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= 037502
(426 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 62/140 (44%), Gaps = 25/140 (17%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH--KVPWK-------------LLKRETPVVRKRVFVCP 101
Y C C + F R +L H+R H + P+K L + + ++ + CP
Sbjct: 22 YACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGEKPYKCP 81
Query: 102 EPSCLHHDPCHALGDLVGIKKHFRRKHSNHKQWVCEKCSKGYAVQSDYKAHLKT-CGTRG 160
E + ++ H +R H+ K + C +C K ++ + +AH +T G +
Sbjct: 82 ECG-------KSFSQRANLRAH-QRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGEKP 133
Query: 161 HSC-DCGRVFSRVESFIEHQ 179
+ C +CG+ FSR ++ HQ
Sbjct: 134 YKCPECGKSFSREDNLHTHQ 153
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 70/167 (41%), Gaps = 35/167 (20%)
Query: 15 EPFSCLENGISHNKRKRRPAGTPDPDAEVVSLSPKTLLESDRYVCEICNQGFQRDQNLQM 74
+P+ C E G S + D + ++ +T Y C C + F + NL+
Sbjct: 48 KPYKCPECGKSFS------------DKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRA 95
Query: 75 HRRRHKVPWKLLKRETPVVRKRVFVCPEPSCLHHDPCHALGDLVGIKKHFRRKHSNHKQW 134
H+R H ++ + CPE + L ++ H +R H+ K +
Sbjct: 96 HQRTH-------------TGEKPYACPECG-------KSFSQLAHLRAH-QRTHTGEKPY 134
Query: 135 VCEKCSKGYAVQSDYKAHLKT-CGTRGHSC-DCGRVFSRVESFIEHQ 179
C +C K ++ + + H +T G + + C +CG+ FSR ++ HQ
Sbjct: 135 KCPECGKSFSREDNLHTHQRTHTGEKPYKCPECGKSFSRRDALNVHQ 181
>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 = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 113 ALGDLVGIKKHFRRKHSNHKQWVCEKCSKGYAVQSDYKAHLKT-CGTRGHSC-DCGRVFS 170
+ ++KH +R H+ K + C +C K ++ SD + H +T G + + C +CG+ FS
Sbjct: 13 SFSQSSNLQKH-QRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFS 71
Query: 171 RVESFIEHQ 179
R + HQ
Sbjct: 72 RSDHLSRHQ 80
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 21/99 (21%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRHKVPWKLLKRETPVVRKRVFVCPEPSCLHHDPCHALGD 116
Y C C + F + NLQ H+R H ++ + CPE +
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTH-------------TGEKPYKCPECG-------KSFSQ 44
Query: 117 LVGIKKHFRRKHSNHKQWVCEKCSKGYAVQSDYKAHLKT 155
++KH +R H+ K + C +C K ++ H +T
Sbjct: 45 SSDLQKH-QRTHTGEKPYKCPECGKSFSRSDHLSRHQRT 82
>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
Length = 155
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 20/115 (17%)
Query: 43 VVSLSPKTLLESDRYVCEICNQGFQRDQNLQMHRRRHKVPWKLLKRETPVVRKRVFVCPE 102
VV + T + + E C + + R +NL+ H R H ++ ++C
Sbjct: 56 VVHMRRHTGEKPHKCTFEGCRKSYSRLENLKTHLRSH-------------TGEKPYMCEH 102
Query: 103 PSCLHHDPCHALGDLVGIKKHFRRKHSNHKQWVCE--KCSKGYAVQSDYKAHLKT 155
C A + KH R HSN K +VC+ C+K Y S + H+KT
Sbjct: 103 EGCSK-----AFSNASDRAKHQNRTHSNEKPYVCKLPGCTKRYTDPSSLRKHVKT 152
>pdb|1DPP|A Chain A, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
pdb|1DPP|C Chain C, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
pdb|1DPP|E Chain E, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
pdb|1DPP|G Chain G, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
Length = 507
Score = 31.6 bits (70), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 47/117 (40%), Gaps = 23/117 (19%)
Query: 231 PTIDTMFLNRIHQGDKSTRNVKHHNLELQLLTTSNPIDVSDDSPKRDHDHNHSTQLQLSI 290
P IDT+ + D S R K E Q++ NP D++ K+D
Sbjct: 209 PQIDTLVFSITP--DASVRYAKLQKNECQVMPYPNPADIA--RMKQDK------------ 252
Query: 291 GSSDISEKNELNVTYLSSTTNGKPAMDIASRLKEQAREQLRLAMAEKACAEEARQAA 347
S ++ E LNV YLS KP D+ + R+ L A+ + A + Q A
Sbjct: 253 -SINLMEMPGLNVGYLSYNVQKKPLDDV------KVRQALTYAVNKDAIIKAVYQGA 302
>pdb|1DPE|A Chain A, Dipeptide-Binding Protein
Length = 507
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 47/117 (40%), Gaps = 23/117 (19%)
Query: 231 PTIDTMFLNRIHQGDKSTRNVKHHNLELQLLTTSNPIDVSDDSPKRDHDHNHSTQLQLSI 290
P IDT+ + D S R K E Q++ NP D++ K+D
Sbjct: 209 PQIDTLVFSITP--DASVRYAKLQKNECQVMPYPNPADIA--RMKQDK------------ 252
Query: 291 GSSDISEKNELNVTYLSSTTNGKPAMDIASRLKEQAREQLRLAMAEKACAEEARQAA 347
S ++ E LNV YLS KP D+ + R+ L A+ + A + Q A
