RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8861
(550 letters)
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D*
1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D*
1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G
2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...
Length = 209
Score = 290 bits (745), Expect = 3e-96
Identities = 92/203 (45%), Positives = 131/203 (64%), Gaps = 4/203 (1%)
Query: 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLR---PGQHGRISGSRTSDYGYQFR 57
M RYIGP +LCRREG+ L+LK R KC ++ R PGQHG+ R SDY + R
Sbjct: 1 MGRYIGPVCRLCRREGVKLYLKG-ERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLR 59
Query: 58 EKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQ 117
EKQK++R+YGI E+QFR F E ++ KG TG + L LLESR DNVVYR+GF+ +R +ARQ
Sbjct: 60 EKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQ 119
Query: 118 LISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAK 177
L+ H VN + V++ SY+++PGD I+V EK++ I +LE + W+++D +
Sbjct: 120 LVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVE 179
Query: 178 KMEGVFKSEPNRSEFANDINDLL 200
M+G F P+R + A +N+ L
Sbjct: 180 GMKGKFLRLPDREDLALPVNEQL 202
>3r8n_D 30S ribosomal protein S4; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D*
2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D*
2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D*
...
Length = 205
Score = 290 bits (744), Expect = 3e-96
Identities = 122/199 (61%), Positives = 156/199 (78%), Gaps = 1/199 (0%)
Query: 2 ARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQK 61
ARY+GPK KL RREG DLFLKS R++D+KCK++ PGQHG R SDYG Q REKQK
Sbjct: 1 ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGA-RKPRLSDYGVQLREKQK 59
Query: 62 VKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISH 121
V+R+YG+LE+QFR Y+ E ARLKG TGE +L LLE R DNVVYRMGF +TR+EARQL+SH
Sbjct: 60 VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH 119
Query: 122 RAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEG 181
+A +VN ++VNIASY++ P D++S+REKAKKQ+R+ +LEL+E +W+ VDA KMEG
Sbjct: 120 KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG 179
Query: 182 VFKSEPNRSEFANDINDLL 200
FK +P RS+ + DIN+ L
Sbjct: 180 TFKRKPERSDLSADINEHL 198
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 201
Score = 268 bits (688), Expect = 7e-88
Identities = 71/200 (35%), Positives = 107/200 (53%), Gaps = 8/200 (4%)
Query: 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQ 60
M+RY GP+ K RR G L + K ++ SG + S Y + EKQ
Sbjct: 1 MSRYRGPRFKKIRRLGALPGLTN-------KRPRAGSDLRNQSRSG-KRSQYRIRLEEKQ 52
Query: 61 KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLIS 120
K++ YGI E+Q +Y + KG TG+++L+LLE R DN+++R+G + T ARQL++
Sbjct: 53 KLRFHYGITERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTIPGARQLVN 112
Query: 121 HRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKME 180
HR LVN +IV+I SY+ KP D I R++ K I NSL+LS +T++ +
Sbjct: 113 HRHILVNGRIVDIPSYRCKPQDTIMARDEQKSIALIQNSLDLSPREELPKHLTLNPFPYK 172
Query: 181 GVFKSEPNRSEFANDINDLL 200
G+ + IN+LL
Sbjct: 173 GLVNQIIDSKWVGLKINELL 192
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology,
possible helix-turn-helix motif, ribosome; NMR
{Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB:
1c06_A 1eg0_A 1qd7_C
Length = 159
Score = 236 bits (604), Expect = 7e-76
Identities = 70/153 (45%), Positives = 103/153 (67%), Gaps = 2/153 (1%)
Query: 48 RTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMG 107
+ S+YG Q +EKQK++ MYG+ E+QFR+ F E ++ GK GE + LLESR DN+VYR+G
Sbjct: 2 KLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLG 61
Query: 108 FSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHST 167
+ TR +ARQL++H LV+ VNI SY++KPG I+VREK++ I +LE + +
Sbjct: 62 LARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALE-ANNYI 120
Query: 168 PFSWITVDAKKMEGVFKSEPNRSEFANDINDLL 200
P +++ D +KMEG + P RSE +IN+ L
Sbjct: 121 P-DYLSFDPEKMEGTYTRLPERSELPAEINEAL 152
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble;
2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Length = 235
Score = 212 bits (543), Expect = 8e-66
Identities = 73/133 (54%), Positives = 98/133 (73%)
Query: 194 NDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIIS 253
+ + LKPR++D++ + S HAKV +EP ERG+G+TLGNALR +LLSSM GCA TEV I
Sbjct: 3 GSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEID 62
Query: 254 GALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIE 313
G LHEYS+ EGVQEDI++I+LNLKG+ +++ +D IL L K G V A+DI D+E
Sbjct: 63 GVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVE 122
Query: 314 LVNPNHIIAHLSD 326
+V P H+I HL+D
Sbjct: 123 IVKPQHVICHLTD 135
Score = 34.0 bits (79), Expect = 0.090
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 328 EEAIRQSARVLVDQLNVFAAL 348
EEAIR++A +L +QL F L
Sbjct: 214 EEAIRRAATILAEQLEAFVDL 234
>3r8s_N 50S ribosomal protein L17; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_N 2wwq_N 3oat_N* 3oas_N* 3ofd_N 3ofc_N 3ofr_N*
3ofz_N* 3og0_N 3ofq_N 3r8t_N 3i1n_N 1p85_L 1p86_L 1vs8_N
1vs6_N 2aw4_N 2awb_N 1vt2_N 2i2v_N ...
