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= 010753
(502 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YUJ|A Chain A, Solution Structure Of Human Ubiquitin Fusion Degradation
Protein 1 Homolog Ufd1
Length = 190
Score = 115 bits (288), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 67/167 (40%), Positives = 91/167 (54%), Gaps = 18/167 (10%)
Query: 91 GDKIKLPPSCFTELSGQGAFDKGPLHFKLSVLHQEGPSNMEDGEKESNRSTHSGVLEFTA 150
G KI +PPS +LS P+ FKL+ K S+R TH GVLEF A
Sbjct: 40 GGKIIMPPSALDQLSRLNI--TYPMLFKLT-------------NKNSDRMTHCGVLEFVA 84
Query: 151 DEGFVGLPPHVWRNLFPSDTPNNSFVEVRYVRLPKGTYAKLQPEGIGFAELPNQKAVLET 210
DEG LP + +NL + V+V V L TY+K QP+ F ++ N KAVLE
Sbjct: 85 DEGICYLPHWMMQNLLLEE---GGLVQVESVNLQVATYSKFQPQSPDFLDITNPKAVLEN 141
Query: 211 SLRQHATLSQDDVLTVNYGELAYKLKVLELKPSSSVSVLETDIEVDI 257
+LR A L+ DV+ +NY E Y+L+V+E KP +VS++E D+ VD
Sbjct: 142 ALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDF 188
>pdb|1ZC1|A Chain A, Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct
Ubiquitin Interaction Sites
Length = 208
Score = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 63/173 (36%), Positives = 94/173 (54%), Gaps = 21/173 (12%)
Query: 91 GDKIKLPPSCFTELSGQGAFDKGPLHFKLSVLHQEGPSNMEDGEKESNRSTHSGVLEFTA 150
G KI LPPS ++LS + P+ FKL+ E+ R TH GVLEF A
Sbjct: 45 GGKIFLPPSALSKLSMLNI--RYPMLFKLTA-------------NETGRVTHGGVLEFIA 89
Query: 151 DEGFVGLPPHVWRNLFPSDTPNNSFVEVRYVRLPKGTYAKLQPEGIGFAELPNQKAVLET 210
+EG V LP + L S +++ +P G + KL+P+ + F ++ + KAVLE
Sbjct: 90 EEGRVYLPQWMMETL---GIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLEN 146
Query: 211 SLRQHATLSQDDVLTVNYGELAYKLKVLELKP---SSSVSVLETDIEVDIVSP 260
LR +TL+ DDV+ ++Y +K+K+LE+KP S S+ V+ETD+ D P
Sbjct: 147 VLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPP 199
>pdb|2R8J|A Chain A, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
pdb|2R8J|B Chain B, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
pdb|2R8K|A Chain A, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
pdb|2R8K|B Chain B, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
Length = 554
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 408 MDTVQ--CKNCKRFIPSRSIVLHEAYCSRHSVACQHAGCGMVLRTEEARDHVHCDKCGQG 465
MDT+Q K C IP + V + H GCG ++ + V K
Sbjct: 97 MDTIQEALKKCSNLIPIHTAVFKKG----EDFWQYHDGCGSWVQDPAKQISVEDHKVSLE 152
Query: 466 LQRREMEKHMKVFHEQC 482
RRE K +K+F C
Sbjct: 153 PYRRESRKALKIFKSAC 169
>pdb|2WTF|A Chain A, Dna Polymerase Eta In Complex With The
Cis-Diammineplatinum (Ii) 1,3-Gtg Intrastrand Cross-Link
pdb|2WTF|B Chain B, Dna Polymerase Eta In Complex With The
Cis-Diammineplatinum (Ii) 1,3-Gtg Intrastrand Cross-Link
pdb|2XGP|A Chain A, Yeast Dna Polymerase Eta In Complex With C8-2-
Acetylaminofluorene Containing Dna
pdb|2XGP|B Chain B, Yeast Dna Polymerase Eta In Complex With C8-2-
Acetylaminofluorene Containing Dna
pdb|2XGQ|A Chain A, Structure Of Yeast Dna Polymerase Eta In Complex With
C8-N- Acetyl-2-Aminoanthracene Containing Dna
pdb|2XGQ|B Chain B, Structure Of Yeast Dna Polymerase Eta In Complex With
C8-N- Acetyl-2-Aminoanthracene Containing Dna
Length = 536
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 408 MDTVQ--CKNCKRFIPSRSIVLHEAYCSRHSVACQHAGCGMVLRTEEARDHVHCDKCGQG 465
MDT+Q K C IP + V + H GCG ++ + V K
Sbjct: 97 MDTIQEALKKCSNLIPIHTAVFKKG----EDFWQYHDGCGSWVQDPAKQISVEDHKVSLE 152
Query: 466 LQRREMEKHMKVFHEQC 482
RRE K +K+F C
Sbjct: 153 PYRRESRKALKIFKSAC 169
>pdb|1JIH|A Chain A, Yeast Dna Polymerase Eta
pdb|1JIH|B Chain B, Yeast Dna Polymerase Eta
Length = 513
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 408 MDTVQ--CKNCKRFIPSRSIVLHEAYCSRHSVACQHAGCGMVLRTEEARDHVHCDKCGQG 465
MDT+Q K C IP + V + H GCG ++ + V K