Sbjct: 253 -SINLMEMPGLNVGYLSYNVQKKPLDDV------KVRQALTYAVNKDAIIKAVYQGA 302
>pdb|2ELZ|A Chain A, Solution Structure Of The 17th Zf-C2h2 Domain From Human
Zinc Finger Protein 224
Length = 46
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH 79
Y CE C +G+ R NL MH+R H
Sbjct: 13 YKCEDCGKGYNRRLNLDMHQRVH 35
>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 = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 23/88 (26%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRHKVPWKLLKRETPVVRKRVFVCPEPSCLHHDPCH-ALG 115
++C+ C + F + NL +H R H +R + C D CH A
Sbjct: 18 FICKFCGRHFTKSYNLLIHERTH-------------TDERPYTC--------DICHKAFR 56
Query: 116 DLVGIKKHFRRKHSNHKQWVCEKCSKGY 143
++ H R HS K + C++C KG+
Sbjct: 57 RQDHLRDH-RYIHSKEKPFKCQECGKGF 83
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 128 HSNHKQWVCEKCSKGYAVQSDYKAH-LKTCGTRGHSCD-CGRVFSRVESFIEH 178
HS+ + + C+ C K + +SD K H G + H C CG+ FS+ + I H
Sbjct: 24 HSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITH 76
>pdb|1ARD|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH 79
+VCE+C + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|1ARE|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH 79
+VCE+C + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEALKRHYRSH 25
>pdb|1ARF|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH 79
+VCE+C + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEYLKRHYRSH 25
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 134 WVCEKCSKGYAVQSDYKAHLKT-CGTRGHSCD-CGRVFSRVESFIEHQDACSKGHI 187
+VCE C++ +A Q K H ++ + + C C R F+R + I H G++
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAFTRRDLLIRHAQKIHSGNL 58
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH 79
+VCE+C + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|3GVP|A Chain A, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|B Chain B, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|C Chain C, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|D Chain D, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
Length = 435
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 339 CAEEARQA--AKRQIELAEQEFANAKRIRQQAQAE 371
C + +QA +R+IE+AEQE +R++AQ E
Sbjct: 15 CVKNIKQAEFGRREIEIAEQEMPALMALRKRAQGE 49
>pdb|3MTG|A Chain A, Crystal Structure Of Human S-Adenosyl Homocysteine
Hydrolase Protein
pdb|3MTG|B Chain B, Crystal Structure Of Human S-Adenosyl Homocysteine
Hydrolase Protein
Length = 444
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 339 CAEEARQA--AKRQIELAEQEFANAKRIRQQAQAE 371
C + +QA +R+IE+AEQ+ + +R++AQ E
Sbjct: 20 CVKNIKQAEFGRREIEIAEQDMSALISLRKRAQGE 54
>pdb|2DLK|A Chain A, Solution Structure Of The First And The Second Zf-C2h2
Domains Of Zinc Finger Protein 692
Length = 79
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 12/48 (25%)
Query: 93 VRKRVFVCPEPSCLHHDPCHALGDLVGIKKHFR---RKHSNHKQWVCE 137
+ ++ F CPEP+C G KKH + + HS+ + ++CE
Sbjct: 34 IHQKSFSCPEPAC---------GKSFNFKKHLKEHMKLHSDTRDYICE 72
>pdb|2YSP|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
507- 539) Of Human Zinc Finger Protein 224
Length = 46
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRH 79
Y CE C +G+ NL MH++ H
Sbjct: 13 YKCEKCGKGYNSKFNLDMHQKVH 35
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 57 YVCEICNQGFQRDQNLQMHRRRHK 80
+ C +CN+ F R +L +H +RH+
Sbjct: 76 FQCGVCNRSFSRSDHLALHMKRHQ 99
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 0.129 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,727,384
Number of Sequences: 62578
Number of extensions: 438263
Number of successful extensions: 1381
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 1302
Number of HSP's gapped (non-prelim): 97
length of query: 426
length of database: 14,973,337
effective HSP length: 102
effective length of query: 324
effective length of database: 8,590,381
effective search space: 2783283444
effective search space used: 2783283444
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: 53 (25.0 bits)