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= 041127
(285 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 742
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 54/270 (20%), Positives = 111/270 (41%), Gaps = 31/270 (11%)
Query: 13 DYLERGFTKLKRIFEGLQERA---FNLEDYMMLYTIVYDICCKPARPHHDEDPDQMYDKY 69
+Y + + KL +Q +NLE+ LY V ++C P +Y +
Sbjct: 40 NYTQDTWRKLHEAVRAVQSSTSIRYNLEE---LYQAVENLCSHKVSP-------MLYKQL 89
Query: 70 QQILADYMPSKVLPYLREKHDEYDLLRELLKSWANHKFLAKWLSRVFLPLQAGYI-PRMA 128
+Q D++ +++LP+ + D L+++ W +H + +FL L Y+
Sbjct: 90 RQACEDHVQAQILPFREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNST 149
Query: 129 LPELNAFGISCFRDLVF--EAMKDKVKDAVVALXXXXXXXXXXXXTLVKNVLDLFVE--- 183
LP + G+ FR + + ++ K D ++ L +L++++L + +
Sbjct: 150 LPSIWDMGLELFRTHIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDLQV 209
Query: 184 ---------IEDMAAYYSRKASNWILQDSF-DYLVNVGECLKNERERASHYLQPSSNRKL 233
+E+ Y+ + + + +YL +V + L+ E +R YL S+ + L
Sbjct: 210 YKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPL 269
Query: 234 ANILSFMQKGEFRCRQLLRG--HKLDGHSI 261
+ GE L +G H LD + +
Sbjct: 270 IACVEKQLLGEHLTAILQKGLDHLLDENRV 299
>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 759
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 54/270 (20%), Positives = 111/270 (41%), Gaps = 31/270 (11%)
Query: 13 DYLERGFTKLKRIFEGLQERA---FNLEDYMMLYTIVYDICCKPARPHHDEDPDQMYDKY 69
+Y + + KL +Q +NLE+ LY V ++C P +Y +
Sbjct: 57 NYTQDTWRKLHEAVRAVQSSTSIRYNLEE---LYQAVENLCSHKVSP-------MLYKQL 106
Query: 70 QQILADYMPSKVLPYLREKHDEYDLLRELLKSWANHKFLAKWLSRVFLPLQAGYI-PRMA 128
+Q D++ +++LP+ + D L+++ W +H + +FL L Y+
Sbjct: 107 RQACEDHVQAQILPFREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNST 166
Query: 129 LPELNAFGISCFRDLVF--EAMKDKVKDAVVALXXXXXXXXXXXXTLVKNVLDLFVE--- 183
LP + G+ FR + + ++ K D ++ L +L++++L + +
Sbjct: 167 LPSIWDMGLELFRTHIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDLQV 226
Query: 184 ---------IEDMAAYYSRKASNWILQDSF-DYLVNVGECLKNERERASHYLQPSSNRKL 233
+E+ Y+ + + + +YL +V + L+ E +R YL S+ + L
Sbjct: 227 YKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPL 286
Query: 234 ANILSFMQKGEFRCRQLLRG--HKLDGHSI 261
+ GE L +G H LD + +
Sbjct: 287 IACVEKQLLGEHLTAILQKGLDHLLDENRV 316
>pdb|1LDK|A Chain A, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 396
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 48/251 (19%), Positives = 100/251 (39%), Gaps = 59/251 (23%)
Query: 39 YMMLYTIVYDICCK-------------PARPHHDEDPD-------QMYDKYQQILADYMP 78
YM LYT VY+ C P++ + P ++Y + ++ L +Y+
Sbjct: 28 YMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLT 87
Query: 79 SKVLPYLREKHDEYD--LLRELLKSWANHKFLAKWLSRVFLPLQAGYI------PRMALP 130
+ L++ D D +L+ + W +++F +K L+ + L ++ R +
Sbjct: 88 N----LLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIY 143
Query: 131 ELNAFGISCFRDLVFEAMKDKVKDAVVALXXXXXXXXXXXXTLVKNVLDLFVE------- 183
E+ + + +RD +F + +V +AV+ L L+ V+ +VE
Sbjct: 144 EIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDD 203
Query: 184 -------------------IEDMAAYYSRKASNWILQDSF-DYLVNVGECLKNERERASH 223
+ D +Y+R+++ ++ Q+ +Y+ L E+ R
Sbjct: 204 AFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQV 263
Query: 224 YLQPSSNRKLA 234
YL S+ +LA
Sbjct: 264 YLHESTQDELA 274
>pdb|1LDJ|A Chain A, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 760
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 48/251 (19%), Positives = 100/251 (39%), Gaps = 59/251 (23%)
Query: 39 YMMLYTIVYDICCK-------------PARPHHDEDPD-------QMYDKYQQILADYMP 78
YM LYT VY+ C P++ + P ++Y + ++ L +Y+
Sbjct: 26 YMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLT 85
Query: 79 SKVLPYLREKHDEYD--LLRELLKSWANHKFLAKWLSRVFLPLQAGYI------PRMALP 130
+ L++ D D +L+ + W +++F +K L+ + L ++ R +
Sbjct: 86 N----LLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIY 141
Query: 131 ELNAFGISCFRDLVFEAMKDKVKDAVVALXXXXXXXXXXXXTLVKNVLDLFVE------- 183
