RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10165
(337 letters)
>3r8n_E 30S ribosomal protein S5; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_E 3fih_E* 3iy8_E 2wwl_E 3oar_E 3oaq_E
3ofb_E 3ofa_E 3ofp_E 3ofx_E 3ofy_E 3ofo_E 3r8o_E 4a2i_E
2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E ...
Length = 150
Score = 94.1 bits (235), Expect = 1e-23
Identities = 39/129 (30%), Positives = 68/129 (52%), Gaps = 1/129 (0%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
GR + + L V G+G G GF GK+ E A+++ A +A + +I V + T+ H
Sbjct: 19 GRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVAL-NNGTLQHPVK 77
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
+++F++ EGTG+I ++ + + G+ ++ AK GSTNP +V+A GL
Sbjct: 78 GVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLEN 137
Query: 274 QKSHQQLAE 282
S + +A
Sbjct: 138 MNSPEMVAA 146
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E
3i1z_E 3i21_E 3izv_I* 3izw_I* 3kc4_E 3or9_E 3ora_E
3sfs_E* 3uoq_E*
Length = 167
Score = 94.5 bits (236), Expect = 1e-23
Identities = 39/129 (30%), Positives = 68/129 (52%), Gaps = 1/129 (0%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
GR + + L V G+G G GF GK+ E A+++ A +A + +I V + T+ H
Sbjct: 28 GRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVAL-NNGTLQHPVK 86
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
+++F++ EGTG+I ++ + + G+ ++ AK GSTNP +V+A GL
Sbjct: 87 GVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLEN 146
Query: 274 QKSHQQLAE 282
S + +A
Sbjct: 147 MNSPEMVAA 155
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E
1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E*
1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E*
1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ...
Length = 162
Score = 92.6 bits (231), Expect = 5e-23
Identities = 38/137 (27%), Positives = 64/137 (46%), Gaps = 1/137 (0%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
GR LVV G+ QG G GK+ E +++ A A + ++ V ++ T+ H+
Sbjct: 23 GRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPL-QNGTIPHEIE 81
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
+FG +KI ++ GTG+I + + I + G+ DI K GS NP I A L Q
Sbjct: 82 VEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQ 141
Query: 274 QKSHQQLAEEQQLHLVE 290
++ + ++
Sbjct: 142 LRTKADVERLRKGEAHA 158
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 308
Score = 95.3 bits (237), Expect = 1e-22
Identities = 28/130 (21%), Positives = 59/130 (45%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
G++ +VV G+ +G G +GK+ E ++++ A A + +I V K T H
Sbjct: 169 GKHMRFRAIVVVGDKKGQVGVGVGKAKEVVSAVQKAAVDARRNIITVPMTKYLTFPHRNE 228
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
+G ++ + GTG+I ++ + + G+++ K GS N +A + +
Sbjct: 229 ADYGAARVMLRPAAPGTGVIAGGAVRTVLEMAGVENALGKQLGSNNALNNARATIVAVQT 288
Query: 274 QKSHQQLAEE 283
+ +A +
Sbjct: 289 MRQFSDVARD 298
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP:
d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D
Length = 150
Score = 89.5 bits (223), Expect = 5e-22
Identities = 44/123 (35%), Positives = 61/123 (49%), Gaps = 1/123 (0%)
Query: 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213
GR S LVV G+ G GF GK+ E ++R A A + LI V T+ H+
