RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031854
(152 letters)
>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O
3jyv_O* 1ysh_E 1s1h_O
Length = 151
Score = 205 bits (523), Expect = 2e-69
Identities = 89/123 (72%), Positives = 111/123 (90%)
Query: 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60
MGRMHS GKGIS+SA+PY R P+W K+SS+ V + I K+A+KGLTPSQIGV+LRD+HG+
Sbjct: 1 MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV 60
Query: 61 AQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVES 120
Q + +TG+KI+RILK++GLAPEIPEDLY+LIKKAV++RKHLERNRKDKD+KFRLIL+ES
Sbjct: 61 TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES 120
Query: 121 RIH 123
RIH
Sbjct: 121 RIH 123
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 202 bits (514), Expect = 5e-68
Identities = 88/125 (70%), Positives = 101/125 (80%), Gaps = 2/125 (1%)
Query: 1 MGRMH--SRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSH 58
MGRM +GKGIS SALP+KR P WL ++ V D K AKKGLTPSQIGVILRD H
Sbjct: 1 MGRMQMKGKGKGISGSALPFKRRSPKWLHMTPSTVVDLSVKLAKKGLTPSQIGVILRDQH 60
Query: 59 GIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILV 118
GI QV+ +TG KILRILK +G AP++PEDLY LIKKA++IRKHLE+NRKDKDSK+RLILV
Sbjct: 61 GIPQVRFLTGQKILRILKKNGCAPQLPEDLYFLIKKALSIRKHLEKNRKDKDSKYRLILV 120
Query: 119 ESRIH 123
ESRIH
Sbjct: 121 ESRIH 125
>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 = 43.3 bits (101), Expect = 9e-06
Identities = 21/126 (16%), Positives = 36/126 (28%), Gaps = 42/126 (33%)
Query: 25 WLKISSQDVEDNICKFAKKGLTPSQIGVILRDS-------HGIAQVKSVTGS-------- 69
W + DV + K K L + + I V
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSL-------VEKQPKESTISIPSIYLELKVKLENEYALHRS 448
Query: 70 -----KILRILKAHGLAPEIPEDLY---HLIKKAVAIRKHLER-NRKDKDSKFRLILVES 120
I + + L P D Y H I HL+ ++ + FR++ ++
Sbjct: 449 IVDHYNIPKTFDSDDLIPP-YLDQYFYSH-------IGHHLKNIEHPERMTLFRMVFLDF 500
Query: 121 RIHDWL 126
R +L
Sbjct: 501 R---FL 503
Score = 29.8 bits (66), Expect = 0.42
Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 9/99 (9%)
Query: 32 DVEDN--ICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLY 89
+V++ F +I + R + + T + I + L P+ E
Sbjct: 252 NVQNAKAWNAFNLS----CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD--EVK- 304
Query: 90 HLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLAT 128
L+ K + R + RL ++ I D LAT
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Score = 27.9 bits (61), Expect = 1.5
Identities = 23/169 (13%), Positives = 48/169 (28%), Gaps = 49/169 (28%)
Query: 1 MGRMHSRGKGISASALPYKRTPPSWLK-ISSQDVEDNICKFAKKGLTPSQIGVILRDSHG 59
G + K I L +++ +DV+D K L+ +I I+
Sbjct: 11 TGEHQYQYKDI----LSVFE--DAFVDNFDCKDVQD----MPKSILSKEEIDHIIMSKDA 60
Query: 60 IAQVKSV------TGSKILRI----------------LKAHGLAPEIPEDLY-----HLI 92
++ + ++++ +K P + +Y L
Sbjct: 61 VSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY 120
Query: 93 KKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFHLYGNM 141
K+ +R K R L+E R + + G +
Sbjct: 121 NDNQVFAKY-NVSRLQPYLKLRQALLELRPAKNVL---------IDG-V 158
>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 = 33.4 bits (75), Expect = 0.012
Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 17/43 (39%)
