RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16169
(139 letters)
>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 = 37.9 bits (87), Expect = 5e-04
Identities = 25/135 (18%), Positives = 49/135 (36%), Gaps = 26/135 (19%)
Query: 13 CSSSSSASTKYD--VDLLKSDV-ALARDRVSR------LKRELEQIRTEMNYTQRGLVPM 63
S + Y D L +D A+ VSR L++ L ++R N G++
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS 161
Query: 64 G-TRLA-EMAR--------------MRL-EYDETRKRIQIIQTQLADLEEKVTPGQAESD 106
G T +A ++ + L + ++++Q L ++ T S
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 107 KDRLILFQEKEQLLR 121
+L + + +L R
Sbjct: 222 NIKLRIHSIQAELRR 236
Score = 28.7 bits (63), Expect = 0.66
Identities = 19/161 (11%), Positives = 48/161 (29%), Gaps = 45/161 (27%)
Query: 12 LCSSS----SSASTKYDVDLLKSDVALARDRVSRL-KRELEQIRTEMNYTQRGLVP---- 62
L S + + + ++ + + L + ++ + L+P
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD 470
Query: 63 ---------------MGTRLAEMARMRLEYDETRKRIQIIQTQ----------LADL--- 94
R+ + L++ ++I+ T L L
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFY 530
Query: 95 EEKVTPGQAESDKDRLI------LFQEKEQLLRSRSMSLIR 129
+ + + +RL+ L + +E L+ S+ L+R
Sbjct: 531 KPYICD--NDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569
>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 = 32.4 bits (74), Expect = 0.035
Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 7/103 (6%)
Query: 16 SSSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRL 75
S S K + + LK + + + +I E+ + + + + +
Sbjct: 173 SGSIQYKKEYEELKEKIEKLSKSATESIKNRRRIHGELKTYKSPGLEVLFQGPRGS---- 228
Query: 76 EYDETRKRIQIIQTQLADLEE---KVTPGQAESDKDRLILFQE 115
YDE R ++I + L+ K+ + K R LF++
Sbjct: 229 RYDEAEGRFEVINNETEQLKAEEKKILNQFLKIKKKRKELFEK 271
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.9 bits (69), Expect = 0.088
Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 20/95 (21%)
Query: 38 RVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLEE- 96
+ RL +E E IR + QR RL E L+ + + DLEE
Sbjct: 76 QADRLTQEPESIR-KWREEQR------KRLQE-----LDAASKVMEQEWREKAKKDLEEW 123
Query: 97 -KVTPGQAESDK--DRLILFQEKEQLLRSRSMSLI 128
+ Q E +K +R + + +I
Sbjct: 124 NQRQSEQVEKNKINNR----IADKAFYQQPDADII 154
>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A
{Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20
c.37.1.20
Length = 854
Score = 31.0 bits (71), Expect = 0.12
Identities = 22/90 (24%), Positives = 47/90 (52%), Gaps = 11/90 (12%)
Query: 40 SRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRL--EYDE-TRKRIQIIQTQLADLEE 96
+RL+ LE E++ +R + + E+ R L E D +++R++ I+ ++A L E
Sbjct: 390 ARLRMALESAPEEIDALERKKLQL-----EIEREALKKEKDPDSQERLKAIEAEIAKLTE 444
Query: 97 KVTPGQA--ESDKDRLILFQE-KEQLLRSR 123
++ +A E +++ L +E + +L R
Sbjct: 445 EIAKLRAEWEREREILRKLREAQHRLDEVR 474
Score = 27.5 bits (62), Expect = 1.7
Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 13/70 (18%)
Query: 37 DRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYD---ETRKRIQIIQTQLAD 93
++ + L+++R E+ +R L A L Y + ++ + +L
Sbjct: 461 RKLREAQHRLDEVRREIELAER-----QYDLNRAA--ELRYGELPKLEAEVEALSEKLRG 513
Query: 94 ---LEEKVTP 100
+ +VT
Sbjct: 514 ARFVRLEVTE 523
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 29.1 bits (64), Expect = 0.50
