RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 036979
(212 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 86.6 bits (215), Expect = 2e-22
Identities = 26/64 (40%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 48 LELTDDELLRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALA 107
L L + EL E K GPGGQ NK V LKHVP+G++ + + RS +NR +A
Sbjct: 41 LPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96
Query: 108 LSRL 111
L
Sbjct: 97 RKVL 100
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation;
2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X
2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Length = 365
Score = 86.5 bits (215), Expect = 2e-20
Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
E + ++SGPGGQ N ++AVR+ H+PTG+ RSQ KN+ LAL L
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKIL 279
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 85.8 bits (213), Expect = 5e-20
Identities = 25/54 (46%), Positives = 39/54 (72%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
+ + Y++SG GGQH N+ E+AVR+ H+PTG++ Q DRSQHKN+ A+ ++
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQM 291
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor
1 (RF-1), structural joint center for structural
genomics, JCSG; 2.34A {Streptococcus mutans}
Length = 371
Score = 84.9 bits (211), Expect = 8e-20
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
Y +SG GGQ+ NK TAVR+ H+PT + + E+R+Q KNR A+ +
Sbjct: 239 IYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKII 287
>2b3t_B RF-1, peptide chain release factor 1; translation termination,
methylation, conformational changes; HET: SAH; 3.10A
{Escherichia coli} SCOP: e.38.1.1
Length = 360
Score = 84.9 bits (211), Expect = 1e-19
Identities = 26/49 (53%), Positives = 39/49 (79%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
T++SSG GGQH N ++A+R+ H+PTG++ + ++RSQHKN+A ALS L
Sbjct: 226 TFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVL 274
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein,
ribosomal protein, RNA-binding, binding, metal-binding,
zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y
3d5c_X 3mr8_V 3ms0_V
Length = 354
Score = 84.1 bits (209), Expect = 1e-19
Identities = 23/49 (46%), Positives = 32/49 (65%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
++SGPGGQ N ++AVR+ H+PTG++ + RSQ KNR AL L
Sbjct: 221 VMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMIL 269
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 83.4 bits (207), Expect = 3e-19
Identities = 23/49 (46%), Positives = 36/49 (73%)
Query: 63 TYKSSGPGGQHRNKCETAVRLKHVPTGVIAQAAEDRSQHKNRALALSRL 111
T+++SG GGQ+ NK E+AVR+ H+PTG++ +RSQ++N+ AL L
Sbjct: 202 TFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRIL 250
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue F
alternative rescue factor, ARFB, release factor, rescue
of ribosomes; 3.20A {Escherichia coli} PDB: 2jy9_A
Length = 140
Score = 63.6 bits (155), Expect = 2e-13
Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 24/83 (28%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLK------------------------HVPTGVIAQ 93
E E+ ++ G GGQH NK TA+ L+ ++ +
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 94 AAEDRSQHKNRALALSRLPTFLA 116
A E RSQ NR AL+RL +
Sbjct: 74 AQEYRSQELNREAALARLVAMIK 96
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 62.6 bits (152), Expect = 3e-13
Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 24/83 (28%)
Query: 58 ECEMHTYKSSGPGGQHRNKCETAVRLKHVPTG------------------------VIAQ 93
E E+ ++ G GGQ+ NK +A+ L+ ++ +
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73
Query: 94 AAEDRSQHKNRALALSRLPTFLA 116
A + R+Q +NRA AL RL +
Sbjct: 74 AQQYRTQEQNRADALLRLSELIV 96
>1j26_A Immature colon carcinoma transcript 1; peptide chain release
factors, RF-1, the GGQ motif, immature carcinoma
transcript 1; NMR {Mus musculus} SCOP: d.50.4.1
Length = 112
Score = 57.1 bits (137), Expect = 5e-11
Identities = 16/86 (18%), Positives = 29/86 (33%), Gaps = 25/86 (29%)
Query: 56 LRECEMHTYKSSGPGGQHRNKCETAVRLKHVPTG-------------------------V 90
