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= psy3572
(245 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J2I|B Chain B, Structure Of Late Pre-60s Ribosomal Subunits With Nuclear
Export Factor Arx1 Bound At The Peptide Exit Tunnel
Length = 245
Score = 392 bits (1007), Expect = e-110, Method: Compositional matrix adjust.
Identities = 178/243 (73%), Positives = 215/243 (88%)
Query: 1 MAVRVQFENNNEVGVFSKLTNSYCLVAIGGSENFYSVFEAELAETIPVIHASLAGCRIIG 60
MA R QFEN+NE+GVFSKLTN+YCLVA+GGSENFYS FEAEL + IP++H ++AG RIIG
Sbjct: 1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG 60
Query: 61 RMSVGNRHGLIVPNATTDTELQHIRNSLPDSVKLQRVEERLSALGNVIACNDYVALVHPD 120
RM+ GNR GL+VP TTD ELQH+RNSLPDSVK+QRVEERLSALGNVI CNDYVALVHPD
Sbjct: 61 RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD 120
Query: 121 LDRETEEILADTLNVEVFRQTVSSNVLVGSYCALTNQGGLVHPHTSPQDQDELSSLLQIP 180
+DRETEE+++D L VEVFRQT+S N+LVGSYC+L+NQGGLVHP TS QDQ+ELSSLLQ+P
Sbjct: 121 IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVP 180
Query: 181 LVAGTVNRGSEVIGAGMVVNDWAAFCGFDTTSTEISVIESVFKLNEAQPSAITTSMRASL 240
LVAGTVNRGS V+GAGMVVND+ A G DTT+ E+SVIES+F+L +AQP +I+ ++R +L
Sbjct: 181 LVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRLQDAQPESISGNLRDTL 240
Query: 241 IDS 243
I++
Sbjct: 241 IET 243
>pdb|1G62|A Chain A, Crystal Structure Of S.Cerevisiae Eif6
pdb|2X7N|B Chain B, Mechanism Of Eif6s Anti-Association Activity
Length = 224
Score = 375 bits (963), Expect = e-104, Method: Compositional matrix adjust.
Identities = 171/224 (76%), Positives = 200/224 (89%)
Query: 1 MAVRVQFENNNEVGVFSKLTNSYCLVAIGGSENFYSVFEAELAETIPVIHASLAGCRIIG 60
MA R QFEN+NE+GVFSKLTN+YCLVA+GGSENFYS FEAEL + IP++H ++AG RIIG
Sbjct: 1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG 60
Query: 61 RMSVGNRHGLIVPNATTDTELQHIRNSLPDSVKLQRVEERLSALGNVIACNDYVALVHPD 120
RM+ GNR GL+VP TTD ELQH+RNSLPDSVK+QRVEERLSALGNVI CNDYVALVHPD
Sbjct: 61 RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD 120
Query: 121 LDRETEEILADTLNVEVFRQTVSSNVLVGSYCALTNQGGLVHPHTSPQDQDELSSLLQIP 180
+DRETEE+++D L VEVFRQT+S N+LVGSYC+L+NQGGLVHP TS QDQ+ELSSLLQ+P
Sbjct: 121 IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQVP 180
Query: 181 LVAGTVNRGSEVIGAGMVVNDWAAFCGFDTTSTEISVIESVFKL 224
LVAGTVNRGS V+GAGMVVND+ A G DTT+ E+SVIES+F+L
Sbjct: 181 LVAGTVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRL 224
>pdb|4A18|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|J Chain J, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 248
Score = 350 bits (897), Expect = 6e-97, Method: Compositional matrix adjust.
Identities = 157/241 (65%), Positives = 203/241 (84%)
Query: 1 MAVRVQFENNNEVGVFSKLTNSYCLVAIGGSENFYSVFEAELAETIPVIHASLAGCRIIG 60
MA R QFEN+N++GVF KLT++YCLV++G SENFYSVFE+EL IPVIH S+ G RI+G
Sbjct: 4 MARRCQFENSNDIGVFCKLTSAYCLVSVGASENFYSVFESELVPHIPVIHTSIGGTRIVG 63
Query: 61 RMSVGNRHGLIVPNATTDTELQHIRNSLPDSVKLQRVEERLSALGNVIACNDYVALVHPD 120
R++ GN++GL+VPN D EL++IRNSLPD+V+++R+EE+LSALGN + NDYVAL+HPD
Sbjct: 64 RVTCGNKNGLLVPNTCNDNELRNIRNSLPDNVRVRRIEEKLSALGNCVVANDYVALIHPD 123
Query: 121 LDRETEEILADTLNVEVFRQTVSSNVLVGSYCALTNQGGLVHPHTSPQDQDELSSLLQIP 180
LDRE+EEI+ADTL VEVFR T+++NVLVG+YC + N+GGLVHP S ++ DEL++LLQIP
Sbjct: 124 LDRESEEIIADTLGVEVFRTTIANNVLVGTYCVINNRGGLVHPLASVEELDELANLLQIP 183
Query: 181 LVAGTVNRGSEVIGAGMVVNDWAAFCGFDTTSTEISVIESVFKLNEAQPSAITTSMRASL 240
L AGT+NRGS+VIGAG+VVNDWAAFCG DTTSTEISV+E++FKLNE + + MR
Sbjct: 184 LCAGTINRGSDVIGAGLVVNDWAAFCGLDTTSTEISVVENIFKLNEMKDENMDNEMRKDF 243
Query: 241 I 241
+
Sbjct: 244 V 244
>pdb|1G61|A Chain A, Crystal Structure Of M.Jannaschii Eif6
pdb|1G61|B Chain B, Crystal Structure Of M.Jannaschii Eif6