Identities = 15/71 (21%), Positives = 35/71 (49%)
Query: 16 SSSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRL 75
S+ TK V+L++ D A A + + K+ E +R+ + +R ++ R+ + +
Sbjct: 85 DSNTLTKNIVELMRGDFAKANNNDNTFKQINEDLRSRIEILRRKVIEQVQRINLLQKNVR 144
Query: 76 EYDETRKRIQI 86
+ KR+++
Sbjct: 145 DQLVDMKRLEV 155
>4e6f_A Uncharacterized protein; PF14730 family protein, DUF4468 with
TBP-like fold,structura genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.49A {Bacteroides
ovatus}
Length = 181
Score = 28.4 bits (63), Expect = 0.55
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 50 RTEMNYTQRGLVPMGTRLAEMARMRLEYDETRK 82
RT +NY G L E+ ++R Y ET K
Sbjct: 92 RTLVNYQITVTCKPGNCLVELEKIRFTYRETEK 124
>3fpp_A Macrolide-specific efflux protein MACA; hexameric assembly,
membrane fusion protein, drug efflux pump, periplasmic
protein; 2.99A {Escherichia coli}
Length = 341
Score = 27.3 bits (61), Expect = 1.5
Identities = 13/93 (13%), Positives = 36/93 (38%), Gaps = 8/93 (8%)
Query: 24 DVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRL----EYDE 79
D + ++ + + L+ + +Q E+ + +R +A+ + + D
Sbjct: 63 DPEQAENQIKEVEATLMELRAQRQQAEAELKLARVTY----SRQQRLAQTQAVSQQDLDN 118
Query: 80 TRKRIQIIQTQLADLEEKVTPGQAESDKDRLIL 112
+ + Q Q+ ++ ++ QA D + L
Sbjct: 119 AATEMAVKQAQIGTIDAQIKRNQASLDTAKTNL 151
>3aek_B Light-independent protochlorophyllide reductase S; iron/sulfur
cluster, oxidoreductase, bacteriochlorophyll
biosynthesis; HET: PMR; 2.30A {Rhodobacter capsulatus}
PDB: 3aeq_B* 3aer_B 3aes_B* 3aeu_B 3aet_B
Length = 525
Score = 27.1 bits (60), Expect = 2.6
Identities = 4/30 (13%), Positives = 12/30 (40%)
Query: 44 RELEQIRTEMNYTQRGLVPMGTRLAEMARM 73
E+ ++ M P+G ++ ++
Sbjct: 173 AEVTKLLATMGIKVNVCAPLGASPDDLRKL 202
>2v66_B Nuclear distribution protein NUDE-like 1; structural protein,
developmental protein, structural protei
phosphorylation, transport, microtubule; 2.10A {Homo
sapiens}
Length = 111
Score = 26.1 bits (57), Expect = 2.7
Identities = 11/61 (18%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRL-AEMARMRLEYDETRKRIQIIQTQLADL 94
+ RLK E+E ++ ++ + + L ++++ R ++ K ++ ++ DL
Sbjct: 9 QADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDL 68
Query: 95 E 95
E
Sbjct: 69 E 69
>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 3.65A {Bacillus subtilis}
Length = 468
Score = 26.4 bits (59), Expect = 3.8
Identities = 8/53 (15%), Positives = 26/53 (49%)
Query: 71 ARMRLEYDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSR 123
+++RL T ++ ++ +L ++ ++ + ++ ++ EQ LR +
Sbjct: 383 SKVRLRSFTTPPNLKELEQKLDEVRKEKDAAVQSQEFEKAASLRDTEQRLREQ 435
>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM,
protein engineering, structural protein; HET: ADP; 2.80A
{Dictyostelium discoideum} SCOP: k.1.1.1
Length = 1010
Score = 26.6 bits (59), Expect = 4.0
Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 18/92 (19%)
Query: 28 LKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQII 87
+ +A+ + +R+ ++LE A + L +ET I +
Sbjct: 880 RQKKIAVLLQKYNRILKKLEN------------------WATTKSVYLGSNETGDSITAV 921
Query: 88 QTQLADLEEKVTPGQAESDKDRLILFQEKEQL 119
Q +L +LE Q+ + L QL
Sbjct: 922 QAKLKNLEAFDGECQSLEGQSNSDLLSILAQL 953
