RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3013
(151 letters)
>3iz5_A 60S ribosomal protein L1 (L1P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_A
Length = 216
Score = 128 bits (323), Expect = 2e-39
Identities = 5/121 (4%), Positives = 20/121 (16%), Gaps = 2/121 (1%)
Query: 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKT 92
M K+ + R+ T + + +
Sbjct: 1 MSKLQSDAVKDAITQIVGEAREKKRKFTETVELQIGLKNYDPQKDKRFSGSVKLPHIPRP 60
Query: 93 LFKKRSKIKPFLKVLNYNHLMPTRYTYPDMQEK--LQPKELKDPMKKKKIRFQIRMKFEE 150
+ + + + + + + +K
Sbjct: 61 KMRVCMLGDAQHVDQAEKMGLDYMDVESLKKMNKNKKLVKKLAKKYHAFLASEAIIKQIP 120
Query: 151 K 151
+
Sbjct: 121 R 121
>3izc_a 60S ribosomal protein RPL27 (L27E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_a
3u5e_Z 3u5i_Z
Length = 136
Score = 127 bits (321), Expect = 6e-39
Identities = 56/121 (46%), Positives = 84/121 (69%), Gaps = 2/121 (1%)
Query: 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKT 92
M K +KAGK+ +V+ GRYAG+K V++K +D+G+ +GHALVAGI+RYP KVTK+
Sbjct: 1 MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAK 60
Query: 93 LFKKRSKIKPFLKVLNYNHLMPTRYTYPDMQEK--LQPKELKDPMKKKKIRFQIRMKFEE 150
KR+KIKPF+KV+NYNHL+PTRYT K + + + P ++++ + ++ FEE
Sbjct: 61 KVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEE 120
Query: 151 K 151
+
Sbjct: 121 R 121
>4a18_N RPL27, ribosomal protein L22; ribosome, eukaryotic initiation
factor 6, EIF6, transla large ribosomal subunit, rRNA;
3.52A {Tetrahymena thermophila} PDB: 4a19_N 4a1b_N
4a1d_N
Length = 144
Score = 126 bits (317), Expect = 3e-38
Identities = 52/121 (42%), Positives = 84/121 (69%), Gaps = 2/121 (1%)
Query: 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKT 92
M K +K G++V++L GR+AG+KAV++K+ +DGT D+++GH LVAG++R P+KVTKRM
Sbjct: 1 MAKFLKYGRVVILLQGRFAGKKAVIVKSSEDGTKDRKFGHVLVAGVERSPKKVTKRMGSK 60
Query: 93 LFKKRSKIKPFLKVLNYNHLMPTRYT--YPDMQEKLQPKELKDPMKKKKIRFQIRMKFEE 150
+KR+ +KPF+K +N NH+MPTRY+ ++L ++ K ++R ++ F E
Sbjct: 61 KIQKRTSVKPFIKYVNLNHIMPTRYSVKELCDFKELVKEDKIKNNAKSEVRDTLKKVFVE 120
Query: 151 K 151
K
Sbjct: 121 K 121
>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 = 37.0 bits (85), Expect = 0.002
Identities = 30/198 (15%), Positives = 53/198 (26%), Gaps = 70/198 (35%)
Query: 3 DTDKYMLNSEEV---------P---TLAHSIFPFLFCRHISKMGKIMK----AGKIVLVL 46
+ Y SE+ P + + F + G I AG
Sbjct: 1713 HSTSYTFRSEKGLLSATQFTQPALTLMEKAAF-----EDLKSKGLIPADATFAG-----H 1762
Query: 47 S-GRY------AG----RKAVVL-----KTYDDGTADKQYGHALVAGIDRYPRKVTKRMN 90
S G Y A V + T + G + I P +V +
Sbjct: 1763 SLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFS 1822
Query: 91 KTLFKK-----RSKIKPFLKVLNYNHLMPTRYTYPDMQ----------EKLQPKELKDPM 135
+ + + ++++NYN + Q + + L +
Sbjct: 1823 QEALQYVVERVGKRTGWLVEIVNYN--------VENQQYVAAGDLRALDTVT-NVLNF-I 1872
Query: 136 KKKKIRF---QIRMKFEE 150
K +KI Q + EE
Sbjct: 1873 KLQKIDIIELQKSLSLEE 1890
>2joy_A 50S ribosomal protein L14E; protein solution structure, structural
genomics, PSI-2, protein structure initiative; NMR
{Sulfolobus solfataricus} SCOP: b.34.5.7 PDB: 2kds_A
Length = 96
Score = 34.8 bits (80), Expect = 0.002
Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 26/104 (25%)
Query: 37 MKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKK 96
++ G+I + + GR AG K V++ DD LV G P+ +T
Sbjct: 4 IEVGRICVKVKGREAGSKCVIVDIIDD-------NFVLVTG----PKDITGVK------- 45
Query: 97 RSKIKPFLKVLNYNHLMPTRYTYPDMQEKLQPKELKDPMKKKKI 140
+ +N HL PT D+Q+ +E+K +++ +
Sbjct: 46 -------RRRVNILHLEPTDKKI-DIQKGASDEEVKKKLEESNL 81
>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 = 36.0 bits (82), Expect = 0.003
Identities = 21/173 (12%), Positives = 51/173 (29%), Gaps = 50/173 (28%)
Query: 6 KYM-LNSEEVPTLAHSIFPFLFCRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDG 64
KY+ +++P + P +S + + ++ G + +
Sbjct: 309 KYLDCRPQDLPREVLTTNPR----RLSIIAESIRDGLA------TW--------DNWKHV 350
Query: 65 TADKQYGHALVAGIDRYPRKVTKRMNKTL--FKKRSKIKPFLKVLN-------------- 108
DK + + ++ ++M L F + I +L+