Sbjct: 28 GRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLIEVPI-VGTTIPHEVI 86
Query: 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ 273
FG +I ++ EGTG+I + + + GI DI +K GS P +V+A F GL Q
Sbjct: 87 GHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRATFDGLKQ 146
Query: 274 QKS 276
K
Sbjct: 147 LKR 149
>2xzm_E Ribosomal protein S5 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_E
Length = 296
Score = 84.6 bits (209), Expect = 5e-19
Identities = 39/226 (17%), Positives = 75/226 (33%), Gaps = 14/226 (6%)
Query: 121 DLNRGQIIGIDTFDGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSV 180
D + + +L+ V + R R VV G+ G G +
Sbjct: 62 DHFYPKNKDVQAEHKLMEEVLQITPVQKQTQAGQRTR-FKGFVVVGDSNGHIGLGWKVAK 120
Query: 181 EGRASMRNAKNRAGQKLIYVQR-------YKDHTVLHDFYTQFGKTKIFVEKKPEGTGLI 233
E + +++ A A ++ V++ HT+ + G +I + P GTG++
Sbjct: 121 EVQGAIKGAITHAKLNMVPVRKGYWGNKIANAHTIPQKITGKSGSVRIRLVPAPRGTGIV 180
Query: 234 CHRIIQEICKAVGIKDIRAKVEGSTNPQA-IVKAFFLGLMQQKSHQQLAEEQQLHL---- 288
I +++ + G++DI +G T + +KA + L + +
Sbjct: 181 AAPIPKKVLQFAGVQDIYTSSQGCTRTRGNFLKATYYALANTYRYLTPDFWGKPEDNELP 240
Query: 289 -VEFSEENDNYPTIVASPSTCKKDSSKAPDFTEVSSWSYRPEIEER 333
FSE K K D +P E++
Sbjct: 241 FETFSEFLHTKAQKKEPKQYENKREKKHFDRPRREHGDRQPRGEKK 286
>3u5c_C Guanine nucleotide-binding protein subunit beta-L protein (ASC1,
RACK1); translation, ribosome, ribosomal, ribosomal R
ribosomal protein, eukaryotic ribosome, RNA-protein C;
3.00A {Saccharomyces cerevisiae} PDB: 3izb_E 3o30_B
3o2z_B 3u5g_C 3jyv_E* 1s1h_E
Length = 254
Score = 83.7 bits (207), Expect = 7e-19
Identities = 50/251 (19%), Positives = 92/251 (36%), Gaps = 25/251 (9%)
Query: 63 TPPLERGWSGGKLGGRSLGPPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARD- 121
P ++ GG G P NT ++ W VT K GR GK+T +
Sbjct: 3 APEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVT-------KLGRLVKAGKITTIEE 55
Query: 122 -LNRGQIIG----IDTFDG-FDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFA 175
+ IDT ++ K V + R R +VV G+ G G
Sbjct: 56 IFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTR-FKAVVVVGDSNGHVGLG 114
Query: 176 LGKSVEGRASMRNAKNRAGQKLIYVQR-------YKDHTVLHDFYTQFGKTKIFVEKKPE 228
+ + E ++R A +I ++R + H++ + G + + P
Sbjct: 115 IKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPR 174
Query: 229 GTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQA-IVKAFFLGLMQQKSHQ--QLAEEQQ 285
G+G++ ++++ + G++D+ + G T +KA F+ + L EQ
Sbjct: 175 GSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQP 234
Query: 286 LHLVEFSEEND 296
L + +D
Sbjct: 235 LPVSPLDIYSD 245
>3iz6_E 40S ribosomal protein S2 (S5P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
2zkq_e 1s1h_E
Length = 274
Score = 83.8 bits (207), Expect = 8e-19
Identities = 49/224 (21%), Positives = 84/224 (37%), Gaps = 23/224 (10%)
Query: 68 RGWSGGKLGGRSLGPPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARD--LNRG 125
RG+ G G R G +E W VT K GR G+ + +
Sbjct: 17 RGFGRGGRGDRGGRRGGRRGPRQEEEKWVPVT-------KLGRLVKEGRFSKIEEIYLHS 69
Query: 126 QIIG----IDTFDG-FDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSV 180
+ ++T +++ V + R R VV G+ G G + +
Sbjct: 70 LPVKEHQIVETLVPGLKDEVMKITPVQKQTRAGQRTR-FKAFVVVGDNNGHVGLGVKCAK 128
Query: 181 EGRASMRNAKNRAGQKLIYVQR-------YKDHTVLHDFYTQFGKTKIFVEKKPEGTGLI 233
