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= psy3483
(99 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3UK3|C Chain C, Crystal Structure Of Znf217 Bound To Dna
pdb|3UK3|D Chain D, Crystal Structure Of Znf217 Bound To Dna
pdb|4F2J|C Chain C, Crystal Structure Of Znf217 Bound To Dna, P6522 Crystal
Form
pdb|4IS1|C Chain C, Crystal Structure Of Znf217 Bound To Dna
pdb|4IS1|D Chain D, Crystal Structure Of Znf217 Bound To Dna
Length = 57
Score = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 45 CCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
C C K+ S+ + H+RTHT ++PYKC +C+Y + ++++++ H+ R H
Sbjct: 7 CSYCGKFFRSNYY-LNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHH 56
>pdb|1BBO|A Chain A, High-Resolution Solution Structure Of The Double
Cys2His2 Zinc Finger From The Human Enhancer Binding
Protein Mbp-1
Length = 57
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 42 RYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHM 91
+Y+C C R S ++ HIRTHT RPY C YC++ + N+ HM
Sbjct: 1 KYICEECG-IRXKKPSMLKKHIRTHTDVRPYHCTYCNFSFKTKGNLTKHM 49
>pdb|2I13|A Chain A, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
Triplets
pdb|2I13|B Chain B, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
Triplets
Length = 190
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSV 97
T + Y C C K SD + H RTHT ++PYKC C ++R+N++AH
Sbjct: 45 TGEKPYKCPECGK-SFSDKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGE 103
Query: 98 KP 99
KP
Sbjct: 104 KP 105
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSV 97
T + Y C C K S + +R+H RTHT ++PYKC C + N+ H
Sbjct: 101 TGEKPYACPECGK-SFSQLAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTHQRTHTGE 159
Query: 98 KP 99
KP
Sbjct: 160 KP 161
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSV 97
T + Y C C K S + +R+H RTHT ++PY C C ++ ++++AH
Sbjct: 73 TGEKPYKCPECGK-SFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGE 131
Query: 98 KP 99
KP
Sbjct: 132 KP 133
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
Y C C K S + + H RTHT ++PYKC C +++ ++ H KP
Sbjct: 22 YACPECGK-SFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGEKP 77
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSV 97
T + Y C C K S + +H RTHT ++PYKC C + R + H R H+
Sbjct: 129 TGEKPYKCPECGK-SFSREDNLHTHQRTHTGEKPYKCPECGKSFSRRDALNVHQ-RTHTG 186
Query: 98 K 98
K
Sbjct: 187 K 187
>pdb|2DMD|A Chain A, Solution Structure Of The N-Terminal C2h2 Type
Zinc-Binding Domain Of The Zinc Finger Protein 64,
Isoforms 1 And 2
Length = 96
Score = 38.9 bits (89), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHM 91
T + Y C C Y +D+S + H+R H+ +RP+KC C Y S S + H+
Sbjct: 32 TGVKPYKCKTCD-YAAADSSSLNKHLRIHSDERPFKCQICPYASRNSSQLTVHL 84
>pdb|1X5W|A Chain A, Solution Structure Of The C2h2 Type Zinc-Binding Domain
Of Human Zinc Finger Protein 64, Isoforms 1 And 2
Length = 70
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 59 MRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
+R H R H DRP+KC YC + + + SN+ HM + H
Sbjct: 25 LRIHERIHCTDRPFKCNYCSFDTKQPSNLSKHMKKFHG 62
>pdb|2DLQ|A Chain A, Solution Structure Of The Tandem Four Zf-C2h2 Domain
Repeats Of Murine Gli-Kruppel Family Member Hkr3
Length = 124
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 27/39 (69%)
Query: 58 KMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
++R H+ +HT + PYKC C + ++ ++++HMI+ HS
Sbjct: 81 ELRLHMVSHTGEMPYKCSSCSQQFMQKKDLQSHMIKLHS 119
>pdb|1MEY|C Chain C, Crystal Structure Of A Designed Zinc Finger Protein
Bound To Dna
pdb|1MEY|F Chain F, Crystal Structure Of A Designed Zinc Finger Protein
Bound To Dna
