RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17514
(159 letters)
>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome
segregation, cell adhesion, kleisin, MIT cell cycle;
HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP:
c.37.1.12
Length = 430
Score = 126 bits (319), Expect = 2e-35
Identities = 48/167 (28%), Positives = 78/167 (46%), Gaps = 14/167 (8%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTL 61
+ + L FKSY ++ + F +I G NG+GKSN++D I FVLG++ +R+N L
Sbjct: 3 RLVGLELSNFKSYRGVTKVGFGESNFTSIIGPNGSGKSNMMDAISFVLGVRSNHLRSNIL 62
Query: 62 QELIY--------KNGQAGVTKASVTLTFDNSDKKNCPIGYENDNT-IVICRQISIPSNT 112
++LIY + AS Y+ N + + R IS +T
Sbjct: 63 KDLIYRGVLNDENSDDYDNEGAASSNPQSAYVKAF-----YQKGNKLVELMRIISRNGDT 117
Query: 113 RYMINGSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
Y I+G +V+ K S + N+ + +FL+ QG V ++ P E
Sbjct: 118 SYKIDGKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVE 164
>3kta_A Chromosome segregation protein SMC; structural maintenance of
chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A,
transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB:
1xex_A* 1xew_X*
Length = 182
Score = 118 bits (299), Expect = 9e-35
Identities = 54/163 (33%), Positives = 87/163 (53%), Gaps = 10/163 (6%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRAN 59
YI+ + L GFKSYG + + F + F AI G NG+GKSNI D I FVLG K +RA+
Sbjct: 2 PYIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRAS 61
Query: 60 TLQELIYKNGQAG---VTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMI 116
+ +LI+ G A V + F+N D+ PI + +VI R++ + Y +
Sbjct: 62 RISDLIF-AGSKNEPPAKYAEVAIYFNNEDRG-FPIDE---DEVVIRRRVYPDGRSSYWL 116
Query: 117 NGSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
NG + D+ ++ ++ + + +++QG +TK + M P E
Sbjct: 117 NGRRATRSEILDILTAAMIS-PDGYNIVLQGDITKFIKMSPLE 158
>1e69_A Chromosome segregation SMC protein; structural maintenance of
chromosomes, coiled coil; 3.1A {Thermotoga maritima}
SCOP: c.37.1.12
Length = 322
Score = 108 bits (271), Expect = 3e-29
Identities = 51/163 (31%), Positives = 80/163 (49%), Gaps = 18/163 (11%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRAN 59
M +K + L GFKS+G I F AI G NG+GKSNI+D I +V G Q K++RA+
Sbjct: 1 MRLKKLYLKGFKSFGRPSLI-GFSDRVTAIVGPNGSGKSNIIDAIKWVFGEQSKKELRAS 59
Query: 60 TLQELIYKNGQAG---VTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMI 116
++I+ G A V L F+ + I + R++ Y +
Sbjct: 60 EKFDMIF-AGSENLPPAGSAYVELVFEEN-----------GEEITVARELKRTGENTYYL 107
Query: 117 NGSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
NGS V K + D F+ L V+ + ++ QG++ +++N P E
Sbjct: 108 NGSPVRLKDIRDRFAGTGLGVDF-YSIVGQGQIDRIVNASPEE 149
>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC
transporter ATPase domain-like; HET: DNA ADP; 2.70A
{Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*
Length = 371
Score = 80.3 bits (198), Expect = 1e-18
Identities = 40/165 (24%), Positives = 64/165 (38%), Gaps = 26/165 (15%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M +K + ++ FKS+ I F++ AI G NG+GKS+I + + F L
Sbjct: 3 MILKEIRMNNFKSHV-NSRI-KFEKGIVAIIGENGSGKSSIFEAVFFALF---GAGSNFN 57
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGSS 120
+I K V L F+ + Y+ I R+ +
Sbjct: 58 YDTIITKGK----KSVYVELDFEVNGNN-----YK------IIREYDSGRGGAKLYKNGK 102
Query: 121 VNPKRVSDLFSSVN--LNVNNPHF----LIMQGRVTKVLNMKPHE 159
+S + +VN L V+ F I QG + K L++KP E
Sbjct: 103 PYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSE 147
>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold,
coiled-coils, ATPase, exonuclease, endonucle binding,
DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB:
3qkr_A*
Length = 203
Score = 77.4 bits (191), Expect = 2e-18
Identities = 26/170 (15%), Positives = 57/170 (33%), Gaps = 30/170 (17%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M ++ + + F+S+ + +F N I G NG+GKS++LD I L ++ ++