E+ + + +RD +F + +V +AV+ L L+ V+ +VE
Sbjct: 142 EIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDD 201
Query: 184 -------------------IEDMAAYYSRKASNWILQDSF-DYLVNVGECLKNERERASH 223
+ D +Y+R+++ ++ Q+ +Y+ L E+ R
Sbjct: 202 AFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQV 261
Query: 224 YLQPSSNRKLA 234
YL S+ +LA
Sbjct: 262 YLHESTQDELA 272
>pdb|1U6G|A Chain A, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
Length = 776
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 48/251 (19%), Positives = 100/251 (39%), Gaps = 59/251 (23%)
Query: 39 YMMLYTIVYDICCK-------------PARPHHDEDPD-------QMYDKYQQILADYMP 78
YM LYT VY+ C P++ + P ++Y + ++ L +Y+
Sbjct: 42 YMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLT 101
Query: 79 SKVLPYLREKHDEYD--LLRELLKSWANHKFLAKWLSRVFLPLQAGYI------PRMALP 130
+ L++ D D +L+ + W +++F +K L+ + L ++ R +
Sbjct: 102 N----LLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIY 157
Query: 131 ELNAFGISCFRDLVFEAMKDKVKDAVVALXXXXXXXXXXXXTLVKNVLDLFVE------- 183
E+ + + +RD +F + +V +AV+ L L+ V+ +VE
Sbjct: 158 EIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDD 217
Query: 184 -------------------IEDMAAYYSRKASNWILQDSF-DYLVNVGECLKNERERASH 223
+ D +Y+R+++ ++ Q+ +Y+ L E+ R
Sbjct: 218 AFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQV 277
Query: 224 YLQPSSNRKLA 234
YL S+ +LA
Sbjct: 278 YLHESTQDELA 288
>pdb|4A64|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
pdb|4A64|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
pdb|4A64|C Chain C, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
pdb|4A64|D Chain D, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
Length = 354
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 71/153 (46%), Gaps = 16/153 (10%)
Query: 13 DYLERGFTKLKRIFEGLQERA---FNLEDYMMLYTIVYDICCKPARPHHDEDPDQMYDKY 69
+Y + + KLK E +Q +NLE+ LY V ++C + +Y +
Sbjct: 8 NYTDETWQKLKEAVEAIQNSTSIKYNLEE---LYQAVENLCSYKISAN-------LYKQL 57
Query: 70 QQILADYMPSKVLPYLREKHDEYDLLRELLKSWANHKFLAKWLSRVFLPLQAGYIPRMA- 128
+QI D++ +++ + + D L+++ + W NH + +FL L Y+ + +
Sbjct: 58 RQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIFLFLDRTYVLQNSM 117
Query: 129 LPELNAFGISCFRDLVF--EAMKDKVKDAVVAL 159
LP + G+ FR + + +++K D ++ L
Sbjct: 118 LPSIWDMGLELFRAHIISDQKVQNKTIDGILLL 150
>pdb|4A0L|E Chain E, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|H Chain H, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 726
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 71/153 (46%), Gaps = 16/153 (10%)
Query: 13 DYLERGFTKLKRIFEGLQERA---FNLEDYMMLYTIVYDICCKPARPHHDEDPDQMYDKY 69
+Y + + KLK E +Q +NLE+ LY V ++C + +Y +
Sbjct: 24 NYTDETWQKLKEAVEAIQNSTSIKYNLEE---LYQAVENLCSYKISAN-------LYKQL 73
Query: 70 QQILADYMPSKVLPYLREKHDEYDLLRELLKSWANHKFLAKWLSRVFLPLQAGYIPRMA- 128
+QI D++ +++ + + D L+++ + W NH + +FL L Y+ + +
Sbjct: 74 RQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIFLFLDRTYVLQNSM 133
Query: 129 LPELNAFGISCFRDLVF--EAMKDKVKDAVVAL 159
LP + G+ FR + + +++K D ++ L
Sbjct: 134 LPSIWDMGLELFRAHIISDQKVQNKTIDGILLL 166
>pdb|4A0C|C Chain C, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|E Chain E, Structure Of The Cand1-Cul4b-Rbx1 Complex
Length = 741
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 71/153 (46%), Gaps = 16/153 (10%)
Query: 13 DYLERGFTKLKRIFEGLQERA---FNLEDYMMLYTIVYDICCKPARPHHDEDPDQMYDKY 69
+Y + + KLK E +Q +NLE+ LY V ++C + +Y +
Sbjct: 39 NYTDETWQKLKEAVEAIQNSTSIKYNLEE---LYQAVENLCSYKISAN-------LYKQL 88
Query: 70 QQILADYMPSKVLPYLREKHDEYDLLRELLKSWANHKFLAKWLSRVFLPLQAGYIPRMA- 128
+QI D++ +++ + + D L+++ + W NH + +FL L Y+ + +
Sbjct: 89 RQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIFLFLDRTYVLQNSM 148
Query: 129 LPELNAFGISCFRDLVF--EAMKDKVKDAVVAL 159
LP + G+ FR + + +++K D ++ L
Sbjct: 149 LPSIWDMGLELFRAHIISDQKVQNKTIDGILLL 181
>pdb|4EX4|A Chain A, The Structure Of Glcb From Mycobacterium Leprae
