RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13254
(132 letters)
>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic
hypermutat protein-DNA complex, DNA mispair, cancer;
HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B*
2o8e_B* 2o8f_B*
Length = 1022
Score = 122 bits (309), Expect = 8e-34
Identities = 63/138 (45%), Positives = 92/138 (66%), Gaps = 8/138 (5%)
Query: 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQ-RVVRREIC 60
+AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++ K RVVRREIC
Sbjct: 117 NWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREIC 176
Query: 61 KITCRGAQTFSIMDVD--ANY-----VDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFE 113
+I +G QT+S+++ D NY + + GVCF+DT++G+F +G+F
Sbjct: 177 RIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFS 236
Query: 114 DDKQFSRLSTLMSHYPPC 131
DD+ SR TL++HYPP
Sbjct: 237 DDRHCSRFRTLVAHYPPV 254
>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B*
3thy_B* 3thz_B*
Length = 918
Score = 69.6 bits (171), Expect = 3e-15
Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 28/134 (20%)
Query: 20 LVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKI----------------T 63
LV KGYKV V+QTE+A I R + R++ +
Sbjct: 81 LVAKGYKVGVVKQTETAALKAIGDNRSSL------FSRKLTALYTKSTLIGEDVNPLIKL 134
Query: 64 CRGAQTFSIMDVDAN------YVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQ 117
IM + + + + K +G+ + GE F+D
Sbjct: 135 DDAVNVDEIMTDTSTSYLLCISENKENVRDKKKGNIFIGIVGVQPATGEVVFDSFQDSAS 194
Query: 118 FSRLSTLMSHYPPC 131
S L T MS P
Sbjct: 195 RSELETRMSSLQPV 208
>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A*
2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*
Length = 934
Score = 54.6 bits (132), Expect = 6e-10
Identities = 19/131 (14%), Positives = 45/131 (34%), Gaps = 20/131 (15%)
Query: 7 GFPEISYGKF-AQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
++++ F L+ + Y+V + + + +
Sbjct: 79 VLSKMNFESFVKDLLLVRQYRVEVYKNRAG-------------NKASKENDWYLAYKASP 125
Query: 66 G--AQTFSIMDVDANYVDN----KFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFS 119
G +Q I+ + + + + ++GV ++D+ + + EF D+ QFS
Sbjct: 126 GNLSQFEDILFGNNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFS 185
Query: 120 RLSTLMSHYPP 130
L L+ P
Sbjct: 186 NLEALLIQIGP 196
>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA
binding, DNA repair, mismatch recognition; HET: DNA ADP;
2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12
c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A*
1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*
Length = 800
Score = 52.1 bits (126), Expect = 5e-09
Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 21/103 (20%)
Query: 18 QTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDA 77
LV +G VA EQ +K V R++ +I G + D
Sbjct: 81 AKLVNQGESVAICEQIGDPAT----SKG--------PVERKVVRIVTPGTIS------DE 122
Query: 78 NYVDNK---FLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQ 117
+ + L + ++ G +D + G F + E D +
Sbjct: 123 ALLQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEPADRET 165
>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein,
mostly mixed alpha-beta structures, one domain is
entirely helical; HET: DNA; 2.20A {Thermus aquaticus}
SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A*
1fw6_A* 1ewr_A*
Length = 765
Score = 48.2 bits (116), Expect = 1e-07
Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 17/100 (17%)
Query: 18 QTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDA 77
+ L++ G+++A +Q E AE+ + +VRRE+ ++ G +
Sbjct: 83 ERLLKMGFRLAVADQVEPAEE----AE--------GLVRREVTQLLTPGTLLQESLLPRE 130
Query: 78 NYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQ 117
N +L + GD G+ F+D + GEF +
Sbjct: 131 A---N-YLAAIA-TGDGWGLAFLDVSTGEFKGTVLKSKSA 165
>3rr1_A GALD, putative D-galactonate dehydratase; enolase, magnesium
binding site, lyase; 1.95A {Ralstonia pickettii} PDB:
3rra_A
Length = 405
Score = 31.1 bits (71), Expect = 0.081
Identities = 8/58 (13%), Positives = 17/58 (29%), Gaps = 1/58 (1%)
Query: 3 YAHSGFPEIS-YGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREI 59
Y+ G + + L G+ ++ E +D D + +R
Sbjct: 118 YSWVGGDRPADVIAGMKALQAGGFDHFKLNGCEEMGIIDTSRAVDAAVARVAEIRSAF 175
>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 = 28.9 bits (64), Expect = 0.55
Identities = 12/101 (11%), Positives = 32/101 (31%), Gaps = 39/101 (38%)
Query: 2 EY----AHSGFPEISY----------GKFAQTLVEKG------YKVARVEQTESAEQMDI 41
