RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16477
(172 letters)
>3iz5_C 60S ribosomal protein L3 (L3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_C
Length = 389
Score = 66.7 bits (162), Expect = 1e-13
Identities = 47/111 (42%), Positives = 68/111 (61%), Gaps = 7/111 (6%)
Query: 1 MMKLLKKRQKKAHLMEIQLNGGSVADRQHITVCLKLAHTEDLYGAHMKLLKKRQKKAHLM 60
K K A EIQL + +++ T+ +AHT+ K+ +QKKAHLM
Sbjct: 130 FTKYALKYDSDAGKKEIQLQLEKM--KKYATIVRVIAHTQ-----IRKMKGLKQKKAHLM 182
Query: 61 EIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGFV 111
EIQ+NGG++ADK+ + + E+ +PV VF +DEM+D IGVTKGKG++G V
Sbjct: 183 EIQVNGGTIADKVDYGYKFFEKEVPVEAVFQKDEMVDIIGVTKGKGYEGVV 233
Score = 44.8 bits (105), Expect = 4e-06
Identities = 15/23 (65%), Positives = 17/23 (73%)
Query: 127 SAKFGHGRFQTPADKLAFMGYLK 149
S+KFGHGRFQT +K F G LK
Sbjct: 366 SSKFGHGRFQTTDEKQKFYGRLK 388
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 403
Score = 63.6 bits (154), Expect = 1e-12
Identities = 55/111 (49%), Positives = 72/111 (64%), Gaps = 8/111 (7%)
Query: 1 MMKLLKKRQKKAHLMEIQLNGGSVADRQHITVCLKLAHTEDLYGAHMKLLKKRQKKAHLM 60
K KK Q +++ + S+ + V +AHT+ M+LL RQKKAHLM
Sbjct: 130 FTKYCKKWQDADGKKQLERDFSSMKK--YCQVIRVIAHTQ------MRLLPLRQKKAHLM 181
Query: 61 EIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGFV 111
E+Q+NGG+VA+K+ WAR+ LEQ +PV QVF QDEMID IGVTKGKG+KG
Sbjct: 182 EVQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVT 232
Score = 55.9 bits (134), Expect = 6e-10
Identities = 22/31 (70%), Positives = 26/31 (83%)
Query: 127 SAKFGHGRFQTPADKLAFMGYLKKDRIREEE 157
++KFGHGRFQT +K AFMG LKKDRI +EE
Sbjct: 371 TSKFGHGRFQTVEEKKAFMGPLKKDRIAKEE 401
>3u5e_B 60S ribosomal protein L3; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 3o5h_C 3o58_C 3u5i_B
3izc_C 3izs_C 1s1i_C 3jyw_C
Length = 387
Score = 62.9 bits (152), Expect = 3e-12
Identities = 36/66 (54%), Positives = 47/66 (71%)
Query: 46 HMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGK 105
++ QKKAHL EIQLNGGS+++K+ WAR+H E+ + V VF Q+EMID I VTKG
Sbjct: 165 QIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGH 224
Query: 106 GFKGFV 111
GF+G
Sbjct: 225 GFEGVT 230
Score = 48.3 bits (114), Expect = 2e-07
Identities = 19/25 (76%), Positives = 22/25 (88%)
Query: 127 SAKFGHGRFQTPADKLAFMGYLKKD 151
++KFG GRFQTPA+K AFMG LKKD
Sbjct: 362 ASKFGKGRFQTPAEKHAFMGTLKKD 386
>1vq8_B 50S ribosomal protein L3P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: b.43.3.2 PDB: 1vq4_B*
1vq5_B* 1vq6_B* 1vq7_B* 1s72_B* 1vq9_B* 1vqk_B* 1vql_B*
1vqm_B* 1vqn_B* 1vqo_B* 1vqp_B* 1yhq_B* 1yi2_B* 1yij_B*
1yit_B* 1yj9_B* 1yjn_B* 1yjw_B* 2otj_B* ...