Length = 120
Score = 206 bits (527), Expect = 4e-65
Identities = 77/115 (66%), Positives = 93/115 (80%)
Query: 430 MRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTL 489
MRHR R+LNR SSHR M RNM SL+R+EIIKTTLPKAKELRRVVEP++TL+K +++
Sbjct: 1 MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV 60
Query: 490 SNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIEL 544
+N+RLAF+ RD +I KLF+ELGPR+ GGY RILK GFR GDNAPMA+IEL
Sbjct: 61 ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIEL 115
>2zjr_K 50S ribosomal protein L17; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.188.1.1 PDB: 1nwx_L* 1nwy_L*
1sm1_L* 1xbp_L* 2zjp_K* 2zjq_K 1nkw_L 3cf5_K* 3dll_K*
3pio_K* 3pip_K* 1pnu_L 1pny_L 1vor_O 1vou_O 1vow_O
1voy_O 1vp0_O
Length = 116
Score = 201 bits (515), Expect = 2e-63
Identities = 52/115 (45%), Positives = 70/115 (60%)
Query: 430 MRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTL 489
MRH RKLNR SS R+ + R +LLR I+TTL KAKELR VE ++T +K L
Sbjct: 1 MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDL 60
Query: 490 SNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIEL 544
++RL + D+ + K+ E+ P+Y + GGY RIL++G R GD MA IEL
Sbjct: 61 HSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIEL 115
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_A
Length = 329
Score = 208 bits (532), Expect = 6e-63
Identities = 74/133 (55%), Positives = 99/133 (74%)
Query: 194 NDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIIS 253
+ + LKPR++D++ + S HAKV +EP ERG+G+TLGNALRR+LLSSM GCA TEV I
Sbjct: 3 GSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEID 62
Query: 254 GALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIE 313
G LHEYS+ EGVQEDI++I+LNLKG+ +++ +D IL L K G V A+DI D+E
Sbjct: 63 GVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVE 122
Query: 314 LVNPNHIIAHLSD 326
+V P H+I HL+D
Sbjct: 123 IVKPQHVICHLTD 135
Score = 159 bits (404), Expect = 2e-44
Identities = 64/99 (64%), Positives = 78/99 (78%), Gaps = 1/99 (1%)
Query: 328 EEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKA 387
EEAIR++A +L +QL F L + + E+ + DPILLRPVDDLELTVRSANCLKA
Sbjct: 214 EEAIRRAATILAEQLEAFVDLRD-VRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKA 272
Query: 388 ENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRG 426
E IH IGDL+QR+E ELL+TPNLG+KSL EIK++LASRG
Sbjct: 273 EAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 311
>3bbo_P Ribosomal protein L17; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 205
Score = 203 bits (518), Expect = 1e-62
Identities = 52/144 (36%), Positives = 85/144 (59%), Gaps = 1/144 (0%)
Query: 402 NELLRTPNLGRKSLNEIKEILASRGKYY-MRHRHGFRKLNRTSSHRLIMLRNMTISLLRY 460
+ LL + S ++ + G+ + MRH KLNR R +LR +T LL++
Sbjct: 61 HPLLSLSSQDSTSFEHSFTVIDNGGRVFAMRHGRKVPKLNRPPDQRRALLRGLTTQLLKH 120
Query: 461 EIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKIN 520
IKTT +A+ +R+ V+ ++T++K +L +R A ++ +++I LF+E+ RY + N
Sbjct: 121 GRIKTTKARARAVRKYVDKMITMAKDGSLHKRRQALGFIYEKQIVHALFAEVPDRYGERN 180
Query: 521 GGYVRILKMGFRVGDNAPMAFIEL 544
GGY RI++ R GDNAPMA+IEL
Sbjct: 181 GGYTRIIRTLPRRGDNAPMAYIEL 204
>1gd8_A 50S ribosomal protein L17; two domains, ribosomal protein S8-like
domain, Trp repressor-like domain, helix-turn-helix
motif; 2.30A {Thermus thermophilus} SCOP: d.188.1.1 PDB:
1vsa_L 1vsp_L 1yl3_0 2b66_R 2b9n_R 2b9p_R 2hgj_Q 2hgq_Q
2hgu_Q 2j01_R 2j03_R 2jl6_R 2jl8_R 2v47_R 2v49_R 2wdi_R
2wdj_R 2wdl_R 2wdn_R 2wh2_R ...
Length = 118
Score = 198 bits (505), Expect = 9e-62
Identities = 58/116 (50%), Positives = 74/116 (63%), Gaps = 1/116 (0%)
Query: 430 MRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTL 489
MRH RKLNR SSHRL + RN SLL + I TT+PKAKELR V+ ++ L+K+ L
Sbjct: 1 MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDHLIHLAKRGDL 60
Query: 490 SNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMG-FRVGDNAPMAFIEL 544
+RL L+D K+ KLF E+ PRY GGY R+LK+ R GD AP+A +EL
Sbjct: 61 HARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKLAERRRGDGAPLALVEL 116
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1
d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A
2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A*
3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A*
1ynn_A* ...
