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= 024840
(262 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 = 203 bits (516), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 94/248 (37%), Positives = 159/248 (64%)
Query: 9 VDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADP 68
+D+D + + L I+G+ + VK+G++HTL++ELHR F L K+ WD+ ALD + A +P
Sbjct: 72 MDFDTKAAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAFALDRVDAACNP 131
Query: 69 TASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQ 128
+ +A++ V++ EGLA+I L+ MTI R RI+ IPRK + Y+ L+KF+++V Q
Sbjct: 132 SRNAEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQ 191
Query: 129 AFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKH 188
+ DF+ ++ ++ASPGF + ++ A + L+ I+++K++ +++H+S+G+ H
Sbjct: 192 SINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIH 251
Query: 189 SLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 248
SL E+L P V + + DTK QE++ L F++++ D +A YGP HV A E A+ L
Sbjct: 252 SLNEILKDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGEL 311
Query: 249 LITDDLFR 256
LI+D LFR
Sbjct: 312 LISDSLFR 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 = 126 bits (316), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 69/249 (27%), Positives = 127/249 (51%), Gaps = 6/249 (2%)
Query: 10 DYDKEGSVLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQ 64
D+D + L+ +G + + N + +G + + ++ F + K ++ L++
Sbjct: 73 DFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNE 132
Query: 65 AADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAGYESALNKFF 123
A + +D A V++QEG+AH+ LV S TI + +IE S+P+K + ++ KF+
Sbjct: 133 ACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFY 192
Query: 124 ENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTS 183
+ + A K ++F+ ++ ++ SPGF + AE + I++NK + H S
Sbjct: 193 KAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCS 252
Query: 184 SGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERM 243
+GY + EVL P + ++DTK ++E+ + +F L D +A YG K V A E
Sbjct: 253 TGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYG 312
Query: 244 AVQTLLITD 252
A+ LL+TD
Sbjct: 313 AISYLLLTD 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 = 124 bits (311), Expect = 6e-29, Method: Compositional matrix adjust.
Identities = 69/249 (27%), Positives = 125/249 (50%), Gaps = 6/249 (2%)
Query: 10 DYDKEGSVLRIRGKNILE-----NEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQ 64
D+D + L+ +G + + N + +G + + ++ F + K ++ L++
Sbjct: 73 DFDXKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFXQKLLNE 132
Query: 65 AADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPA-IAGYESALNKFF 123
A + +D A V++QEG+AH+ LV S TI + +IE S P+K + ++ KF+
Sbjct: 133 ACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSXPKKKRTTDVLKFDEKTEKFY 192
Query: 124 ENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTS 183
+ + A K ++F+ ++ ++ SPGF + AE + I++NK + H S
Sbjct: 193 KAIYSAXKKDLNFDKLKTIILCSPGFYAKILXDKIFQYAEEEHNKKILDNKGXFFIAHCS 252
Query: 184 SGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERM 243
+GY + EVL P + ++DTK ++E+ +F L D +A YG K V A E
Sbjct: 253 TGYLQGINEVLKNPLYASKLQDTKYSKEIXVXDEFLLHLNKDDDKAWYGEKEVVKAAEYG 312
Query: 244 AVQTLLITD 252
A+ LL+TD
Sbjct: 313 AISYLLLTD 321
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 65/256 (25%), Positives = 123/256 (48%), Gaps = 19/256 (7%)
Query: 6 SQVVDYDKEGSVLRIRGKNILEN-EHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQ 64
++ +++ K + +R+ G + + E V +G +HT+ IE ++K W ++ L +
Sbjct: 67 AEKINFHKFANQVRVTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHIERLKE 126
Query: 65 AADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGY----ESALN 120
