RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13255
(156 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 = 104 bits (261), Expect = 7e-27
Identities = 38/89 (42%), Positives = 54/89 (60%), Gaps = 1/89 (1%)
Query: 1 ILDSTALANLHVLTN-SDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
+LD+ L NL + N ++ +TEGTL+E++D C T FGKR+L+ L PL N AI R D
Sbjct: 396 VLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLD 455
Query: 60 AISVLLDQKHITEQMRAKMKDLRDLERML 88
AI L+ ++ +K L DLER+L
Sbjct: 456 AIEDLMVVPDKISEVVELLKKLPDLERLL 484
Score = 95.5 bits (238), Expect = 7e-24
Identities = 31/59 (52%), Positives = 44/59 (74%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
GC VPA+ LTP+DR+FTR+GA D + +ST+ EL+E+ +I+ HA+ +SL LVDEL
Sbjct: 819 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 877
>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 = 90.8 bits (226), Expect = 3e-22
Identities = 44/162 (27%), Positives = 73/162 (45%), Gaps = 12/162 (7%)
Query: 1 ILDSTALANLHVLTN-SDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
++ T L NL +L N +D T+G+L+ LDH TSFG+R L+ + +PL L I R D
Sbjct: 320 TINGTTLRNLEILQNQTDMKTKGSLLWVLDHTKTSFGRRKLKKWVTQPLLKLREINARLD 379
Query: 60 AISVLLDQKHIT-EQMRAKMKDLRDLERMLPSSTFLSFQGCRVPAD--SL--TLTPVDRI 114
A+S +L + Q+ ++ L D+ER L + + C + + TL +
Sbjct: 380 AVSEVLHSESSVFGQIENHLRKLPDIERGL---CSIYHKKCS-TQEFFLIVKTLYHLKSE 435
Query: 115 FTRMGAKDNLSGAQSTYLAELTES-ETIMRHASKYSLALVDE 155
F + S QS L + ++ Y L ++
Sbjct: 436 FQAI-IPAVNSHIQSDLLRTVILEIPELLSPVEHYLKILNEQ 476
Score = 87.3 bits (217), Expect = 5e-21
Identities = 29/59 (49%), Positives = 41/59 (69%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA+ T+ VD IFTRMGA DN+ +ST++ ELT++ I+R A+ SL ++DEL
Sbjct: 703 GSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKATSQSLVILDEL 761
>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 = 82.5 bits (205), Expect = 2e-19
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 2/88 (2%)
Query: 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
L L L V + TL LD T+ G+R+L++ L PL + ++ R D
Sbjct: 251 RLPEATLRALEVFEPL--RGQDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEARLDR 308
Query: 61 ISVLLDQKHITEQMRAKMKDLRDLERML 88
+ + + + E +R + L DLER+
Sbjct: 309 VEGFVREGALREGVRRLLYRLADLERLA 336
Score = 79.1 bits (196), Expect = 3e-18
Identities = 25/59 (42%), Positives = 40/59 (67%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA+ L D I+TR+GA D+L+G +ST++ E+ E I++ A++ SL L+DE+
Sbjct: 606 GSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEV 664
>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 = 82.0 bits (203), Expect = 4e-19
Identities = 26/59 (44%), Positives = 40/59 (67%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
GC VP +S ++ VD I R+GA D+ ST++AE+ E+ +I+R A+K SL ++DEL
Sbjct: 692 GCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDEL 750
Score = 78.9 bits (195), Expect = 5e-18
Identities = 20/91 (21%), Positives = 45/91 (49%), Gaps = 3/91 (3%)
Query: 1 ILDSTALANLHVLTNS--DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQ 58
LD A+ L++ S D T +L L+ C T G+R++ + +PL + + I++R
Sbjct: 301 KLDIAAVRALNLFQGSVEDTTGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERL 360
Query: 59 DAISVLLDQKHITEQMRAK-MKDLRDLERML 88
+ + ++ + + ++ ++ DL R+
Sbjct: 361 NLVEAFVEDAELRQTLQEDLLRRFPDLNRLA 391
>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 = 81.4 bits (202), Expect = 6e-19
Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
I+D+ NL + N E TL LD VT G RML+ L P+ + + +RQ
Sbjct: 268 IMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQT 327
Query: 61 ISVLLDQKHITEQMRAKMKDLRDLERML 88
I L D ++ ++ + DLER+L
Sbjct: 328 IGALQDFT---AGLQPVLRQVGDLERIL 352
Score = 79.1 bits (196), Expect = 5e-18
Identities = 28/59 (47%), Positives = 45/59 (76%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA + + P+DRIFTR+GA D+L+ +ST++ E+TE+ I+ +A++YSL L+DE+
Sbjct: 637 GSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEI 695
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.8 bits (79), Expect = 0.009
