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= 028178
(212 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1EK5|A Chain A, Structure Of Human Udp-Galactose 4-Epimerase In Complex
With Nad+
pdb|1EK6|A Chain A, Structure Of Human Udp-Galactose 4-Epimerase Complexed
With Nadh And Udp-Glucose
pdb|1EK6|B Chain B, Structure Of Human Udp-Galactose 4-Epimerase Complexed
With Nadh And Udp-Glucose
Length = 348
Score = 30.8 bits (68), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 77 SIVRALKGTSGDKFVFK--APRSGMYQFCFHNPTSTPEEVSFYIHIGHIPNEHDLAKDEH 134
+V+A++ SG K +K A R G C+ NP+ EE+ + +G DL + +
Sbjct: 279 QMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQK 338
Query: 135 LDP 137
+P
Sbjct: 339 QNP 341
>pdb|1I3K|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3K|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3L|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3L|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3M|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3M|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3N|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3N|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
Length = 348
Score = 30.8 bits (68), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 77 SIVRALKGTSGDKFVFK--APRSGMYQFCFHNPTSTPEEVSFYIHIGHIPNEHDLAKDEH 134
+V+A++ SG K +K A R G C+ NP+ EE+ + +G DL + +
Sbjct: 279 QMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQK 338
Query: 135 LDP 137
+P
Sbjct: 339 QNP 341
>pdb|1HZJ|A Chain A, Human Udp-Galactose 4-Epimerase: Accommodation Of Udp-N-
Acetylglucosamine Within The Active Site
pdb|1HZJ|B Chain B, Human Udp-Galactose 4-Epimerase: Accommodation Of Udp-N-
Acetylglucosamine Within The Active Site
Length = 348
Score = 30.8 bits (68), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 77 SIVRALKGTSGDKFVFK--APRSGMYQFCFHNPTSTPEEVSFYIHIGHIPNEHDLAKDEH 134
+V+A++ SG K +K A R G C+ NP+ EE+ + +G DL + +
Sbjct: 279 QMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQK 338
Query: 135 LDP 137
+P
Sbjct: 339 QNP 341
>pdb|3RWM|B Chain B, Crystal Structure Of Ypt32 In Complex With Gppnhp
pdb|3RWO|B Chain B, Crystal Structure Of Ypt32 In Complex With Gdp
pdb|3RWO|A Chain A, Crystal Structure Of Ypt32 In Complex With Gdp
Length = 185
Score = 30.0 bits (66), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 83 KGTSGDKFVFKAPRSGMYQFCFHNPTSTPEEVSFYIHIGHIPNEHDLA 130
+G G V+ +S Y+ C H T E + +G I N+ DLA
Sbjct: 81 RGAVGALIVYDISKSSSYENCNHWLTELRENADDNVAVGLIGNKSDLA 128
>pdb|2R7G|A Chain A, Structure Of The Retinoblastoma Protein Pocket Domain In
Complex With Adenovirus E1a Cr1 Domain
pdb|2R7G|C Chain C, Structure Of The Retinoblastoma Protein Pocket Domain In
Complex With Adenovirus E1a Cr1 Domain
Length = 347
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 41/149 (27%), Positives = 56/149 (37%), Gaps = 16/149 (10%)
Query: 4 RSAQVCLVIGFILSFIRHVSTLSITVTDTECVYEHVIYKEDTITGNVFVTTD-------H 56
RS L G LSF ++ L++ D V E I E +T + +
Sbjct: 121 RSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIME 180
Query: 57 ELFWNSDHPGIDFTVTCPDGSIVRALKGTSGDKFVFKAPRSG---MYQFCFHNPTSTPE- 112
L W SD P D D R K TS F K R + C + PE
Sbjct: 181 SLAWLSDSPLFDLIKQSKD----REGKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPEL 236
Query: 113 EVSFYIHIGH-IPNEHDLAKDEHLDPIYV 140
E + H + NE++L +D HLD I +