EY + + +S G Q V + Y + + + ++
Sbjct: 1766 EYAALASLADV--MSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAI----NPGRVAA 1819
Query: 42 RTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVDN 82
++ + + + + G +T ++++ NY N
Sbjct: 1820 SFSQEAL--------QYVVE--RVGKRTGWLVEI-VNY--N 1847
>1jfr_A Lipase; serine hydrolase; 1.90A {Streptomyces exfoliatus} SCOP:
c.69.1.16
Length = 262
Score = 26.9 bits (59), Expect = 2.0
Identities = 7/38 (18%), Positives = 14/38 (36%)
Query: 6 SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRT 43
+ S L +G+ V ++ + +Q D R
Sbjct: 63 FTAYQSSIAWLGPRLASQGFVVFTIDTNTTLDQPDSRG 100
>3pe6_A Monoglyceride lipase; alpha-beta hydrolase fold,
2-arachidonyl-glycerol, M associated, hydrolase,
hydrolase-hydrolase inhibitor comple; HET: ZYH; 1.35A
{Homo sapiens} PDB: 3jw8_A 3jwe_A*
Length = 303
Score = 26.5 bits (59), Expect = 2.7
Identities = 7/23 (30%), Positives = 10/23 (43%), Gaps = 4/23 (17%)
Query: 5 HSGFPEISYGKFAQTLVEKGYKV 27
HSG Y + A+ L+ V
Sbjct: 54 HSGR----YEELARMLMGLDLLV 72
>3hju_A Monoglyceride lipase; alpha/beta hydrolase, hydrolase, serine
esterase; 2.20A {Homo sapiens}
Length = 342
Score = 26.6 bits (59), Expect = 3.0
Identities = 7/23 (30%), Positives = 10/23 (43%), Gaps = 4/23 (17%)
Query: 5 HSGFPEISYGKFAQTLVEKGYKV 27
HSG Y + A+ L+ V
Sbjct: 72 HSGR----YEELARMLMGLDLLV 90
>1w9y_A 1-aminocyclopropane-1-carboxylate oxidase 1; oxygenase, 2OG
oxygenase, ACCO, ACC oxidase; 2.1A {Petunia hybrida}
SCOP: b.82.2.1 PDB: 1wa6_X
Length = 319
Score = 26.0 bits (58), Expect = 4.3
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 111 EFEDDKQFSRLSTLMSHYPPC 131
F K + T +S+YPPC
Sbjct: 146 AFYGSKGPN-FGTKVSNYPPC 165
>3lmc_A Peptidase, zinc-dependent; structural genomics, PSI-2, protein
structure initiative, no structural genomics consortium,
NESG, MUR16; 2.00A {Methanocorpusculum labreanum}
Length = 210
Score = 25.5 bits (55), Expect = 5.9
Identities = 10/88 (11%), Positives = 25/88 (28%)
Query: 40 DIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCF 99
R + ++ + + K + + D F+ G+ + +
Sbjct: 62 MFRRRMPQIFKPADMDLEFYNKFNHLHEKILLVTPGDLYEPLADFVFGLAYPKLGVAIVS 121
Query: 100 IDTTIGEFHVGEFEDDKQFSRLSTLMSH 127
EF+ +D R+ +H
Sbjct: 122 PHRLQNEFYGKYADDSALIDRIVKEGAH 149
>2e3j_A Epoxide hydrolase EPHB; epoxide hydrolase B, structural
mycobacterium tuberculosis structural proteomics
project, X hydrolase; 2.10A {Mycobacterium
tuberculosis} PDB: 2zjf_A*
Length = 356
Score = 25.3 bits (55), Expect = 6.6
Identities = 9/23 (39%), Positives = 10/23 (43%), Gaps = 2/23 (8%)
Query: 7 GFPEISYG--KFAQTLVEKGYKV 27
GFPE Y L GY+V
Sbjct: 35 GFPESWYSWRHQIPALAGAGYRV 57
>1llm_C Chimera of ZIF23-GCN4; dimerization, DNA recognition, leucine
zipper, X-RAY crystallography, structure-based design,
zinc fingers; 1.50A {Mus musculus} SCOP: g.37.1.1
g.37.1.1 PDB: 1xf7_A
Length = 88
Score = 24.4 bits (54), Expect = 7.4
Identities = 3/13 (23%), Positives = 6/13 (46%)
Query: 115 DKQFSRLSTLMSH 127
++F+R H
Sbjct: 38 GRKFARSDERKRH 50
Score = 24.4 bits (54), Expect = 7.7
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 115 DKQFSRLSTLMSH 127
+ FSR L +H
Sbjct: 10 MRNFSRSDHLTTH 22
Score = 24.4 bits (54), Expect = 7.9
Identities = 2/18 (11%), Positives = 7/18 (38%)
Query: 115 DKQFSRLSTLMSHYPPCR 132
++ S+ L + +
Sbjct: 65 EELLSKNYHLENEVARLK 82
>2gli_A Protein (five-finger GLI); protein/DNA complex, transcription/DNA
complex; HET: DNA; 2.60A {Homo sapiens} SCOP: g.37.1.1
g.37.1.1 g.37.1.1 g.37.1.1 g.37.1.1
Length = 155
Score = 24.9 bits (55), Expect = 8.3
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 116 KQFSRLSTLMSH 127
K +SRL L +H
Sbjct: 77 KSYSRLENLKTH 88
>3ksr_A Putative serine hydrolase; catalytic triad, structural genomics,
JOIN for structural genomics, JCSG; 2.69A {Xanthomonas
campestris PV}
Length = 290
Score = 24.8 bits (54), Expect = 9.8
Identities = 8/55 (14%), Positives = 13/55 (23%), Gaps = 16/55 (29%)
Query: 3 YAHSGFPEI--SYGKFAQTLVEKGYKVARV-------------EQTESAEQMDIR 42
+ H G+ A+ V G T + DI+
Sbjct: 33 FVH-GWGGSQHHSLVRAREAVGLGCICMTFDLRGHEGYASMRQSVTRAQNLDDIK 86
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
0.321 0.136 0.402
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,932,670
Number of extensions: 101967
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 38
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
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 (21.8 bits)
S2: 52 (23.7 bits)