Query: 62 QVKSVTGSKILRILKAHGLAPE-IPEDLYHLIKKAVAIRKHLE 103
+K + S LK + A + P A+AI+ +E
Sbjct: 21 ALKKLQAS-----LKLY--ADDSAP---------ALAIKATME 47
Score = 26.5 bits (57), Expect = 3.4
Identities = 8/18 (44%), Positives = 10/18 (55%), Gaps = 2/18 (11%)
Query: 132 QRSFHLYGNMSQPLPALS 149
Q S LY + S PAL+
Sbjct: 26 QASLKLYADDSA--PALA 41
>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 = 33.9 bits (77), Expect = 0.017
Identities = 28/135 (20%), Positives = 47/135 (34%), Gaps = 38/135 (28%)
Query: 11 ISASALPYKRTPPSW-LKI---SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSV 66
I +L PS L I + + V+D + K Q+ + L + V V
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK-NLV--V 379
Query: 67 TGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRK-----HLERNRKDKDSKFRLILVESR 121
+G P+ LY L + +RK L+++R S+ R + +R
Sbjct: 380 SGP---------------PQSLYGL---NLTLRKAKAPSGLDQSRI-PFSE-RKLKFSNR 419
Query: 122 IHDWLATTRRQRSFH 136
+L FH
Sbjct: 420 ---FLPVASP---FH 428
Score = 32.3 bits (73), Expect = 0.053
Identities = 20/96 (20%), Positives = 28/96 (29%), Gaps = 25/96 (26%)
Query: 7 RGKGISASALPYKRTPPSWLKISSQDVEDNICKFAK--KGLTPSQIGVILRDSHGI---- 60
+GK I + Y + + + D K K K + R G+
Sbjct: 1680 KGKRIREN---Y-------SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT 1729
Query: 61 --AQVKSVTGSK-ILRILKAHGLAPEIPEDLY---H 90
Q K LK+ GL IP D H
Sbjct: 1730 QFTQPALTLMEKAAFEDLKSKGL---IPADATFAGH 1762
Score = 27.7 bits (61), Expect = 2.1
Identities = 20/118 (16%), Positives = 33/118 (27%), Gaps = 46/118 (38%)
Query: 36 NICKFAKK-GLTPSQIGVILR----DSHGI--AQVKSVTGS---------KILRIL---- 75
+ AK G TP ++ L+ S G+ A + T S K + +L
Sbjct: 248 HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIG 307
Query: 76 -KAH------GLAPEIPED-------------------LYHLIKKAVAIRKHLERNRK 107
+ + L P I ED + HL ++
Sbjct: 308 VRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
>3l76_A Aspartokinase; allostery, ACT domains, kinase transferase; HET:
LYS; 2.54A {Synechocystis}
Length = 600
Score = 29.5 bits (67), Expect = 0.48
Identities = 7/37 (18%), Positives = 18/37 (48%)
Query: 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81
LT +Q+G++ H A++ + ++ L+ +
Sbjct: 95 LTGAQVGIVTEAEHSRARILEIRPDRLEHHLREGKVV 131
>3ab4_A Aspartokinase; aspartate kinase, concerted inhibition, alternative
initiati amino-acid biosynthesis, ATP-binding; HET: LYS;
2.47A {Corynebacterium glutamicum} PDB: 3aaw_A* 3ab2_A
Length = 421
Score = 29.0 bits (66), Expect = 0.55
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81
T SQ GV+ + HG A++ VT ++ L +
Sbjct: 95 FTGSQAGVLTTERHGNARIVDVTPGRVREALDEGKIC 131
>3j15_A Protein pelota; ribosome recycling, ribosome, archaea,
translation-transport complex; HET: ADP; 6.60A
{Pyrococcus furiosus}
Length = 357
Score = 28.6 bits (63), Expect = 0.93
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 7/78 (8%)
Query: 70 KILRILKAHG---LAPEIPEDLYHL---IKKAVAIRKHLERNRKDKDSKFRLILVESRIH 123
+IL G + E +DL+HL I + R + + R VE I
Sbjct: 2 EILEEKPKEGKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVE-VIP 60
Query: 124 DWLATTRRQRSFHLYGNM 141
+L + +FH + N
Sbjct: 61 VFLGVQAEKINFHKFANQ 78
>3obw_A Protein pelota homolog; SM fold, hydrolase; 2.60A {Sulfolobus
solfataricus}
Length = 364
