RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16868
(109 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 = 85.5 bits (212), Expect = 3e-21
Identities = 26/99 (26%), Positives = 37/99 (37%), Gaps = 9/99 (9%)
Query: 2 YIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSDS 61
+ + + FKSY+ T V + ++G NGSGKSN AI FVL S LR S+
Sbjct: 3 RLVGLELSNFKSYRGVTKVGFGESNFTSIIGPNGSGKSNMMDAISFVLGVRSNHLR-SNI 61
Query: 62 RQALLHEGTGPR--------VVNAYVEIVFDNTDHRVPG 92
+ L++ G A
Sbjct: 62 LKDLIYRGVLNDENSDDYDNEGAASSNPQSAYVKAFYQK 100
>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 = 77.2 bits (191), Expect = 2e-19
Identities = 37/95 (38%), Positives = 49/95 (51%), Gaps = 4/95 (4%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDEST-SLRHS 59
YI+++ + GFKSY + VV PF K +VG NGSGKSN AI FVL S ++R +
Sbjct: 2 PYIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMR-A 60
Query: 60 DSRQALLHEGTGPR--VVNAYVEIVFDNTDHRVPG 92
L+ G+ A V I F+N D P
Sbjct: 61 SRISDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPI 95
>1e69_A Chromosome segregation SMC protein; structural maintenance of
chromosomes, coiled coil; 3.1A {Thermotoga maritima}
SCOP: c.37.1.12
Length = 322
Score = 74.6 bits (184), Expect = 1e-17
Identities = 30/93 (32%), Positives = 52/93 (55%), Gaps = 5/93 (5%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDEST-SLRHS 59
M +K++ + GFKS+ +++ F R +VG NGSGKSN AI++V ++S LR +
Sbjct: 1 MRLKKLYLKGFKSFGRPSLIG-FSDRVTAIVGPNGSGKSNIIDAIKWVFGEQSKKELR-A 58
Query: 60 DSRQALLHEGTGPR--VVNAYVEIVFDNTDHRV 90
+ ++ G+ +AYVE+VF+ +
Sbjct: 59 SEKFDMIFAGSENLPPAGSAYVELVFEENGEEI 91
>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 = 74.5 bits (183), Expect = 3e-17
Identities = 25/107 (23%), Positives = 51/107 (47%), Gaps = 12/107 (11%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSD 60
M +K++ ++ FKS+ + F+K ++G NGSGKS+ F A+ F L ++ +
Sbjct: 3 MILKEIRMNNFKSHVNSRI--KFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDT 60
Query: 61 SRQALLHEGTGPRVVNAYVEIVF--DNTDHRVPGFIRCRSTSVDLYR 105
++ +G + YVE+ F + ++++ LY+
Sbjct: 61 ----IITKGKK----SVYVELDFEVNGNNYKIIREYDSGRGGAKLYK 99
>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 = 70.0 bits (172), Expect = 2e-16
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSD 60
M +++V + F+S+ + V F + N+++G+NGSGKS+ AI L
Sbjct: 1 MKLERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAILVGLYWPLR--IKDI 56
Query: 61 SRQALLHEGTGPRVVNAYVEIVFDNTDHR 89
+ G + Y++++F+ +
Sbjct: 57 KKDEFTKVGAR----DTYIDLIFEKDGTK 81
>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 = 67.4 bits (165), Expect = 8e-16
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSD 60
M +++V + F+S+ + V F + N+++G+NGSGKS+ AI L
Sbjct: 1 MKLERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAILVGLYWPLR--IKDI 56
Query: 61 SRQALLHEGTGPRVVNAYVEIVFDNTDHR 89
+ G + Y++++F+ +
Sbjct: 57 KKDEFTKVGAR----DTYIDLIFEKDGTK 81
>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 = 62.4 bits (151), Expect = 6e-13
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSD 60
M +++V + F+S+ + V F + N+++G+NGSGKS+ AI L
Sbjct: 1 MKLERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKK 58
Query: 61 SRQALLHEGTGPRVVNAYVEIVFDNTDHR 89
G + Y++++F+ +
Sbjct: 59 DE--FTKVGAR----DTYIDLIFEKDGTK 81
>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 = 52.6 bits (127), Expect = 1e-09
Identities = 15/91 (16%), Positives = 28/91 (30%), Gaps = 10/91 (10%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSD 60
+ + + +++ T+ F + + G NG+GK+N A L +
Sbjct: 4 VRLSALSTLNYRNLAPGTL--NFPEGVTGIYGENGAGKTNLLEAAYLAL---TGQTDAPR 58
Query: 61 SRQALLHEGTGPRVVNAYVEIVFDNTDHRVP 91
Q + T AYV
Sbjct: 59 IEQLIQAGETE-----AYVRADLQQGGSLSI 84
>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga
maritima} PDB: 3qg5_A 3tho_A*
Length = 365
Score = 47.9 bits (114), Expect = 6e-08
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 7/89 (7%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSD 60