pdb|1MEY|G Chain G, Crystal Structure Of A Designed Zinc Finger Protein
Bound To Dna
Length = 87
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
Y C C K S +S ++ H RTHT ++PYKC C ++ S+++ H KP
Sbjct: 5 YKCPECGK-SFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKP 60
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSV 97
T + Y C C K S +S ++ H RTHT ++PYKC C +S RS+ + R H
Sbjct: 28 TGEKPYKCPECGK-SFSQSSDLQKHQRTHTGEKPYKCPECG-KSFSRSDHLSRHQRTHQN 85
Query: 98 K 98
K
Sbjct: 86 K 86
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 56 ASKMRSHIRTHTKDRPYKCFY--CDYRSNERSNVKAHMIRRHSVKP 99
+S +++H+RTHT ++PYKC + CD+R + H + KP
Sbjct: 30 SSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKHTGAKP 75
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 51 YRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
+R + + ++ H R HT +P++C C+ RS RS+ A ++RH
Sbjct: 55 WRFARSDELTRHYRKHTGAKPFQCGVCN-RSFSRSDHLALHMKRH 98
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 26/36 (72%), Gaps = 2/36 (5%)
Query: 59 MRSHIRTHTKDRPYKCFY--CDYRSNERSNVKAHMI 92
+R+H+R HT DRPY C + C+ + + +N+K+H++
Sbjct: 80 LRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHIL 115
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFY--CDYRSNERSNVKAHM 91
+VC C K ++SK++ H HT ++P++C + C R + N++ H+
Sbjct: 35 HVCAECGKA-FVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHV 84
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 56 ASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
+S + +H+ H+ RPY C YC R +++S++K H KP
Sbjct: 14 SSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKP 57
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
Y C C K H S M+ H HT ++P+KC C ++ SN+ H R+H+
Sbjct: 30 YPCQYCGKRFH-QKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITHS-RKHT 81
>pdb|2CT1|A Chain A, Solution Structure Of The Zinc Finger Domain Of
Transcriptional Repressor Ctcf Protein
Length = 77
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 23/33 (69%)
Query: 64 RTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
RTH+ ++PY+C+ C R + +K H++++H+
Sbjct: 8 RTHSGEKPYECYICHARFTQSGTMKMHILQKHT 40
>pdb|1X6E|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain
Of Human Zinc Finger Protein 24
Length = 72
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
Y C C K S +S + H R HT ++PYKC C ++ S + H R H+ P
Sbjct: 15 YGCVECGK-AFSRSSILVQHQRVHTGEKPYKCLECGKAFSQNSGLINHQ-RIHTSGP 69
>pdb|2ELQ|A Chain A, Solution Structure Of The 14th C2h2 Zinc Finger Of Human
Zinc Finger Protein 406
Length = 36
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 65 THTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVK 98
+ + +P+KC C+Y + +SN+KAHM RHS +
Sbjct: 3 SGSSGKPFKCSLCEYATRSKSNLKAHM-NRHSTE 35
>pdb|2COT|A Chain A, Solution Structure Of The First And Second Zf-C2h2
Domain Of Zinc Finger Protein 435
Length = 77
Score = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 41 QRYVCCLCSK-YRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAH 90
+RY C C K + HS S + H RTHT ++PYKC C +RS++ H
Sbjct: 17 RRYKCDECGKSFSHS--SDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGH 65
>pdb|5ZNF|A Chain A, Alternating Zinc Fingers In The Human Male Associated
Protein Zfy: 2d Nmr Structure Of An Even Finger And
Implications For "jumping-Linker" Dna Recognition
Length = 30
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 70 RPYKCFYCDYRSNERSNVKAHMIRRHS 96
+ Y+C YC+YRS + SN+K H+ +HS
Sbjct: 1 KTYQCQYCEYRSADSSNLKTHIKTKHS 27
>pdb|1KLR|A Chain A, Nmr Structure Of The Zfy-6t[y10f] Zinc Finger
Length = 30
Score = 32.0 bits (71), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 70 RPYKCFYCDYRSNERSNVKAHMIRRHS 96