Length = 315
Score = 198 bits (505), Expect = 4e-59
Identities = 56/134 (41%), Positives = 85/134 (63%), Gaps = 2/134 (1%)
Query: 196 INDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGA 255
++ LK + V+T G + + ++EP ERG+G TLGN LRR+LLSS+ G A T V I
Sbjct: 2 LDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDV 61
Query: 256 LHEYSSLEGVQEDIIDIILNLKGVILKLYNRD--YAILNLKKFGKCVVLASDIELLSDIE 313
LHE+S++ GV+ED+++IILNLK ++++ N L LK G V A D ++D+E
Sbjct: 62 LHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVE 121
Query: 314 LVNPNHIIAHLSDN 327
++NP+ IA L +
Sbjct: 122 IMNPDLHIATLEEG 135
Score = 155 bits (395), Expect = 2e-43
Identities = 28/103 (27%), Positives = 50/103 (48%), Gaps = 4/103 (3%)
Query: 328 EEAIRQSARVLVDQLNVFAAL----ENTPVKKELDSSLEKVDPILLRPVDDLELTVRSAN 383
EA+ Q+ +L + L F+ P + + + + + L P+++L L+ R +
Sbjct: 208 LEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLH 267
Query: 384 CLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRG 426
LK E I + L+ + +L P +G +SL EIKE L +G
Sbjct: 268 SLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKG 310
>2cqm_A Ribosomal protein L17 isolog; alpha and beta (A+B), structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.188.1.1 PDB: 2ftc_J 3iy9_S
Length = 122
Score = 170 bits (433), Expect = 3e-51
Identities = 35/104 (33%), Positives = 53/104 (50%), Gaps = 2/104 (1%)
Query: 443 SSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSN--KRLAFSYLR 500
SS +LRN+ L+R+E I+ + E+R E ++ K + R+A +L
Sbjct: 2 SSGSSGLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLIDYGKLGDTNERAMRMADFWLT 61
Query: 501 DRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIEL 544
++ + KLF L PRY GGY R+L++ R D A MA IE
Sbjct: 62 EKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKMAVIEY 105
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl
transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB:
2jzb_A
Length = 98
Score = 114 bits (287), Expect = 7e-31
Identities = 53/75 (70%), Positives = 62/75 (82%)
Query: 352 PVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLG 411
+ E+ + DPILLRPVDDLELTVRSANCLKAE IH IGDL+QR+E ELL+TPNLG
Sbjct: 6 VREPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 65
Query: 412 RKSLNEIKEILASRG 426
+KSL EIK++LASRG
Sbjct: 66 KKSLTEIKDVLASRG 80
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex,
cytoplasm, redox-active center, stress response,
transcription; 2.30A {Bacillus subtilis}
Length = 79
Score = 110 bits (276), Expect = 2e-29
Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 4/75 (5%)
Query: 352 PVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLG 411
P KE D + + +L +++L+L+VRS NCLK I+ + +L ++E ++++ NLG
Sbjct: 2 PHMKEED----QKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLG 57
Query: 412 RKSLNEIKEILASRG 426
RKSL E+K L G
Sbjct: 58 RKSLEEVKAKLEELG 72
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription
regulation, disulfide stress; 1.50A {Bacillus subtilis}
SCOP: a.60.3.1 PDB: 3ihq_B
Length = 73
Score = 106 bits (268), Expect = 2e-28
Identities = 24/64 (37%), Positives = 42/64 (65%)
Query: 363 KVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422
+ + +L +++L+L+VRS NCLK I+ + +L ++E ++++ NLGRKSL E+K L
Sbjct: 2 EKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKL 61
Query: 423 ASRG 426
G
Sbjct: 62 EELG 65
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription
regulation, DNA-directed RNA polymer
nucleotidyltransferase; HET: MLY; 2.05A {Escherichia
coli k-12} PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D
Length = 86
Score = 96.8 bits (241), Expect = 1e-24
Identities = 49/65 (75%), Positives = 54/65 (83%)
Query: 362 EKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEI 421
+ DPILLRPVDDLELTVRSANCL AE IH IGDL+QR+E ELL TPNLG SL EI ++
Sbjct: 4 PEFDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDV 63
Query: 422 LASRG 426
LASRG
Sbjct: 64 LASRG 68
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Length = 181
Score = 81.7 bits (201), Expect = 3e-18
Identities = 24/125 (19%), Positives = 49/125 (39%), Gaps = 4/125 (3%)
Query: 31 KCKLDLRPGQHGRISGSRTSDYGYQFREKQK--VKRMYGILEKQFRRYFIE--GARLKGK 86
K K ++ Q + + K + +L + F+ + +L
Sbjct: 37 KNKREVWRVQMILAKFRKAARELLTLDPKDPRRLFEGSALLRRMFKYGLLSEQERKLDYV 96
Query: 87 TGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146
G I KL+E R V+++ +++ +R LI R V K +VN+ S+ ++ S+
Sbjct: 97 LGLTIHKLMERRLQTRVFKLNLANSIHHSRVLIRQRHIKVGKNLVNVPSFMVRTDSEKSI 156
Query: 147 REKAK 151
+
Sbjct: 157 DFAST 161
