RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13610
(123 letters)
>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 140
Score = 90.8 bits (226), Expect = 7e-25
Identities = 25/84 (29%), Positives = 46/84 (54%)
Query: 21 KFKNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKK 80
+ +++++ + NNTI++++D +G V S G GF+ ++GT AAQ A +
Sbjct: 25 RKIPKGVIHVQASFNNTIVTVTDVRGRVVSWASAGTCGFRGTKRGTPFAAQTAAGNAIRT 84
Query: 81 ALEIGVSSVRINVRGLGPGRLKAL 104
+E G+ + ++G G GR AL
Sbjct: 85 VVEQGMQRAEVMIKGPGLGRDAAL 108
>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.55.4.1
PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K* 1hr0_K 1ibk_K*
1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N* 1jgq_N* 1ml5_N*
1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K* 1xmq_K* 1xnq_K*
...
Length = 129
Score = 89.7 bits (223), Expect = 2e-24
Identities = 32/78 (41%), Positives = 46/78 (58%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKKALEIGV 86
I + NNTI++++D G S G+ G+K +RKGT AAQ A + KKA+ G+
Sbjct: 18 RAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGM 77
Query: 87 SSVRINVRGLGPGRLKAL 104
SV + VRG G GR +A+
Sbjct: 78 QSVDVIVRGTGAGREQAI 95
>3r8n_K 30S ribosomal protein S11; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_K 3fih_K* 3iy8_K 2wwl_K
3oar_K 3oaq_K 3ofb_K 3ofa_K 3ofp_K 3ofx_K 3ofy_K 3ofo_K
3r8o_K 4a2i_K 3i1m_K 1vs7_K* 3e1a_C 3e1c_C 1vs5_K 3i1o_K
...
Length = 117
Score = 88.8 bits (221), Expect = 2e-24
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 23 KNLP--IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGKK 80
K + + +I + NNTI++++D +G + G GF+ +RK T AAQ A
Sbjct: 2 KQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADA 61
Query: 81 ALEIGVSSVRINVRGLGPGRLKAL 104
E G+ ++ + V+G GPGR +
Sbjct: 62 VKEYGIKNLEVMVKGPGPGRESTI 85
>3u5c_O RP59A, 40S ribosomal protein S14-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_K 3o30_H 3o2z_H 3u5g_O 1s1h_K
3jyv_K*
Length = 137
Score = 68.5 bits (168), Expect = 3e-16
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 15/97 (15%)
Query: 27 IMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNAR-KGTNIAAQAAGITIGKKALEIG 85
+ I + N+T + ++D G + R G K R + + AA A + K E+G
Sbjct: 16 VARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAAQDVAAKCKEVG 75
Query: 86 VSSVRINVRGLGPGRLKALEIGVSSVRINVRGLGPGR 122
+++V + +R G R K GPG
Sbjct: 76 ITAVHVKIRATGGTRTK--------------TPGPGG 98
>2xzm_K RPS14E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_K 3j0o_K 3j0l_K 2zkq_k 3iz6_K 3jyv_K*
Length = 151
Score = 62.9 bits (153), Expect = 7e-14
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 9/93 (9%)
Query: 21 KFKNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARK-GTNIAAQAAGITIGK 79
+ +I T N+T + ++D G L+R G K R+ + AA A I +
Sbjct: 24 NENVFGVCHIMATWNDTFIHVTDLSGRETLVRVTGGMKVKADREESSPYAAMQAAIDVVN 83
Query: 80 KALEIGVSSVRINVR--------GLGPGRLKAL 104
+ E+ ++++ I +R GPG AL
Sbjct: 84 RCKELKINALHIKLRAKGGVETKQPGPGAQSAL 116
>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 = 43.1 bits (101), Expect = 6e-06
Identities = 25/134 (18%), Positives = 49/134 (36%), Gaps = 36/134 (26%)
Query: 4 KDIFP--DENTPDLIFDGLKFKNLPIMNIRVTKNNT---ILSLSDAKGVVKLLRSCGMEG 58
+ IF +E++ F + T+ T + + A + L+S +G
Sbjct: 1704 EKIFKEINEHSTSYTFRS------EKGLLSATQ-FTQPALTLMEKA--AFEDLKS---KG 1751
Query: 59 FKNARK---G------TNIAAQAAGITIGKKALEIGVSSVRINVRGLGPGR-LKALEIGV 108
A G +A+ A ++I + +E+ V RG+ + E+G
Sbjct: 1752 LIPADATFAGHSLGEYAALASLADVMSI-ESLVEV----VFY--RGMTMQVAVPRDELGR 1804
Query: 109 SSVRINVRGLGPGR 122
S+ + + PGR
Sbjct: 1805 SNYGMI--AINPGR 1816
>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus
stearothermophilus} SCOP: c.55.4.1
Length = 120
Score = 27.6 bits (62), Expect = 0.63
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 62 ARKGTNI-AAQAAGITIGKKALEIGVSSV 89
NI AA+ G + K+ALE G+ V
Sbjct: 65 LDSTNNIEAAKKVGELVAKRALEKGIKQV 93
>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 161
Score = 27.4 bits (61), Expect = 0.85
Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 56 MEGFKNARKGTNI-AAQAAGITIGKKALEIGVSSV 89
+ + I A+ G I LE G++ V
Sbjct: 100 ISEELDYSSSPTIEVAKKVGEVIASACLEKGITKV 134
>3r8s_O 50S ribosomal protein L18; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_O 2wwq_O 3oat_O* 3oas_O* 3ofd_O 3ofc_O 3ofr_O*
3ofz_O* 3og0_O 3ofq_O 3r8t_O 3i1n_O 1p85_M 1p86_M
1vs8_O 1vs6_O 2aw4_O 2awb_O 1vt2_O 2i2v_O ...