+ Y+C YC++RS + SN+K H+ +HS
Sbjct: 1 KTYQCQYCEFRSADSSNLKTHIKTKHS 27
>pdb|1G2F|C Chain C, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX
(Tatazf;clone #6)
pdb|1G2F|F Chain F, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX
(Tatazf;clone #6)
Length = 90
Score = 32.0 bits (71), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
R S + + +HIR HT +P++C C ++++++ AH+ KP
Sbjct: 15 RFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAHIRTHTGEKP 62
Score = 28.9 bits (63), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD 78
T + + C +C + AS + +HIRTHT ++P+ C C
Sbjct: 30 TGQKPFQCRICMRNFSQQAS-LNAHIRTHTGEKPFACDICG 69
>pdb|2RPC|A Chain A, Solution Structure Of The Tandem Zf-C2h2 Domains From The
Human Zinc Finger Protein Zic 3
Length = 155
Score = 31.2 bits (69), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 56 ASKMRSHIRTHTKDRPYKCFY--CDYRSNERSNVKAHM 91
+ ++ H RTHT ++P+KC + CD R S+ K HM
Sbjct: 105 SENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHM 142
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 58 KMRSHIRTHTKDRPYKCFY 76
K+ +HIR HT ++P+ C +
Sbjct: 77 KLVNHIRVHTGEKPFPCPF 95
>pdb|2LCE|A Chain A, Chemical Shift Assignment Of Hr4436b From Homo Sapiens,
Northeast Structural Genomics Consortium
Length = 74
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 57 SKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
+ SH HT ++PY+C C + N +N+K H KP
Sbjct: 31 GNLASHKTVHTGEKPYRCNICGAQFNRPANLKTHTRIHSGEKP 73
>pdb|1A1F|A Chain A, Dsnr (Zif268 Variant) Zinc Finger-Dna Complex (Gacc
Site)
pdb|1A1G|A Chain A, Dsnr (Zif268 Variant) Zinc Finger-Dna Complex (Gcgt
Site)
Length = 90
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R SD+S + HIR HT +P++C C R+ RS+ IR H+
Sbjct: 15 RFSDSSNLTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 58
Score = 28.5 bits (62), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 30 TGQKPFQCRICMRN-FSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 86
>pdb|1KLS|A Chain A, Nmr Structure Of The Zfy-6t[y10l] Zinc Finger
Length = 30
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 70 RPYKCFYCDYRSNERSNVKAHMIRRHS 96
+ Y+C YC+ RS + SN+K H+ +HS
Sbjct: 1 KTYQCQYCELRSADSSNLKTHIKTKHS 27
>pdb|1XRZ|A Chain A, Nmr Structure Of A Zinc Finger With Cyclohexanylalanine
Substituted For The Central Aromatic Residue
Length = 30
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 70 RPYKCFYCDYRSNERSNVKAHMIRRHS 96
+ Y+C YC+ RS + SN+K H+ +HS
Sbjct: 1 KTYQCQYCEXRSADSSNLKTHIKTKHS 27
>pdb|2JP9|A Chain A, Structure Of The Wilms Tumor Suppressor Protein Zinc
Finger Domain Bound To Dna
pdb|2JPA|A Chain A, Structure Of The Wilms Tumor Suppressor Protein Zinc
Finger Domain Bound To Dna
pdb|2PRT|A Chain A, Structure Of The Wilms Tumor Suppressor Protein Zinc
Finger Domain Bound To Dna
Length = 119
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 57 SKMRSHIRTHTKDRPYKCFY--CDYRSNERSNVKAHMIRRHSVKP 99
S ++ H R HT ++PY+C + C+ R + +K H R VKP
Sbjct: 22 SHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKP 66
>pdb|1TF6|A Chain A, Co-crystal Structure Of Xenopus Tfiiia Zinc Finger
Domain Bound To The 5s Ribosomal Rna Gene Internal
Control Region
pdb|1TF6|D Chain D, Co-crystal Structure Of Xenopus Tfiiia Zinc Finger
Domain Bound To The 5s Ribosomal Rna Gene Internal
Control Region
Length = 190
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 37 PTKYQRYVCCLCS-KYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
P Y+RY+C ++ K+++H+ HT ++P F C E+ H + RH
Sbjct: 7 PVVYKRYICSFADCGAAYNKNWKLQAHLCKHTGEKP---FPCKEEGCEKGFTSLHHLTRH 63