Sbjct: 1 MKLERVTVKNFRSHS-DTVV-EFKEGINLIIGQNGSGKSSLLDAILVGLYWPLR-IKDIK 57
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGSS 120
E + L F+ K Y I R+ ++ +
Sbjct: 58 KDEFTKVGA----RDTYIDLIFEKDGTK-----YR------ITRRFLKGYSSGEIHAMKR 102
Query: 121 VNPKRVSDLFSSVNLNVNNPHFLIM------------QGRVTKVLNMKPH 158
+ + + ++ ++ QG++ +L
Sbjct: 103 LVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEA 152
>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication;
1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB:
1f2u_A* 1us8_A*
Length = 149
Score = 72.8 bits (179), Expect = 3e-17
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 7/88 (7%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M ++ + + F+S+ + +F N I G NG+GKS++LD I L ++ ++
Sbjct: 1 MKLERVTVKNFRSHS-DTVV-EFKEGINLIIGQNGSGKSSLLDAILVGLYWPLR-IKDIK 57
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKK 88
E G + L F+ K
Sbjct: 58 KDEFTKV----GARDTYIDLIFEKDGTK 81
>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga
maritima} PDB: 3qg5_A 3tho_A*
Length = 365
Score = 65.3 bits (159), Expect = 3e-13
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 8/89 (8%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVL-GIQVKQVRAN 59
M + + + F V+I +F + G NG GKS++ + I F L G +R
Sbjct: 1 MRPERLTVRNFLGLKN-VDI-EFQSGITVVEGPNGAGKSSLFEAISFALFG---NGIRYP 55
Query: 60 TLQELIYKNGQAGVTKASVTLTFDNSDKK 88
+ + +N A A + F+ K+
Sbjct: 56 NSYDYVNRN--AVDGTARLVFQFERGGKR 82
>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold,
coiled-coils, ATP binding, DNA bindi MRE11, replication;
HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A*
1ii8_A 3qks_B* 3qkr_B* 1ii8_B
Length = 339
Score = 65.1 bits (158), Expect = 3e-13
Identities = 29/158 (18%), Positives = 59/158 (37%), Gaps = 12/158 (7%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M ++ + + F+S+ + +F N I G NG+GKS++LD I L +++
Sbjct: 1 MKLERVTVKNFRSHS-DTVV-EFKEGINLIIGQNGSGKSSLLDAILVGLYWP-LRIKDIK 57
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKK---NCPIGYENDNTIVICRQISIPSNTRYMIN 117
E G + L F+ K + + + + + +++
Sbjct: 58 KDEFTKV----GARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTE 113
Query: 118 GSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNM 155
SS + N+ +N I QG++ +L
Sbjct: 114 PSSKAISAFMEKLIPYNIFLNA--IYIRQGQIDAILES 149
>2o5v_A DNA replication and repair protein RECF; ABC ATPase, walker A
motif, P-loop, signature motif,
replication/recombination complex; HET: DNA; 1.61A
{Deinococcus radiodurans}
Length = 359
Score = 57.2 bits (139), Expect = 1e-10
Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
+ + ++ +++ + +F I G NG GK+N+L+ L Q A
Sbjct: 4 VRLSALSTLNYRNL-APGTL-NFPEGVTGIYGENGAGKTNLLEAAYLALT---GQTDAPR 58
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKK 88
+++LI QAG T+A V
Sbjct: 59 IEQLI----QAGETEAYVRADLQQGGSL 82
>1qhl_A Protein (cell division protein MUKB); SMC, chromosome partitioning;
2.20A {Escherichia coli} SCOP: c.37.1.12
Length = 227
Score = 41.4 bits (96), Expect = 4e-05
Identities = 18/99 (18%), Positives = 31/99 (31%), Gaps = 10/99 (10%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQ 62
+S+ L + + R D D ++G NG GKS + L + +
Sbjct: 7 FRSLTLINWNGFFARTF--DLDELVTTLSGGNGAGKSTTMAAFVTALIPDLTLLHFRNTT 64
Query: 63 EL--------IYKNGQAGVTKASVTLTFDNSDKKNCPIG 93
E +G+ L NS + +G
Sbjct: 65 EAGATSGSRDKGLHGKLKAGVCYSMLDTINSRHQRVVVG 103
>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome
condensation, condensin, SMC, N subunit, ABC-type
ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus
ducreyi} PDB: 3euk_A*
Length = 483
Score = 41.4 bits (96), Expect = 5e-05
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQ 62
+S+ L + + R DFD ++G NG GKS + G L + +
Sbjct: 9 FRSLTLINWNGFFARTF--DFDELVTTLSGGNGAGKSTTMAGFVTALIPDLTLLNFRNTT 66
