BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 030017
(184 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 144 bits (362), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 67/178 (37%), Positives = 111/178 (62%)
Query: 1 MQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFNV 60
+ EGLA+I L+ MTI R RI+ IPRK + Y+ L+KF+++V Q+ DF+
Sbjct: 142 LDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQSINSEFDFDK 201
Query: 61 VRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPN 120
++ ++ASPGF + ++ A + L+ I+++K++ +++H+S+G+ HSL E+L P
Sbjct: 202 LKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIHSLNEILKDPA 261
Query: 121 VMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 178
V + + DTK QE++ L F++++ D +A YGP HV A E A+ LLI+D LFR
Sbjct: 262 VESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSLFR 319
>pdb|2VGM|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-Go Decay.
pdb|3IZQ|0 Chain 0, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
pdb|3J16|A Chain A, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 386
Score = 109 bits (273), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 56/175 (32%), Positives = 94/175 (53%), Gaps = 1/175 (0%)
Query: 1 MQEGLAHILLVGRSMTITRSRIETSIPRKH-GPAIAGYESALNKFFENVLQAFLKHVDFN 59
+QEG+AH+ LV S TI + +IE S+P+K + ++ KF++ + A K ++F+
Sbjct: 147 LQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFYKAIYSAMKKDLNFD 206
Query: 60 VVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAP 119
++ ++ SPGF + AE + I++NK + H S+GY + EVL P
Sbjct: 207 KLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGINEVLKNP 266
Query: 120 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITD 174
+ ++DTK ++E+ + +F L D +A YG K V A E A+ LL+TD
Sbjct: 267 LYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTD 321
>pdb|2VGN|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay.
pdb|2VGN|B Chain B, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay
Length = 386
Score = 107 bits (268), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 56/175 (32%), Positives = 92/175 (52%), Gaps = 1/175 (0%)
Query: 1 MQEGLAHILLVGRSMTITRSRIETSIPRKH-GPAIAGYESALNKFFENVLQAFLKHVDFN 59
+QEG+AH+ LV S TI + +IE S P+K + ++ KF++ + A K ++F+
Sbjct: 147 LQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDVLKFDEKTEKFYKAIYSAXKKDLNFD 206
Query: 60 VVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAP 119
++ ++ SPGF + AE + I++NK + H S+GY + EVL P
Sbjct: 207 KLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILDNKGXFFIAHCSTGYLQGINEVLKNP 266
Query: 120 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITD 174
+ ++DTK ++E+ +F L D +A YG K V A E A+ LL+TD
Sbjct: 267 LYASKLQDTKYSKEIXVXDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTD 321
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 73.2 bits (178), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 34/59 (57%), Positives = 44/59 (74%)
Query: 120 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 178
V + + DTKAA EV+AL DF+ ML ++P RA YG K VE A+E MA+ TLLI+D+LFR
Sbjct: 8 TVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFR 66
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 57.4 bits (137), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 39/141 (27%), Positives = 70/141 (49%), Gaps = 8/141 (5%)
Query: 38 ESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKS 97
ES KFF +V + + + V A++A PGF K+ F++ L ++ P E
Sbjct: 176 ESEEMKFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFL------KEKYP--ELAK 227
Query: 98 RIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKH 157
++++ TS + + EV+ V + ++ + A+EVQ ++ + + YG K
Sbjct: 228 KVVIEDTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVAYGLKE 287
Query: 158 VEVAHERMAVQTLLITDDLFR 178
VE A AV+TLL+ D+L +
Sbjct: 288 VEEAVNYGAVETLLVLDELLK 308
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 63/129 (48%), Gaps = 13/129 (10%)
Query: 49 LQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGY 108
L ++K D + + ++A PGF K++ + ++ I++NK +I + SS
Sbjct: 197 LAEYVKQYDPDAI---LLAGPGFFKEEVSK---------KVNAILKNK-KIYIDSVSSAT 243
Query: 109 KHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQ 168
+ L EVL + ++ D + A + ++ +L P YG + V+ A E AV+
Sbjct: 244 RAGLHEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVE 303
Query: 169 TLLITDDLF 177
T+L+ +DL
Sbjct: 304 TVLVIEDLL 312
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/177 (25%), Positives = 78/177 (44%), Gaps = 25/177 (14%)
Query: 9 LLVGRSMTITRSRIETSIPRKH---GPAIAGYE----SALNKFFENVLQA----FLKHVD 57
LL G + + + +E +P KH G + YE +++FF+ V + + +
Sbjct: 157 LLKGARLEVLKE-LEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKKVGEEASNLLVPLAE 215
Query: 58 FNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLD 117
V++ ++A PG K +F L+ +L+ I+ + + G K + V+
Sbjct: 216 KGVLKGVIVAGPGLAKQEFVEGNYLDY---RLKKILAPELVDVAYQGLQGLKEA---VMK 269
Query: 118 APNVM--NMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLI 172
A V+ M +D V A+++F L YG K VE A E AV+TLLI
Sbjct: 270 AEKVVEAQMYRDA-----VNAMEEFKLHLAKGTGMIVYGEKDVEAALEMGAVKTLLI 321
>pdb|3E20|C Chain C, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|B Chain B, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|H Chain H, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|K Chain K, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
Length = 441
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 41/170 (24%), Positives = 67/170 (39%), Gaps = 28/170 (16%)
Query: 21 RIETSIPRKHGPAIAGYESALN--------------KFFENVLQAFLKHVDFNVVRCAVI 66
R +P+KHG G +SAL K E +Q F+ NV +
Sbjct: 176 RFTVDLPKKHG---RGGQSALRFARLRDEKRHNYVRKVAEGAVQHFITDDKPNVAGIVLA 232
Query: 67 ASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIK 126
S F + L +R Q R I K+ + +G+ ++ D +
Sbjct: 233 GSADFKTELGQSDLF--DQRLQSRII---KTVDVSYGGDAGFNQAIELAADT------LS 281
Query: 127 DTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 176
+ K QE + ++ FF+ ++ D + C+G A + AV+TLL DL
Sbjct: 282 NVKYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFADL 331
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 32/135 (23%), Positives = 63/135 (46%), Gaps = 18/135 (13%)
Query: 44 FFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVH 103
+F+ ++ A LK N +I PGF +D+F R+ +R + I +
Sbjct: 177 YFDQIVNA-LK----NYSNSIIILGPGFARDRFARY----CAQRGVNVIGSFPAN----R 223
Query: 104 TSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHE 163
T SG ++ E + + + ++ + + A++ + + +F + D YG E A +
Sbjct: 224 TDSG---AVYEFITSADGAKLLSNERIARDKEIVDEFLVAVKKDM--GVYGRDQTESALQ 278
Query: 164 RMAVQTLLITDDLFR 178
A+ L+ITD++FR
Sbjct: 279 MGALSDLIITDEMFR 293
>pdb|3IR9|A Chain A, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei.