Query: 96 SV 97
S+
Sbjct: 64 SL 65
>pdb|2EN4|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
284- 316) Of Human Zinc Finger Protein 347
Length = 46
Score = 29.3 bits (64), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 65 THTKDRPYKCFYCDYRSNERSNVKAHMI 92
+ TK++PYKC+ C RSN+ H +
Sbjct: 6 SGTKEKPYKCYECGKAFRTRSNLTTHQV 33
>pdb|1LLM|C Chain C, Crystal Structure Of A Zif23-Gcn4 Chimera Bound To Dna
pdb|1LLM|D Chain D, Crystal Structure Of A Zif23-Gcn4 Chimera Bound To Dna
Length = 88
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 3/34 (8%)
Query: 54 SDASKMRSHIRTHTKDRPYKCFYCD---YRSNER 84
S + + +HIRTHT ++P+ C C RS+ER
Sbjct: 14 SRSDHLTTHIRTHTGEKPFACDICGRKFARSDER 47
>pdb|1G2D|C Chain C, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX
(CLONE #2)
pdb|1G2D|F Chain F, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX
(CLONE #2)
Length = 90
Score = 28.9 bits (63), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 24/48 (50%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
R S + + +HIR HT +P++C C ++ + + H+ KP
Sbjct: 15 RFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQHTGLNQHIRTHTGEKP 62
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYC 77
T + + C +C + S + + HIRTHT ++P+ C C
Sbjct: 30 TGQKPFQCRICMR-NFSQHTGLNQHIRTHTGEKPFACDIC 68
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac
Site)
Length = 90
Score = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 30 TGQKPFQCRICMR-NFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 86
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R S + + HIR HT +P++C C R+ RS+ IR H+
Sbjct: 15 RFSQSGSLTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 58
>pdb|1JK1|A Chain A, Zif268 D20a Mutant Bound To Wt Dna Site
pdb|1JK2|A Chain A, Zif268 D20a Mutant Bound To The Gct Dna Site
Length = 90
Score = 28.5 bits (62), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 30 TGQKPFQCRICMRN-FSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 86
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R S ++++ HIR HT +P++C C R+ RS+ IR H+
Sbjct: 15 RFSRSAELTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 58
>pdb|1A1I|A Chain A, Radr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac
Site)
pdb|1A1J|A Chain A, Radr (Zif268 Variant) Zinc Finger-Dna Complex (Gcgt
Site)
pdb|1A1K|A Chain A, Radr (Zif268 Variant) Zinc Finger-Dna Complex (Gacc
Site)
Length = 90
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 30 TGQKPFQCRICMRN-FSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 86
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R S ++ + HIR HT +P++C C R+ RS+ IR H+
Sbjct: 15 RFSRSADLTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 58
>pdb|2EPA|A Chain A, Solution Structure Of The First And Second Zf-C2h2
Domains From Human Krueppel-Like Factor 10
Length = 72
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 56 ASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
+S +++H RTHT ++P F C ++ ER ++ + RH
Sbjct: 32 SSHLKAHTRTHTGEKP---FSCSWKGCERRFARSDELSRH 68
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 43 YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
+VC +C++ + ++ H R+HT ++PY C C+ R + H + HS
Sbjct: 3 FVCEVCTRA-FARQEHLKRHYRSHTNEKPYPCGLCNRAFTRRDLLIRHAQKIHS 55
>pdb|1P47|A Chain A, Crystal Structure Of Tandem Zif268 Molecules Complexed
To Dna
pdb|1P47|B Chain B, Crystal Structure Of Tandem Zif268 Molecules Complexed
To Dna
Length = 87
Score = 28.5 bits (62), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 29 TGQKPFQCRICMRN-FSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 85