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*
Length = 197
Score = 72.8 bits (178), Expect = 5e-15
Identities = 32/152 (21%), Positives = 59/152 (38%), Gaps = 6/152 (3%)
Query: 3 RYIGPKAKLCRREGIDLFLKSARRS-LDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQK 61
Y PK + +D LK A L +K ++ Q +I + ++ ++
Sbjct: 11 TYSTPK-RPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKR 69
Query: 62 VKRMYGILEKQFRRYFIE--GARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLI 119
+ ++ + R + +L + LE R VY++G + + AR LI
Sbjct: 70 LFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLI 129
Query: 120 SHRAFLVNKKIVNIASYKIKPG--DIISVREK 149
+ R V K+IVNI S+ ++ I
Sbjct: 130 TQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPT 161
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 195
Score = 71.6 bits (175), Expect = 1e-14
Identities = 25/125 (20%), Positives = 46/125 (36%), Gaps = 6/125 (4%)
Query: 31 KCKLDLRPGQHGRISGSRTSDYGYQFREKQK--VKRMYGILEKQFRRYFI--EGARLKGK 86
+CK +L Q+ + + EK + +L + R + +L
Sbjct: 39 RCKRELWRVQYALSRIRNNARHLLTLDEKNPRRIFEGEALLRRMNRYGLLADGQNKLDYV 98
Query: 87 TGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG--DII 144
+ L R +V++ G + + AR LI R V ++IVNI S+ ++ I
Sbjct: 99 LALTVENFLARRLQTLVFKAGMAKSIHHARVLIRQRHIRVGRQIVNIPSFMVRVESEKHI 158
Query: 145 SVREK 149
Sbjct: 159 DFSLT 163
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog;
S4 domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 71
Score = 59.6 bits (145), Expect = 1e-11
Identities = 7/60 (11%), Positives = 20/60 (33%), Gaps = 2/60 (3%)
Query: 94 LLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG--DIISVREKAK 151
R V+ ++ + A + V +V ++ + D ++ + +K
Sbjct: 5 SSGRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSSK 64
>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 = 65.6 bits (159), Expect = 2e-11
Identities = 81/526 (15%), Positives = 154/526 (29%), Gaps = 152/526 (28%)
Query: 10 KLCRREGIDLFLKSARRSLDSKCKLD-LRPGQHGRISGSRTSDYGYQFR-EKQKVKRMYG 67
+ ++ + +F + + D K D + I D+ + R++
Sbjct: 15 QYQYKDILSVFEDAFVDNFDCKDVQDMPKS-----ILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 68 ILE-KQFRRY--FIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQ------- 117
L KQ F+E L N Y+ S ++E RQ
Sbjct: 70 TLLSKQEEMVQKFVEEV-------------LR---IN--YKFLMSPIKTEQRQPSMMTRM 111
Query: 118 LISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAK 177
I R L N + ++ R + + R A LEL P + +D
Sbjct: 112 YIEQRDRLYN------DNQVFAKYNV--SRLQPYLKLRQA-LLELR----PAKNVLIDG- 157
Query: 178 KMEGVFKS----EPNRSEFANDINDLLKPRI--IDVKTLGSNHAKVIMEPFERGYGYTLG 231
+ G K+ + S + + +I +++K S ++E ++
Sbjct: 158 -VLGSGKTWVALDVCLSY---KVQCKMDFKIFWLNLKNCNSPET--VLEMLQK------- 204
Query: 232 NALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAIL 291
L I T S+++ I + L + K Y +L
Sbjct: 205 -------LLYQIDPNWTS-----RSDHSSNIKLRIHSIQAELRRL--LKSKPYENCLLVL 250
Query: 292 N-------LKKFG-KC--VVLASDIELLSDIELVNPNHI-IAHLSDN---EEAIRQSARV 337
F C ++ ++ + HI + H S +E +
Sbjct: 251 LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310
Query: 338 L---VDQL------------NVFAAL--------------ENTPVKKELDSSLEKVDPIL 368
L L ++ A + ++SSL ++P
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAE 370
Query: 369 LRPV-DDLELTVRSANCLKAENIHCI--GDLIQRSENELLRTPNLGRKSLNEIKEILASR 425
R + D L + SA+ + + D+I+ ++ L + SL + +
Sbjct: 371 YRKMFDRLSVFPPSAHI--PTILLSLIWFDVIKSDVMVVVNK--LHKYSL------VEKQ 420
Query: 426 GKYYMRHRHG-FRKL-----NRTSSHRLIMLRNMTISLLRYEIIKT 465
K + +L N + HR I + Y I KT
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHRSI--------VDHYNIPKT 458
Score = 46.8 bits (110), Expect = 2e-05
Identities = 63/370 (17%), Positives = 109/370 (29%), Gaps = 122/370 (32%)
Query: 11 LCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILE 70
L E L LK LD + + DL P + + R S R+ +
Sbjct: 298 LTPDEVKSLLLKY----LDCRPQ-DL-PREVLTTNPRRLSIIAESIRDG--LATW----- 344
Query: 71 KQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKI 130
++ + +L E L +LE +E R++ V
Sbjct: 345 DNWKHVNCD--KLT-TIIESSLNVLEP---------------AEYRKM--FDRLSVFPPS 384
Query: 131 VNIASYKIKPGDIISV--REKAKKQTR-IANSLELSEHSTPFSWITVDAKKMEGVFKSEP 187
+I P ++S+ + K + N L + V K
Sbjct: 385 AHI------PTILLSLIWFDVIKSDVMVVVNKLH--------------KYSL--VEKQPK 422
Query: 188 NRSEFANDINDLLKPRIIDVKTLGSNHAKVI--------------MEPFERGY-----GY 228
+ I LK ++ + L H ++ + P+ Y G+
Sbjct: 423 ESTISIPSIYLELKVKLENEYAL---HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 229 TLGNA--------LRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVI 280
