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= 004582
(744 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T1H|A Chain A, Nmr Solution Structure Of The U Box Domain From Atpub14,
An Armadillo Repeat Containing Protein From Arabidopsis
Thaliana
Length = 78
Score = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 40/77 (51%), Positives = 54/77 (70%)
Query: 257 GVLEPPEEFKCSISLRLMYDPVVIASGKTFERVWIQKWFNAGHTTCPKTHMRLDNVSVTP 316
G E PE F+C ISL LM DPV++++G+T+ER IQKW +AGH TCPK+ L + +TP
Sbjct: 1 GSPEFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTP 60
Query: 317 NVAIKELISQWCLKHGI 333
N +K LI+ WC +GI
Sbjct: 61 NYVLKSLIALWCESNGI 77
>pdb|2C2L|A Chain A, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|B Chain B, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|C Chain C, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|D Chain D, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
Length = 281
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 262 PEEFKCSISLRLMYDPVVIASGKTFERVWIQKWFN-AGHTTCPKTHMRLDNVSVTPNVAI 320
P+ IS LM +P + SG T++R I++ GH P T L + PN+A+
Sbjct: 206 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN-PVTRSPLTQEQLIPNLAM 264
Query: 321 KELISQWCLKHG 332
KE+I + ++G
Sbjct: 265 KEVIDAFISENG 276
>pdb|2C2V|S Chain S, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|T Chain T, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|U Chain U, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|V Chain V, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
Length = 78
Score = 36.2 bits (82), Expect = 0.072, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 262 PEEFKCSISLRLMYDPVVIASGKTFERVWIQKWFN-AGHTTCPKTHMRLDNVSVTPNVAI 320
P+ IS LM +P + SG T++R I++ GH P T L + PN+A+
Sbjct: 3 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN-PVTRSPLTQEQLIPNLAM 61
Query: 321 KELISQWCLKHG 332
KE+I + ++G
Sbjct: 62 KEVIDAFISENG 73
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 260 EPPEEFKCSISLRLMYDPVVIASGKTFERVWIQKWFN-AGHTTCPKTHMRLDNVSVTPNV 318
E P+ IS LM +P + SG T++R I++ GH P T L + PN+
Sbjct: 102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFD-PVTRSPLTQDQLIPNL 160
Query: 319 AIKELISQWCLKHG 332
A+KE+I + ++G
Sbjct: 161 AMKEVIDAFIQENG 174
>pdb|2OXQ|C Chain C, Structure Of The Ubch5 :chip U-Box Complex
pdb|2OXQ|D Chain D, Structure Of The Ubch5 :chip U-Box Complex
Length = 80
Score = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 260 EPPEEFKCSISLRLMYDPVVIASGKTFERVWIQKWFN-AGHTTCPKTHMRLDNVSVTPNV 318
E P+ IS LM +P + SG T++R I++ GH P T L + PN+
Sbjct: 9 EIPDYLCGKISFELMAEPCITPSGITYDRKDIEEHLQRVGHFD-PVTRSPLTQDQLIPNL 67
Query: 319 AIKELI 324
A+KE+I
Sbjct: 68 AMKEVI 73
>pdb|4FBK|A Chain A, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With One Manganese Ion Per Active Site
pdb|4FBK|B Chain B, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With One Manganese Ion Per Active Site
pdb|4FBQ|A Chain A, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With Two Manganese Ions Per Active Site
pdb|4FBQ|B Chain B, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With Two Manganese Ions Per Active Site
Length = 472
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 34/79 (43%), Gaps = 1/79 (1%)
Query: 448 KDNGQSRHLAFLNSYVKPLIKFLKDAHNLCDAKAQKDGAEVLLAILSQSRDEMPLFHKDE 507
K N SRH + S K KF K A D A G+E + IL S + KD
Sbjct: 35 KSNANSRHTSKYYSGRKNFKKFQKKASQKVDGSAGSAGSENTIRILISSDPHVGYGEKDP 94
Query: 508 ICTFALFLD-SEIMEEALE 525
+ F+ +EI+E A E
Sbjct: 95 VRGNDSFVSFNEILEIARE 113
>pdb|2KRE|A Chain A, Solution Structure Of E4bUFD2A U-Box Domain
pdb|3L1X|A Chain A, Crystal Structure Of U-Box Domain Of Human E4b Ubiquitin
Ligase
pdb|3L1Z|B Chain B, Crystal Structure Of The U-Box Domain Of Human E4b
Ubiquitin Ligase In Complex With Ubch5c E2 Ubiquitin
Conjugating Enzyme
Length = 100
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 262 PEEFKCSISLRLMYDPVVIASGKTFER-VWIQKWFNAGHTTCPKTHMRLDNVSVTPNVAI 320
P+EF+ + LM DPV + SG +R + ++ N+ T P L + P +
Sbjct: 27 PDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNS--PTDPFNRQTLTESMLEPVPEL 84
Query: 321 KELISQWC 328
KE I W
Sbjct: 85 KEQIQAWM 92
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 256 SGVLEPPE-EFKCSISLRLMYDPVVIASGKTFERVWIQKWF 295
SG LE + E CS+ L + +PV+I G F + I +W+
Sbjct: 6 SGALENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWW 46
>pdb|1WGM|A Chain A, Solution Structure Of The U-Box In Human Ubiquitin
Conjugation Factor E4a
Length = 98
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 263 EEFKCSISLRLMYDPVVIASGK-TFERVWIQKWFNAGHTTCPKTHMRLDNVSVTPNVAIK 321
+EF I LM DPVV+ S + T +R I + + T P L + PN +K
Sbjct: 21 DEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTD-PFNRSPLTMDQIRPNTELK 79
Query: 322 ELISQW 327
E I +W
Sbjct: 80 EKIQRW 85
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 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,756,331
Number of Sequences: 62578
Number of extensions: 745471
Number of successful extensions: 1610
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1604
Number of HSP's gapped (non-prelim): 11
length of query: 744
length of database: 14,973,337
effective HSP length: 106
effective length of query: 638
effective length of database: 8,340,069
effective search space: 5320964022
effective search space used: 5320964022
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: 55 (25.8 bits)