RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2272
(276 letters)
>1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding
protein, gene regulation; NMR {Homo sapiens} SCOP:
b.40.4.5
Length = 143
Score = 117 bits (294), Expect = 3e-33
Identities = 74/101 (73%), Positives = 82/101 (81%), Gaps = 1/101 (0%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLGNGRLEAMCFDG KRLCHIRGKLRKKVWIN DIIL+GLRDYQD KADVILKY DEA
Sbjct: 40 MLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEA 99
Query: 61 RNLKTYGEFPETVRINDTVTFVEEGYDEDIEFGDEISDDEE 101
R+LK YGE PE +IN+T TF G D++I+F D DDE+
Sbjct: 100 RSLKAYGELPEHAKINETDTF-GPGDDDEIQFDDIGDDDED 139
>2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic
initiation facto SGC, structural genomics; 1.80A
{Cryptosporidium parvum iowa II}
Length = 117
Score = 103 bits (257), Expect = 5e-28
Identities = 57/77 (74%), Positives = 68/77 (88%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLGNGRL+A CFDG KRLCHIRGK+RKKVW+N GDI+L+ LRD+QD+K D+ILKYTPDEA
Sbjct: 41 MLGNGRLDAYCFDGQKRLCHIRGKMRKKVWVNPGDIVLVSLRDFQDSKGDIILKYTPDEA 100
Query: 61 RNLKTYGEFPETVRIND 77
R LK+ GE PET +IN+
Sbjct: 101 RALKSKGEIPETTKINE 117
>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel,
translation factor; NMR {Methanocaldococcus jannaschii}
SCOP: b.40.4.5
Length = 102
Score = 100 bits (249), Expect = 5e-27
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQ-DAKADVILKYTPDE 59
MLG R+ C DG RL I G+L+ ++W+ +GD++++ + Q D K D+I +YT +
Sbjct: 29 MLGASRVRVRCLDGKTRLGRIPGRLKNRIWVREGDVVIVKPWEVQGDQKCDIIWRYTKTQ 88
Query: 60 ARNLKTYGEFPETV 73
LK G E +
Sbjct: 89 VEWLKRKGYLDELL 102
>2dgy_A MGC11102 protein; EIF-1A, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 111
Score = 99 bits (249), Expect = 8e-27
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIG-LRDYQDAKADVILKYTPDE 59
GN E G + L + K RK +WI +GD +++ + + + KA++ D
Sbjct: 24 TPGNNLHEVETAQGQRFLVSMPSKYRKNIWIKRGDFLIVDPIEEGEKVKAEISFVLCKDH 83
Query: 60 ARNLKTYGEFPE 71
R+L+ G +PE
Sbjct: 84 VRSLQKEGFWPE 95
>3i4o_A Translation initiation factor IF-1; cytoplasm, protein
biosynthesis; 1.47A {Mycobacterium tuberculosis}
Length = 79
Score = 40.3 bits (95), Expect = 4e-05
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKY 55
L N +G K L HI GK+R+ + I D +++ L Y ++ ++ +Y
Sbjct: 23 PLPNAMFRIELENGHKVLAHISGKMRQHYIRILPEDRVVVELSPYDLSRGRIVYRY 78
>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 = 42.9 bits (100), Expect = 8e-05
Identities = 35/258 (13%), Positives = 77/258 (29%), Gaps = 68/258 (26%)
Query: 34 GDIILIGLRDYQDAKADVILKYTPDEARNLKTYGEFPETVRINDTVT------------- 80
DI+ + + + K D +++ + E + D V+
Sbjct: 19 KDILSVFEDAF---VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQ 75
Query: 81 ------FVEEGYDEDIEF-GDEISDDEEGNAVD-NLYLQMHMSKF---PWFSIHFKLSFL 129
FVEE + +F I ++ ++ +Y++ + F+ + +S L
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN-VSRL 134
Query: 130 KKVGTV-SSIQEARPSYTLQYQNSAEVSYLC--------KGALLKKVLNSKNIAGGINKR 180
+ + ++ E RP+ + K + V S + +
Sbjct: 135 QPYLKLRQALLELRPA-----------KNVLIDGVLGSGKTWVALDVCLSY----KVQCK 179
Query: 181 FFKNRF--ARGNYNCQGLIVPKED----RIGKN---------QPFQENKNLKRVIRHLLA 225
F N N ++ +I N +++ +R LL
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239
Query: 226 PKLDSSDTLHLDN-WISE 242
K + L L N ++
Sbjct: 240 SKPYENCLLVLLNVQNAK 257
Score = 36.0 bits (82), Expect = 0.015
Identities = 48/310 (15%), Positives = 95/310 (30%), Gaps = 92/310 (29%)
Query: 21 IRGKLRKKVWINQGDIILIGLRDYQDAKA----DV---ILKYTPDEARNLKTYGEFPETV 73
I+ +LR+ + + L+ L + Q+AKA ++ IL T + + + T
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRF--KQVTDFLSAATTT 287
Query: 74 RINDTVTFVEEGYDED------IEFGDEISDD--EEGNAVDNLYLQM---HMSKFPWFSI 122
I ++ D +++ D D E + L + +
Sbjct: 288 HI--SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345
Query: 123 HFKLSFLKKVGTV--SSIQ-----EARPSY---------------TLQ--YQNSAE---- 154
++K K+ T+ SS+ E R + L + + +
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405
Query: 155 --VSYLCKGALLKKVLNSKNIAGGINKRFFKNRFARGNYNCQGLIVPKEDRIGKNQPFQE 212
V+ L K +L++K K I + + + +
Sbjct: 406 VVVNKLHKYSLVEK--QPKESTISIPSIYLELK----------------------VKLEN 441
Query: 213 NKNL-KRVIRHLLAPK-LDSSDTL--HLDNWISEEYQLLSYR-PEGRQDRKKPAIPR--- 264
L + ++ H PK DS D + +LD + Y + + +
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF---YSHIGHHLKNIEHPERMTLFRMVFL 498
Query: 265 -----EQKFR 269
EQK R
Sbjct: 499 DFRFLEQKIR 508
>1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA
