RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032468
(140 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 = 226 bits (577), Expect = 7e-78
Identities = 100/140 (71%), Positives = 123/140 (87%)
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 RIHRLARYYKKTKKLPPVWK 140
RIHRLARYY+ LPP WK
Sbjct: 121 RIHRLARYYRTVAVLPPNWK 140
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 222 bits (566), Expect = 4e-76
Identities = 100/142 (70%), Positives = 115/142 (80%), Gaps = 2/142 (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 ESRIHRLARYYKKTKKLPPVWK 140
ESRIHRL+RYYK +KLPP WK
Sbjct: 121 ESRIHRLSRYYKLNQKLPPKWK 142
>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 = 42.1 bits (98), Expect = 2e-05
Identities = 20/121 (16%), Positives = 34/121 (28%), Gaps = 39/121 (32%)
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 R 121
R
Sbjct: 501 R 501
Score = 27.9 bits (61), Expect = 1.4
Identities = 22/111 (19%), Positives = 37/111 (33%), Gaps = 14/111 (12%)
Query: 32 DVEDN--ICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLY 89
+V++ F +I + R + + T + I + L P+ E
Sbjct: 252 NVQNAKAWNAFNLS----CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD--EVK- 304
Query: 90 HLIKKAVAIRKHLERNRKDKDSKFRL-ILVESRIHRLAR--YYKK--TKKL 135
L+ K + R + RL I+ ES LA +K KL
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL 355
>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 = 34.3 bits (78), Expect = 0.009
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 32/120 (26%)
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
Score = 33.1 bits (75), Expect = 0.022
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 = 28.5 bits (63), Expect = 0.79
Identities = 29/161 (18%), Positives = 48/161 (29%), Gaps = 58/161 (36%)
Query: 3 RMHSRGKGI-----SASALP---YKRTPP-SWLKIS-SQDVEDNICKFAKK-GLTPSQIG 51
++ ++G I + S P Y + P S I Q + AK G TP ++
Sbjct: 207 KVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA--HYVVTAKLLGFTPGELR 264
Query: 52 VILR----DSHGI--AQVKSVTGS---------KILRIL-----KAH------GLAPEIP 85
L+ S G+ A + T S K + +L + + L P I
Sbjct: 265 SYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSIL 324
Query: 86 ED-------------------LYHLIKKAVAIRKHLERNRK 107
ED + HL ++
Sbjct: 325 EDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
>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 = 31.8 bits (71), Expect = 0.037
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
>3l76_A Aspartokinase; allostery, ACT domains, kinase transferase; HET:
LYS; 2.54A {Synechocystis}
Length = 600
Score = 29.1 bits (66), 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 = 28.7 bits (65), 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
>3dxq_A Choline/ethanolamine kinase family protein; NP_106042.1, STR
genomics, joint center for structural genomics, JCSG,
prote structure initiative; HET: MSE; 2.55A
{Mesorhizobium loti}
Length = 301
Score = 27.4 bits (60), Expect = 1.6
Identities = 9/76 (11%), Positives = 21/76 (27%), Gaps = 8/76 (10%)
Query: 70 KILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNR-----KDKDSKFRLILVESRIHR 124
R G++PE+ L+ V + +++ + K K +
Sbjct: 60 VAAREAAKAGVSPEV---LHVDPATGVMVTRYIAGAQTMSPEKFKTRPGSPARAGEAFRK 116
Query: 125 LARYYKKTKKLPPVWK 140
L ++
Sbjct: 117 LHGSGAVFPFRFELFA 132
>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system,
helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP;
2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*
Length = 1038
Score = 27.6 bits (61), Expect = 1.8
Identities = 8/61 (13%), Positives = 16/61 (26%), Gaps = 3/61 (4%)
Query: 83 EIPEDLYHLIKKAVAIRKHLERNRKDKDS---KFRLILVESRIHRLARYYKKTKKLPPVW 139
+ + + I + + F +L S + YY K+L
Sbjct: 505 QAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEA 564
Query: 140 K 140
Sbjct: 565 A 565
>3obw_A Protein pelota homolog; SM fold, hydrolase; 2.60A {Sulfolobus
solfataricus}
Length = 364
Score = 27.0 bits (59), Expect = 2.4
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
>3j15_A Protein pelota; ribosome recycling, ribosome, archaea,
translation-transport complex; HET: ADP; 6.60A
{Pyrococcus furiosus}
Length = 357
Score = 26.7 bits (58), Expect = 3.2
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 11/64 (17%)
Query: 70 KILRILKAHG---LAPEIPEDLYHL---IKK-----AVAIRKHLERNRKDKDSKFRLILV 118
+IL G + E +DL+HL I A +RK +R + K +I V
Sbjct: 2 EILEEKPKEGKVKVKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPV 61
Query: 119 ESRI 122
+
Sbjct: 62 FLGV 65
>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 = 3.6
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 33 VEDNICKFAKKGLTPSQIGVI 53
VE K K G P QIG+I
Sbjct: 659 VEKITTKLLKAGAKPDQIGII 679
>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 = 4.0
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
>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 = 4.0
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 33 VEDNICKFAKKGLTPSQIGVI 53
VE K K G P QIG+I
Sbjct: 483 VEKITTKLLKAGAKPDQIGII 503
>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 = 4.2
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
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 26.1 bits (57), Expect = 4.8
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 33 VEDNICKFAKKGLTPSQIGVI 53
E I K + G+ P QIGVI
Sbjct: 661 CERIITKLFRDGVKPEQIGVI 681
>4adn_A FAR1; antibiotic resistance; 1.65A {Staphylococcus aureus} PDB:
4ado_A
Length = 222
Score = 25.7 bits (56), Expect = 5.1
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 78 HGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKD 110
HG+ I Y+ I+ + K++ + DK+
Sbjct: 8 HGMKTMIYPHQYNYIRSVILRLKNVYKTVNDKE 40
>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 = 5.3
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
>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 = 25.5 bits (56), Expect = 7.5
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
>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc
genomics, protein structure initiative; 2.20A
{Campylobacter jejuni}
Length = 464
Score = 25.3 bits (56), Expect = 8.0
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
>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 = 25.1 bits (54), Expect = 8.8
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
>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional
regulator, transcription; 2.00A {Streptococcus
pneumoniae}
Length = 146
Score = 24.8 bits (54), Expect = 9.3
Identities = 9/74 (12%), Positives = 29/74 (39%), Gaps = 19/74 (25%)
Query: 40 FAKKGLTPSQIGVILRDSHG------IAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIK 93
++ LT +Q +++ S +A+ +V+ + + + +K L+K
Sbjct: 31 TSEVALTNTQEHILMLLSEESLTNSELARRLNVSQAAVTKAIK-------------SLVK 77
Query: 94 KAVAIRKHLERNRK 107
+ + ++ +
Sbjct: 78 EGMLETSKDSKDAR 91
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 0.136 0.399
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: 2,159,839
Number of extensions: 121826
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 423
Number of HSP's successfully gapped: 41
Length of query: 140
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 56
Effective length of database: 4,356,429
Effective search space: 243960024
Effective search space used: 243960024
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 (23.8 bits)