A + A + +V++ +G A + LV R + I SI +H Y ES
Sbjct: 127 AVAASKRARVMIVVIDDGEADMALV-REYGV---EILNSI--RHNLGGKRYNTDRESEEM 180
Query: 121 KFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILV 180
KFF +V + + + V A++A PGF K+ F++ L ++ P E ++++
Sbjct: 181 KFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFL------KEKYP--ELAKKVVIE 232
Query: 181 HTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAH 240
TS + + EV+ V + ++ + A+EVQ ++ + + YG K VE A
Sbjct: 233 DTSVTGRTGIYEVIKRGVVDRVYQENRVAKEVQLVEKVLENIARNNGLVAYGLKEVEEAV 292
Query: 241 ERMAVQTLLITDDLFR 256
AV+TLL+ D+L +
Sbjct: 293 NYGAVETLLVLDELLK 308
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 34/59 (57%), Positives = 44/59 (74%)
Query: 198 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 256
V + + DTKAA EV+AL DF+ ML ++P RA YG K VE A+E MA+ TLLI+D+LFR
Sbjct: 8 TVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFR 66
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 43/234 (18%)
Query: 34 GAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSM 93
GA HT+ +++ ++ K W+ LD L + A+ + +A+V E L
Sbjct: 110 GAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANKRSRIIIALVDFDEYL---------- 159
Query: 94 TITRSRIETSIPRKHGPAIAGYES--ALNK----FFENVLQ------AFLKHVDFNVVRC 141
+IP + G I +S LN+ +N L+ ++K D + +
Sbjct: 160 --------IAIPFEQGIKILSEKSLRPLNEEEGIIEQNALEIATELAEYVKQYDPDAI-- 209
Query: 142 AVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMN 201
++A PGF K++ + ++ I++NK +I + SS + L EVL +
Sbjct: 210 -LLAGPGFFKEEVSK---------KVNAILKNK-KIYIDSVSSATRAGLHEVLKRDIIDK 258
Query: 202 MIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 255
++ D + A + ++ +L P YG + V+ A E AV+T+L+ +DL
Sbjct: 259 IMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVIEDLL 312
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 57/239 (23%), Positives = 100/239 (41%), Gaps = 24/239 (10%)
Query: 18 LRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVV 77
LRI G I E K G ++ + + + K+ WD +D L +A D V
Sbjct: 79 LRILGTVIEGPEDTK-GKHQSITVTVDSEISITKE-WDDQHIDLLKEATDEKYVTVYTAV 136
Query: 78 LMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHVDFN 137
M E A I L+ ++ T + G G S + +F+ ++ A LK N
Sbjct: 137 AMDEDEAQIFLI---HPYGIQQVGTVYSGRSGKYAEGNYSEAS-YFDQIVNA-LK----N 187
Query: 138 VVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAP 197
+I PGF +D+F R+ +R + I T SG ++ E + +
Sbjct: 188 YSNSIIILGPGFARDRFARY----CAQRGVNVI----GSFPANRTDSG---AVYEFITSA 236
Query: 198 NVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFR 256
+ ++ + + A++ + + +F + D YG E A + A+ L+ITD++FR
Sbjct: 237 DGAKLLSNERIARDKEIVDEFLVAVKKDM--GVYGRDQTESALQMGALSDLIITDEMFR 293
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 54/247 (21%), Positives = 105/247 (42%), Gaps = 24/247 (9%)
Query: 9 VDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADP 68
V++ + + LR+ GK + ++ +HTL I + + + K W L+ L +A +
Sbjct: 70 VEFHRFANRLRVSGKIVA---GIEESGYHTLNITVGKELSIIKK-WKPEQLERLRRAVED 125
Query: 69 TASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQ 128
+ ++ ++ ++EG A + + + +E + G G + +FF V
Sbjct: 126 SNRPEIVMLTIEEGYAV------AGVLRQWGVEEIFEERMGYG-KGMGDSRKEFFGEV-A 177
Query: 129 AFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKH 188
A L+ DF + ++A PGF K+ F L ++ P E ++V SS
Sbjct: 178 AKLESFDFKYL---IVAGPGFAKNDFLDFL------KERYP--EMAKNAVVVDVSSVGSR 226
Query: 189 SLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 248
E+L V ++ + + A+E + + + R YG V AH A++ L
Sbjct: 227 GFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAK-GERVAYGLDEVREAHNYRAIEVL 285
Query: 249 LITDDLF 255
L+ D+
Sbjct: 286 LVADEFL 292
>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 = 0.004, Method: Compositional matrix adjust.
