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= 048626
(260 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X52|A Chain A, Solution Structures Of The C-Terminal Domain Of The Human
Pelota Homolog (Cgi-17)
Length = 124
Score = 87.4 bits (215), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 52/114 (45%), Positives = 71/114 (62%), Gaps = 23/114 (20%)
Query: 137 ASSVMNMIKDTKAAQEV----------QH-----------VEVAHQRMAVQTLHITDDLF 175
+ +V + + DTKAA EV QH VE A++ MA+ TL I+D+LF
Sbjct: 6 SGTVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELF 65
Query: 176 RNTAIATRKKYVDLVNSVKDSGGTAHVFSSM--SQGNLGQLTGVAAILRFPLPN 227
R+ +ATR +YV LV+SVK++ GT +FSS+ S L QLTGVAAILRFP+P+
Sbjct: 66 RHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPS 119
>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 = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 57/89 (64%), Gaps = 2/89 (2%)
Query: 146 DTKAAQEVQHVEVAHQRMAVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGTAHVFSS 205
D KA + V A + A+ L +TD + + IA R++Y+ L++SV+ +GG A V S+
Sbjct: 295 DDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLMDSVESNGGKALVLST 354
Query: 206 M-SQG-NLGQLTGVAAILRFPLPNLTKND 232
+ S G L QLTG+A IL++PLP+L ++D
Sbjct: 355 LHSLGEELDQLTGIACILKYPLPDLDEDD 383
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 4 VRKDLIPNGPRSVKMIPVDSDDLWFAYNLVAGKDPFLAITLRKVVRQTKSGG--KDAEWV 61
++KD G + ++P D +DL+ Y +V D I +K + G K + V
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLV 63
Query: 62 KLKSEI 67
KLK ++
Sbjct: 64 KLKIKV 69
>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 = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 56/89 (62%), Gaps = 2/89 (2%)
Query: 146 DTKAAQEVQHVEVAHQRMAVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGTAHVFSS 205
D KA + V A + A+ L +TD + + IA R++Y+ L +SV+ +GG A V S+
Sbjct: 295 DDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLXDSVESNGGKALVLST 354
Query: 206 M-SQG-NLGQLTGVAAILRFPLPNLTKND 232
+ S G L QLTG+A IL++PLP+L ++D
Sbjct: 355 LHSLGEELDQLTGIACILKYPLPDLDEDD 383
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 4 VRKDLIPNGPRSVKMIPVDSDDLWFAYNLVAGKDPFLAITLRKVVRQTKSGG--KDAEWV 61
++KD G + ++P D +DL+ Y +V D I +K + G K + V
Sbjct: 6 LKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDEL--IFKKKFTSKLDEAGKKKSTDLV 63
Query: 62 KLKSEI 67
KLK ++
Sbjct: 64 KLKIKV 69
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 38/88 (43%), Positives = 53/88 (60%), Gaps = 3/88 (3%)
Query: 140 VMNMIKDTKAAQEVQHVEVAHQRMAVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGT 199
VMN D KA HV A + A+ L I+D LFR++ IATRKK+V LV VK+
Sbjct: 284 VMNE-DDRKAWYGPNHVLKAFELGAIGELLISDSLFRSSDIATRKKWVSLVEGVKEINCP 342
Query: 200 AHVFSSMSQG--NLGQLTGVAAILRFPL 225
++FSS+ + L L+G+AAIL +P+
Sbjct: 343 VYIFSSLHESGKQLDLLSGIAAILTYPV 370
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 37/67 (55%)
Query: 1 MRIVRKDLIPNGPRSVKMIPVDSDDLWFAYNLVAGKDPFLAITLRKVVRQTKSGGKDAEW 60
M++++K++ NG + M P + +D+W YN++ D A T+R+VV+ +G
Sbjct: 1 MKLIQKNIEKNGSGWITMCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSR 60
Query: 61 VKLKSEI 67
V +K I
Sbjct: 61 VVMKLRI 67
>pdb|2QI2|A Chain A, Crystal Structure Of The Thermoplasma Acidophilum Pelota
Protein
Length = 347
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 1 MRIVRKDLIPNGPRSVKMIPVDS-DDLWFAYNLVAGKDPFLAITLRKV 47
MRI+ +DL S I ++S DDLW+ N+++ D AIT R+V
Sbjct: 1 MRILEEDL----KNSTYRIRIESLDDLWYLRNILSEGDEVSAITFRRV 44
>pdb|3IGY|B Chain B, Crystal Structures Of Leishmania Mexicana Phosphoglycerate
Mutase At High Cobalt Concentrations
pdb|3IGZ|B Chain B, Crystal Structures Of Leishmania Mexicana Phosphoglycerate
Mutase At Low Cobalt Concentration
Length = 561
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%)
Query: 152 EVQHVEVAHQRMAVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGTAHVFSSMSQGNL 211
EV H + R+A+Q + DD ++ I T + Y L + G T H+ +S G +
Sbjct: 76 EVGHNALGAGRVALQGASLVDDAIKSGEIYTGEGYRYLHGAFSKEGSTLHLIGLLSDGGV 135
>pdb|2IFY|A Chain A, Structure Of Bacillus Anthracis Cofactor-Independent
Phosphoglucerate Mutase
Length = 508
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 152 EVQHVEVAHQRMAVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGTAHVFSSMSQGNL 211
EV H+ + R+ Q+L + R + + + SVK+ G H+F +S G +
Sbjct: 61 EVGHLNIGAGRIVYQSLTRVNVAIREGEFDKNETFQSAIKSVKEKGTALHLFGLLSDGGV 120
Query: 212 -GQLTGVAAILRF 223
+ + A+LR
Sbjct: 121 HSHMNHMFALLRL 133
>pdb|3NVL|A Chain A, Crystal Structure Of Phosphoglycerate Mutase From
Trypanosoma Brucei
pdb|3NVL|B Chain B, Crystal Structure Of Phosphoglycerate Mutase From
Trypanosoma Brucei
Length = 571
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 152 EVQHVEVAHQRMAVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGTAHVFSSMSQGNL 211
EV H + R+ +Q + DD + I T + Y L + G T H+ +S G +
Sbjct: 95 EVGHNALGAGRVVLQGASLVDDALESGEIFTSEGYRYLHGAFSQPGRTLHLIGLLSDGGV 154
>pdb|3AGJ|B Chain B, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|D Chain D, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|F Chain F, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|H Chain H, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
Length = 358
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 158 VAHQRM-AVQTLHITDDLFRNTAIATRKKYVDLVNSVKDSGGTAHVFSSMSQGN--LGQL 214
+A RM AV T+ + D L + A R+ + + V+ GG + S L
Sbjct: 281 LAVARMGAVDTVLLVDTLLHSPDDAVREAVDEALRLVESMGGRVIIIPGDSPAGERLVSF 340
Query: 215 TGVAAILRFPLPN 227
GV A+LR+P+P
Sbjct: 341 GGVIALLRYPVPQ 353
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
0.319 0.133 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,272,198
Number of Sequences: 62578
Number of extensions: 274872
Number of successful extensions: 613
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 12
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)