E ++R A A ++ V+R + HTV + G + + P G+G++
Sbjct: 129 EVATAIRGAIILAKLSVVPVRRGYWGNKIGQPHTVPCKVTGKCGSVTVRMVPAPRGSGIV 188
Query: 234 CHRIIQEICKAVGIKDIRAKVEGSTNPQA-IVKAFFLGLMQQKS 276
R+ +++ + GI+D+ GST VKA F LM+
Sbjct: 189 AARVPKKVLQFAGIEDVFTSSRGSTKTLGNFVKATFDCLMKTYG 232
>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 = 42.7 bits (100), Expect = 1e-04
Identities = 37/198 (18%), Positives = 73/198 (36%), Gaps = 55/198 (27%)
Query: 117 LTARDLNRGQIIGIDTFDGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFAL 176
L+ +L + Q+ D + ++ + K V N + LVV+G Q L G L
Sbjct: 339 LSISNLTQEQVQ--DYVNKTNSHLPAGKQVEISLVNGAK-----NLVVSGPPQSLYGLNL 391
Query: 177 GKSVEGRASMRNAKNRAG--Q-KLIYVQRYKDHTVLHDFYTQFGKTKIFVEKKP------ 227
++R AK +G Q ++ + +R K F +F + P
Sbjct: 392 --------TLRKAKAPSGLDQSRIPFSER-KLK-----FSNRFL--PVAS---PFHSHLL 432
Query: 228 -EGTGLICHRIIQEIC----KAVGI--------KDIRAKVEGSTNPQAIVKAFFLGLMQQ 274
+ LI +++ K + I D+R + GS + IV +++
Sbjct: 433 VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLR-VLSGSISE-RIVDC----IIRL 486
Query: 275 KSH-QQLAEEQQLHLVEF 291
+ + + H+++F
Sbjct: 487 PVKWETTTQFKATHILDF 504
Score = 39.6 bits (92), Expect = 0.002
Identities = 41/236 (17%), Positives = 73/236 (30%), Gaps = 104/236 (44%)
Query: 143 YKAVFCMKKNSGRYRTVSTL---VVTGN--------GQGLAG--FALGKSVEGRASMRNA 189
A K+ + S L V GN GQG F E +R+
Sbjct: 127 ITARIMAKRPFDKKSN-SALFRAVGEGNAQLVAIFGGQGNTDDYFE-----E----LRD- 175
Query: 190 KNRAGQKLIYVQRYKDHTVLHDFYTQFGKT------------KIFVE--------KKPEG 229
+Y Q Y ++ D +T K+F + + P
Sbjct: 176 --------LY-QTYH--VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSN 224
Query: 230 T----------------GLI--CHRIIQEICKAVGI--KDIRAKVEGSTN-PQAIVKA-- 266
T G+I H ++ K +G ++R+ ++G+T Q +V A
Sbjct: 225 TPDKDYLLSIPISCPLIGVIQLAHYVV--TAKLLGFTPGELRSYLKGATGHSQGLVTAVA 282
Query: 267 ---------------------FFLGLMQQKSHQQLAEEQQLHLVEFSEENDN-YPT 300
FF+G+ +++ + ++E S EN+ P+
Sbjct: 283 IAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPS--ILEDSLENNEGVPS 336
>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO,
genome stability, DNA damage, DNA recombination,
nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe}
PDB: 3rcz_A*
Length = 82
Score = 29.9 bits (67), Expect = 0.28
Identities = 6/55 (10%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 235 HRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEEQQLHLV 289
H++I + ++ +D+R + + ++K + + +++ +++ L
Sbjct: 7 HKLITLLLRSSKSEDLRLSIPVDFTVKDLIKRY-------CTEVKISFHERIRLE 54
>3szt_A QCSR, quorum-sensing control repressor; quorum sensing
acyl-homoserine lactone, helix-turn-helix, transcription
factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas
aeruginosa}
Length = 237
Score = 29.9 bits (67), Expect = 0.86
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 9/42 (21%)
Query: 239 QEICKAVGI---------KDIRAKVEGSTNPQAIVKAFFLGL 271
EI + I + K+ S +A +KA+ +GL
Sbjct: 194 GEIGLILSIDQRTVKFHIVNAMRKLNSSNKAEATMKAYAIGL 235
>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 = 30.6 bits (68), Expect = 0.92
Identities = 23/150 (15%), Positives = 51/150 (34%), Gaps = 40/150 (26%)
Query: 202 RYKDHTVLHDFYTQFGKTKIFVEKKPEGTGLICHRIIQEICKAV----GIKDI---RAKV 254
+YKD +L F F C + +Q++ K++ I I + V