M +++ + F K + F VV G NG+GKS+ F AI F L R+ +
Sbjct: 1 MRPERLTVRNFLGLKNVDI--EFQSGITVVEGPNGAGKSSLFEAISFALFGNGI--RYPN 56
Query: 61 SRQALLHEGTGPRVVNAYVEIVFDNTDHR 89
S ++ A + F+ R
Sbjct: 57 SYD-YVNRNAVDGT--ARLVFQFERGGKR 82
>1qhl_A Protein (cell division protein MUKB); SMC, chromosome
partitioning; 2.20A {Escherichia coli} SCOP: c.37.1.12
Length = 227
Score = 39.0 bits (90), Expect = 6e-05
Identities = 21/96 (21%), Positives = 34/96 (35%), Gaps = 13/96 (13%)
Query: 3 IKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLR----- 57
+ + + + + +T D+ + G NG+GKS A L + T L
Sbjct: 7 FRSLTLINWNGFFARTF--DLDELVTTLSGGNGAGKSTTMAAFVTALIPDLTLLHFRNTT 64
Query: 58 ----HSDSRQALLHEGTGPRVVNAYVEIVFDNTDHR 89
S SR LH V Y + N+ H+
Sbjct: 65 EAGATSGSRDKGLHGKLKAGV--CYSMLDTINSRHQ 98
>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 = 37.2 bits (85), Expect = 4e-04
Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 11/89 (12%)
Query: 3 IKQVIIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLR----- 57
+ + + + + +T FD+ + G NG+GKS L + T L
Sbjct: 9 FRSLTLINWNGFFARTF--DFDELVTTLSGGNGAGKSTTMAGFVTALIPDLTLLNFRNTT 66
Query: 58 ----HSDSRQALLHEGTGPRVVNAYVEIV 82
S SR L+ V A +E V
Sbjct: 67 EAGSTSSSRDKGLYGKLKAGVCYAVLETV 95
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.5 bits (78), Expect = 0.002
Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 52 ESTSLRHSDSRQALLHEGTGPRV-VNAYVE 80
E +L+ + L + + P + + A +E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>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 = 32.9 bits (74), Expect = 0.013
Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 38/91 (41%)
Query: 11 FKSYKE--QTVVEPFDKRH---------------------NVVV-GRNGSGKSNFFFAIQ 46
+ ++ + F K + NV++ G GSGK+ + A+
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT--WVALD 169
Query: 47 FVLSDEST-----------SLRHSDSRQALL 66
V +L++ +S + +L
Sbjct: 170 -VCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199
>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 = 29.2 bits (65), Expect = 0.24
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 30 VVGRNGSGKSNFFFAI 45
+ G NG GKS AI
Sbjct: 466 ICGPNGCGKSTLMRAI 481
>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 = 0.32
Identities = 18/105 (17%), Positives = 32/105 (30%), Gaps = 37/105 (35%)
Query: 15 KEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQ--FVLSDESTSLRHSDSRQALLHEGTGP 72
+Q+ + PF +R R F + F HS LL
Sbjct: 402 LDQSRI-PFSERKLKFSNR--------FLPVASPF----------HSH----LL-VPASD 437
Query: 73 RVVN--AYVEIVFDNTDHRVPGF-------IRCRSTSV--DLYRC 106
+ + F+ D ++P + +R S S+ + C
Sbjct: 438 LINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC 482
Score = 25.4 bits (55), Expect = 5.2
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 68 EGTGPRVVNA 77
+GTG RV+ A
Sbjct: 521 DGTGVRVIVA 530
>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur
cluster, adenosine diphosphate, nucleotide-binding; HET:
ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*
Length = 607
Score = 28.0 bits (63), Expect = 0.67
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 29 VVVGRNGSGKSNFF 42
+VG NG GK+ F
Sbjct: 386 GIVGPNGIGKTTFV 399
Score = 26.9 bits (60), Expect = 1.5
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 29 VVVGRNGSGKS 39
+VG NG+GK+
Sbjct: 121 GIVGPNGTGKT 131
>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis,
hydrolyase/translation complex; HET: ADP; 1.90A
{Pyrococcus furiosus}
Length = 538
Score = 27.6 bits (62), Expect = 0.69
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 11 FKSYKEQTV-VEPFDKRHN---VVVGRNGSGKSNF 41
K Y + VEP + + +VG NG GK+ F
Sbjct: 294 VKDYGSFRLEVEPGEIKKGEVIGIVGPNGIGKTTF 328
>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET:
ATP; NMR {Saccharomyces cerevisiae}
Length = 608
Score = 27.7 bits (62), Expect = 0.88
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 29 VVVGRNGSGKS 39
