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= 007366
(606 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RNO|A Chain A, Solution Structure Of The N-Terminal Sap Domain Of Sumo
E3 Ligases From Oryza Sativa
Length = 110
Score = 119 bits (299), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 56/92 (60%), Positives = 77/92 (83%), Gaps = 2/92 (2%)
Query: 2 DLIASCKEKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKM--WAKKSP 59
DL++SCK+KLA+FRIKELKD+L QLGL KQGKKQDL+DR+LA+L+D+Q + W +K+
Sbjct: 8 DLVSSCKDKLAYFRIKELKDILNQLGLPKQGKKQDLIDRVLALLTDEQGQRHHGWGRKNS 67
Query: 60 VSKEEVAKLVDDTHRKLQVSVAPDLASKGGQG 91
++KE VAK+VDDT+RK+Q+ APDLA++ G
Sbjct: 68 LTKEAVAKIVDDTYRKMQIQCAPDLATRSHSG 99
>pdb|1WEW|A Chain A, Solution Structure Of Phd Domain In Dna-Binding Family
Protein Aam98074
Length = 78
Score = 99.8 bits (247), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 44/67 (65%), Positives = 55/67 (82%)
Query: 105 DDYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCE 164
+D Q + KV C CG+SLET+SMI+CEDPRC VWQH+ CVI+P+KP +GNPP+PE FYCE
Sbjct: 8 EDPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCE 67
Query: 165 ICRLSRA 171
ICRL+
Sbjct: 68 ICRLTSG 74
>pdb|2RSD|A Chain A, Solution Structure Of The Plant Homeodomain (Phd) Of The
E3 Sumo Ligase Siz1 From Rice
Length = 68
Score = 82.8 bits (203), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 39/67 (58%), Positives = 51/67 (76%), Gaps = 1/67 (1%)
Query: 106 DYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELFYCEI 165
D Q + KV C C S++ +SMI+CED RC VWQH++CV+IP+KP E + VP +FYCE+
Sbjct: 3 DSFQPEAKVRCICSSTMVNDSMIQCEDQRCQVWQHLNCVLIPDKPGE-SAEVPPVFYCEL 61
Query: 166 CRLSRAD 172
CRLSRAD
Sbjct: 62 CRLSRAD 68
>pdb|4FO9|A Chain A, Crystal Structure Of The E3 Sumo Ligase Pias2
Length = 360
Score = 72.4 bits (176), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 56/95 (58%), Gaps = 4/95 (4%)
Query: 352 EVVADSIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYS 411
E+ S+ V+L CP+ R+ + R C H+ CFD +++++N++ W CP+C + +
Sbjct: 206 EIATTSLRVSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAA 265
Query: 412 LENIIIDPYFNRITSKMRNCGEDITELEVKPDGSW 446
E++I+D F I + +C D+ E++ + DGSW
Sbjct: 266 YESLILDGLFMEI---LNDCS-DVDEIKFQEDGSW 296
>pdb|3I2D|A Chain A, Crystal Structure Of S. Cerevisiae Sumo E3 Ligase Siz1
Length = 371
Score = 68.6 bits (166), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 57/250 (22%), Positives = 113/250 (45%), Gaps = 28/250 (11%)
Query: 207 FPITRADKDLLSK-----QEYDVQAWCMLLNDKVPFRMQWPQYADLQVNGVPVR-----A 256
F +++AD +LLS + Y L + +Q+P +L+ N V ++
Sbjct: 100 FKLSKADYNLLSNPNSKHRLYLFSGMINPLGSRGNEPIQFPFPNELRCNNVQIKDNIRGF 159
Query: 257 INRPGSQLLGANGRDDGPIITPWTKDGINKIVLTGCDARIFCLGVRIVKRRSVQQVLNLI 316
++PG+ A D P + P+T+ N ++ + + L IV+ + +Q+L
Sbjct: 160 KSKPGT----AKPADLTPHLKPYTQQN-NVELIYAFTTKEYKLFGYIVEMITPEQLL--- 211
Query: 317 PKESEGEHFEDALTRVCRCVXXXXXXXXXXXXXXLEVVADSIGVNLRCPMSGSRIKVAGR 376
E +H ++ + + + S ++L+CP+S +R+K +
Sbjct: 212 --EKVLQH-----PKIIKQATLLYLKKTLREDEEMGLTTTSTIMSLQCPISYTRMKYPSK 264
Query: 377 FKPCVHMGCFDLDVFVELNQRSRKWQCPICLRNYSLENIIIDPYFNRITSKMRNCGEDIT 436
C H+ CFD F+ + WQCP+C + +LEN+ I + + I ++NC +++
Sbjct: 265 SINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDI---LQNCQKNVE 321
Query: 437 ELEVKPDGSW 446
++E+ DG W
Sbjct: 322 QVELTSDGKW 331