L + +SSGPGGQ+ NK + ++ +
Sbjct: 19 LDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGEL 78
Query: 91 IAQAAEDRSQHKNRALALSRLPTFLA 116
+ + R Q +N A L ++ +A
Sbjct: 79 VLTSESSRYQFRNLAECLQKIRDMIA 104
>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 = 38.9 bits (90), Expect = 0.001
Identities = 43/229 (18%), Positives = 64/229 (27%), Gaps = 66/229 (28%)
Query: 19 GLDWADW-AGPSIRMGFHH-CSCPASKKKNYLELTDDELLRECEMHTYKSSG--PGGQHR 74
GL+ +W PS + S P S + + +L + T K G PG
Sbjct: 212 GLNILEWLENPSNTPDKDYLLSIPISCP--LIGVI--QLA--HYVVTAKLLGFTPGELRS 265
Query: 75 NKCETAVRLKHVPTGV-IAQAAEDRSQHKNRALALSRL------------PTFLALK-VR 120
+ + T V IA+ S + A++ L T L +
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE 325
Query: 121 SSVNLGAYSP-P------LQLLQI----------LPPKSTIRSSEVGPQIGPNNPKFALV 163
S+ P P L Q+ LP + S V G N LV
Sbjct: 326 DSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV---NGAKN----LV 378
Query: 164 LLYSLLLRLLLSTGALSRLILSDDSLRMAVNEFRTSKCLMAYFNSNLPH 212
+ +G SL R +K S +P
Sbjct: 379 V-----------SGPPQ-------SLYGLNLTLRKAKAPSGLDQSRIPF 409
>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 = 34.1 bits (77), Expect = 0.034
Identities = 36/183 (19%), Positives = 60/183 (32%), Gaps = 28/183 (15%)
Query: 46 NYLELTDDELLRE-CEMHTYKSSGPGGQHRNKCETAVRLKHVP----TGVIAQAAEDRSQ 100
YL+ +L RE + + S R+ T KHV T +I +
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368
Query: 101 HKNRALALSRLPTFLALKV-RSSVNLGAYSPPLQLLQILPPKSTIRSSEVGPQIGPN--- 156
+ R + F L V S ++ P LL ++ V
Sbjct: 369 AEYRKM-------FDRLSVFPPSAHI-----PTILLSLIWFDVIKSDVMVVVNKLHKYSL 416
Query: 157 ---NPKFALVLLYSLLLRLLLST---GALSRLILSDDSLRMAVNEFRTSK-CLMAYFNSN 209
PK + + + S+ L L + AL R I+ ++ + L YF S+
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476
Query: 210 LPH 212
+ H
Sbjct: 477 IGH 479
Score = 31.4 bits (70), Expect = 0.24
Identities = 24/98 (24%), Positives = 37/98 (37%), Gaps = 32/98 (32%)
Query: 113 TFLALKVRSS-------------VNLGAYSPPLQLLQIL-------PPKSTIRSSEVGPQ 152
T++AL V S +NL + P +L++L P T RS
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD----- 218
Query: 153 IGPNNPKFALVLLYSLLLRLLLSTG---ALSRLILSDD 187
+N K + + + L RLL S L L+L +
Sbjct: 219 -HSSNIKLRIHSIQAELRRLLKSKPYENCL--LVL-LN 252
>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 2.51A {Homo
sapiens}
Length = 300
Score = 30.8 bits (70), Expect = 0.23
Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 20/89 (22%)
Query: 83 LKHVPTGVIAQA----------------AEDRSQHKNRALALSRLPTF-LALKVRSSVN- 124
L P +IAQ+ + + + L LS PT+ LAL+ +
Sbjct: 127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS--PTYELALQTGKVIEQ 184
Query: 125 LGAYSPPLQLLQILPPKSTIRSSEVGPQI 153
+G + P L+L + R ++ QI
Sbjct: 185 MGKFYPELKLAYAVRGNKLERGQKISEQI 213
>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA
dependent ATPase, mRNA export, nucleocytoplasmic
transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens}
PDB: 3ews_A* 3g0h_A* 3fhc_B
Length = 412
Score = 31.0 bits (71), Expect = 0.28
Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 20/89 (22%)
Query: 83 LKHVPTGVIAQA----------------AEDRSQHKNRALALSRLPTF-LALKVRSSVN- 124
L P +IAQ+ + + + L LS PT+ LAL+ +
Sbjct: 60 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS--PTYELALQTGKVIEQ 117
Query: 125 LGAYSPPLQLLQILPPKSTIRSSEVGPQI 153
+G + P L+L + R ++ QI
Sbjct: 118 MGKFYPELKLAYAVRGNKLERGQKISEQI 146
>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 3.19A {Homo
sapiens}
Length = 479
Score = 30.4 bits (69), Expect = 0.41
Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 20/89 (22%)
Query: 83 LKHVPTGVIAQA----------------AEDRSQHKNRALALSRLPTF-LALKVRSSVN- 124
L P +IAQ+ + + + L LS PT+ LAL+ +
Sbjct: 127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS--PTYELALQTGKVIEQ 184
Query: 125 LGAYSPPLQLLQILPPKSTIRSSEVGPQI 153
+G + P L+L + R ++ QI
Sbjct: 185 MGKFYPELKLAYAVRGNKLERGQKISEQI 213
>3giu_A Pyrrolidone-carboxylate peptidase; IDP00836, hydrolase, PROT thiol
protease, structural genomics; HET: MSE PG4; 1.25A
{Staphylococcus aureus subsp}
Length = 215
Score = 28.6 bits (63), Expect = 1.2