Length = 338
Score = 55.4 bits (133), Expect = 8e-10
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 48 KLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQP--IPVGQVFAQDEMIDCIGVTKGK 105
+ +KK +ME ++ GGSV+D++ A +E + +F E D GVTKGK
Sbjct: 151 AVPSVPKKKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGK 210
Query: 106 GFKGFV 111
G +G V
Sbjct: 211 GTQGPV 216
>4a17_B RPL3, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_B 4a1c_B 4a1e_B
Length = 391
Score = 54.8 bits (131), Expect = 1e-09
Identities = 35/70 (50%), Positives = 52/70 (74%)
Query: 42 LYGAHMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGV 101
+ +M L RQKK H++EIQ+NGG VA+K+A+A+ LE+ + V +FA++EM+D +GV
Sbjct: 159 IAHTNMSKLNLRQKKNHILEIQVNGGKVAEKVAFAKSLLEKEVKVDSIFAENEMLDVLGV 218
Query: 102 TKGKGFKGFV 111
TKGKGF G +
Sbjct: 219 TKGKGFAGVI 228
Score = 53.2 bits (127), Expect = 6e-09
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 127 SAKFGHGRFQTPADKLAFMGYLKKDRIREEEK 158
S+K GHGRFQT +K F G + ++ + +
Sbjct: 360 SSKIGHGRFQTVEEKDKFFGRDRTKKVEAKSE 391
>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 = 37.7 bits (87), Expect = 0.001
Identities = 36/194 (18%), Positives = 66/194 (34%), Gaps = 80/194 (41%)
Query: 12 AHL-----MEIQL-NGGSVADRQHITVCLKLAHTEDLYGAHMKLLKKR------QKKA-- 57
+HL +EI L NG +++ V + LYG ++ L K + Q +
Sbjct: 358 SHLPAGKQVEISLVNG-----AKNLVVS---GPPQSLYGLNLTLRKAKAPSGLDQSRIPF 409
Query: 58 --------------------HLMEI---QLNGGSVADKIAWARQHLEQPIPV-----GQV 89
HL+ +N V + +++ + ++ IPV G
Sbjct: 410 SERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ--IPVYDTFDGSD 467
Query: 90 FAQ------DEMIDCIGVTKGKGFKGFVN--SSLLFRDSKITSIISAKFGHGRFQTPADK 141
+ ++DCI + V ++ F K T I+ FG G
Sbjct: 468 LRVLSGSISERIVDCI-------IRLPVKWETTTQF---KATHILD--FGPG-------G 508
Query: 142 LAFMGYLKKDRIRE 155
+ +G L R ++
Sbjct: 509 ASGLGVLTH-RNKD 521
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 259
Score = 34.2 bits (79), Expect = 0.014
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 82 QPIPVGQVFAQDEMIDCIGVTKGKGFKG 109
Q + G++F + +++D G T GKGF+G
Sbjct: 137 QKLDFGELFKEGDLVDVSGTTIGKGFQG 164
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial
ribosome, large ribosomal subunit, ribosomal R ribosome;
12.10A {Bos taurus}
Length = 211
Score = 32.5 bits (75), Expect = 0.045
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 5/34 (14%)
Query: 81 EQPIPVGQ-----VFAQDEMIDCIGVTKGKGFKG 109
I G F + +D T GKGF+G
Sbjct: 89 NAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQG 122
>3r8s_D 50S ribosomal protein L3; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_B
1p86_B 1vs8_D 1vs6_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vt2_D
2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D
2qbg_D 2qbi_D* 2qbk_D* 2qov_D ...
Length = 209
Score = 31.7 bits (73), Expect = 0.064
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 84 IPVGQ-----VFAQDEMIDCIGVTKGKGFKG 109
VGQ +FA + +D G +KGKGF G
Sbjct: 90 FTVGQSISVELFADVKKVDVTGTSKGKGFAG 120
>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 = 32.5 bits (73), Expect = 0.071
Identities = 27/177 (15%), Positives = 53/177 (29%), Gaps = 37/177 (20%)
Query: 6 KKRQKKAHLMEIQ------LNG--GS-----VADRQHITVCLKLAHTEDL-YGAH-MKLL 50
+ + L+E++ ++G GS D VCL + + + L
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALD-----VCLSYKVQCKMDFKIFWLNL- 189
Query: 51 KKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGF 110
K ++E+ D +R I + Q E+ + K K ++
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL---KSKPYE-- 244
Query: 111 VNSSLLFRDSKITSIISAKFGHG-------RFQTPADKLAFMGYLKKDRIREEEKKA 160
N L+ + + +A F RF+ D L+ +
Sbjct: 245 -NCLLVLLNVQNAKAWNA-FNLSCKILLTTRFKQVTDFLS--AATTTHISLDHHSMT 297
Score = 31.0 bits (69), Expect = 0.21
Identities = 30/188 (15%), Positives = 59/188 (31%), Gaps = 44/188 (23%)