Length = 116
Score = 26.7 bits (60), Expect = 1.1
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 60 KNARKGTNI-AAQAAGITIGKKALEIGVSSV 89
+ + N AA A G + ++ALE G+ V
Sbjct: 59 EQLKYTGNKDAAAAVGKAVAERALEKGIKDV 89
>3v2d_S 50S ribosomal protein L18; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_M 2hgj_R 2hgq_R 2hgu_R 1vsa_M 2j03_S 2jl6_S 2jl8_S
2v47_S 2v49_S 2wdi_S 2wdj_S 2wdl_S 2wdn_S 2wh2_S 2wh4_S
2wrj_S 2wrl_S 2wro_S 2wrr_S ...
Length = 112
Score = 26.4 bits (59), Expect = 1.6
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 64 KGTNI-AAQAAGITIGKKALEIGVSSVRINVRG--LGPGRLKAL 104
KG A+ G + +KAL +G+ V + RG GR+KAL
Sbjct: 59 KGNKTEVARQVGRALAEKALALGIKQVAFD-RGPYKYHGRVKAL 101
>2zjr_L 50S ribosomal protein L18; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.55.4.1 PDB: 1sm1_M* 2zjp_L* 2zjq_L
1nkw_M 3cf5_L* 3dll_L* 3pio_L* 3pip_L* 1nwy_M* 1nwx_M*
1xbp_M* 1pnu_M 1pny_M 1vor_P 1vou_P 1vow_P 1voy_P 1vp0_P
Length = 114
Score = 26.0 bits (58), Expect = 2.2
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 64 KGTNI-AAQAAGITIGKKALEIGVSSVRINVRG--LGPGRLKAL 104
G A A G + A E G+ V + RG GR+KAL
Sbjct: 61 SGNKTDTAAAVGKALAAAAAEKGIKQVVFD-RGSYKYHGRVKAL 103
>1egd_A Medium chain acyl-COA dehydrogenase; flavoprotein, electron
transfer; HET: FAD; 2.40A {Homo sapiens} SCOP: a.29.3.1
e.6.1.1 PDB: 1egc_A* 1ege_A* 1t9g_A* 2a1t_A* 1udy_A*
3mdd_A* 3mde_A*
Length = 396
Score = 25.9 bits (58), Expect = 4.2
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 7/32 (21%)
Query: 57 EGFKNARKG-----TNIAAQAAGITIGKKALE 83
GFK A +AA A G + ++AL+
Sbjct: 243 AGFKVAMGAFDKERPVVAAGAVG--LAQRALD 272
>1rx0_A Acyl-COA dehydrogenase family member 8, mitochondrial;
flavoprotein, coenzyme A, oxidoreductase; HET: FAD 2MC;
1.77A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1
Length = 393
Score = 25.6 bits (57), Expect = 4.8
Identities = 8/36 (22%), Positives = 15/36 (41%), Gaps = 7/36 (19%)
Query: 57 EGFKNARKG-----TNIAAQAAGITIGKKALEIGVS 87
+GF A +G NIA+ + G ++ +
Sbjct: 242 QGFLIAVRGLNGGRINIASCSLGAAHA--SVILTRD 275
>1r2j_A Protein FKBI; polyketide synthase, polyketide, acyl-COA
dehydrogenase, , aldehyde dehydrogenase, oxidoreductase;
HET: FAD; 2.10A {Streptomyces hygroscopicus} SCOP:
a.29.3.1 e.6.1.1
Length = 366
Score = 25.6 bits (57), Expect = 5.8
Identities = 10/71 (14%), Positives = 15/71 (21%), Gaps = 30/71 (42%)
Query: 11 NTPDLIFDGLKFKNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGT---- 66
DL D +RV +L G +
Sbjct: 190 GHADLHLD----------QVRVPAGA-------------VLAGSG-ASLPMLVAASLAYG 225
Query: 67 --NIAAQAAGI 75
++A GI
Sbjct: 226 RKSVAWGCVGI 236
>2jif_A Short/branched chain specific acyl-COA dehydrogen; mitochondrion,
oxidoreductase, transit peptide, fatty acid metabolism,
FAD, flavoprotein; HET: FAD COS; 2.0A {Homo sapiens}
Length = 404
Score = 25.2 bits (56), Expect = 6.4
Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 31/81 (38%)
Query: 11 NTPDLIFDGLKFKNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKGTN--- 67
+T L F+ N++V + N +L G G+K A N
Sbjct: 231 STCPLTFE----------NVKVPEAN-------------ILGQIG-HGYKYAIGSLNEGR 266
Query: 68 --IAAQAAGITIGKKALEIGV 86
IAAQ G+ G + +
Sbjct: 267 IGIAAQMLGLAQG--CFDYTI 285
>2gpy_A O-methyltransferase; structural genomics, PSI, protein structure
initiative, NEW research center for structural genomics,
nysgxrc; HET: MSE; 1.90A {Bacillus halodurans}
Length = 233
Score = 25.3 bits (56), Expect = 6.4