Sbjct: 74 MDTIQEALKKCSNLIPIHTAVFKKG----EDFWQYHDGCGSWVQDPAKQISVEDHKVSLE 129
Query: 466 LQRREMEKHMKVFHEQC 482
RRE K +K+F C
Sbjct: 130 PYRRESRKALKIFKSAC 146
>pdb|3HUR|A Chain A, Crystal Structure Of Alanine Racemase From Oenococcus Oeni
Length = 395
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 169 DTPNNSFVEVRYVRLPKGTYAKLQPEGIGFAELPNQKAVLETSLRQHATLSQ-DDVLTVN 227
D ++ E+R K YA L+ +G G +P KA ET+ +S D+ L +
Sbjct: 17 DAAAHNLQEIREWTKAKKVYAVLKADGYGLGAIPLAKAFQETASADALIVSNLDEALELR 76
Query: 228 YGELAYKLKVL 238
+L + VL
Sbjct: 77 QADLTLPIWVL 87
>pdb|2FMD|A Chain A, Structural Basis Of Carbohydrate Recognition By Bowringia
Milbraedii Seed Agglutinin
Length = 240
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 226 VNYGELAYKLKVLELKPSSSVSVLETDIEVDIVSPD----DMSAGTDQYT 271
++Y + +L V+ P+SS V+ D+E++ V P SA T QYT
Sbjct: 171 ISYNSASKRLSVVSSYPNSSPVVVSFDVELNNVXPXWVRVGFSATTGQYT 220
>pdb|3A25|A Chain A, Crystal Structure Of P. Horikoshii Tyw2 In Complex With
Adomet
pdb|3A26|A Chain A, Crystal Structure Of P. Horikoshii Tyw2 In Complex With
Mesado
Length = 301
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 14/114 (12%)
Query: 198 FAELPNQKAVL-------ETSLRQHATLSQDDVLTVNYGE-LAYKLKVLELKPSSSVSVL 249
+AE+ K VL ET + L D +TV+ + YKL V ++ S + +V
Sbjct: 79 YAEVLGVKTVLRKGHIHGETRKPDYELLYGSDTVTVHVENGIKYKLDVAKIMFSPA-NVK 137
Query: 250 ETDIEVDIVSPD----DMSAGTDQYTLKPLLFGKSESGMVEEGKYVFYKFTIDD 299
E + PD DM AG +L ++GK++ +E+ Y F KF +++
Sbjct: 138 ERVRMAKVAKPDELVVDMFAGIGHLSLPIAVYGKAKVIAIEKDPYTF-KFLVEN 190
>pdb|1UBD|C Chain C, Co-Crystal Structure Of Human Yy1 Zinc Finger Domain Bound
To The Adeno-Associated Virus P5 Initiator Element
Length = 124
Score = 28.9 bits (63), Expect = 6.2, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 436 SVACQHAGCGMVLRTEEA-RDHVH--------CDKCGQGLQRREMEKHMKVFH 479
++AC H GC + R A R H+H C +CG+ K ++ H
Sbjct: 5 TIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVH 57
>pdb|2D2I|A Chain A, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|B Chain B, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|O Chain O, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|P Chain P, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|Q Chain Q, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|R Chain R, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2DUU|A Chain A, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|B Chain B, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|O Chain O, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|P Chain P, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|Q Chain Q, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|R Chain R, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp
Length = 380
Score = 28.9 bits (63), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 25/89 (28%)
Query: 306 VSGEKRAEVRVDSE---IDGGDTSIYVSRHPLLFPTRHLHEW------------------ 344
V G A++ D ++G I R+PL P + EW
Sbjct: 52 VLGRFNADISYDENSITVNGKTMKIVCDRNPLNLPWK---EWDIDLVIESTGVFVTAEGA 108
Query: 345 SSH-DAGSKVVILSSKDKSVDVGTYSIGV 372
S H AG+K V++++ K+ VGTY IGV
Sbjct: 109 SKHIQAGAKKVLITAPGKAEGVGTYVIGV 137
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 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,665,326
Number of Sequences: 62578
Number of extensions: 587451
Number of successful extensions: 1164
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1158
Number of HSP's gapped (non-prelim): 15
length of query: 502
length of database: 14,973,337
effective HSP length: 103
effective length of query: 399
effective length of database: 8,527,803
effective search space: 3402593397
effective search space used: 3402593397
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)