Sbjct: 17 QYKD--ILSVFEDAFVDN------------FDC-KDVQDMPKSILSKEEIDHIIMSKDAV 61
Query: 255 EGS--------TNPQAIVKAFFLGLMQQKSHQQLAEEQQLHLVEFSEENDNYPTIVASPS 306
G+ + + +V+ F ++ + +++ L + + S Y +
Sbjct: 62 SGTLRLFWTLLSKQEEMVQKFVEEVL-RINYKFLMSPIKTEQRQPSMMTRMY---IEQRD 117
Query: 307 TCKKDSSKAPDFTEVSSWSYRPE-IEERRK 335
D+ + VS R + + R+
Sbjct: 118 RLYNDNQVFAKYN-VS----RLQPYLKLRQ 142
Score = 29.1 bits (64), Expect = 2.5
Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 173 GFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHD-FYTQFGKTKI-FVEKKPEGT 230
F L + + ++ NA L ++ YK + +D Y + + F+ K
Sbjct: 501 RF-LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKI--EE 557
Query: 231 GLICHR---IIQ 239
LIC + +++
Sbjct: 558 NLICSKYTDLLR 569
>1r62_A Nitrogen regulation protein NR(II); PII, histidine kinase, two
component system, transfera; 1.60A {Escherichia coli}
SCOP: d.122.1.3
Length = 160
Score = 29.4 bits (67), Expect = 1.0
Identities = 7/22 (31%), Positives = 10/22 (45%), Gaps = 3/22 (13%)
Query: 222 FVEKKPEGTGL---ICHRIIQE 240
V + GTGL I +I +
Sbjct: 115 MVSGREGGTGLGLSIARNLIDQ 136
>1wiw_A Glucose-6-phosphate isomerase like protein; riken structural
genomics/proteomics initiative, RSGI, structural
genomics; 2.00A {Thermus thermophilus} SCOP: c.80.1.1
Length = 290
Score = 30.0 bits (67), Expect = 1.1
Identities = 12/63 (19%), Positives = 18/63 (28%), Gaps = 2/63 (3%)
Query: 30 RELVQQTRLPPDPDREAKLIALRDKQFQGKYRK--TPPLERGWSGGKLGGRSLGPPDPVG 87
R+L ++ D A + P G+ G+ G PD
Sbjct: 2 RDLDREETYLVDRTGLALELRDLVGTGPVPGEAYPGPHAALGYGEGQFAALLSGLPDWGE 61
Query: 88 ENT 90
E T
Sbjct: 62 EGT 64
>3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I
two-component histidine kinase, phosphoprotein; HET:
ADP; 2.03A {Geobacillus stearothermophilus}
Length = 244
Score = 29.8 bits (68), Expect = 1.1
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 12/32 (37%)
Query: 212 FYTQFGKTKIFVEKKPEGTGL---ICHRIIQE 240
++T TK +GTGL + +RII+
Sbjct: 179 YFT----TK-----GVKGTGLGMMVVYRIIES 201
>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase,
two-component regulatory system; 1.57A {Thermotoga
maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A
Length = 152
Score = 29.1 bits (66), Expect = 1.3
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 3/18 (16%)
Query: 226 KPEGTGL---ICHRIIQE 240
K +GTGL IC +II++
Sbjct: 107 KTQGTGLGLSICRKIIED 124
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 29.2 bits (66), Expect = 2.1
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 3/18 (16%)
Query: 226 KPEGTGL---ICHRIIQE 240
K +GTGL IC +II++
Sbjct: 304 KTQGTGLGLSICRKIIED 321
>2pg9_A Phosphomevalonate kinase; GHMP kinase superfamily, transferase;
HET: PMV ANP; 1.90A {Streptococcus pneumoniae} PDB:
1k47_A* 3gon_A*
Length = 337
Score = 28.8 bits (64), Expect = 2.9
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 164 VTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRY 203
+G G G G AL + +++N G +L+Y +R
Sbjct: 292 SSGAGGGDCGIALSFDAQSTKTLKNRWADLGIELLYQERI 331
>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist,
antagonist, LUXR, acylated homoseri lactone,
transcription factor; HET: HL6; 2.00A {Chromobacterium
violaceum} PDB: 3qp5_A*
Length = 265
Score = 28.3 bits (63), Expect = 3.3