Identities = 8/32 (25%), Positives = 16/32 (50%), Gaps = 5/32 (15%)
Query: 79 KKALEIGV----SSVRINVRGLGPGRLKALEI 106
+ LEIG S++R+ + L + ++E
Sbjct: 56 ARILEIGTAIGYSAIRM-AQALPEATIVSIER 86
>2z1q_A Acyl-COA dehydrogenase; FAD, structural genomics, NPPSFA, Na
project on protein structural and functional analyses;
HET: FAD; 2.30A {Thermus thermophilus}
Length = 577
Score = 25.4 bits (56), Expect = 6.5
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 57 EGFKNARKGTN-----IAAQAAGITIGKKALEIGV 86
+G K A N + A A G K+ALE+
Sbjct: 251 KGHKIAFNVLNVGRYKLGAGAVG--GAKRALELSA 283
>3mkh_A Nitroalkane oxidase; oxidoreductase flavoenzyme, acyl-COA
dehydrogen flavoprotein, oxidoreductase; HET: FAD; 2.00A
{Podospora anserina}
Length = 438
Score = 25.3 bits (56), Expect = 7.0
Identities = 13/78 (16%), Positives = 22/78 (28%), Gaps = 31/78 (39%)
Query: 11 NTPDLIFDGLKFKNLPIMNIRVTKNNTILSLSDAKGVVKLLRSCGMEGFKNARKG----- 65
+ P + + N+RV N +L G +G K A
Sbjct: 239 SGPHVRYT----------NVRVPTKN-------------VLCPAG-QGAKVAFGAFDGSA 274
Query: 66 TNIAAQAAGITIGKKALE 83
+ A G+ A +
Sbjct: 275 VLVGAMGVGLMRA--AFD 290
>3owa_A Acyl-COA dehydrogenase; structural genomics, center for structural
genomics of infec diseases, csgid, alpha-structure,
beta-barrel; HET: MSE FAD 1PE; 1.97A {Bacillus
anthracis}
Length = 597
Score = 25.4 bits (56), Expect = 7.4
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 7/35 (20%)
Query: 57 EGFKNARKGTN-----IAAQAAGITIGKKALEIGV 86
+G A N + G K+A+EI
Sbjct: 256 KGHIIAFNILNIGRYKLGVGTVG--SAKRAVEISA 288
>1ukw_A Acyl-COA dehydrogenase; oxidoreductase, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; HET: FAD; 2.40A {Thermus thermophilus} SCOP:
a.29.3.1 e.6.1.1
Length = 379
Score = 25.1 bits (56), Expect = 8.2
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 57 EGFKNARKG-----TNIAAQAAGITIGKKALE 83
EGFK A + +AA + G + ++AL+
Sbjct: 229 EGFKIAMQTLNKTRIPVAAGSVG--VARRALD 258
>1vz6_A Ornithine acetyl-transferase; clavulanic acid, N-acetyl- ornithine,
N-acetyl-glutamate, antibiotic; 2.75A {Streptomyces
clavuligerus} SCOP: d.154.1.2 PDB: 1vz7_A 1vz8_A
Length = 393
Score = 24.8 bits (55), Expect = 8.5
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 55 GMEGFKNARKGTNIAAQAAGITIGKKALEIGVSS 88
G+EG +NAR+ A+A G+ E+ ++S
Sbjct: 81 GLEGEENAREVREAVARALGL----PEGEMLIAS 110
>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid; HET:
FDA; 2.10A {Mycobacterium thermoresistibile}
Length = 393
Score = 24.8 bits (55), Expect = 8.8
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 7/32 (21%)
Query: 57 EGFKNARKG-----TNIAAQAAGITIGKKALE 83
GFK A I AQA G I + AL+
Sbjct: 243 TGFKTALATLDHTRPTIGAQAVG--IAQGALD 272
>1ee6_A Pectate lyase; parallel beta-helix, high-alkaline,
low-molecular-weight; 2.30A {Bacillus SP} SCOP: b.80.1.1
Length = 197
Score = 24.6 bits (53), Expect = 9.8
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 44 AKGVVKLLRSCGMEGFKNARKGTNIAAQAAGITIGK 79
A + KL+R G +K N I +
Sbjct: 124 ADDIGKLVRQNGGTTYKVVMNVENCNISRVKDAILR 159
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 0.140 0.391
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,883,306
Number of extensions: 107963
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 293
Number of HSP's successfully gapped: 53
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
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 (21.7 bits)
S2: 51 (23.3 bits)