>pdb|2LV9|A Chain A, Solution Nmr Structure Of The Phd Domain Of Human Mll5,
Northeast Structural Genomics Consortium Target Hr6512a
Length = 98
Score = 37.0 bits (84), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 93 SNSSNIKIKGEMDDYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTE 152
S N+ +G D +D C CG + + MI C+ +C VWQH+ C+ I +
Sbjct: 9 SGRENLYFQGSEDGSYGTDVTRC-ICGFTHDDGYMICCD--KCSVWQHIDCMGIDRQ--- 62
Query: 153 GNPPVPELFYCEICR 167
+P+ + CE C+
Sbjct: 63 ---HIPDTYLCERCQ 74
>pdb|3IYJ|F Chain F, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|A Chain A, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|B Chain B, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|C Chain C, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|D Chain D, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|E Chain E, Bovine Papillomavirus Type 1 Outer Capsid
Length = 495
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 14/79 (17%)
Query: 137 VWQHMSCVIIPEKPTEGNPPVPELFYCEICRLSRADPFW-------VTIGHPLYPLKLTT 189
+WQ + +P PT PV ++ C + R F+ +TIGHP YP+ +
Sbjct: 3 LWQQGQKLYLP--PT----PVSKVL-CSETYVQRKSIFYHAETERLLTIGHPYYPVSIGA 55
Query: 190 TNIPTDGTNPARILEKTFP 208
+P N R+ + P
Sbjct: 56 KTVPKVSANQYRVFKIQLP 74
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 351 LEVVAD--SIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408
LE+V S+ L CP+ +K K C+H C D + RS +CP C +
Sbjct: 42 LEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITA---LRSGNKECPTCRK 98
Query: 409 NY-SLENIIIDPYFNRITSKM 428
S ++ DP F+ + SK+
Sbjct: 99 KLVSKRSLRPDPNFDALISKI 119
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 351 LEVVAD--SIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408
LE+V S+ L CP+ +K K C+H C D + RS +CP C +
Sbjct: 41 LEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITA---LRSGNKECPTCRK 97
Query: 409 NY-SLENIIIDPYFNRITSKM 428
S ++ DP F+ + SK+
Sbjct: 98 KLVSKRSLRPDPNFDALISKI 118
>pdb|3O70|A Chain A, Phd-Type Zinc Finger Of Human Phd Finger Protein 13
Length = 68
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 102 GEMDDYIQSDTKVCCPCGSSLETESMIKCEDPRCPVWQHMSCVIIPEKPTEGNPPVPELF 161
G + Y Q V C C MI+C + C W H+SC I + VPE+F
Sbjct: 10 GRENLYFQG--LVTCFCMKPFAGRPMIECNE--CHTWIHLSCAKIRKSN------VPEVF 59
Query: 162 YCEICRLSR 170
C+ CR S+
Sbjct: 60 VCQKCRDSK 68
>pdb|1YVL|A Chain A, Structure Of Unphosphorylated Stat1
pdb|1YVL|B Chain B, Structure Of Unphosphorylated Stat1
Length = 683
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 243 QYADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWT---KDGIN 285
Q++ + G+ V +N G +LLG N DG I PWT K+ IN
Sbjct: 505 QFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLI--PWTRFCKENIN 548
>pdb|1BF5|A Chain A, Tyrosine Phosphorylated Stat-1DNA COMPLEX
Length = 575
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 239 MQWPQYADLQVNGVPVRAINRPGSQLLGANGRDDGPIITPWT---KDGIN 285
+ W Q++ + G+ V +N G +LLG N DG I PWT K+ IN
Sbjct: 367 LSW-QFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLI--PWTRFCKENIN 413
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 351 LEVVAD--SIGVNLRCPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPICLR 408
LE+V S+ L CP+ +K K C+H C D + RS +CP C +
Sbjct: 22 LEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITA---LRSGNKECPTCRK 78
Query: 409 NY-SLENIIIDPYFNRITSKM 428
S ++ DP F+ + SK+
Sbjct: 79 KLVSKRSLRPDPNFDALISKI 99