Score = 28.2 bits (62), Expect = 1.3
Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 11/75 (14%)
Query: 57 SHGIAQVKSVTGSKILRILKAHG---LAPEIPEDL---YHLIKK-----AVAIRKHLERN 105
H V + +IL + L E +DL + +++K A R
Sbjct: 9 HHSSGLVPRGSHMRILEFDEKRQAVKLHIESEDDLWLLHLILEKDDKVVAKTTRDVGLGK 68
Query: 106 RKDKDSKFRLILVES 120
+ ++ V+
Sbjct: 69 ESRRIPMTIILKVDY 83
>3agj_B Protein pelota homolog; GTP binding, translation-hydrolase complex;
HET: GTP; 2.30A {Aeropyrum pernix}
Length = 358
Score = 26.6 bits (58), Expect = 3.4
Identities = 12/65 (18%), Positives = 20/65 (30%), Gaps = 9/65 (13%)
Query: 80 LAPEIPEDL---YHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFH 136
L PE EDL ++ +RK R+ + + R+ L F
Sbjct: 17 LRPESEEDLWLLRITLRPGDVVRKRTSRDVPVGSGR------KERVVMTLRIRLDSIEFQ 70
Query: 137 LYGNM 141
+
Sbjct: 71 PFTGK 75
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 26.5 bits (58), Expect = 4.1
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 33 VEDNICKFAKKGLTPSQIGVI 53
VE K K G P QIG+I
Sbjct: 659 VEKITTKLLKAGAKPDQIGII 679
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 26.3 bits (58), Expect = 4.4
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 33 VEDNICKFAKKGLTPSQIGVI 53
VE K K G P QIG+I
Sbjct: 483 VEKITTKLLKAGAKPDQIGII 503
>2qi2_A Pelota, cell division protein pelota related protein; DOM34, cell
cycle; 2.90A {Thermoplasma acidophilum} SCOP: b.38.4.1
c.55.4.2 d.79.3.2
Length = 347
Score = 26.3 bits (57), Expect = 4.5
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 11/64 (17%)
Query: 70 KILRILKAHG---LAPEIPEDL---YHLIKK-----AVAIRKHLERNRKDKDSKFRLILV 118
+IL + + E +DL +++ + A+ R+ E + + I +
Sbjct: 2 RILEEDLKNSTYRIRIESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPI 61
Query: 119 ESRI 122
R+
Sbjct: 62 TIRL 65
>4adn_A FAR1; antibiotic resistance; 1.65A {Staphylococcus aureus} PDB:
4ado_A
Length = 222
Score = 26.1 bits (57), Expect = 4.7
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 78 HGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKD 110
HG+ I Y+ I+ + K++ + DK+
Sbjct: 8 HGMKTMIYPHQYNYIRSVILRLKNVYKTVNDKE 40
>4dgf_A Sulfate transporter sulfate transporter family PR; STAS domain,
anion exchange, membrane, transport protein; HET: MSE;
1.60A {Wolinella succinogenes} PDB: 3oir_A*
Length = 135
Score = 25.8 bits (57), Expect = 4.8
Identities = 7/40 (17%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 70 KILRILKAHGLAPEIPED-LYHLIKKAV-AIRKHLERNRK 107
++ L G + E+ ++ I KA+ + +E +
Sbjct: 95 RLYGALNRFGFIEALGEERVFDHIDKALAYAKLLVETAEE 134
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 26.4 bits (58), Expect = 5.3
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 33 VEDNICKFAKKGLTPSQIGVI 53
E I K + G+ P QIGVI
Sbjct: 661 CERIITKLFRDGVKPEQIGVI 681
>3qw4_B UMP synthase; N-terminal orotidine monophosphate decarboxylase
domain C-TE orotate phosphoribosyltransferase domain,
transferase, LYAS; HET: U5P; 3.00A {Leishmania donovani}
Length = 453
Score = 25.9 bits (57), Expect = 5.9
Identities = 10/65 (15%), Positives = 19/65 (29%), Gaps = 12/65 (18%)
Query: 42 KKGLTPSQIGVIL-RD--------SHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLI 92
GL I V++ RD G V ++L + + I +
