RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4875
(100 letters)
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX,
paired domain, DNA-binding protein, gene regulation/DNA
complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP:
a.4.1.5
Length = 128
Score = 77.8 bits (191), Expect = 3e-20
Identities = 36/65 (55%), Positives = 49/65 (75%)
Query: 9 PLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSN 68
+++RY ETGSIRP IGGSKPR+AT E+ ++I YKR P +F+WEIR++L++EGVC
Sbjct: 52 KILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDR 111
Query: 69 DNIPS 73
PS
Sbjct: 112 STAPS 116
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple
frequency, 3D NMR, induced FIT, alternative splicing,
developmental protein; NMR {Homo sapiens}
Length = 159
Score = 74.9 bits (183), Expect = 9e-19
Identities = 45/64 (70%), Positives = 53/64 (82%)
Query: 10 LVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSND 69
++ RYYETGSIRP IGGSKP+VAT +VV KI YKR+ P++FAWEIRDRLL EGVC ND
Sbjct: 61 ILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDND 120
Query: 70 NIPS 73
+PS
Sbjct: 121 TVPS 124
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription
factor, transcription/DNA complex; 2.25A {Homo sapiens}
SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A
Length = 149
Score = 74.4 bits (182), Expect = 9e-19
Identities = 43/64 (67%), Positives = 53/64 (82%)
Query: 10 LVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSND 69
++ RYYETGSI+P IGGSKP+VAT +VV KI+ YKR+ P++FAWEIRDRLL E VC ND
Sbjct: 68 ILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDND 127
Query: 70 NIPS 73
+PS
Sbjct: 128 TVPS 131
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 40.6 bits (94), Expect = 2e-05
Identities = 6/39 (15%), Positives = 15/39 (38%)
Query: 35 AEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPS 73
A + + +E P A ++ L Q + + + +
Sbjct: 14 AHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDT 52
Score = 32.2 bits (72), Expect = 0.014
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 74 RECPSIFAWEIRDRLLQEGVCSNDNIP 100
+E P A ++ L Q + + +
Sbjct: 25 QEDPWRVAKMVKSYLQQHNIPQREVVD 51
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 37.7 bits (86), Expect = 2e-04
Identities = 9/86 (10%), Positives = 25/86 (29%), Gaps = 20/86 (23%)
Query: 35 AEVVSKISHYKRECPSIFAWEIRDRLLQEGVC--------------------SNDNIPSR 74
AE +++ E P A I+ + Q + + ++
Sbjct: 15 AEQRAEVDRMLSEDPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGTPMKTQ 74
Query: 75 ECPSIFAWEIRDRLLQEGVCSNDNIP 100
+ +++ W +R + +
Sbjct: 75 KRAALYTWYVRKQREILRQFNQTVQS 100
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 28.5 bits (63), Expect = 0.42
Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 36/92 (39%)
Query: 32 VATAEVVS-----KISHYKRECPSIFAWEIRDRLLQEGV------CSNDNI----PSREC 76
+ A+V+S ++ Y R +Q V SN + P R
Sbjct: 1771 ASLADVMSIESLVEVVFY------------RGMTMQVAVPRDELGRSNYGMIAINPGRVA 1818
Query: 77 PSIFAWE----IRDRLLQE--GVCS--NDNIP 100
S F+ E + +R+ + + N N+
Sbjct: 1819 AS-FSQEALQYVVERVGKRTGWLVEIVNYNVE 1849
Score = 25.4 bits (55), Expect = 4.2
Identities = 8/55 (14%), Positives = 14/55 (25%), Gaps = 19/55 (34%)
Query: 20 IRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCS--NDNIP 72
I P + S + A VV ++ + N N+
Sbjct: 1812 INPGRVAASFSQEALQYVVERVGKR-----------------TGWLVEIVNYNVE 1849
>1zcj_A Peroxisomal bifunctional enzyme; peroxisomal multifunctional enzyme
type 1, L-bifunction enzyme, MFE-1, fatty acid beta
oxidation; 1.90A {Rattus norvegicus}
Length = 463
Score = 25.3 bits (56), Expect = 4.5
Identities = 9/40 (22%), Positives = 14/40 (35%)
Query: 53 AWEIRDRLLQEGVCSNDNIPSRECPSIFAWEIRDRLLQEG 92
W+IR G P R+ + + D L + G
Sbjct: 270 GWKIRKGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAG 309
>3zxs_A Cryptochrome B, rscryb; lyase, cryPro, lumazine,
iron-sulfur-cluster; HET: FAD DLZ; 2.70A {Rhodobacter
sphaeroides}
Length = 522
Score = 25.1 bits (55), Expect = 5.5
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 27 GSKPRVATAEVVSKISHYKREC 48
GSKP V++ + ++S Y R C
Sbjct: 430 GSKPYVSSGAYIDRMSDYCRGC 451
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 24.6 bits (53), Expect = 5.7
Identities = 5/18 (27%), Positives = 7/18 (38%)
Query: 52 FAWEIRDRLLQEGVCSND 69
FA + R L G+
Sbjct: 9 FAKNFKIRRLSLGLTQTQ 26
Score = 24.6 bits (53), Expect = 5.7
Identities = 5/18 (27%), Positives = 7/18 (38%)
Query: 80 FAWEIRDRLLQEGVCSND 97
FA + R L G+
Sbjct: 9 FAKNFKIRRLSLGLTQTQ 26
>2wyr_A Cobalt-activated peptidase TET1; hydrolase, large SELF-assembled
dodecamer, hyperthermophilic; 2.24A {Pyrococcus
horikoshii} PDB: 2cf4_A
Length = 332
Score = 24.5 bits (54), Expect = 7.4
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 10 LVHRYYETGSIRPRAIGGSKPRVATAEVV 38
L+ + G +R R +GG R+ V
Sbjct: 69 LITGITDEGKLRFRKVGGIDDRLLYGRHV 97
>3zwc_A Peroxisomal bifunctional enzyme; beta oxidation pathway,
oxidoreductase, lipid metabolism, LY isomerase,
peroxisome, fatty acid metabolism; HET: NAD HSC; 2.30A
{Rattus norvegicus} PDB: 3zw9_A* 3zw8_A* 3zwa_A* 3zwb_A*
2x58_A*
Length = 742
Score = 24.5 bits (54), Expect = 8.0
Identities = 9/40 (22%), Positives = 14/40 (35%)
Query: 53 AWEIRDRLLQEGVCSNDNIPSRECPSIFAWEIRDRLLQEG 92
W+IR G P R+ + + D L + G
Sbjct: 549 GWKIRKGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAG 588
>3isx_A Endoglucanase; TM1050, structural genomics, joint center for
structural genomics, JCSG, protein structure initiative,
PSI-2, hydrolase; HET: MSE; 1.40A {Thermotoga maritima}
Length = 343
Score = 24.2 bits (53), Expect = 9.7
Identities = 5/29 (17%), Positives = 12/29 (41%)
Query: 10 LVHRYYETGSIRPRAIGGSKPRVATAEVV 38
+V + G + +GG P + + +
Sbjct: 79 VVTNVDDKGFLTIEPVGGVSPYMLLGKRI 107
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.139 0.444
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,554,966
Number of extensions: 77522
Number of successful extensions: 136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 133
Number of HSP's successfully gapped: 21
Length of query: 100
Length of database: 6,701,793
Length adjustment: 66
Effective length of query: 34
Effective length of database: 4,859,007
Effective search space: 165206238
Effective search space used: 165206238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.6 bits)