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R S + ++ HIR HT +P++C C R+ RS+ IR H+
Sbjct: 14 RFSRSDELTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 57
>pdb|1AAY|A Chain A, Zif268 Zinc Finger-Dna Complex
pdb|1A1L|A Chain A, Zif268 Zinc Finger-Dna Complex (Gcac Site)
Length = 90
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 30 TGQKPFQCRICMRN-FSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 86
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R S + ++ HIR HT +P++C C R+ RS+ IR H+
Sbjct: 15 RFSRSDELTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 58
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 38 TKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCD---YRSNERS-NVKAHM 91
T + + C +C + S + + +HIRTHT ++P+ C C RS+ER + K H+
Sbjct: 30 TGQKPFQCRICMRN-FSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 86
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 52 RHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
R S + ++ HIR HT +P++C C R+ RS+ IR H+
Sbjct: 15 RFSRSDELTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 58
>pdb|1X6H|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain
Of Human Transcriptional Repressor Ctcf
Length = 86
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 61 SHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
S RTHT ++PY C +CD ++ + H R H
Sbjct: 5 SSGRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYH 39
>pdb|2WBU|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4
Bound To Its Target Dna
Length = 90
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 17/21 (80%)
Query: 56 ASKMRSHIRTHTKDRPYKCFY 76
+S +++H+RTHT ++PY C +
Sbjct: 21 SSHLKAHLRTHTGEKPYHCDW 41
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 51 YRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
++ + + ++ H R HT RP++C CD R+ RS+ A ++RH
Sbjct: 46 WKFARSDELTRHYRKHTGHRPFQCQKCD-RAFSRSDHLALHMKRH 89
>pdb|2WBS|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4
Bound To Its Target Dna
Length = 89
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 17/21 (80%)
Query: 56 ASKMRSHIRTHTKDRPYKCFY 76
+S +++H+RTHT ++PY C +
Sbjct: 20 SSHLKAHLRTHTGEKPYHCDW 40
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 51 YRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRH 95
++ + + ++ H R HT RP++C CD R+ RS+ A ++RH
Sbjct: 45 WKFARSDELTRHYRKHTGHRPFQCQKCD-RAFSRSDHLALHMKRH 88
>pdb|1F2I|G Chain G, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|H Chain H, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|I Chain I, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|J Chain J, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|K Chain K, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|L Chain L, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
Length = 73
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 39 KYQRYVCCLCS-KYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
K + Y C + S R S + ++ HIR HT +P++C C R+ RS+ IR H+
Sbjct: 16 KMRPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRIC-MRNFSRSDHLTTHIRTHT 73
>pdb|1TF3|A Chain A, Tfiiia Finger 1-3 Bound To Dna, Nmr, 22 Structures
Length = 92
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 62 HIRTHTKDRPYKCF--YCDYRSNERSNVKAHMIRRHSVK 98
H THT ++ + C CD R ++N+K H R H++K
Sbjct: 54 HSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIK 92
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 41 QRYVCCLCS-KYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSV 97
+RY+C ++ K+++H+ HT ++P F C E+ H + RHS+
Sbjct: 2 KRYICSFADCGAAYNKNWKLQAHLSKHTGEKP---FPCKEEGCEKGFTSLHHLTRHSL 56
