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= 038715
(332 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 = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 53/115 (46%), Gaps = 22/115 (19%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGHNLPWKLMQRPTTQVKKGVYVCPKPNCVHHHPSRALGD 65
Y C C K F R +L H++ H ++P Y CP+ C ++ D
Sbjct: 22 YACPECGKSFSRSDHLAEHQRTHT-----GEKP--------YKCPE--C-----GKSFSD 61
Query: 66 LTGVKKHFCRKHGEKKWKCDKCSKCYAVQSDWKAHTKI-CGTREHRC-DCGIIFS 118
+ +H GEK +KC +C K ++ +++ +AH + G + + C +CG FS
Sbjct: 62 KKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFS 116
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 22/118 (18%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGHNLPWKLMQRPTTQVKKGVYVCPKPNCVHHHPSRALGD 65
Y C C K F + NL+ H++ H ++P Y CP+ C ++
Sbjct: 78 YKCPECGKSFSQRANLRAHQRTHT-----GEKP--------YACPE--C-----GKSFSQ 117
Query: 66 LTGVKKHFCRKHGEKKWKCDKCSKCYAVQSDWKAHTKI-CGTREHRC-DCGIIFSSQN 121
L ++ H GEK +KC +C K ++ + + H + G + ++C +CG FS ++
Sbjct: 118 LAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTHQRTHTGEKPYKCPECGKSFSRRD 175
>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 = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 61 RALGDLTGVKKHFCRKHGEKKWKCDKCSKCYAVQSDWKAHTKI-CGTREHRC-DCGIIFS 118
++ + ++KH GEK +KC +C K ++ SD + H + G + ++C +CG FS
Sbjct: 12 KSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFS 71
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 20/98 (20%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGHNLPWKLMQRPTTQVKKGVYVCPKPNCVHHHPSRALGD 65
Y C C K F + NLQ H++ H ++P Y CP+ C ++
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTH-----TGEKP--------YKCPE--C-----GKSFSQ 44
Query: 66 LTGVKKHFCRKHGEKKWKCDKCSKCYAVQSDWKAHTKI 103
+ ++KH GEK +KC +C K ++ H +
Sbjct: 45 SSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRT 82
>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 = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGHN--LPWKLMQ 36
Y C++CHK F+R +L+ HR H+ P+K +
Sbjct: 46 YTCDICHKAFRRQDHLRDHRYIHSKEKPFKCQE 78
>pdb|2E6R|A Chain A, Solution Structure Of The Phd Domain In Smcy Protein
Length = 92
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 4 NRYICEVCHKGFQRDQNLQLHRKGHNLPWKLMQRPTTQVKKGVYVCPK 51
+ YIC+VC +G + D+ L N + P ++ +G++ CPK
Sbjct: 15 DSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPK 62
>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 = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 20/43 (46%)
Query: 61 RALGDLTGVKKHFCRKHGEKKWKCDKCSKCYAVQSDWKAHTKI 103
R TG+ +H GEK + CD C + +A HTKI
Sbjct: 42 RNFSQHTGLNQHIRTHTGEKPFACDICGRKFATLHTRDRHTKI 84
>pdb|2COT|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domain
Of Zinc Finger Protein 435
Length = 77
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 80 KKWKCDKCSKCYAVQSDWKAHTKI-CGTREHRCD-CGIIF 117
+++KCD+C K ++ SD H + G + ++CD CG F
Sbjct: 17 RRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAF 56
>pdb|1ARD|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGH 28
++CEVC + F R ++L+ H + H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac Site)
Length = 90
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 78 GEKKWKCDKCSKCYAVQSDWKAHTKI 103
GEK + CD C + +A + K HTKI
Sbjct: 59 GEKPFACDICGRKFARSDERKRHTKI 84
>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 = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 78 GEKKWKCDKCSKCYAVQSDWKAHTKI 103
GEK + CD C + +A + K HTKI
Sbjct: 59 GEKPFACDICGRKFARSDERKRHTKI 84
>pdb|3LDV|A Chain A, 1.77 Angstrom Resolution Crystal Structure Of Orotidine
5'- Phosphate Decarboxylase From Vibrio Cholerae O1
Biovar Eltor Str. N16961
pdb|3LDV|B Chain B, 1.77 Angstrom Resolution Crystal Structure Of Orotidine
5'- Phosphate Decarboxylase From Vibrio Cholerae O1
Biovar Eltor Str. N16961
pdb|3UWQ|A Chain A, 1.80 Angstrom Resolution Crystal Structure Of Orotidine
5'-Phosphate Decarboxylase From Vibrio Cholerae O1
Biovar Eltor Str. N16961 In Complex With
Uridine-5'-Monophosphate (Ump)
pdb|3UWQ|B Chain B, 1.80 Angstrom Resolution Crystal Structure Of Orotidine
5'-Phosphate Decarboxylase From Vibrio Cholerae O1
Biovar Eltor Str. N16961 In Complex With
Uridine-5'-Monophosphate (Ump)
Length = 255
Score = 28.1 bits (61), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 50/124 (40%), Gaps = 22/124 (17%)
Query: 204 ACAMAIGSSFTSSTALLQKAAEMGTMMRFTVFXXXXXXXXGFLRQGSSNGLYVDKNLEPG 263
A A+A ST L+ EM FT+F F+R+ G V +L+
Sbjct: 40 ADALAFVDKIDPSTCRLKVGKEM-----FTLFGPD------FVRELHKRGFSVFLDLKFH 88
Query: 264 DQRESCSLLQSKNGNAASALVQVHMGGSEKMTADFLWAEVEQPVGSGHSNYGKKRSL--G 321
D +CS +V VH G E+M A E+ +P YGK+R L G
Sbjct: 89 DIPNTCSKAVKAAAELGVWMVNVHASGGERMMA--ASREILEP-------YGKERPLLIG 139
Query: 322 GTVV 325
TV+
Sbjct: 140 VTVL 143
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGH 28
++CEVC + F R ++L+ H + H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|2EP0|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
528- 560) Of Human Zinc Finger Protein 28 Homolog
Length = 46
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGHN 29
Y C+VCHK F+ +L +H++ H
Sbjct: 13 YKCDVCHKSFRYGSSLTVHQRIHT 36
>pdb|2ELZ|A Chain A, Solution Structure Of The 17th Zf-C2h2 Domain From Human
Zinc Finger Protein 224
Length = 46
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 6 YICEVCHKGFQRDQNLQLHRKGH 28
Y CE C KG+ R NL +H++ H
Sbjct: 13 YKCEDCGKGYNRRLNLDMHQRVH 35
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
0.319 0.132 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,611,367
Number of Sequences: 62578
Number of extensions: 295898
Number of successful extensions: 902
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 803
Number of HSP's gapped (non-prelim): 101
length of query: 332
length of database: 14,973,337
effective HSP length: 99
effective length of query: 233
effective length of database: 8,778,115
effective search space: 2045300795
effective search space used: 2045300795
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)