>pdb|1WES|A Chain A, Solution Structure Of Phd Domain In Inhibitor Of Growth
Family, Member 1-Like
Length = 71
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 127 MIKCEDPRCPV-WQHMSCVIIPEKPTEGNPPVPELFYCEICR 167
MI C++ +CP+ W H SCV + KP +YC CR
Sbjct: 29 MIGCDNEQCPIEWFHFSCVSLTYKPK-------GKWYCPKCR 63
>pdb|2VSQ|A Chain A, Structure Of Surfactin A Synthetase C (Srfa-C), A
Nonribosomal Peptide Synthetase Termination Module
Length = 1304
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/104 (22%), Positives = 51/104 (49%), Gaps = 4/104 (3%)
Query: 2 DLIASCKEKLAHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKMWAKKSPVS 61
D+ A K++L + + + L +L L+ GK + R+L DQ+++ W
Sbjct: 917 DVKAHLKKQLPAYMVPQTFTFLDELPLTTNGK---VNKRLLPKPDQDQLAEEWIGPRNEM 973
Query: 62 KEEVAKLVDDTHRKLQVSVAPDLASKGGQGV-SNSSNIKIKGEM 104
+E +A++ + + Q+ + D + GG + + ++ +IK E+
Sbjct: 974 EETIAQIWSEVLGRKQIGIHDDFFALGGHALKAMTAASRIKKEL 1017
>pdb|3VK6|A Chain A, Crystal Structure Of A Phosphotyrosine Binding Domain
Length = 101
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 364 CPMSGSRIKVAGRFKPCVHMGCFDLDVFVELNQRSRKWQCPIC 406
C G IKV GR PC H+ C+D + L+++ CP C
Sbjct: 4 CDKCGLPIKVYGRMIPCKHVFCYDCAI---LHEKKGDKMCPGC 43
>pdb|1H1J|S Chain S, The Sap Domain Is A Dna-Binding Domain Capable Of
Binding SMAR DNA
Length = 51
Score = 28.9 bits (63), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 12 AHFRIKELKDVLTQLGLSKQGKKQDLVDRILAILSDDQVSKMWAKKSP 59
+ + +LKD+LT+ LS G K +LV R++ DD+ SK ++ SP
Sbjct: 6 SSLTVVQLKDLLTKRNLSVGGLKNELVQRLIK---DDEESKGESEVSP 50
>pdb|2G6Q|A Chain A, Crystal Structure Of Ing2 Phd Domain In Complex With
H3k4me3 Peptide
Length = 62
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 127 MIKCEDPRCPV-WQHMSCVIIPEKPTEGNPPVPELFYCEICR 167
MI C++ +CP+ W H SCV + KP +YC CR
Sbjct: 24 MIGCDNEQCPIEWFHFSCVSLTYKPKGK-------WYCPKCR 58
>pdb|2JMI|A Chain A, Nmr Solution Structure Of Phd Finger Fragment Of Yeast
Yng1 Protein In Free State
pdb|2JMJ|A Chain A, Nmr Solution Structure Of The Phd Domain From The Yeast
Yng1 Protein In Complex With H3(1-9)k4me3 Peptide
Length = 90
Score = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 91 GVSNSSNIKIKGEMDDYIQSDTKVCCPCGSSLETESMIKCEDPRCPV-WQHMSCVIIPEK 149
G +S +G++ + + +V C C ++ M+ C++P CP W H CV + +
Sbjct: 4 GSHMASEFINQGDVTEGNNNQEEVYCFC-RNVSYGPMVACDNPACPFEWFHYGCVGLKQA 62
Query: 150 P 150
P
Sbjct: 63 P 63
>pdb|3C6W|A Chain A, Crystal Structure Of The Ing5 Phd Finger In Complex With
H3k4me3 Peptide
pdb|3C6W|C Chain C, Crystal Structure Of The Ing5 Phd Finger In Complex With
H3k4me3 Peptide
Length = 59
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 127 MIKCEDPRCPV-WQHMSCVIIPEKP 150
MI C++P CP+ W H +CV + KP
Sbjct: 22 MIGCDNPDCPIEWFHFACVDLTTKP 46
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
0.318 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,921,189
Number of Sequences: 62578
Number of extensions: 823253
Number of successful extensions: 1666
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1655
Number of HSP's gapped (non-prelim): 27
length of query: 606
length of database: 14,973,337
effective HSP length: 104
effective length of query: 502
effective length of database: 8,465,225
effective search space: 4249542950
effective search space used: 4249542950
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: 54 (25.4 bits)