interaction, OB fold; NMR {Escherichia coli} SCOP:
b.40.4.5
Length = 71
Score = 38.0 bits (89), Expect = 2e-04
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKY 55
L N +G HI GK+RK + I GD + + L Y +K ++ +
Sbjct: 15 TLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRS 70
>1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1;
3.20A {Escherichia coli} SCOP: b.40.4.5 PDB: 1zo1_W
Length = 71
Score = 37.2 bits (87), Expect = 4e-04
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVI 52
L N G + L +I GK+R + I GD +++ + Y + ++
Sbjct: 16 ALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIV 68
>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 = 32.2 bits (72), Expect = 0.089
Identities = 9/33 (27%), Positives = 11/33 (33%), Gaps = 11/33 (33%)
Query: 48 KADVILK-YTPDEARNLKTYGEFPETVRINDTV 79
K LK Y D A P + I T+
Sbjct: 24 KLQASLKLYADDSA---------P-ALAIKATM 46
Score = 29.1 bits (64), Expect = 0.83
Identities = 10/51 (19%), Positives = 14/51 (27%), Gaps = 28/51 (54%)
Query: 212 ENKNLKRVIRHLLAPKLDSSDTLHLDNWISEEYQLLSYRPEGRQDRKKPAI 262
E + LK KL +S L Y + PA+
Sbjct: 18 EKQALK---------KLQASLKL--------------YADD-----SAPAL 40
>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 = 31.6 bits (71), Expect = 0.39
Identities = 19/125 (15%), Positives = 38/125 (30%), Gaps = 29/125 (23%)
Query: 8 EAMCFDGTKRLCHIRGKLRKK--------------VWINQGDIILIGLRDYQDAKADVIL 53
+ M + + RG + + IN G + ++ + +
Sbjct: 1775 DVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVG 1834
Query: 54 KYTPDEARNLKTYGEFPETVRINDTV---TFVEEGYDEDIEFGDEISDDEEGNAVDNLYL 110
K T G E V N V +V G ++ + + + +D + L
Sbjct: 1835 KRT----------GWLVEIV--NYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIEL 1882
Query: 111 QMHMS 115
Q +S
Sbjct: 1883 QKSLS 1887
Score = 28.9 bits (64), Expect = 2.7
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 19/53 (35%)
Query: 190 NYNCQGL-IV-----------------PKEDRIGKNQPFQENKNLKRVIRHLL 224
NYN + V K +I Q++ +L+ V HL
Sbjct: 1845 NYNVENQQYVAAGDLRALDTVTNVLNFIKLQKI-DIIELQKSLSLEEVEGHLF 1896
>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; HET: GDP; 1.90A
{Aquifex aeolicus}
Length = 302
Score = 29.5 bits (67), Expect = 1.1
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 3/45 (6%)
Query: 13 DGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTP 57
DG RGK+ KK I GD + + D I +
Sbjct: 26 DGKTYRGIPRGKVLKKTKIYAGDYVWGEVVDPNTF---AIEEVEE 67
>2rdy_A BH0842 protein; PSI-II, structural genomics, protein structure
initiative, NEW YORK SGX research center for structural
genomics; 2.03A {Bacillus halodurans c-125}
Length = 803
Score = 28.3 bits (62), Expect = 3.0
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 13/70 (18%)
Query: 2 LGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEAR 61
+GNG L AM F ++ ++ +N+ + +D+ + KA +L + R
Sbjct: 20 IGNGNLGAMVFGKVEKE---------RIALNEDTLWSGYPKDWNNPKAKEVL----PKVR 66
Query: 62 NLKTYGEFPE 71
L ++ E
Sbjct: 67 ELIAQEKYEE 76
>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'-
D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP
*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator;
HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8
PDB: 1xs9_A
Length = 129
Score = 26.1 bits (58), Expect = 8.9
Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 18/60 (30%)
Query: 74 RINDTVTFVEEGYDEDIEFGDEISDDEEGNAVDNLYLQMHMSKFPWFSIHFKLSFLKKVG 133
I+ + ++E+ + + +++S+ + SK+ H + F K+ G
Sbjct: 12 TIHSILDWIEDNLESPLSL-EKVSE------------RSGYSKW-----HLQRMFKKETG 53
>2fa8_A Hypothetical protein ATU0228; ALPH-beta structure, 4 helix bundle,
structural genomics, PS protein structure initiative;
1.90A {Agrobacterium tumefaciens str} SCOP: c.47.1.23
Length = 105
Score = 25.5 bits (56), Expect = 9.3
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 210 FQENKNLKRVIRHLLAPKLD 229
F K LK+ IR L+ P+ D
Sbjct: 70 FPGPKELKQRIRDLIDPERD 89
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 0.137 0.405
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,296,793
Number of extensions: 256127
Number of successful extensions: 510
Number of sequences better than 10.0: 1
Number of HSP's gapped: 504
Number of HSP's successfully gapped: 24
Length of query: 276
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 184
Effective length of database: 4,133,061
Effective search space: 760483224
Effective search space used: 760483224
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: 57 (25.7 bits)