RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 038082
(149 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 87.0 bits (216), Expect = 2e-23
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 5 PNYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNR 64
P L L + EL E K GPGGQ NK + V LKH P+G++ + + RS +NR
Sbjct: 38 PALLPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNR 93
Query: 65 ASALSRLRTLL 75
A L+ +
Sbjct: 94 KIARKVLQEKV 104
>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 = 89.6 bits (223), Expect = 3e-22
Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRT-LLA 76
E +D ++SGPGGQ N +SAVR+ H PTG+ RSQ KN+ AL L+ L
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYE 285
Query: 77 LKVR 80
L+ +
Sbjct: 286 LERK 289
>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 = 88.5 bits (220), Expect = 8e-22
Identities = 28/58 (48%), Positives = 41/58 (70%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
+ +D Y++SG GGQH N+ ESAVR+ H PTG++ Q DRSQHKN+ A+ +++ L
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKL 295
>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 = 87.2 bits (217), Expect = 2e-21
Identities = 29/74 (39%), Positives = 47/74 (63%), Gaps = 1/74 (1%)
Query: 3 VLPNYLELTDDEL-FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQH 61
V+P + ++ + +D ++SSG GGQH N +SA+R+ H PTG++ + ++RSQH
Sbjct: 205 VMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQH 264
Query: 62 KNRASALSRLRTLL 75
KN+A ALS L +
Sbjct: 265 KNKAKALSVLGARI 278
>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 = 87.2 bits (217), Expect = 2e-21
Identities = 23/58 (39%), Positives = 36/58 (62%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
+ +D Y +SG GGQ+ NK +AVR+ H PT + + E+R+Q KNR A+ +R +
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARV 291
>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 = 86.5 bits (215), Expect = 3e-21
Identities = 28/58 (48%), Positives = 37/58 (63%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
E +D ++SGPGGQ N +SAVR+ H PTG++ + RSQ KNR AL LR+ L
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRL 273
>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 = 85.3 bits (212), Expect = 8e-21
Identities = 25/55 (45%), Positives = 39/55 (70%)
Query: 21 MDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
++ +++SG GGQ+ NK ESAVR+ H PTG++ +RSQ++N+ +AL LR L
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARL 254
>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 = 65.6 bits (160), Expect = 9e-15
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 24/83 (28%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLK------------------------HAPTGVIAQ 53
E E+ A ++ G GGQH NK +A+ L+ + ++ +
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 54 AAEDRSQHKNRASALSRLRTLLA 76
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 = 63.8 bits (155), Expect = 2e-14
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 24/83 (28%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTG------------------------VIAQ 53
E E+ A ++ G GGQ+ NK SA+ L+ ++ +
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73
Query: 54 AAEDRSQHKNRASALSRLRTLLA 76
A + R+Q +NRA AL RL L+
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 = 56.7 bits (136), Expect = 2e-11
Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 25/84 (29%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTG-------------------------VIA 52
+ +SSGPGGQ+ NK S ++ ++
Sbjct: 21 RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVL 80
Query: 53 QAAEDRSQHKNRASALSRLRTLLA 76
+ R Q +N A L ++R ++A
Sbjct: 81 TSESSRYQFRNLAECLQKIRDMIA 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 = 30.0 bits (67), Expect = 0.30
Identities = 25/128 (19%), Positives = 34/128 (26%), Gaps = 51/128 (39%)
Query: 50 VIAQAAEDRSQHKNRASALSRL------------RTLLALK-VRSSVNLDAYSPPPQLH- 95
IA+ S + A++ L T L + S+ + P P L
Sbjct: 282 AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 96 ----------------QILPPKSTIRSSEVGPQIGPNNPKFALVL---PYSLLLPFVINA 136
LP + S V G N LV+ P SL
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVEISLV---NGAKN----LVVSGPPQSL-------- 386
Query: 137 AKIYGLKS 144
YGL
Sbjct: 387 ---YGLNL 391
Score = 30.0 bits (67), Expect = 0.31
Identities = 25/144 (17%), Positives = 35/144 (24%), Gaps = 53/144 (36%)
Query: 52 AQAAEDRSQHKNRASALSR-------------------------LRTL--------LALK 78
A+ R K SAL R LR L L
Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLI 188
Query: 79 VRSSVNL-----DAYSPPPQLHQILPPKSTIRSSEVGPQIGPNNPKFALVLPYSLLLPFV 133
S+ L Q L + P P+ + P S P +
Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQGLNILEWLE----NPSNTPDKDYLLSI-PIS--CPLI 241
Query: 134 --------INAAKIYGLKSGEIQE 149
+ AK+ G GE++
Sbjct: 242 GVIQLAHYVVTAKLLGFTPGELRS 265
>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 = 29.1 bits (64), Expect = 0.35
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 8/29 (27%)
Query: 78 KVRSSVNLDAYSP--PPQLHQILPPKSTI 104
K+++S+ L Y+ P L I K+T+
Sbjct: 24 KLQASLKL--YADDSAPAL-AI---KATM 46
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.4 bits (60), Expect = 1.7
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 4/55 (7%)
Query: 75 LALKVRSSVNLDAYSPPPQLHQILPPKSTIRSSEVGPQIGPNNPKFALVL---PY 126
+A++V S + S +PP I S KF LV+ P+
Sbjct: 118 MAIQVNYSSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKKF-LVIAYEPF 171
>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 = 27.2 bits (60), Expect = 1.8
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 30 GGQHRNKRESAVRLKHAPTGV 50
G+ K++ VRL+H T
Sbjct: 134 SGKTW-KQDQRVRLQHIDTSG 153
>3p01_A Two-component response regulator; PSI-2, midwest center for
structural genomics, protein struc initiative, MCSG,
signali protein; 2.65A {Nostoc SP}
Length = 184
Score = 26.8 bits (60), Expect = 2.1
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 50 VIAQAAEDRSQHKNRASALSR----LRTL--LALKVRSSVNLDA 87
V+ +AAE K R L R + L L ++S +L+A
Sbjct: 4 VVQRAAETYDLLKQRTEELRRANAQMSLLTVLVQVTQASNSLEA 47
>2hp7_A Flagellar motor switch protein FLIM; bacterial chemotaxis,
flagellar switch complex, signaling protein; 2.00A
{Thermotoga maritima} PDB: 3soh_A
Length = 183
Score = 26.9 bits (59), Expect = 2.3
Identities = 12/40 (30%), Positives = 16/40 (40%)
Query: 92 PQLHQILPPKSTIRSSEVGPQIGPNNPKFALVLPYSLLLP 131
PQ QI+PP + G + P+SLL P
Sbjct: 140 PQFVQIVPPNEIVLLVTASVSWGEFTSFINVCWPFSLLEP 179
>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 = 26.8 bits (59), Expect = 2.4
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 36 KRESAVRLKHAPTGV 50
+L+HA TG
Sbjct: 127 LESEQFKLRHAVTGS 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
0.315 0.132 0.375
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: 2,120,263
Number of extensions: 111510
Number of successful extensions: 169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 166
Number of HSP's successfully gapped: 20
Length of query: 149
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 64
Effective length of database: 4,328,508
Effective search space: 277024512
Effective search space used: 277024512
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: 42 (22.0 bits)
S2: 53 (24.3 bits)