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 15 TCWTGLDWADWAGPSIRMGFHHC---SCPASKKKNYLELTDDELLR 57
T + D P +R GF H K + + ++++
Sbjct: 147 TLYHLGYLQDKHYPHLRFGFIHVPYIPEQVIGKPDTPSMPLEKIVA 192
>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor
biosynthesis, transferase; 1.45A {Escherichia coli}
SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D
1nvi_D
Length = 81
Score = 27.2 bits (61), Expect = 1.2
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 169 LLRLLLSTGALSRLILSDDSLRMAVNE 195
L + + + L L D L AVN+
Sbjct: 31 LRQHMAAQSDRWALALEDGKLLAAVNQ 57
>4ash_A NS6 protease; hydrolase, trypsin-like, calicivirus; 1.58A {Murine
norovirus 1}
Length = 185
Score = 27.1 bits (59), Expect = 3.3
Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 4/105 (3%)
Query: 19 GLDWADWAGPSIRMGFHHCSCPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKCE 78
G W W + + H + P + + D + + Y + R
Sbjct: 15 GTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYYFTSA---VRPDIP 71
Query: 79 TAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSV 123
V GV+A R+ + ALA+ R+ + A+K+ S+V
Sbjct: 72 AMVLENGCQEGVVASVLVKRASGEMLALAV-RMGSQAAIKIGSAV 115
>1v90_A Delta-paluit1, delta-palutoxin IT1; insecticidal toxin, spider
toxin, ICK fold, structure; NMR {Paracoelotes
luctuosus} PDB: 1v91_A
Length = 38
Score = 24.7 bits (53), Expect = 4.7
Identities = 11/17 (64%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 23 ADWAGPSIRMGFHHCSC 39
ADW+GPS GF +CSC
Sbjct: 10 ADWSGPSCCDGF-YCSC 25
>3mal_A Stromal cell-derived factor 2-like protein; trefoil fold, MIR
motifs, unfolded protein response, putativ binding
protein, plant protein; 1.95A {Arabidopsis thaliana}
Length = 199
Score = 26.4 bits (58), Expect = 5.5
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 70 GGQHRNKCETAVRLKHVPTGV 90
G+ K + VRL+H+ T
Sbjct: 134 SGKTW-KQDQRVRLQHIDTSG 153
>2fyq_A Chymotrypsin-like cysteine proteinase; protease, norovirus,
calicivirus, viral protein; 1.50A {Norwalk virus} PDB:
2fyr_A 2iph_A* 1wqs_A*
Length = 194
Score = 26.3 bits (57), Expect = 6.2
Identities = 17/105 (16%), Positives = 37/105 (35%), Gaps = 4/105 (3%)
Query: 19 GLDWADWAGPSIRMGFHHCSCPASKKKNYLELTDDELLRECEMHTYKSSGPGGQHRNKCE 78
G W W P++ + H K+ L+ + + E ++ S R
Sbjct: 26 GSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKK---MRPDLT 82
Query: 79 TAVRLKHVPTGVIAQAAEDRSQHKNRALALSRLPTFLALKVRSSV 123
V + P G + R + LA+ R+ +++++ +
Sbjct: 83 GMVLEEGCPEGTVCSVLIKRDSGELLPLAV-RMGAIASMRIQGRL 126
>1ffv_B CUTL, molybdoprotein of carbon monoxide dehydrogenase; hydrolase;
HET: ARO PCD FAD; 2.25A {Hydrogenophaga pseudoflava}
SCOP: d.41.1.1 d.133.1.1 PDB: 1ffu_B*
Length = 803
Score = 26.6 bits (59), Expect = 8.5
Identities = 5/17 (29%), Positives = 8/17 (47%)
Query: 113 TFLALKVRSSVNLGAYS 129
L L+V + GA+
Sbjct: 324 KILGLRVNVVADHGAFD 340
>1t3q_B Quinoline 2-oxidoreductase large subunit; QOR, molybdenum, MCD;
HET: FAD MCN; 1.80A {Pseudomonas putida} SCOP: d.41.1.1
d.133.1.1
Length = 788
Score = 26.4 bits (59), Expect = 8.6
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 113 TFLALKVRSSVNLGAYS 129
FLAL+ RS + GAY+
Sbjct: 311 RFLALENRSITDGGAYN 327
>1t9f_A Protein 1D10; structural genomics, PSI, protein structure
initiative, southeast collaboratory for structural
genomics, secsg; 2.00A {Caenorhabditis elegans} SCOP:
b.42.6.1
Length = 187
Score = 26.1 bits (57), Expect = 9.0
Identities = 6/41 (14%), Positives = 11/41 (26%), Gaps = 10/41 (24%)
Query: 60 EMHTYKSSGPGGQHRN----------KCETAVRLKHVPTGV 90
E+ + S + +L+H TG
Sbjct: 101 EVSAFGSEAESDTGDDWTVICNGDEWLESEQFKLRHAVTGS 141
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
0.320 0.134 0.408
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,100,889
Number of extensions: 168744
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 29
Length of query: 212
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 123
Effective length of database: 4,216,824
Effective search space: 518669352
Effective search space used: 518669352
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: 55 (25.1 bits)