Sbjct: 390 SAGLEVVSIVVLVDRDMGAKAFLNKLGYDFEAVVGLHQLLPLWRKSNA---ITSQQEADV 446
Query: 93 KKAVA 97
+ +
Sbjct: 447 RAFLG 451
>2wg3_C Hedgehog-interacting protein; lipoprotein, development, membrane,
secreted, protease, PALM hydrolase, developmental
protein, autocatalytic cleavage; HET: NAG; 2.60A {Homo
sapiens} PDB: 2wg4_B 2wfx_B 2wft_A 3ho3_A 3ho4_A 3ho5_A
Length = 463
Score = 26.1 bits (57), Expect = 6.7
Identities = 6/36 (16%), Positives = 9/36 (25%), Gaps = 3/36 (8%)
Query: 55 RDSHGIAQVKSVTGSKILRIL---KAHGLAPEIPED 87
D S +LR+ + IP
Sbjct: 163 LDDMEEMDGLSDFTGSVLRLDVDTDMCNVPYSIPRS 198
>2pmv_A Gastric intrinsic factor; cobalamin transport protein alpha6-alpha6
motif two domain P transport protein; HET: NAG B12;
2.60A {Homo sapiens} PDB: 3kq4_A*
Length = 399
Score = 25.9 bits (56), Expect = 6.8
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 124 DWLATTRRQRSFHLYGNMSQPLPALSW 150
D + +Q FH +++Q LP+L
Sbjct: 233 DMILNEIKQGKFHNPMSIAQILPSLKG 259
>1rcq_A Catabolic alanine racemase DADX; alpha-beta barrel,
beta-structure for C-terminal domain, internal/external
aldimine forms, isomerase; HET: KCX PLP DLY; 1.45A
{Pseudomonas aeruginosa} SCOP: b.49.2.2 c.1.6.1 PDB:
2odo_A*
Length = 357
Score = 25.9 bits (58), Expect = 7.2
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 4/29 (13%)
Query: 58 HGIAQVKSVTGSKILRILKA----HGLAP 82
H + TG++ L ++KA HG
Sbjct: 15 HNYRLAREATGARALAVIKADAYGHGAVR 43
>3oby_A Protein pelota homolog; SM fold, hydrolase; 2.90A {Archaeoglobus
fulgidus}
Length = 352
Score = 25.8 bits (56), Expect = 7.2
Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 6/65 (9%)
Query: 80 LAPEIPEDL---YHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFH 136
L PE +DL +I+K + +R + D + + L + FH
Sbjct: 17 LIPETLDDLWHLRFIIEKGDVVFATTKRASQSSDKLRS---DKEMVTVRLGIEVEKVEFH 73
Query: 137 LYGNM 141
+ N
Sbjct: 74 RFANR 78
>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc
genomics, protein structure initiative; 2.20A
{Campylobacter jejuni}
Length = 464
Score = 25.6 bits (57), Expect = 8.5
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 61 AQVKSVTGSKILRILKAH-GLAPEIPEDLYH 90
Q+ + S +L + ++ E PE Y
Sbjct: 81 NQIYLLGLSILLSVKESILHENVEYPEQYYK 111
>3mca_B Protein DOM34, elongation factor 1 alpha-like protein; protein
protein complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 390
Score = 25.5 bits (55), Expect = 9.3
Identities = 12/65 (18%), Positives = 21/65 (32%), Gaps = 5/65 (7%)
Query: 80 LAPEIPEDLYHL---IKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFH 136
+ PE PED++HL ++ ++ R+ SR+ L F
Sbjct: 18 MCPEEPEDMWHLYNILQVGDQLKAS--TVRRVVKVGATGSTSGSRVVMKLRILVENMDFD 75
Query: 137 LYGNM 141
Sbjct: 76 TKAAQ 80
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
0.320 0.135 0.406
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,331,558
Number of extensions: 130058
Number of successful extensions: 367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 365
Number of HSP's successfully gapped: 38
Length of query: 152
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,328,508
Effective search space: 290010036
Effective search space used: 290010036
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: 53 (24.2 bits)