Sbjct: 351 NCDK-LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT--ILLSLIWFDVIKSDVMVV 407
Query: 109 YNHLM----------PTRYTYPDMQEKLQPKELKDPMKKKKI--RFQIRMKFE 149
N L + + P + +L+ K + + I + I F+
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460
Score = 29.8 bits (66), Expect = 0.39
Identities = 18/104 (17%), Positives = 29/104 (27%), Gaps = 20/104 (19%)
Query: 37 MK-AGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFK 95
+ +GK + L V D L P V + + K L+
Sbjct: 158 VLGSGKTWVALD---VCLSYKVQCKMDFKI------FWLNLKNCNSPETVLEMLQKLLY- 207
Query: 96 KRSKIKPFLKVLNYNHLMPTRYTYPDMQEKLQPKELKDPMKKKK 139
+I P N+ +Q EL+ +K K
Sbjct: 208 ---QIDP-----NWTSRSDHSSNIKLRIHSIQ-AELRRLLKSKP 242
>3izc_G 60S ribosomal protein RPL6 (L6E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins; NMR {Saccharomyces cerevisiae} PDB:
3izs_G 3o58_F 3o5h_F 3u5e_E 3u5i_E
Length = 176
Score = 30.8 bits (69), Expect = 0.11
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 26 FCRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDG 64
K+ + G ++++L+GR+ G++ V LK +D
Sbjct: 23 KAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDN 61
>3izc_n 60S ribosomal protein RPL38 (L38E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_n
3u5e_k 3u5i_k
Length = 78
Score = 28.4 bits (63), Expect = 0.52
Identities = 0/106 (0%), Positives = 0/106 (0%), Gaps = 28/106 (26%)
Query: 35 KIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLF 94
++ + + + T
Sbjct: 13 ELTRRADVKTATVKINKKLNKAGKPFRQT-------KFKVRGS----SSLYTLV------ 55
Query: 95 KKRSKIKPFLKVLNYNHLMPTRYTYPDMQEKLQPKELKDPMKKKKI 140
+
Sbjct: 56 ----------INDAGKAKKLIQSLP- 90
>4a17_Q RPL17, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_Q 4a1c_Q 4a1e_Q
Length = 183
Score = 28.0 bits (62), Expect = 0.93
Identities = 8/67 (11%), Positives = 17/67 (25%)
Query: 27 CRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVT 86
+ + K + L ++ + + H R+P K
Sbjct: 31 TYEVVRAIKGLNLENAKRYLKAVIDRKRCIPFTRFTGCIGRTAQAHEFGRTQGRWPVKSV 90
Query: 87 KRMNKTL 93
K + L
Sbjct: 91 KVILGLL 97
>2ri0_A Glucosamine-6-phosphate deaminase; carbohydrate metabolism,; HET:
BTB; 1.60A {Streptococcus mutans} PDB: 2ri1_A*
Length = 234
Score = 27.6 bits (62), Expect = 1.5
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 17/52 (32%)
Query: 10 NSEEVPTLAHSIFPFLFCRHISKMG--KIMKAGKIVLVLSGRYAGRKAVVLK 59
+E+VP A IS MG IM A I+L+ G KA +
Sbjct: 164 KAEDVPKQA-----------IS-MGLASIMSAKMILLMAFGE---EKAEAVA 200
>2do3_A Transcription elongation factor SPT5; KOW motif, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
SCOP: b.34.5.5
Length = 69
Score = 25.9 bits (57), Expect = 1.7
Identities = 8/35 (22%), Positives = 19/35 (54%)
Query: 29 HISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDD 63
++ K K G V V++GR+ G ++++ ++
Sbjct: 10 PAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEEN 44
>3iz5_N 60S ribosomal protein L14 (L14E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_N
Length = 134
Score = 26.8 bits (59), Expect = 2.2
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 35 KIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTA 66
+ ++ G++ LV G+ GR V++ D A
Sbjct: 5 RFVEIGRVALVNYGKDYGRLVVIVDVVDQNRA 36
>2bkx_A Glucosamine-6-phosphate deaminase; hydrolase, substrate inhibition,
fructose-6-phosphate; HET: F6R; 1.4A {Bacillus subtilis}
PDB: 2bkv_A*
Length = 242
Score = 26.9 bits (60), Expect = 2.2
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 17/52 (32%)
Query: 10 NSEEVPTLAHSIFPFLFCRHISKMG--KIMKAGKIVLVLSGRYAGRKAVVLK 59
+ + VP A ++ MG I+ + +I+L++SG+ KA ++
Sbjct: 171 SIDSVPKKA-----------LT-MGIQTILSSKRILLLISGK---SKAEAVR 207
>3iz5_G 60S ribosomal protein L6 (L6E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_G
Length = 219
Score = 26.5 bits (58), Expect = 3.2
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 28 RHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDG 64
H +K+ + G ++++L+GRY G++ V LK G
Sbjct: 66 PHPTKLRSTITPGTVLILLAGRYMGKRVVFLKQLQSG 102