Identities = 48/191 (25%), Positives = 86/191 (45%), Gaps = 26/191 (13%)
Query: 74 LAVVLMQEGLAHI-LLVGRSMTITRSRIETSIPRKH---GPAIAGYE----SALNKFFEN 125
+ +++++ A I LL G + + + +E +P KH G + YE +++FF+
Sbjct: 143 IGIIIVERDQATIGLLKGARLEVLKE-LEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKK 201
Query: 126 VLQA----FLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVH 181
V + + + V++ ++A PG K +F L+ +L+ I+ + +
Sbjct: 202 VGEEASNLLVPLAEKGVLKGVIVAGPGLAKQEFVEGNYLDY---RLKKILAPELVDVAYQ 258
Query: 182 TSSGYKHSLREVLDAPNVM--NMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVA 239
G K + V+ A V+ M +D V A+++F L YG K VE A
Sbjct: 259 GLQGLKEA---VMKAEKVVEAQMYRDA-----VNAMEEFKLHLAKGTGMIVYGEKDVEAA 310
Query: 240 HERMAVQTLLI 250
E AV+TLLI
Sbjct: 311 LEMGAVKTLLI 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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 41/170 (24%), Positives = 67/170 (39%), Gaps = 28/170 (16%)
Query: 99 RIETSIPRKHGPAIAGYESALN--------------KFFENVLQAFLKHVDFNVVRCAVI 144
R +P+KHG G +SAL K E +Q F+ NV +
Sbjct: 176 RFTVDLPKKHG---RGGQSALRFARLRDEKRHNYVRKVAEGAVQHFITDDKPNVAGIVLA 232
Query: 145 ASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIK 204
S F + L +R Q R I K+ + +G+ ++ D +
Sbjct: 233 GSADFKTELGQSDLF--DQRLQSRII---KTVDVSYGGDAGFNQAIELAADT------LS 281
Query: 205 DTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 254
+ K QE + ++ FF+ ++ D + C+G A + AV+TLL DL
Sbjct: 282 NVKYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEGAVETLLCFADL 331
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 187 KHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQ 246
+ L E+++A ++D + + A++DFF L D + YG V E +V
Sbjct: 7 ESGLSELVNAAG--EKLQDLELXGQKNAVRDFFKELIADSGKVAYGESQVRANLEINSVD 64
Query: 247 TLLITDDL 254
LL+++DL
Sbjct: 65 VLLLSEDL 72
>pdb|4DB5|A Chain A, Crystal Structure Of Rabbit Gitrl
Length = 125
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 197 PNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 248
P+ +N I D K L + + DPT + P V++ + A+QTL
Sbjct: 24 PSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTL 75
>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 = 6.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 191 REVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTL 248
++VL V + K+T E + DF ML P Y K++ AH+ M +Q L
Sbjct: 26 KKVLADERVKHFFKNTDMDHETKQQTDFLTMLLGGPNH--YKGKNMTEAHKGMNLQNL 81
>pdb|1HN0|A Chain A, Crystal Structure Of Chondroitin Abc Lyase I From Proteus
Vulgaris At 1.9 Angstroms Resolution
Length = 1021
Score = 27.7 bits (60), Expect = 7.2, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 7 QVVDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKD 52
Q++ Y E L + K + +N +V +G + TL + RA+VL KD
Sbjct: 313 QIIIYQPEN--LNSQDKQLFDN-YVILGNYTTLMFNISRAYVLEKD 355
>pdb|1RWS|A Chain A, Backbone Solution Structure Of Mixed AlphaBETA PROTEIN
PF1061
pdb|1SF0|A Chain A, Backbone Solution Structure Of Mixed AlphaBETA PROTEIN
PF1061
Length = 77
Score = 27.3 bits (59), Expect = 8.7, Method: Composition-based stats.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 5 VSQVVDYDKEGSVLRIRGKNILENEHVKIGAF 36
+ + V ++ E ++ ++ GK +LE++ VK G F
Sbjct: 36 ILRAVGFNTESAIAKVNGKVVLEDDEVKDGDF 67
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
0.323 0.136 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,181,430
Number of Sequences: 62578
Number of extensions: 261828
Number of successful extensions: 744
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 727
Number of HSP's gapped (non-prelim): 18
length of query: 262
length of database: 14,973,337
effective HSP length: 97
effective length of query: 165
effective length of database: 8,903,271
effective search space: 1469039715
effective search space used: 1469039715
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)