>pdb|2ELT|A Chain A, Solution Structure Of The 3rd C2h2 Zinc Finger Of Human
Zinc Finger Protein 406
Length = 36
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 65 THTKDRPYKCFYCDYRSNERSNVKAHMIRRHS 96
+ + +PYKC C Y S ++N+ H+ R+H+
Sbjct: 3 SGSSGKPYKCPQCSYASAIKANLNVHL-RKHT 33
>pdb|7ZNF|A Chain A, Alternating Zinc Fingers In The Human Male Associated
Protein Zfy: 2d Nmr Structure Of An Even Finger And
Implications For "jumping-Linker" Dna Recognition
Length = 30
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 70 RPYKCFYCDYRSNERSNVKAHMIRRHS 96
+ Y+C YC+ R + SN+K H+ +HS
Sbjct: 1 KTYQCQYCEKRFADSSNLKTHIKTKHS 27
>pdb|2EE8|A Chain A, Solution Structure Of Three Zf-C2h2 Domains From Mouse
Protein Odd-Skipped-Related 2 Splicing Isoform 2
Length = 106
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 37 PTKYQR-YVCCLCSKYRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAH 90
P+K ++ ++C C ++ + + + H RTHT +RPY C C + +++ H
Sbjct: 11 PSKTKKEFICKFCGRH-FTKSYNLLIHERTHTDERPYTCDICHKAFRRQDHLRDH 64
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 43 YVCCLCSK-YRHSDASKMRSHIRTHTKDRPYKCFYCD 78
Y C +C K +R D +R H H+K++P+KC C
Sbjct: 46 YTCDICHKAFRRQD--HLRDHRYIHSKEKPFKCQECG 80
>pdb|4GZN|C Chain C, Mouse Zfp57 Zinc Fingers In Complex With Methylated Dna
Length = 60
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 43 YVCCLCSK-YRHSDASKMRSHIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
+ C C K YR DAS + H R H RP C C ++S V H+ + H KP
Sbjct: 5 FFCNFCGKTYR--DASGLSRHRRAHLGYRPRSCPECGKCFRDQSEVNRHL-KVHQNKP 59
>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
Length = 155
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 54 SDASKMRSHIRTHTKDRPYKCFY--CDYRSNERSNVKAHMIRRHS 96
S +++H+R+HT ++PY C + C + S+ H R HS
Sbjct: 80 SRLENLKTHLRSHTGEKPYMCEHEGCSKAFSNASDRAKHQNRTHS 124
>pdb|3KY9|A Chain A, Autoinhibited Vav1
pdb|3KY9|B Chain B, Autoinhibited Vav1
Length = 587
Score = 25.8 bits (55), Expect = 6.8, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 15 KILTYETETIMNHCKFCKAVSRPTKYQRYVCCLCSKYRHSDASKMRSHIRTHTKDRP 71
++ ++E T CK C+ + R T YQ Y C C H + H +D P
Sbjct: 522 QMFSFEETT---SCKACQMLLRGTFYQGYRCHRCRASAHKECLGRVPPCGRHGQDFP 575
>pdb|3ZNF|A Chain A, High-Resolution Three-Dimensional Structure Of A Single
Zinc Finger From A Human Enhancer Binding Protein In
Solution
pdb|4ZNF|A Chain A, High-Resolution Three-Dimensional Structure Of A Single
Zinc Finger From A Human Enhancer Binding Protein In
Solution
Length = 30
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 70 RPYKCFYCDYRSNERSNVKAHM 91
RPY C YC++ + N+ HM
Sbjct: 1 RPYHCSYCNFSFKTKGNLTKHM 22
>pdb|2CSH|A Chain A, Solution Structure Of Tandem Repeat Of The Zf-C2h2
Domains Of Human Zinc Finger Protein 297b
Length = 110
Score = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 62 HIRTHTKDRPYKCFYCDYRSNERSNVKAHMIRRHSVKP 99
H+ H RPY C C + + ++ HM +KP
Sbjct: 28 HMSMHLGLRPYGCGVCGKKFKMKHHLVGHMKIHTGIKP 65
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
0.327 0.132 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,639,939
Number of Sequences: 62578
Number of extensions: 82112
Number of successful extensions: 418
Number of sequences better than 100.0: 70
Number of HSP's better than 100.0 without gapping: 62
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 305
Number of HSP's gapped (non-prelim): 116
length of query: 99
length of database: 14,973,337
effective HSP length: 65
effective length of query: 34
effective length of database: 10,905,767
effective search space: 370796078
effective search space used: 370796078
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)