L N R V L + + S+ I++ + LK
Sbjct: 480 HLKNIEHPERMTLFRMVFLDFRF--------LEQKIRHDSTAWNASGSILNTLQQLK--- 528
Query: 281 LKLYNRDY-------------AILN-LKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD 326
Y + Y AIL+ L K + ++ + +LL I L+ + I
Sbjct: 529 --FY-KPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR-IALMAEDEAIF---- 580
Query: 327 NEEAIRQSAR 336
EEA +Q R
Sbjct: 581 -EEAHKQVQR 589
Score = 32.5 bits (73), Expect = 0.44
Identities = 33/238 (13%), Positives = 70/238 (29%), Gaps = 70/238 (29%)
Query: 10 KLCRREGIDLFLKSARRSL-----DSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKR 64
KL + ++ K + S+ + K KL+ H I Y +
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH------YNIPKT---FD 460
Query: 65 MYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAF 124
++ +YF + ++ + + + E L F
Sbjct: 461 SDDLIPPYLDQYF---------------------YSHIGHHL-KNIEHPERMTLFR-MVF 497
Query: 125 L----VNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKME 180
L + +KI + ++ G I+ N+L+ K +
Sbjct: 498 LDFRFLEQKIRHDSTAWNASGSIL-------------NTLQ-------------QLKFYK 531
Query: 181 G-VFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRV 237
+ ++P N I D L P+ I+ + S + ++ A ++V
Sbjct: 532 PYICDNDPKYERLVNAILDFL-PK-IEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1
d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C
1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C*
1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C
1y77_C* ...
Length = 318
Score = 56.2 bits (134), Expect = 8e-09
Identities = 23/150 (15%), Positives = 52/150 (34%), Gaps = 28/150 (18%)
Query: 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVII---------SG 254
+ ++ ++ I+ + N+LRRV+++ + A V +
Sbjct: 7 QVKIREASKDNVDFILS----NVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEF 62
Query: 255 ALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGK----CVVLASDIELLS 310
H + DI + + ++ +L L+ FG+ V + D+ ++S
Sbjct: 63 IAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 311 DIELVNPNH-----------IIAHLSDNEE 329
++ N H +I L +E
Sbjct: 123 NLMGRNIGHPIIQDKEGNGVLICKLRKGQE 152
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 297
Score = 53.8 bits (128), Expect = 5e-08
Identities = 20/141 (14%), Positives = 39/141 (27%), Gaps = 22/141 (15%)
Query: 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVII---------SGA 255
I ++ + N ++ + N+LRRV+L+ + A V I
Sbjct: 7 ITIRNISKNSVDFVLT----NTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFL 62
Query: 256 LHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKF---------GKCVVLASDI 306
H + +I + Y + G + A D+
Sbjct: 63 AHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDL 122
Query: 307 ELLSDIELVNPNHIIAHLSDN 327
+ S+ L +P
Sbjct: 123 VVSSNSSLGHPILADPKSRGP 143
>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 = 53.9 bits (129), Expect = 1e-07
Identities = 47/311 (15%), Positives = 101/311 (32%), Gaps = 99/311 (31%)
Query: 264 GVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIEL-------LSDIELVN 316
G QE +G+ + LY A + V +D + DI + N
Sbjct: 1625 GSQE---------QGMGMDLYKTSKAA-------QDVWNRADNHFKDTYGFSILDIVINN 1668
Query: 317 PNHIIAHLS-DNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDL 375
P ++ H + + IR++ ++ + V L+ + KE++ L
Sbjct: 1669 PVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSY--TFRSEKGLL 1726
Query: 376 ELT---------VRSA--NCLKAENI---------H---------CIGDLIQRSENELLR 406
T + A LK++ + H + D++
Sbjct: 1727 SATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM--------- 1777
Query: 407 TPNLGRKSLNEIKEILASRGKYYM----RHRHGFRKLNRTSSHRLIMLRNMTISL-LRYE 461
S+ + E++ RG R G S++ +I + ++ E
Sbjct: 1778 -------SIESLVEVVFYRGMTMQVAVPRDELG------RSNYGMIAINPGRVAASFSQE 1824
Query: 462 IIKTTLPK-AKELRRVVEP----------IL--TLSKKNTLSNKRLAFSYLRDRKITI-K 507
++ + + K +VE + L +T++N ++++ +KI I +
Sbjct: 1825 ALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTN---VLNFIKLQKIDIIE 1881
Query: 508 LFSELGPRYIK 518
L L ++
Sbjct: 1882 LQKSLSLEEVE 1892
Score = 48.5 bits (115), Expect = 5e-06
Identities = 34/224 (15%), Positives = 66/224 (29%), Gaps = 74/224 (33%)
Query: 302 LASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSL 361
A+D E + ELV + ++S E +
Sbjct: 48 FAADDEPTTPAELV--GKFLGYVSSLVEPSKVGQF------------------------- 80
Query: 362 EKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEI 421
D +L + + E L+ +IH + + +L + KE+
Sbjct: 81 ---DQVLNLCLTEFE-----NCYLEGNDIHAL----------AAKLLQENDTTLVKTKEL 122
Query: 422 LASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLR-YEI------IKTTLPKAKELR 474
