1-Ubiquitin Aldehyde-Ubc13~ub
Length = 288
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 47/104 (45%), Gaps = 12/104 (11%)
Query: 5 YIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIH-----RHM 59
++ +N E + PFI++ + +YC+ E + W L SL+ + + R
Sbjct: 184 FLKQNSEEYAPFIDEGMTVAQYCEQ-EIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTA 242
Query: 60 SPR--WY--IRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGS 99
+P W+ I + D A I L Y G HY+ V K+DS S
Sbjct: 243 APNGGWHYDIPSDDQQIAPEITLLYRPG-HYD-VIYKKDSTEAS 284
>pdb|4DHI|B Chain B, Structure Of C. Elegans Otub1 Bound To Human Ubc13
pdb|4DHJ|A Chain A, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
pdb|4DHJ|E Chain E, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
pdb|4DHJ|I Chain I, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
pdb|4DHJ|L Chain L, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
Length = 284
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 47/104 (45%), Gaps = 12/104 (11%)
Query: 5 YIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIH-----RHM 59
++ +N E + PFI++ + +YC+ E + W L SL+ + + R
Sbjct: 180 FLKQNSEEYAPFIDEGMTVAQYCEQ-EIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTA 238
Query: 60 SPR--WY--IRNFDYHEARMIHLSYHDGEHYNGVRLKEDSCIGS 99
+P W+ I + D A I L Y G HY+ V K+DS S
Sbjct: 239 APNGGWHYDIPSDDQQIAPEITLLYRPG-HYD-VIYKKDSTEAS 280
>pdb|2KNZ|A Chain A, Nmr Structure Of Cip75 Uba Domain
Length = 53
Score = 27.7 bits (60), Expect = 3.9, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 148 NSEKVEEVLLQVGGDVDAAIEFLIAEQ 174
N E + L+ GGD++AAIE L+ Q
Sbjct: 25 NREANLQALIATGGDINAAIERLLGSQ 51
>pdb|3S5N|A Chain A, Crystal Structure Of Human 4-Hydroxy-2-Oxoglutarate
Aldolase
Length = 304
Score = 27.3 bits (59), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 20/28 (71%), Gaps = 3/28 (10%)
Query: 138 KLVMAGSGCENSEKVEEV---LLQVGGD 162
+L++AGSGCE+++ E+ + QVG D
Sbjct: 81 RLLLAGSGCESTQATVEMTVSMAQVGAD 108
>pdb|3S5O|A Chain A, Crystal Structure Of Human 4-Hydroxy-2-Oxoglutarate
Aldolase Bound To Pyruvate
Length = 307
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 20/28 (71%), Gaps = 3/28 (10%)
Query: 138 KLVMAGSGCENSEKVEEV---LLQVGGD 162
+L++AGSGCE+++ E+ + QVG D
Sbjct: 84 RLLLAGSGCESTQATVEMTVSMAQVGAD 111
>pdb|3BWW|A Chain A, Crystal Structure Of A Duf692 Family Protein (Hs_1138)
From Haemophilus Somnus 129pt At 2.20 A Resolution
Length = 307
Score = 26.6 bits (57), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 52 NICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEH 85
N H + P +I N D IH++ HD EH
Sbjct: 179 NAVNHGLLDPHVFIDNVDLKRVNYIHIAGHDDEH 212
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 0.133 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,118,772
Number of Sequences: 62578
Number of extensions: 181970
Number of successful extensions: 422
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 417
Number of HSP's gapped (non-prelim): 12
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
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: 48 (23.1 bits)