pdb|3IR9|B Chain B, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei
Length = 166
Score = 33.5 bits (75), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 109 KHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQ 168
+ L E+++A ++D + + A++DFF L D + YG V E +V
Sbjct: 7 ESGLSELVNAAG--EKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINSVD 64
Query: 169 TLLITDDL 176
LL+++DL
Sbjct: 65 VLLLSEDL 72
>pdb|3OBY|A Chain A, Crystal Structure Of Archaeoglobus Fulgidus Pelota Reveals
Inter- Domain Structural Plasticity
pdb|3OBY|B Chain B, Crystal Structure Of Archaeoglobus Fulgidus Pelota Reveals
Inter- Domain Structural Plasticity
Length = 352
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 35/142 (24%), Positives = 59/142 (41%), Gaps = 13/142 (9%)
Query: 36 GYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIEN 95
G + +FF V A L+ DF + ++A PGF K+ F L ++ P E
Sbjct: 164 GMGDSRKEFFGEV-AAKLESFDF---KYLIVAGPGFAKNDFLDFL------KERYP--EM 211
Query: 96 KSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGP 155
++V SS E+L V ++ + + A+E + + + R YG
Sbjct: 212 AKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAK-GERVAYGL 270
Query: 156 KHVEVAHERMAVQTLLITDDLF 177
V AH A++ LL+ D+
Sbjct: 271 DEVREAHNYRAIEVLLVADEFL 292
>pdb|4DB5|A Chain A, Crystal Structure Of Rabbit Gitrl
Length = 125
Score = 30.0 bits (66), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 119 PNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 170
P+ +N I D K L + + DPT + P V++ + A+QTL
Sbjct: 24 PSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTL 75
>pdb|2E1B|A Chain A, Crystal Structure Of The Alax-M Trans-Editing Enzyme From
Pyrococcus Horikoshii
Length = 216
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 11/54 (20%)
Query: 4 GLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVD 57
G + LVG M++ + R + + P LNK+ E ++ F K+VD
Sbjct: 114 GEGNWQLVGSGMSVEKGRYDIAYP-----------ENLNKYKEQIISLFNKYVD 156
>pdb|3AQ8|A Chain A, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Q46e Mutant, Fe(Iii) Form
pdb|3AQ8|B Chain B, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Q46e Mutant, Fe(Iii) Form
Length = 121
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 113 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 170
++VL V + K+T E + DF ML P Y K++ AH+ M +Q L
Sbjct: 26 KKVLADERVKHFFKNTDMDHETKQQTDFLTMLLGGPNH--YKGKNMTEAHKGMNLQNL 81
>pdb|3AQ7|A Chain A, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Y25f Mutant, Fe(Iii) Form
pdb|3AQ7|B Chain B, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Y25f Mutant, Fe(Iii) Form
Length = 121
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 112 LREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 170
++VL V + K+T + + DF ML P Y K++ AH+ M +Q L
Sbjct: 25 FKKVLADERVKHFFKNTDMDHQTKQQTDFLTMLLGGPNH--YKGKNMTEAHKGMNLQNL 81
>pdb|3AQ5|A Chain A, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Fe(Ii)-O2 Form
pdb|3AQ5|B Chain B, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Fe(Ii)-O2 Form
pdb|3AQ6|A Chain A, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Fe(Iii) Form
pdb|3AQ6|B Chain B, Crystal Structure Of Truncated Hemoglobin From Tetrahymena
Pyriformis, Fe(Iii) Form
Length = 121
Score = 26.6 bits (57), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 113 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 170
++VL V + K+T + + DF ML P Y K++ AH+ M +Q L
Sbjct: 26 KKVLADERVKHFFKNTDMDHQTKQQTDFLTMLLGGPNH--YKGKNMTEAHKGMNLQNL 81
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.136 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,052,091
Number of Sequences: 62578
Number of extensions: 179424
Number of successful extensions: 528
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 513
Number of HSP's gapped (non-prelim): 20
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)