+ + Y R ++ S+ L R + + I +ELR
Sbjct: 123 IKN---YITARIMAKRPFDKKSNSAL--FRAVGEGNAQLVAIFGGQGNTDDYF---EELR 174
Query: 475 RV-------VEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSE 511
+ V ++ S + TLS +R K+F++
Sbjct: 175 DLYQTYHVLVGDLIKFSAE-TLS------ELIRTTLDAEKVFTQ 211
Score = 46.6 bits (110), Expect = 2e-05
Identities = 58/312 (18%), Positives = 105/312 (33%), Gaps = 107/312 (34%)
Query: 106 MG--FSSTRSEARQLISHRA--FLVNK---KIVNIASYKIKPGDIISVREKAKKQTRI-A 157
MG T A+ + +RA + I++I P ++ + +K RI
Sbjct: 1631 MGMDLYKTSKAAQDVW-NRADNHFKDTYGFSILDIV--INNPVNLT-IHFGGEKGKRIRE 1686
Query: 158 NSLELSEHSTPFSWITVDAK-KMEGVFKSEPNRSE---FANDINDLLK------PRII-- 205
N + + D K K E +FK S F ++ LL P +
Sbjct: 1687 NYSAMIFETIV------DGKLKTEKIFKEINEHSTSYTFRSE-KGLLSATQFTQPALTLM 1739
Query: 206 ------DVKTLGSN--------H-----------AKVIMEPFE--------RGYGYTLGN 232
D+K+ G H A V+ E RG T+
Sbjct: 1740 EKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM--SIESLVEVVFYRGM--TMQV 1795
Query: 233 ALRRVLLS----SMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDY 288
A+ R L MI P V S S E +Q +++ + G ++++ N Y
Sbjct: 1796 AVPRDELGRSNYGMIAINPGRVAASF------SQEALQY-VVERVGKRTGWLVEIVN--Y 1846
Query: 289 AILNLKKFGKCVVLA---SDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVF 345
N++ + V A ++ ++++ L N ++ ++ + +L
Sbjct: 1847 ---NVE--NQQYVAAGDLRALDTVTNV-L------------NFIKLQ---KIDIIELQKS 1885
Query: 346 AALENTPVKKEL 357
+LE V+ L
Sbjct: 1886 LSLE--EVEGHL 1895
Score = 37.7 bits (87), Expect = 0.012
Identities = 25/140 (17%), Positives = 48/140 (34%), Gaps = 45/140 (32%)
Query: 412 RKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAK 471
K+ +++ +R + + +GF L+ I++ N +L I K K
Sbjct: 1636 YKTSKAAQDVW-NRADNHFKDTYGFSILD-------IVINNPV-NL----TIHFGGEKGK 1682
Query: 472 ELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKI-TIKLFSELGPRYIKINGGYVRILKMG 530
+R +N + + F + D K+ T K+F E+
Sbjct: 1683 RIR-----------ENYSA---MIFETIVDGKLKTEKIFKEINEHSTSYT---------- 1718
Query: 531 FRVGDNAPMAFIELLNQTKN 550
FR + LL+ T+
Sbjct: 1719 FR-SEK------GLLSATQF 1731
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding
motif, platform for RNA polymer assembly, transferase;
1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D
2waq_D 2wb1_D 2y0s_D
Length = 265
Score = 47.2 bits (111), Expect = 6e-06
Identities = 20/139 (14%), Positives = 46/139 (33%), Gaps = 19/139 (13%)
Query: 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVII---------SGA 255
I++ ++ E GY NA+RR + + A +V
Sbjct: 3 INLLHKDDTRIDLVFE----GYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEIL 58
Query: 256 LHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKC-----VVLASDIELLS 310
H + + + E+ +D + I N + + + ++ + DI+
Sbjct: 59 AHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSED 118
Query: 311 D-IELVNPNHIIAHLSDNE 328
+ ++ + I L N+
Sbjct: 119 PSVVPISGDIPIVLLGTNQ 137
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding,
lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB:
2ist_A 1qyu_A 1prz_A
Length = 325
Score = 38.7 bits (91), Expect = 0.003
Identities = 13/59 (22%), Positives = 29/59 (49%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRI 156
R D + M +RS ++ I + LVN K+ + K+ G+ +++ + +++ R
Sbjct: 18 RLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARF 76
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding,
unknown function; NMR {Helicobacter pylori}
Length = 92
Score = 34.7 bits (80), Expect = 0.009
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVR 147
R D + +G R A + + A +N AS ++K GD IS+
Sbjct: 2 RIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAK-ASKEVKAGDTISLH 50
>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 = 34.2 bits (77), Expect = 0.039
Identities = 7/24 (29%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 58 EKQKVKRMYGILEKQFRRYFIEGA 81
EKQ +K+ L+ + Y + A
Sbjct: 18 EKQALKK----LQASLKLYADDSA 37
Score = 31.5 bits (70), Expect = 0.36
Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 16/41 (39%)
Query: 349 ENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCL--KA 387
E +KK L +SL+ D SA L KA
Sbjct: 18 EKQALKK-LQASLKLYAD------D-------SAPALAIKA 44
Score = 29.1 bits (64), Expect = 2.0
Identities = 6/31 (19%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 332 RQSARVLVDQLNVFAALENTPVKKELDSSLE 362
+Q+ + L L ++A ++ P + +++E
Sbjct: 19 KQALKKLQASLKLYAD-DSAPALA-IKATME 47
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural
genomics, lyase; 1.59A {Haemophilus influenzae} SCOP:
d.265.1.3 d.66.1.5
Length = 243