Identities = 16/86 (18%), Positives = 29/86 (33%), Gaps = 17/86 (19%)
Query: 11 HVLTNSDNTTEGTLIEQ--LDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD-- 66
H L N ++ TL LD F R L ++ T +A ++ L
Sbjct: 480 H-LKNIEHPERMTLFRMVFLD-----F--RFLEQKIRHDSTAWNA---SGSILNTLQQLK 528
Query: 67 --QKHITEQMRAKMKDLRDLERMLPS 90
+ +I + + + + LP
Sbjct: 529 FYKPYICDNDPKYERLVNAILDFLPK 554
Score = 28.3 bits (62), Expect = 1.4
Identities = 21/154 (13%), Positives = 46/154 (29%), Gaps = 50/154 (32%)
Query: 48 LTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERML------------------- 88
D + +DA D K + + ++ + +++ ++
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSK 74
Query: 89 PSSTFLSFQG-----------------CRVPADSLTL--TPVDRIFT--RMGAKDNLSGA 127
F R P+ + DR++ ++ AK N+S
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL 134
Query: 128 QS-----TYLAELTESETIMRH----ASKYSLAL 152
Q L EL ++ ++ + K +AL
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL 168
>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 = 32.7 bits (74), Expect = 0.044
Identities = 28/156 (17%), Positives = 51/156 (32%), Gaps = 45/156 (28%)
Query: 11 HVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQ----LVKPLTNLD--AIKQRQDAISVL 64
+V + + + G + L+ C+T F L L L + + + ++ I
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNY 126
Query: 65 LDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNL 124
+ A++ R ++ S+ F + V + L IF
Sbjct: 127 I---------TARIMAKRPFDKKSNSALFRA-----VGEGNAQLVA---IF--------- 160
Query: 125 SGAQ---STYLAELTE-SETIMRHASKYSLALVDEL 156
G Q Y EL + +T Y LV +L
Sbjct: 161 -GGQGNTDDYFEELRDLYQT-------YH-VLVGDL 187
Score = 29.2 bits (65), Expect = 0.71
Identities = 25/152 (16%), Positives = 49/152 (32%), Gaps = 46/152 (30%)
Query: 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVT-SF--GKRMLRAQLVKPLTNLDAIKQR 57
++ + A+A +D + + + +T F G +R P T+L
Sbjct: 277 LVTAVAIAE------TD--SWESFFVSVRKAITVLFFIG---VRCYEAYPNTSLPP-SIL 324
Query: 58 QDAI-----------SVL-LDQKHITEQMRAKMKDLRDLERMLPSSTFLS---FQGCR-- 100
+D++ S+ L Q+ + + LP+ + G +
Sbjct: 325 EDSLENNEGVPSPMLSISNLTQEQVQ-------DYVNKTNSHLPAGKQVEISLVNGAKNL 377
Query: 101 V---PADSLTLTPVDRIFTRMGAKDNLSGAQS 129
V P SL ++ + A L QS
Sbjct: 378 VVSGPPQSLYG--LNLTLRKAKAPSGLD--QS 405
>2olv_A Penicillin-binding protein 2; transpeptidase fold,
glycosyltransferase family 51, lysozyme transferase;
HET: M0E; 2.80A {Staphylococcus aureus} SCOP: d.2.1.10
e.3.1.1 PDB: 2olu_A* 3dwk_A*
Length = 669
Score = 27.7 bits (62), Expect = 1.6
Identities = 9/40 (22%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 47 PLTNLDAIKQRQDAI-SVLLDQKHITEQM--RAKMKDLRD 83
+ A + R++ + ++ K IT++ AK DL+
Sbjct: 181 IYDHPKAAEDRKNTVLYLMHYHKRITDKQWEDAKKIDLKA 220
>3vk8_A Probable formamidopyrimidine-DNA glycosylase; DNA glycosylase,
hneil1 ortholog, DNA lesion, thymine glycol zincless
finger; HET: DNA CTG; 2.00A {Acanthamoeba polyphaga
mimivirus} PDB: 3vk7_A* 3a42_A 3a46_A* 3a45_A*
Length = 295
Score = 26.5 bits (59), Expect = 3.6
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 5/29 (17%)
Query: 47 PLTNLD----AIKQRQDAI-SVLLDQKHI 70
L N D IK+ + I ++L+DQK I
Sbjct: 139 FLKNDDIDISKIKKYKQPIVALLMDQKKI 167
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 24.3 bits (53), Expect = 7.1
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 8/49 (16%)
Query: 105 SLTLTPVDRIFTRMG-------AKDNLSGAQSTYLAELT-ESETIMRHA 145
L + PVDR+ + G A L+ Y E+ ++ RHA
Sbjct: 6 ELPIAPVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHA 54
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
0.318 0.130 0.353
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,159,772
Number of extensions: 117175
Number of successful extensions: 295
Number of sequences better than 10.0: 1
Number of HSP's gapped: 291
Number of HSP's successfully gapped: 28
Length of query: 156
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 70
Effective length of database: 4,300,587
Effective search space: 301041090
Effective search space used: 301041090
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)