Sbjct: 237 EHIIWTLFQHTLQNEYELMRDRHLDQIMM 265
>pdb|4ELJ|A Chain A, Crystal Structure Of The Inactive Retinoblastoma Protein
Phosphorylated At T373
Length = 656
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 41/149 (27%), Positives = 56/149 (37%), Gaps = 14/149 (9%)
Query: 4 RSAQVCLVIGFILSFIRHVSTLSITVTDTECVYEHVIYKEDTITGNVFVTTD-------H 56
RS L G LSF ++ L++ D V E I E +T + +
Sbjct: 428 RSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIME 487
Query: 57 ELFWNSDHPGIDFTVTCPDGSIVRALKGTSGDKFVFKAPRSG---MYQFCFHNPTSTPE- 112
L W SD P D D LK TS F K R + C + PE
Sbjct: 488 SLAWLSDSPLFDLIKQSKDRE--GPLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPEL 545
Query: 113 EVSFYIHIGH-IPNEHDLAKDEHLDPIYV 140
E + H + NE++L +D HLD I +
Sbjct: 546 EHIIWTLFQHTLQNEYELMRDRHLDQIMM 574
>pdb|3POM|A Chain A, Crystal Structure Of The Unliganded Retinoblastoma Protein
Pocket Domain
pdb|3POM|B Chain B, Crystal Structure Of The Unliganded Retinoblastoma Protein
Pocket Domain
Length = 352
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 58/152 (38%), Gaps = 20/152 (13%)
Query: 4 RSAQVCLVIGFILSFIRHVSTLSITVTDTECVYEHVIYKEDTITGNVFVTTD-------H 56
RS L G LSF ++ L++ D V E I E +T + +
Sbjct: 124 RSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIME 183
Query: 57 ELFWNSDHPGIDF---TVTCPDGSIVRALKGTSGDKFVFKAPRSG---MYQFCFHNPTST 110
L W SD P D + P GS K TS F K R + C +
Sbjct: 184 SLAWLSDSPLFDLIKQSKLVPRGS-----KSTSLSLFYKKVYRLAYLRLNTLCERLLSEH 238
Query: 111 PE-EVSFYIHIGH-IPNEHDLAKDEHLDPIYV 140
PE E + H + NE++L +D HLD I +
Sbjct: 239 PELEHIIWTLFQHTLQNEYELMRDRHLDQIMM 270
>pdb|1N4M|A Chain A, Structure Of Rb Tumor Suppressor Bound To The
Transactivation Domain Of E2f-2
pdb|1N4M|B Chain B, Structure Of Rb Tumor Suppressor Bound To The
Transactivation Domain Of E2f-2
Length = 345
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 41/149 (27%), Positives = 56/149 (37%), Gaps = 16/149 (10%)
Query: 4 RSAQVCLVIGFILSFIRHVSTLSITVTDTECVYEHVIYKEDTITGNVFVTTD-------H 56
RS L G LSF ++ L++ D V E I E +T + +
Sbjct: 121 RSTSQNLDSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIME 180
Query: 57 ELFWNSDHPGIDFTVTCPDGSIVRALKGTSGDKFVFKAPRSG---MYQFCFHNPTSTPE- 112
L W SD P D S R K TS F K R + C + PE
Sbjct: 181 SLAWLSDSPLFDLI----KQSKTREGKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPEL 236
Query: 113 EVSFYIHIGH-IPNEHDLAKDEHLDPIYV 140
E + H + NE++L +D HLD I +
Sbjct: 237 EHIIWTLFQHTLQNEYELMRDRHLDQIMM 265
>pdb|1QDM|A Chain A, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley
Vacuolar Aspartic Proteinase.
pdb|1QDM|B Chain B, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley
Vacuolar Aspartic Proteinase.
pdb|1QDM|C Chain C, Crystal Structure Of Prophytepsin, A Zymogen Of A Barley
Vacuolar Aspartic Proteinase
Length = 478
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 22/51 (43%)
Query: 41 YKEDTITGNVFVTTDHELFWNSDHPGIDFTVTCPDGSIVRALKGTSGDKFV 91
+ ED++T V D E + PGI F V DG + K S K V
Sbjct: 125 FSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAV 175
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
0.323 0.137 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,070,177
Number of Sequences: 62578
Number of extensions: 247523
Number of successful extensions: 656
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 654
Number of HSP's gapped (non-prelim): 10
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)