Score = 34.8 bits (81), Expect = 0.049
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 111 TRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146
TRS+A + I A +N +IV S +I D I
Sbjct: 16 TRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYF 51
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG,
structural genomics, PSI-2, protein structure
initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}
Length = 213
Score = 33.6 bits (76), Expect = 0.097
Identities = 8/45 (17%), Positives = 20/45 (44%)
Query: 105 RMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149
+ S EA +++++ V+ K V + + D+I + +
Sbjct: 17 YLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFMDVIEINGE 61
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein,
E.coli, montreal-kingston structural genomics
initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6
Length = 79
Score = 31.2 bits (71), Expect = 0.13
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 107 GFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146
G+S + ++A+ I+ V+ + KI G +S
Sbjct: 31 GWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSF 70
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase;
2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB:
1ksl_A 1ksv_A*
Length = 234
Score = 32.8 bits (76), Expect = 0.20
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146
R D + + S R+ A + I V+ +IV A++K+ P ++
Sbjct: 5 RLDKFIAQQLGVS-RAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAY 52
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein
STR initiative, midwest center for structural genomics,
MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}
Length = 291
Score = 32.6 bits (75), Expect = 0.25
Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 98 RFDNVVYRMGFSSTRSEARQLI-SHRAF-LVNKKIVNIASYKIKPGDIISVREKAKK 152
R D + Y+ G TR +A++ + + ++N + + KI G + ++ + +
Sbjct: 8 RVDVLAYKQGLFETREQAKRGVMAGLVVNVINGERYDKPGEKIDDGTELKLKGEKLR 64
>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design,
ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP:
c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*
Length = 420
Score = 32.9 bits (76), Expect = 0.25
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 107 GFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDII 144
G S ++ +AR+ +++ A +N + +Y + P D I
Sbjct: 363 GISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI 400
>1u6g_C TIP120 protein, CAND1; cullin repeat, heat repeat, ring finger,
ligase; 3.10A {Homo sapiens} SCOP: a.118.1.2 PDB: 4a0c_A
Length = 1230
Score = 33.2 bits (74), Expect = 0.28
Identities = 45/274 (16%), Positives = 96/274 (35%), Gaps = 26/274 (9%)
Query: 265 VQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHL 324
+ I ++K R A+L+L + G + L+ +EL + I+
Sbjct: 814 GPAVVGQFIQDVKNSRSTDSIRLLALLSLGEVGHHIDLSGQLEL--------KSVILEAF 865
Query: 325 SDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANC 384
S E ++ +A + ++V E P + +S K +LL + ++ ++ S
Sbjct: 866 SSPSEEVKSAASYALGSISVGNLPEYLPFVLQEITSQPKRQYLLLHSLKEI-ISSASVVG 924
Query: 385 LKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSS 444
LK + L++ E T N+ + L ++ I +L
Sbjct: 925 LKPYVENIWALLLKHCECAEEGTRNVVAECLGKLTLIDPETL---------LPRLKGYLI 975
Query: 445 HRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYL----- 499
R+ ++ +++ I P L+ + L + L+ +R+A
Sbjct: 976 SGSSYARSSVVTAVKFTISDHPQPIDPLLKNCIGDFLKTLEDPDLNVRRVALVTFNSAAH 1035
Query: 500 RDRKITIKLFSELGPRYI---KINGGYVRILKMG 530
+ L + P K+ +R ++MG
Sbjct: 1036 NKPSLIRDLLDTVLPHLYNETKVRKELIREVEMG 1069
>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus
stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E*
1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A
Length = 419
Score = 32.5 bits (75), Expect = 0.31
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 107 GFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDII 144
G S ++ +AR+ I + A VN + + + +
Sbjct: 362 GISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL 399
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA
synthetase, tyrrs, ligase, tyrosine, RNA-binding,
ATP-binding; 2.9A {Mycobacterium tuberculosis}
Length = 432
Score = 32.6 bits (75), Expect = 0.31
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 107 GFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDII 144
G S+++ AR+ I VN V+ + + D +
Sbjct: 366 GLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFL 403
>2x7i_A Mevalonate kinase; transferase; HET: CIT; 2.20A {Staphylococcus