pdb|4EX4|B Chain B, The Structure Of Glcb From Mycobacterium Leprae
Length = 735
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 42/98 (42%), Gaps = 13/98 (13%)
Query: 45 IVYDICCKPARPHHDEDPDQMYDKYQQILADYMPSKVLPYLREKHDEYDLLRELLKSWAN 104
++YD A P D +P+ + +++AD P L DE L+ + W
Sbjct: 19 VLYDFVNNEALPGTDINPNSFWSGVAKVVADLTPQN--QSLLNSRDE---LQAQIDKWHR 73
Query: 105 HKFLAKW---LSRVFLPLQAGYIPRMALPELNAFGISC 139
H+ + + R FL + GY+ LPE + F IS
Sbjct: 74 HRVIEPFDVDAYRQFL-IDIGYL----LPEPDDFTIST 106
>pdb|2HL1|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'- Aminoadenosine
pdb|2HL1|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'- Aminoadenosine
pdb|3PD2|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'-Aminoadenosine
pdb|3PD2|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'-Aminoadenosine
pdb|3PD3|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Threonyl-3'-Aminoadenosine
pdb|3PD3|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Threonyl-3'-Aminoadenosine
pdb|3PD4|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Glycyl-3'-Aminoadenosine
pdb|3PD4|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
Glycyl-3'-Aminoadenosine
pdb|3PD5|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Threonyl- Adenylate
pdb|3PD5|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Threonyl- Adenylate
Length = 147
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 22 LKRIFEGLQERAFNLEDYMMLYTIVYDICCK 52
L R+++GL+ER FN+ Y + I CK
Sbjct: 98 LNRVYQGLKERGFNVGKAPFGYYKAFKISCK 128
>pdb|1Y2Q|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi
pdb|2HKZ|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With
L-Serine
pdb|2HL0|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-trna
Synthetase From Pyrococcus Abyssi In Complex With
Seryl-3'- Aminoadenosine
pdb|2HL2|A Chain A, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Seryladenylate
pdb|2HL2|B Chain B, Crystal Structure Of The Editing Domain Of Threonyl-Trna
Synthetase From Pyrococcus Abyssi In Complex With An
Analog Of Seryladenylate
Length = 143
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 22 LKRIFEGLQERAFNLEDYMMLYTIVYDICCK 52
L R+++GL+ER FN+ Y + I CK
Sbjct: 98 LNRVYQGLKERGFNVGKAPFGYYKAFKISCK 128
>pdb|3TR7|A Chain A, Structure Of A Uracil-Dna Glycosylase (Ung) From Coxiella
Burnetii
Length = 232
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 93 DLLRELLKSWANHKFLAKWLSRVFLPLQAGYIPRMALPELNA-FGISCFRDLVFEAMKDK 151
+L +L S +H FL KW + L L A P+ +A G F D V E++ D
Sbjct: 101 ELHADLGVSIPSHGFLEKWAKQGVLLLNAALTVEAGKPQSHANIGWHRFTDKVIESLNDH 160
Query: 152 VKDAVVAL 159
+ V L
Sbjct: 161 PEGIVFLL 168
>pdb|3AHX|A Chain A, Crystal Structure Of Beta-Glucosidase A From Bacterium
Clostridium Cellulovorans
pdb|3AHX|B Chain B, Crystal Structure Of Beta-Glucosidase A From Bacterium
Clostridium Cellulovorans
pdb|3AHX|C Chain C, Crystal Structure Of Beta-Glucosidase A From Bacterium
Clostridium Cellulovorans
pdb|3AHX|D Chain D, Crystal Structure Of Beta-Glucosidase A From Bacterium
Clostridium Cellulovorans
Length = 453
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 12/101 (11%)
Query: 59 DEDPDQMYDKYQQILADYMPSKVLPYLREKHDEYDLLRELLKSWA--NHKFLAKWLSRVF 116
DE + ++D++ I + + + Y +LLKS +++F W R+F
Sbjct: 28 DEKGESIWDRFSHIPGNVAKMHNGDIACDHYHRYKEDVQLLKSLGIKSYRFSIAW-PRIF 86
Query: 117 LPLQAGYIPRMALPELNAFGISCFRDLVFEAMKDKVKDAVV 157
P+ E+N GI +RDL+ E +K+ ++ A+
Sbjct: 87 --------PK-GFGEINQKGIQFYRDLIDELIKNDIEPAIT 118
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 0.138 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,230,528
Number of Sequences: 62578
Number of extensions: 321159
Number of successful extensions: 780
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 766
Number of HSP's gapped (non-prelim): 15
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)