>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels,
nucleotide-binding, nucleotide binding protein; 2.00A
{Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A
3kxk_A
Length = 364
Score = 26.1 bits (58), Expect = 4.4
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 36 RDRVSRLKRELEQIRT 51
+ R+++L +ELE I+
Sbjct: 150 KRRINKLMKELESIKI 165
>3lkz_A Non-structural protein 5; flavivirus, methyltransferase, inhibitor,
P nucleotide-binding, RNA replication, viral protein;
HET: SFG; 2.00A {West nile virus}
Length = 321
Score = 25.7 bits (56), Expect = 5.3
Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 2/86 (2%)
Query: 7 GICLRLCSSSSSASTKYDVDLLKSDVALARDRVSR--LKRELEQIRTEMNYTQRGLVPMG 64
G +R S +S Y V +V + + S+ L R ++ Y + + G
Sbjct: 225 GGLVRNPLSRNSTHEMYWVSRASGNVVHSVNMTSQVLLGRMEKRTWKGPQYEEDVNLGSG 284
Query: 65 TRLAEMARMRLEYDETRKRIQIIQTQ 90
TR + + + + RI+ ++ +
Sbjct: 285 TRAVGKPLLNSDTSKIKNRIERLRRE 310
>3gpv_A Transcriptional regulator, MERR family; protein structure
initiative II(PSI II), NYSGXRC, structural genomics;
1.90A {Bacillus thuringiensis serovarkonkukian}
Length = 148
Score = 25.0 bits (55), Expect = 8.7
Identities = 9/53 (16%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 46 LEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLEEKV 98
+++I+ ++++ G + RL M + + IQ + L +++K+
Sbjct: 76 IQKIKQFIDWSMEGDSTILHRLKLMKQQE---ANVLQLIQDTEKNLKKIQQKI 125
>2il5_A Hypothetical protein; structural genomics, APC23650, PSI-2,
structure initiative; 2.30A {Staphylococcus aureus
subsp} SCOP: d.129.3.5
Length = 171
Score = 24.8 bits (54), Expect = 8.7
Identities = 8/60 (13%), Positives = 19/60 (31%)
Query: 45 ELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLEEKVTPGQAE 104
E E T+M + R LV R + + + + + + + + +
Sbjct: 112 ERETGGTQMLFYYRSLVEKERRFTNLEYKQKKKEYHDAMVHGFELMFDKMYHVIETSTQQ 171
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 25.3 bits (55), Expect = 9.5
Identities = 12/115 (10%), Positives = 26/115 (22%), Gaps = 14/115 (12%)
Query: 22 KYDVDLLKSDVALARDR-VSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDET 80
K + + + V+ L Q M + + DE
Sbjct: 49 KINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFE-----EYINPVIV--------DER 95
Query: 81 RKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSRSMSLIRWPIKDT 135
Q +A L+ L + + +S + ++
Sbjct: 96 DIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHKESLQKI 150
>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 = 25.4 bits (56), Expect = 9.6
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 76 EYDETRKRIQIIQTQLADLEEK 97
+YD+ I+ + L + EK
Sbjct: 598 DYDQALADIRENEQSLLEYLEK 619
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
0.319 0.132 0.360
Gapped
Lambda K H
0.267 0.0563 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,998,284
Number of extensions: 111741
Number of successful extensions: 420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 411
Number of HSP's successfully gapped: 59
Length of query: 139
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 55
Effective length of database: 4,356,429
Effective search space: 239603595
Effective search space used: 239603595
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 (24.2 bits)