Query: 63 E 63
E
Sbjct: 67 E 67
>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 = 32.3 bits (73), Expect = 0.057
Identities = 28/150 (18%), Positives = 43/150 (28%), Gaps = 66/150 (44%)
Query: 26 EFNAITGLNGTGKSNILDGICFVLGIQ--VKQV--RANTLQELIYKN-------GQAGVT 74
E+ A+ L V+ I+ V+ V R T+Q + ++ G +
Sbjct: 1766 EYAALASLAD------------VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN 1813
Query: 75 KASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGSSVNPKRVSDLFSSVN 134
V +F + + ++ KR L VN
Sbjct: 1814 PGRVAASFSQEALQY------------VVERVG----------------KRTGWLVEIVN 1845
Query: 135 LNVNNPHFLIMQ----G------RVTKVLN 154
NV N Q G VT VLN
Sbjct: 1846 YNVEN-----QQYVAAGDLRALDTVTNVLN 1870
>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 = 31.0 bits (69), Expect = 0.18
Identities = 22/148 (14%), Positives = 38/148 (25%), Gaps = 56/148 (37%)
Query: 29 AITGLNGTGKSNILDGICFVLGIQVKQVRANTLQEL----IYKNGQAGVTKASVTLTFDN 84
I G+ G+GK+ + + V + +Q I+ L N
Sbjct: 154 LIDGVLGSGKT--------WVALDV--CLSYKVQCKMDFKIF------------WLNLKN 191
Query: 85 SDKKNCPIGYENDNTIVICRQI--------SIPSNTRYMINGSSVNPKRVSDLFSSVNL- 135
+ + E + QI SN + I+ + L S
Sbjct: 192 CNSPETVL--EMLQK--LLYQIDPNWTSRSDHSSNIKLRIHSIQ---AELRRLLKSKPYE 244
Query: 136 -------NVNNPHFLIMQGRVTKVLNMK 156
NV N + N+
Sbjct: 245 NCLLVLLNVQNA-------KAWNAFNLS 265
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
Length = 986
Score = 28.1 bits (62), Expect = 1.6
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 12 KSYGTRVEINDFDREFN-----AITGLNGTGKSNILDGI 45
+YG ++ +N I G NG GKS ++ I
Sbjct: 443 LAYGAKILLNKTQLRLKRARRYGICGPNGCGKSTLMRAI 481
>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette,
hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}
Length = 279
Score = 27.2 bits (61), Expect = 2.4
Identities = 7/36 (19%), Positives = 14/36 (38%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDFD-----REFNAITGLNGTGKSNIL 42
+ + + + + GLNG GK+ +L
Sbjct: 29 RMKQGKTILKKISWQIAKGDKWILYGLNGAGKTTLL 64
>3tif_A Uncharacterized ABC transporter ATP-binding prote;
nucleotide-binding domain, ABC transporter ATPase; HET:
ADP; 1.80A {Methanocaldococcus jannaschii dsm
2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*
Length = 235
Score = 26.0 bits (58), Expect = 5.8
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 10/49 (20%)
Query: 26 EFNAITGLNGTGKS---NIL-------DGICFVLGIQVKQVRANTLQEL 64
EF +I G +G+GKS NI+ +G ++ I+ + + L ++
Sbjct: 32 EFVSIMGPSGSGKSTMLNIIGCLDKPTEGEVYIDNIKTNDLDDDELTKI 80
>2it1_A 362AA long hypothetical maltose/maltodextrin transport
ATP-binding protein; structural genomics, NPPSFA; 1.94A
{Pyrococcus horikoshii}
Length = 362
Score = 25.6 bits (57), Expect = 7.5
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDF-----DREFNAITGLNGTGKSNIL 42
K +G +N+ D EF A+ G +G+GKS +L
Sbjct: 11 KKFGNFTALNNINLKIKDGEFMALLGPSGSGKSTLL 46
>2r2a_A Uncharacterized protein; zonular occludens toxin, structural
genomics, APC84050.2, PS protein structure initiative;
HET: MSE; 1.82A {Neisseria meningitidis MC58}
Length = 199
Score = 25.4 bits (55), Expect = 9.0
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 25 REFNAITGLNGTGKS 39
E ITG G+GK+
Sbjct: 5 AEICLITGTPGSGKT 19
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 0.136 0.389
Gapped
Lambda K H
0.267 0.0839 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,294,675
Number of extensions: 123369
Number of successful extensions: 349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 334
Number of HSP's successfully gapped: 34
Length of query: 159
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,300,587
Effective search space: 313942851
Effective search space used: 313942851
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 (21.7 bits)
S2: 53 (24.0 bits)