Query: 4 LLKKRQKKA--HLMEIQLN-GGSVADRQ--H--------ITVCLKLAH----TEDLY--- 43
L++K+ K++ + I L + + H I D Y
Sbjct: 416 LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYS 475
Query: 44 --GAHMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQ-----DEMI 96
G H+K ++ ++ + L+ + KI + Q +
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC 535
Query: 97 DCIGVTKGKGFKGFVNSSLLFRDSKITSIISAKFGHGRFQTPAD--KLAFMGYLKKDRIR 154
D ++ VN+ L F ++I +K+ D ++A M + + I
Sbjct: 536 D-----NDPKYERLVNAILDFLPKIEENLICSKY--------TDLLRIALMA--EDEAIF 580
Query: 155 EEEKKASA 162
EE K
Sbjct: 581 EEAHKQVQ 588
Score = 26.4 bits (57), Expect = 7.4
Identities = 19/153 (12%), Positives = 37/153 (24%), Gaps = 60/153 (39%)
Query: 23 SVAD------RQHITV-----CLKLAHTEDLYG--AHMKL--LKKRQKKAHLMEIQLNGG 67
V D HI++ L + L + L + + + +
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE 335
Query: 68 SVADKIA----WA-----------------------RQHLEQ--------PIPVGQVFA- 91
S+ D +A W R+ ++ IP + +
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT-ILLSL 394
Query: 92 ---QDEMIDCIGVTKGKGFKGFVNSSLLFRDSK 121
D + V SL+ + K
Sbjct: 395 IWFDVIKSDVMVVVNK-----LHKYSLVEKQPK 422
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.43.3.2 PDB: 1nwx_B* 1nwy_B* 1sm1_B*
1xbp_B* 2ogm_B* 2ogn_B* 2ogo_B* 2zjp_B* 2zjq_B 1nkw_B
3cf5_B* 3dll_B* 3pio_B* 3pip_B* 1pnu_B 1pny_B 1vor_E
1vou_E 1vow_E 1voy_E ...
Length = 211
Score = 31.7 bits (73), Expect = 0.074
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 85 PVGQ-----VFAQDEMIDCIGVTKGKGFKG 109
P G +FA+ E ID G +KGKG +G
Sbjct: 86 PDGDSVNVDIFAEGEKIDATGTSKGKGTQG 115
>3v2d_E 50S ribosomal protein L3; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_C 2hgj_E 2hgq_E 2hgu_E 1vsa_C 2j03_E 2jl6_E 2jl8_E
2v47_E 2v49_E 2wdi_E 2wdj_E 2wdl_E 2wdn_E 2wh2_E 2wh4_E
2wrj_E 2wrl_E 2wro_E 2wrr_E ...
Length = 206
Score = 31.3 bits (72), Expect = 0.10
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 85 PVGQ-----VFAQDEMIDCIGVTKGKGFKG 109
P G +F E +D G +KG+GF G
Sbjct: 86 PEGDTVTVEIFKPGERVDVTGTSKGRGFAG 115
>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 358
Score = 30.0 bits (67), Expect = 0.40
Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 10 KKAHLMEIQLNGGSVADRQHITVCLKLA--HTEDLYGAHMKLLKKRQKKAHLMEIQLNGG 67
K + IQ +GG + + + C K+A ++ +K L+ QK
Sbjct: 244 KHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAE 303
Query: 68 SVADKIAWARQHLEQP 83
S+A++ A + + P
Sbjct: 304 SIANQRITAFKMEKAP 319
>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 278
Score = 29.5 bits (66), Expect = 0.42
Identities = 8/49 (16%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 10 KKAHLMEIQLNGGSVADRQHITVCLKLA--HTEDLYGAHMKLLKKRQKK 56
++ L + GGS + C+ A +++ +++K + K
Sbjct: 230 EEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKLMDEVIKSMKPK 278
>3lxu_X Tripeptidyl-peptidase 2; spindle complex, aminopeptidase, hydrolase,
phosphoprotein, protease; 3.14A {Drosophila melanogaster}
Length = 1354
Score = 29.4 bits (65), Expect = 0.76
Identities = 9/66 (13%), Positives = 22/66 (33%), Gaps = 2/66 (3%)
Query: 23 SVADRQHITVCLKLAHTEDLYGAHMKLLKKRQKKAHLMEIQLNGGSVADKIAWA--RQHL 80
D + I L A+ YG K + K ++ + + ++ + R +
Sbjct: 1280 DANDSKAIQFALWHAYAHGHYGRMYKYVVKLIEEKRTRDHFVELAAINGALGHEHIRTVI 1339
Query: 81 EQPIPV 86
+ +
Sbjct: 1340 NRMMIT 1345
>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 305
Score = 28.1 bits (62), Expect = 1.2
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 13 HLMEIQLNGGSVADRQHITVCLKLA--HTEDLYGAHMKLLK----KRQKKAHLME 61
++++ GG D + C A E + ++LLK KR K A ++
Sbjct: 244 EVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLT 298
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.8 bits (61), Expect = 1.4
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 48 KLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQ 82