Identities = 8/42 (19%), Positives = 14/42 (33%), Gaps = 9/42 (21%)
Query: 239 QEICKAVGI---------KDIRAKVEGSTNPQAIVKAFFLGL 271
EI + I ++ K+ + AIV L +
Sbjct: 216 WEIATILNISERTVKFHVANVIRKLNANNRTHAIVLGMHLAM 257
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix,
two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}
Length = 236
Score = 27.7 bits (61), Expect = 4.4
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 247 IKDIRAKVEGSTNPQAIVKAFFLGL 271
+ RAK++ + PQ + A GL
Sbjct: 211 LDKARAKLDAESVPQLVAIAKDRGL 235
>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA
binding motif, alpha/beta/alpha sandwich; HET: LAE;
1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2
d.110.5.1 PDB: 1h0m_A*
Length = 234
Score = 27.7 bits (61), Expect = 5.0
Identities = 2/25 (8%), Positives = 8/25 (32%)
Query: 247 IKDIRAKVEGSTNPQAIVKAFFLGL 271
+++ + + + A L
Sbjct: 209 LREAMKRFDVRSKAHLTALAIRRKL 233
>1nxm_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; jelly roll-like
structure, beta sheet, isomerase; 1.30A {Streptococcus
suis} SCOP: b.82.1.1 PDB: 1nyw_A* 1nzc_A* 2ixl_A*
Length = 197
Score = 26.8 bits (60), Expect = 7.3
Identities = 3/19 (15%), Positives = 8/19 (42%)
Query: 9 IWNLGKINIQWPGLSAPVI 27
+ ++I+W L +
Sbjct: 158 NYADPSLDIKWENLEEAEV 176
>1tif_A IF3-N, translation initiation factor 3; IF3 N-terminal domain,
ribosome binding factor; 1.80A {Geobacillus
stearothermophilus} SCOP: d.15.8.1
Length = 78
Score = 25.6 bits (57), Expect = 7.5
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 8/41 (19%)
Query: 269 LGLMQQKSHQQLAEEQQLHLVEFSEENDNYPTIVASPSTCK 309
LG+ ++ ++A + L LV + P A P C+
Sbjct: 26 LGIKSKQEALEIAARRNLDLVLVA------PN--AKPPVCR 58
>3fd2_A DNA endonuclease I-MSOI, linker, DNA endonuclease; protein-DNA
complex, chloroplast, hydrolase-DNA complex; HET: DNA;
2.69A {Monomastix SP}
Length = 373
Score = 27.2 bits (59), Expect = 9.1
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 171 LAGFALG-----KSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFYTQFGKTKIFVEK 225
+AGF G + R ++ K + + ++QR L D Y Q GK +
Sbjct: 15 IAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKD 74
Query: 226 KPEGT 230
+ +G
Sbjct: 75 RGDGI 79
>2qsf_A RAD4, DNA repair protein RAD4; alpha-beta structure, beta hairpin,
transglutaminase fold, DNA-damage recognition, DNA
repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB:
2qsg_A* 2qsh_A*
Length = 533
Score = 27.2 bits (59), Expect = 10.0
Identities = 7/39 (17%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 215 QFGKTKIFVEK-KPEGTGLICHRIIQEICKAVGIKDIRA 252
FG ++F P L+ + + + + +G++ A
Sbjct: 456 TFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPA 494
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
0.317 0.136 0.408
Gapped
Lambda K H
0.267 0.0619 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,279,305
Number of extensions: 325353
Number of successful extensions: 636
Number of sequences better than 10.0: 1
Number of HSP's gapped: 622
Number of HSP's successfully gapped: 28
Length of query: 337
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 243
Effective length of database: 4,077,219
Effective search space: 990764217
Effective search space used: 990764217
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.0 bits)