V++G NG+GK+
Sbjct: 382 VMMGENGTGKT 392
Score = 27.3 bits (61), Expect = 1.2
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 29 VVVGRNGSGKS 39
+VG NG GKS
Sbjct: 107 GLVGTNGIGKS 117
>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions,
DNA HYDR sodium ION, quadruplex DNA, DNA-binding
protein-DNA complex; 1.86A {Sterkiella nova} SCOP:
b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A
1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A
1ph9_A 1ph5_A* 1ph2_A* 1k8g_A
Length = 495
Score = 27.3 bits (59), Expect = 1.2
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 1/84 (1%)
Query: 7 IIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSL-RHSDSRQAL 65
+ S ++ V K + SGK + F +QF++ D ST L ++
Sbjct: 375 VTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLY 434
Query: 66 LHEGTGPRVVNAYVEIVFDNTDHR 89
+G G N + + N D R
Sbjct: 435 TQDGLGANFFNVKADNLHKNADAR 458
>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase,
translation; HET: ADP; 2.05A {Sulfolobus solfataricus}
Length = 538
Score = 26.9 bits (60), Expect = 1.2
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 29 VVVGRNGSGKSNF 41
++G NG GK+ F
Sbjct: 298 GILGPNGIGKTTF 310
Score = 26.5 bits (59), Expect = 2.1
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 29 VVVGRNGSGKS 39
V+G+NG GK+
Sbjct: 29 GVLGKNGVGKT 39
>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance
regulator, residues 1193-1427...; CFTR, ABC
transporter, nucleotide binding domain, NBD; HET: B44;
2.70A {Homo sapiens}
Length = 390
Score = 27.0 bits (60), Expect = 1.4
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 29 VVVGRNGSGKSNFFFAI 45
++GR GSGKS A
Sbjct: 51 GLLGRTGSGKSTLLSAF 67
>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics,
cell membrane, cobalt transport, hydrolase, ION
transport; 2.30A {Clostridium perfringens atcc 13124}
Length = 275
Score = 26.7 bits (60), Expect = 1.5
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 30 VVGRNGSGKSNFF 42
++G NG GKS F
Sbjct: 39 ILGGNGVGKSTLF 51
>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt
transport, TM02 hydrolase, inner membrane, membrane,
nucleotide-binding; 2.30A {Thermotoga maritima}
Length = 266
Score = 26.4 bits (59), Expect = 1.7
Identities = 7/13 (53%), Positives = 7/13 (53%)
Query: 30 VVGRNGSGKSNFF 42
V G GSGKS
Sbjct: 38 VAGNTGSGKSTLL 50
>4df3_A Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase; NADP rossmann
superfamily, S-adenosyl-L-M (SAM) binding, nucleolus;
HET: SAM; 1.73A {Aeropyrum pernix}
Length = 233
Score = 26.6 bits (58), Expect = 1.7
Identities = 8/31 (25%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 3 IKQVIIHGFKSYKEQTVVEPFDKRHNVVVGR 33
IK ++ G + K+ ++PFD+ H ++
Sbjct: 201 IKTLMDGGLEI-KDVVHLDPFDRDHAMIYAV 230
>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette,
hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}
Length = 279
Score = 26.4 bits (59), Expect = 1.9
Identities = 6/33 (18%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 12 KSYKEQTVVEPFDKR-----HNVVVGRNGSGKS 39
+ + +T+++ + ++ G NG+GK+
Sbjct: 29 RMKQGKTILKKISWQIAKGDKWILYGLNGAGKT 61
>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane,
membrane, transmembrane, transport, ATP- binding,
hydrolase, nucleotide-binding, periplasm; HET: 1PE;
2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C
Length = 249
Score = 26.4 bits (59), Expect = 2.2
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 29 VVVGRNGSGKS 39
+VG NG+GKS
Sbjct: 30 HLVGPNGAGKS 40
>2xgv_A PSIV capsid N-terminal domain; retroviral capsid, viral protein;
2.00A {Microcebus murinus}
Length = 142
Score = 26.0 bits (57), Expect = 2.2
Identities = 5/20 (25%), Positives = 8/20 (40%)
Query: 63 QALLHEGTGPRVVNAYVEIV 82
Q +E R V A++
Sbjct: 7 QGWAYEPMSTRTVAAWIRQT 26
>3id6_C Fibrillarin-like rRNA/TRNA 2'-O-methyltransferase; C/D guide RNA,
2'-O-methylation, coiled-coil, methyltransfer binding,