K L++ + +ME + + D W ++ EQ
Sbjct: 96 KRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQ 130
>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 305
Score = 27.3 bits (60), Expect = 2.5
Identities = 6/51 (11%), Positives = 18/51 (35%), Gaps = 2/51 (3%)
Query: 10 KKAHLMEIQLNGGSVADRQHITVCLKLA--HTEDLYGAHMKLLKKRQKKAH 58
K + ++ G D + I ++ + L+ + ++ K +
Sbjct: 246 SKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEESLGP 296
>3en9_A Glycoprotease, O-sialoglycoprotein endopeptidase/protein kinase;
endopeptidase activity, protein kinase activity; HET:
TBR; 2.67A {Methanocaldococcus jannaschii} PDB: 3enh_A*
2vwb_A*
Length = 540
Score = 27.3 bits (61), Expect = 2.6
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 76 ARQHLEQPIPV-GQVFAQDEM--IDCIGVTKGKG 106
A H E + + F + ID I ++G G
Sbjct: 50 ADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPG 83
>2po1_B Probable exosome complex exonuclease 2; RNAse PH,
hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*
Length = 277
Score = 27.4 bits (61), Expect = 2.6
Identities = 6/48 (12%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 10 KKAHLMEIQLNGGSVADRQHITVCLKLA--HTEDLYGAHMKLLKKRQK 55
+ H+ +Q + G + + ++ A E++ ++ ++K ++
Sbjct: 230 ETGHISAVQKSEGGAFKLEEVMYAVETAFKKAEEIRKLILEAVEKAKQ 277
>3eno_A Putative O-sialoglycoprotein endopeptidase; hydrolase,
metal-binding, metalloprotease, protease, zinc, keops
complex, ATPase, metal ION binding; 3.02A {Thermoplasma
acidophilum}
Length = 334
Score = 26.0 bits (58), Expect = 6.6
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 76 ARQHLEQPIPV-GQVFAQDEM----IDCIGVTKGKG 106
A H E V + + ++ ID IG + G G
Sbjct: 49 AVHHSEVIDTVISRALEKAKISIHDIDLIGFSMGPG 84
>2ivn_A O-sialoglycoprotein endopeptidase; UP1 keops complex, Fe/Zn
dependent nucleotide phosphatase, metalloprotease,
hypothetical protein, zinc; HET: ANP; 1.65A {Pyrococcus
abyssi} PDB: 2ivo_A 2ivp_A*
Length = 330
Score = 25.9 bits (58), Expect = 6.8
Identities = 8/36 (22%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 76 ARQHLEQPIPV-GQVFAQDEM----IDCIGVTKGKG 106
A H P+ + ++ + ID I ++G G
Sbjct: 44 AEHHARLMKPLLRKALSEAGVSLDDIDVIAFSQGPG 79
>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 271
Score = 25.8 bits (57), Expect = 8.7
Identities = 6/45 (13%), Positives = 14/45 (31%), Gaps = 6/45 (13%)
Query: 13 HLMEIQLNGGSVADRQHITVCLKLAHTEDLYGAHMKLLKKRQKKA 57
+ +Q G R + + +A + L + K+
Sbjct: 230 SICAMQKGGEGPLTRDDVLKAVSIAV------EKVPQLIEYLDKS 268
>2hpi_A DNA polymerase III alpha subunit; POL-beta-like
nucleotidyltransferase fold, transferase; HET: DNA;
3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A*
Length = 1220
Score = 26.1 bits (58), Expect = 8.8
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 3/19 (15%)
Query: 69 VADKIAWARQHLEQPIPVG 87
V D I WAR H + VG
Sbjct: 406 VQDYINWARGH---GVSVG 421
>2hnh_A DNA polymerase III alpha subunit; DNA replication,
nucleotidyltransferase, beta, PHP, transferase; HET:
DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Length = 910
Score = 25.9 bits (58), Expect = 9.2
Identities = 6/19 (31%), Positives = 11/19 (57%), Gaps = 3/19 (15%)
Query: 69 VADKIAWARQHLEQPIPVG 87
V + I W++ + +PVG
Sbjct: 344 VMEFIQWSKDN---GVPVG 359
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 0.132 0.374
Gapped
Lambda K H
0.267 0.0501 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,530,654
Number of extensions: 144230
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 288
Number of HSP's successfully gapped: 42
Length of query: 172
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 85
Effective length of database: 4,272,666
Effective search space: 363176610
Effective search space used: 363176610
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: 54 (25.1 bits)