Length = 228
Score = 110 bits (275), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 71/228 (31%), Positives = 125/228 (54%), Gaps = 7/228 (3%)
Query: 1 MAVRVQFENNNEVGVFSKLTNSYCLVAIGGSENFYSVFEAELAETIPVIHASLAGCRIIG 60
M +R F +GV + T L+ I ++ + +E+ ET + ++ G ++G
Sbjct: 3 MIIRKYFSGIPTIGVLALTTEEITLLPIFLDKDDVNEV-SEVLET-KCLQTNIGGSSLVG 60
Query: 61 RMSVGNRHGLIVPNATTDTELQHIRNSLPDS---VKLQRVEERLSALGNVIACNDYVALV 117
+SV N++GL++P D EL I+N L ++ + ++ ++ + +ALGN+I ND AL+
Sbjct: 61 SLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKGALI 120
Query: 118 HPDLDRETEEILADTLNVEVFRQTVSSNVLVGSYCALTNQGGLVHPHTSPQDQDELSSLL 177
P+L ++ ++ + D+LNVEV T++ VGS +TN+G L HP + + L SL
Sbjct: 121 SPEL-KDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVEDDELEFLKSLF 179
Query: 178 QIPLVA-GTVNRGSEVIGAGMVVNDWAAFCGFDTTSTEISVIESVFKL 224
++ + GT N+G+ +GA ++ N A G DTT E+ +IE L
Sbjct: 180 KVEYIGKGTANKGTTSVGACIIANSKGAVVGGDTTGPELLIIEDALGL 227
>pdb|4ADX|I Chain I, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 222
Score = 106 bits (265), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 69/227 (30%), Positives = 113/227 (49%), Gaps = 5/227 (2%)
Query: 1 MAVRVQFENNNEVGVFSKLTNSYCLVAIGGSENFYSVFEAELAETIPVIHASLAGCRIIG 60
M R+ N +GV+ +T+S L+ E F V L + V+ S++G + G
Sbjct: 1 MIRRINLSGNPNLGVYISVTDSVALIPQNTPEKFEGVLREAL--EVEVLKVSISGSSLNG 58
Query: 61 RMSVGNRHGLIVPNATTDTELQHIRNSLPDSVKLQRVEERLSALGNVIACNDYVALVHPD 120
++VGN +G +V N D E+ + + V+ R+ ER +A+GN++ ND A+ P
Sbjct: 59 ALAVGNSNGFVVSNQAMDREIDALAAA---GVEAVRIPERFTAVGNLVLANDNGAVASPL 115
Query: 121 LDRETEEILADTLNVEVFRQTVSSNVLVGSYCALTNQGGLVHPHTSPQDQDELSSLLQIP 180
L + +++ D L V+V T++ +VGS A TN+G L++P S ++ + L +
Sbjct: 116 LSDDALQVIGDVLEVDVKVSTLAGLNIVGSMGAATNRGALLNPQASSEEIGIIEDTLGVE 175
Query: 181 LVAGTVNRGSEVIGAGMVVNDWAAFCGFDTTSTEISVIESVFKLNEA 227
GTVN G +IGA V N G +TT E++ IE E
Sbjct: 176 ADVGTVNHGVTLIGACSVANSNGVLVGEETTGPELARIEEALGFLEG 222
>pdb|2QPQ|A Chain A, Structure Of Bug27 From Bordetella Pertussis
pdb|2QPQ|B Chain B, Structure Of Bug27 From Bordetella Pertussis
pdb|2QPQ|C Chain C, Structure Of Bug27 From Bordetella Pertussis
Length = 301
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 68 HGLIVPNATTDTELQHIRNSLPDSVKLQRVEERLSALGNVIACND---YVALVHPDLDR 123
HGL+VP AT Q + + + ++ V+++L+ LG A + + +V D+DR
Sbjct: 230 HGLLVPGATPMAVRQKLYDGIAKVMQRDDVQKKLADLGYSTASDGPEVFQKMVETDIDR 288
>pdb|2IO5|A Chain A, Crystal Structure Of The Cia- Histone H3-H4 Complex
Length = 175
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 11/76 (14%)
Query: 53 LAGCRIIGRMSVGNRHGLIVPNATTDTELQHIRNSLPDSVKLQRVEERLSALGNVIACND 112
L C G+ + R G V N T+TEL+ PD KLQR N++A N
Sbjct: 99 LITCTYRGQEFI--RVGYYVNNEYTETELRENPPVKPDFSKLQR---------NILASNP 147
Query: 113 YVALVHPDLDRETEEI 128
V H + + TE++
Sbjct: 148 RVTRFHINWEDNTEKL 163
>pdb|3PU6|A Chain A, The Crystal Structure Of An Uncharacterized Protein From
Wolinella Succinogenes
Length = 157
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 12/67 (17%)
Query: 175 SLLQIPLVAGTVNRGSE--VIGAGMVVND----WAAFCGFDTTSTEISVIESVFKLNEAQ 228
SL ++ L G RG + I G +V + W+ F G+DT +E KL E
Sbjct: 2 SLKKVLLCVGNELRGDDGVAIALGRLVEEQXPEWSVFFGYDTPESEFG------KLRELA 55
Query: 229 PSAITTS 235
P I +
Sbjct: 56 PDVIVVA 62
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
0.317 0.132 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,585,130
Number of Sequences: 62578
Number of extensions: 254148
Number of successful extensions: 643
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 625
Number of HSP's gapped (non-prelim): 15
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)