>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 191
Score = 26.4 bits (58), Expect = 3.5
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 7/52 (13%)
Query: 28 RHISKMGKI-MKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGI 78
+ K+ K +K G V V+SG G+ + K + ++ +
Sbjct: 59 NSLPKLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHN------STVIIKDL 104
>1fs5_A Glucosamine-6-phosphate deaminase; allosteric enzyme, entropic
effects, aldose-ketose isomerase multiple conformers,
isomerase; HET: 16G TLA; 1.73A {Escherichia coli} SCOP:
c.124.1.1 PDB: 1cd5_A 1fqo_A* 1frz_A* 1dea_A* 1fs6_A
1fsf_A 1hor_A* 1hot_A* 2wu1_A* 1jt9_A
Length = 266
Score = 26.2 bits (58), Expect = 4.7
Identities = 9/48 (18%), Positives = 24/48 (50%), Gaps = 13/48 (27%)
Query: 12 EEVPTLAHSIFPFLFCRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLK 59
+VP A ++ +G ++ A ++++++ G +KA+ L+
Sbjct: 179 NQVPKYALTV----------GVGTLLDAEEVMILVLGS---QKALALQ 213
>1ne7_A Glucosamine-6-phosphate isomerase; V-type like allosteric enzyme,
conformational disorder, conformational differences,
hydrolase; HET: GLC 16G AGP; 1.75A {Homo sapiens} SCOP:
c.124.1.1
Length = 289
Score = 26.2 bits (58), Expect = 5.0
Identities = 7/27 (25%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 33 MGKIMKAGKIVLVLSGRYAGRKAVVLK 59
+G +M A +++++++G KA L
Sbjct: 190 VGTVMDAREVMILITGA---HKAFALY 213
>2zkr_r 60S ribosomal protein L17; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 184
Score = 25.7 bits (56), Expect = 5.6
Identities = 12/68 (17%), Positives = 22/68 (32%)
Query: 27 CRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVT 86
R ++ K M K L ++ V + Y+ G R+P+K
Sbjct: 29 TRETAQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSA 88
Query: 87 KRMNKTLF 94
+ + L
Sbjct: 89 EFLLHMLK 96
>3hn6_A Glucosamine-6-phosphate deaminase; niaid, ssgcid, decode, UW, SBRI,
infectious disease, LYME DI non-hodgkin lymphomas,
neuroborreliosis; 2.20A {Borrelia burgdorferi}
Length = 289
Score = 25.8 bits (57), Expect = 5.8
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 13/48 (27%)
Query: 12 EEVPTLAHSIFPFLFCRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLK 59
+VP A ++ +G IM + +++++++G KA LK
Sbjct: 200 NKVPKNALTV----------GIGTIMDSQEVLIIVNGH---NKARALK 234
>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
2j28_U* 3fik_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U
3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U
1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U 3i20_U ...
Length = 102
Score = 25.2 bits (56), Expect = 5.9
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 35 KIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGI 78
KI + V+VL+G+ G++ V G +V GI
Sbjct: 3 KI-RRDDEVIVLTGKDKGKRGKVKNVLSS-------GKVIVEGI 38
>1b9p_A Protein (collagen alpha 1); collagen facit XIV, heparin-binding
site; NMR {Synthetic} SCOP: j.49.1.1 PDB: 1b9q_A
Length = 34
Score = 23.7 bits (50), Expect = 6.4
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 77 GIDRYPRKVTKRMNKTLFKKRSKIK 101
GI R+ RK+ KR KTL KR K
Sbjct: 9 GISRFRRKIAKRSIKTLEHKRENAK 33
>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear
protein; 1.45A {Homo sapiens}
Length = 127
Score = 24.9 bits (54), Expect = 7.9
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 38 KAGKIVLVLSGRYAGRKAVVLK 59
GK +LVL+G Y G + +
Sbjct: 72 APGKRILVLNGGYRGNEGTLES 93
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
0.322 0.137 0.396
Gapped
Lambda K H
0.267 0.0505 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,320,628
Number of extensions: 133660
Number of successful extensions: 355
Number of sequences better than 10.0: 1
Number of HSP's gapped: 352
Number of HSP's successfully gapped: 33
Length of query: 151
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 66
Effective length of database: 4,328,508
Effective search space: 285681528
Effective search space used: 285681528
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 (21.9 bits)
S2: 53 (24.7 bits)