rRNA processing; HET: SAM; 2.60A {Sulfolobus
solfataricus} PDB: 3id5_B* 3pla_E*
Length = 232
Score = 26.2 bits (57), Expect = 2.3
Identities = 6/31 (19%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 3 IKQVIIHGFKSYKEQTVVEPFDKRHNVVVGR 33
++++ F++ + ++P+DK H +V+ +
Sbjct: 200 VEKLENSNFET-IQIINLDPYDKDHAIVLSK 229
>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative
iron chelatin ABC transporter, nucleotide binding
domain; 2.40A {Haemophilus influenzae}
Length = 253
Score = 26.0 bits (58), Expect = 3.0
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 29 VVVGRNGSGKSNFFFAI 45
V+G+NG GKS +
Sbjct: 35 AVLGQNGCGKSTLLDLL 51
>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium,
SGC, limited proteolysis, GTP-binding,
nucleotide-binding, signaling protein; HET: GDP; 1.85A
{Homo sapiens}
Length = 187
Score = 25.6 bits (57), Expect = 3.0
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 9 HGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFV 48
H S +E + + + ++GR G+GKS ++F+
Sbjct: 5 HHHSSGRENLYFQGPLEVNLAILGRRGAGKSA--LTVKFL 42
>1v10_A Laccase; multicopper blue oxidase, oxidase; 1.7A {Rigidoporus
lignosus} SCOP: b.6.1.3 b.6.1.3 b.6.1.3
Length = 521
Score = 26.1 bits (58), Expect = 3.0
Identities = 14/82 (17%), Positives = 22/82 (26%), Gaps = 5/82 (6%)
Query: 12 KSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAIQFVLSDESTSLRHSDSRQALLHEGTG 71
V D N+ +GRN + F+ L+ G
Sbjct: 336 PGAPGNPVPGGADINLNLRIGRNATTADFTINGAPFIPPTVPVLLQILSGVTNPNDLLPG 395
Query: 72 PRVV----NAYVEIVFDNT-DH 88
V+ N +EI +H
Sbjct: 396 GAVISLPANQVIEISIPGGGNH 417
>1fbn_A MJ fibrillarin homologue; MJ proteins, ribosomal RNA processing,
snoRNP, structural genomics, BSGC structure funded by
NIH; 1.60A {Methanocaldococcus jannaschii} SCOP:
c.66.1.3 PDB: 1g8s_A
Length = 230
Score = 25.8 bits (56), Expect = 3.1
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 1 MYIKQVIIHGFKSYKEQTVVEPFDKRHNVVVGR 33
+ + GFK ++ +EPF+K H + VG
Sbjct: 195 EQKEILEAGGFKI-VDEVDIEPFEKDHVMFVGI 226
>1g6h_A High-affinity branched-chain amino acid transport ATP-binding
protein; beta-core domain; HET: ADP; 1.60A
{Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB:
1gaj_A 1g9x_A*
Length = 257
Score = 25.5 bits (57), Expect = 3.3
Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 9/39 (23%)
Query: 7 IIHGFKSYKEQTVVEPFDKRHNVVVGRNGSGKSNFFFAI 45
K E TV+E N+++G G+S
Sbjct: 90 TPQPLK---EMTVLE------NLLIGEICPGESPLNSLF 119
>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial
conjugation, F1-ATPase-like quaternary structure, ring
helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB:
1e9s_A 1gki_A* 1gl7_A* 1gl6_A*
Length = 437
Score = 25.6 bits (56), Expect = 3.5
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 23 FDKRHNVVVGRNGSGKSNFFFAI 45
+ RH +V G G+GKS +
Sbjct: 51 AEPRHLLVNGATGTGKSVLLREL 73
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 25.5 bits (55), Expect = 4.0
Identities = 4/22 (18%), Positives = 8/22 (36%)
Query: 9 HGFKSYKEQTVVEPFDKRHNVV 30
S E + + K+ V+
Sbjct: 145 IRIVSGLELSDTKQKGKKFLVI 166
>2ipx_A RRNA 2'-O-methyltransferase fibrillarin; FBL, structural genomics,
structural genomics consortium, SGC; HET: MTA; 1.82A
{Homo sapiens}
Length = 233
Score = 25.4 bits (55), Expect = 4.3
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 3 IKQVIIHGFKSYKEQTVVEPFDKRHNVVVGR 33
+K++ K +EQ +EP+++ H VVVG
Sbjct: 201 VKKMQQENMK-PQEQLTLEPYERDHAVVVGV 230
>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding
cassette, transport protein; HET: ATP; 2.05A {Homo
sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A*
1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A*
1xfa_A*
Length = 290
Score = 25.0 bits (55), Expect = 5.2
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 30 VVGRNGSGKSNFFFAI 45
V G G+GK++ I
Sbjct: 69 VAGSTGAGKTSLLMMI 84
>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET:
GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A*
2j3e_A*
Length = 262
Score = 25.2 bits (55), Expect = 5.3
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 29 VVVGRNGSGKS 39
+V+G+ G GKS
Sbjct: 40 LVLGKGGVGKS 50
>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon;
HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB:
3bb1_A*
Length = 270
Score = 25.3 bits (55), Expect = 5.3
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 29 VVVGRNGSGKS 39
+V+G+ G GKS
Sbjct: 43 LVMGKGGVGKS 53
>2cbz_A Multidrug resistance-associated protein 1; ABC proteins,
MRP1/ABCC1, nucleotide-binding domain, ATP- binding,
hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}
Length = 237
Score = 24.8 bits (55), Expect = 6.8
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 30 VVGRNGSGKSNFFFAI 45
VVG+ G GKS+ A+
Sbjct: 36 VVGQVGCGKSSLLSAL 51
>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC
transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo
sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A
1ckz_A
Length = 229
Score = 24.8 bits (55), Expect = 6.9
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 30 VVGRNGSGKSNFFFAI 45
V G G+GK++ I
Sbjct: 39 VAGSTGAGKTSLLMMI 54
>3lxw_A GTPase IMAP family member 1; immunity, structural genomics
consortium, SGC, immune system; HET: GDP; 2.21A {Homo
sapiens} PDB: 3v70_A*
Length = 247
Score = 24.6 bits (53), Expect = 7.5
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 15 KEQTVVEPFDKRHNVVVGRNGSGKSNFFFAI 45
+E + R ++VGR G+GKS +I
Sbjct: 11 RENLYFQGESTRRLILVGRTGAGKSATGNSI 41
>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 = 24.7 bits (53), Expect = 7.9
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 28 NVVVGRNGSGKSNFFFAIQFVLSDE 52
++ G GSGK+ + + +DE
Sbjct: 8 CLITGTPGSGKT--LKMVSMMANDE 30
>3t61_A Gluconokinase; PSI-biology, structural genomics, protein
structure initiati YORK structural genomics research
consortium, nysgrc; 2.20A {Sinorhizobium meliloti}
Length = 202
Score = 24.6 bits (53), Expect = 8.3
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 13 SYKEQTVVEPFDKRHNVVVGRNGSGKS 39
YK + VV+G +GSGKS
Sbjct: 6 EYKSEAAAVRRFPGSIVVMGVSGSGKS 32
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 24.8 bits (55), Expect = 8.6
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 13/51 (25%)
Query: 55 SLRHSDSRQALLHEGTGPRVVNAYVEIVFDNTDHRVPGFIRCRSTSVDLYR 105
SL+H SR+A+ +G G ++++ VE ++ T DL++
Sbjct: 439 SLKHFVSRRAMDVDGMGDKIIDQLVE----------KEYVH---TPADLFK 476
>2ctz_A O-acetyl-L-homoserine sulfhydrylase; crystal, O-acetyl homoserine
sulfhydrase, structural genomic structural
genomics/proteomics initiative; HET: PLP; 2.60A
{Thermus thermophilus} SCOP: c.67.1.3
Length = 421
Score = 24.4 bits (54), Expect = 9.4
Identities = 12/44 (27%), Positives = 15/44 (34%), Gaps = 15/44 (34%)
Query: 66 LHEG------TGPRVVNAY--VEIVFDNTDH-------RVPGFI 94
LH G T R V Y VF + +H + G I
Sbjct: 8 LHAGYEPEPTTLSRQVPIYPTTSYVFKSPEHAANLFALKEFGNI 51
>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster,
ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding;
HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A
Length = 267
Score = 24.4 bits (54), Expect = 9.8
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 32 GRNGSGKS 39
G NGSGKS
Sbjct: 53 GPNGSGKS 60
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 0.138 0.412
Gapped
Lambda K H
0.267 0.0529 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,642,227
Number of extensions: 84279
Number of successful extensions: 304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 294
Number of HSP's successfully gapped: 71
Length of query: 109
Length of database: 6,701,793
Length adjustment: 73
Effective length of query: 36
Effective length of database: 4,663,560
Effective search space: 167888160
Effective search space used: 167888160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.9 bits)