aureus}
Length = 308
Score = 32.4 bits (74), Expect = 0.36
Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 7/85 (8%)
Query: 350 NTPVKKELDSSLEKV-----DPILLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENE 403
+T VK ++ V DP + V + +L +R+++ ++ + D+ +
Sbjct: 180 DTGVKGSTRQAVHDVHKLCEDPQYMSHVKHIGKLVLRASDVIEHHKFEALADIFNEC-HA 238
Query: 404 LLRTPNLGRKSLNEIKEILASRGKY 428
L+ + + ++ +I G
Sbjct: 239 DLKALTVSHDKIEQLMKIGKENGAI 263
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat
shock proteins, protein-RNA interactions, ribosome,
structural genomics; 2.00A {Escherichia coli} SCOP:
d.66.1.3 PDB: 3bbu_A
Length = 133
Score = 31.0 bits (70), Expect = 0.42
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIA 157
R D ++ F TR+ AR++I N + S ++ +++R+ ++T
Sbjct: 10 RLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQGNDERT--V 66
Query: 158 NSLELSEHSTPFSWI 172
++E P S
Sbjct: 67 IVKAITEQRRPASEA 81
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET:
TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1
d.66.1.4 PDB: 1h3e_A*
Length = 432
Score = 30.5 bits (69), Expect = 1.5
Identities = 7/41 (17%), Positives = 21/41 (51%)
Query: 107 GFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVR 147
G + + +EAR+LI +R ++ +++ ++ ++
Sbjct: 379 GLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQ 419
>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics
center for infectious disease, SMT, transcription; 2.25A
{Reston ebolavirus}
Length = 227
Score = 30.1 bits (67), Expect = 1.6
Identities = 16/92 (17%), Positives = 36/92 (39%), Gaps = 1/92 (1%)
Query: 134 ASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGVFK-SEPNRSEF 192
++ DII + +A L+++EH ++ K+ + +F
Sbjct: 77 EDLDMEDNDIIEAHREQIGGLTLAVLLQIAEHWATRDLRQIEDSKLRALLTLCAVLTRKF 136
Query: 193 ANDINDLLKPRIIDVKTLGSNHAKVIMEPFER 224
+ LL + + LG + A ++E ++R
Sbjct: 137 SKSQLGLLCETHLRHEGLGQDQADSVLEVYQR 168
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 29.4 bits (65), Expect = 3.9
Identities = 15/114 (13%), Positives = 28/114 (24%), Gaps = 21/114 (18%)
Query: 288 YAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFA- 346
IL+ F + ++L + I S ++ + NV
Sbjct: 176 KEILSRVNFEEDLILVPGRQAAEMIR---------------RRANASGIIVATKDNVRTV 220
Query: 347 --ALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQ 398
L N +D L+ + + + GD Q
Sbjct: 221 DSFLMNYGKGARCQFKRLFIDEGLMLHTGCVNFL---VEMSLCDIAYVYGDTQQ 271
>2oqt_A Hypothetical protein SPY0176; APC29699, putative PTS IIA domain,
streptococcus pyogenes M1 GAS, structural genomics,
PSI-2; 2.41A {Streptococcus pyogenes serotype M1}
Length = 162
Score = 28.1 bits (63), Expect = 5.4
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 313 ELVNPNHII--AHLSDNEEAIRQSARVLVDQ 341
L++ N I +EA+R + + L+D
Sbjct: 7 ALIDNNSIRLGLSADTWQEAVRLAVQPLIDS 37
>1zbo_A Hypothetical protein BPP1347; alpha-beta protein, structural
genomics, PSI, protein struct initiative; 2.60A
{Bordetella parapertussis} SCOP: b.122.1.10
Length = 210
Score = 27.9 bits (62), Expect = 6.9
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 404 LLRTPNLGRKSLNEIKEILASRGKYYMRHRH 434
LL P L R L EI +LA+ G H H
Sbjct: 180 LLLLPPLDR--LREIDAVLAADGHALEHHHH 208
>2oq3_A Mannitol-specific cryptic phosphotransferase enzyme IIA component;
solution structure; NMR {Escherichia coli}
Length = 150
Score = 27.3 bits (61), Expect = 9.1
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 313 ELVNPNHII--AHLSDNEEAIRQSARVLVDQ 341
+ + I D +EAI S L+D+
Sbjct: 8 DYFPESSISVIHSAKDWQEAIDFSMVSLLDK 38
>3oxp_A Phosphotransferase enzyme II, A component; structural genomics,
center for structural genomics of infec diseases, csgid,
pestis CO92; HET: GOL; 1.20A {Yersinia pestis}
Length = 150
Score = 27.2 bits (61), Expect = 9.4
Identities = 8/31 (25%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 313 ELVNPNHII--AHLSDNEEAIRQSARVLVDQ 341
L+ + I + D +AI S + L+D
Sbjct: 7 TLLTSDVIQVVSQAKDWRDAIAISCQPLIDN 37
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
0.321 0.138 0.385
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,377,006
Number of extensions: 533361
Number of successful extensions: 1456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1431
Number of HSP's successfully gapped: 71
Length of query: 550
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 452
Effective length of database: 3,965,535
Effective search space: 1792421820
Effective search space used: 1792421820
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: 60 (26.7 bits)