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= 030052
(183 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 = 263 bits (673), Expect = 3e-71, Method: Compositional matrix adjust.
Identities = 126/178 (70%), Positives = 144/178 (80%)
Query: 1 MATRLMFENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIG 60
MATR FENS E+GVFSKLTN +CLVA+GGSE+FYS FEAEL D IP+V T+I G RIIG
Sbjct: 1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG 60
Query: 61 RLCVGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTD 120
R+ GN+ GLL+P TTDQELQHLRNSLPD V +QR+EERLSALGN I CND+VAL H D
Sbjct: 61 RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD 120
Query: 121 LDRETEEIIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVRHRISSSRHLLKHFLLQ 178
+DRETEE+I+DVLGVEVFRQTI+GNILVGSYCS SN+GGLV + S LLQ
Sbjct: 121 IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSVQDQEELSSLLQ 178
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 58/112 (51%), Gaps = 5/112 (4%)
Query: 39 EAELADV--IPVVKTSIGGNRIIGRLC-VGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQ 95
E ++DV + V + +I GN ++G C + N+ GL+ P T+ Q+ + L + L +V
Sbjct: 126 EELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSV-QDQEELSSLLQVPLVAG 184
Query: 96 RIEERLSALGNCIACNDHVALAHTDLDRETEEIIADVLGVEVFR-QTIAGNI 146
+ S +G + ND++A+ D +I + ++ + ++I+GN+
Sbjct: 185 TVNRGSSVVGAGMVVNDYLAVTGLDTTAPELSVIESIFRLQDAQPESISGNL 236
>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 = 263 bits (671), Expect = 5e-71, Method: Compositional matrix adjust.
Identities = 123/166 (74%), Positives = 141/166 (84%)
Query: 1 MATRLMFENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIG 60
MATR FENS E+GVFSKLTN +CLVA+GGSE+FYS FEAEL D IP+V T+I G RIIG
Sbjct: 1 MATRTQFENSNEIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIG 60
Query: 61 RLCVGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTD 120
R+ GN+ GLL+P TTDQELQHLRNSLPD V +QR+EERLSALGN I CND+VAL H D
Sbjct: 61 RMTAGNRRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPD 120
Query: 121 LDRETEEIIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVRHRIS 166
+DRETEE+I+DVLGVEVFRQTI+GNILVGSYCS SN+GGLV + S
Sbjct: 121 IDRETEELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTS 166
Score = 34.3 bits (77), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 6/93 (6%)
Query: 39 EAELADV--IPVVKTSIGGNRIIGRLC-VGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQ 95
E ++DV + V + +I GN ++G C + N+ GL+ P T+ Q+ + L + L +V
Sbjct: 126 EELISDVLGVEVFRQTISGNILVGSYCSLSNQGGLVHPQTSV-QDQEELSSLLQVPLVAG 184
Query: 96 RIEERLSALGNCIACNDHVALAHTDLDRETEEI 128
+ S +G + ND++A+ T LD E+
Sbjct: 185 TVNRGSSVVGAGMVVNDYLAV--TGLDTTAPEL 215
>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 = 231 bits (589), Expect = 2e-61, Method: Compositional matrix adjust.
Identities = 112/171 (65%), Positives = 138/171 (80%), Gaps = 1/171 (0%)
Query: 1 MATRLMFENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIG 60
MA R FENS ++GVF KLT+A+CLV++G SE+FYS FE+EL IPV+ TSIGG RI+G
Sbjct: 4 MARRCQFENSNDIGVFCKLTSAYCLVSVGASENFYSVFESELVPHIPVIHTSIGGTRIVG 63
Query: 61 RLCVGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTD 120
R+ GNKNGLL+P+T D EL+++RNSLPD V V+RIEE+LSALGNC+ ND+VAL H D
Sbjct: 64 RVTCGNKNGLLVPNTCNDNELRNIRNSLPDNVRVRRIEEKLSALGNCVVANDYVALIHPD 123
Query: 121 LDRETEEIIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVRHRISSSRHL 171
LDRE+EEIIAD LGVEVFR TIA N+LVG+YC +NRGGLV H ++S L
Sbjct: 124 LDRESEEIIADTLGVEVFRTTIANNVLVGTYCVINNRGGLV-HPLASVEEL 173
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 32/75 (42%)
Query: 46 IPVVKTSIGGNRIIGRLCVGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALG 105
+ V +T+I N ++G CV N G L+ + +EL L N L + I +G
Sbjct: 138 VEVFRTTIANNVLVGTYCVINNRGGLVHPLASVEELDELANLLQIPLCAGTINRGSDVIG 197
Query: 106 NCIACNDHVALAHTD 120
+ ND A D
Sbjct: 198 AGLVVNDWAAFCGLD 212
>pdb|4ADX|I Chain I, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 222
Score = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 55/167 (32%), Positives = 89/167 (53%), Gaps = 5/167 (2%)
Query: 1 MATRLMFENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIG 60
M R+ + +GV+ +T++ L+ E F L + V+K SI G+ + G
Sbjct: 1 MIRRINLSGNPNLGVYISVTDSVALIPQNTPEKFEGVLREALE--VEVLKVSISGSSLNG 58
Query: 61 RLCVGNKNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTD 120
L VGN NG ++ + D+E+ L + + V RI ER +A+GN + ND+ A+A
Sbjct: 59 ALAVGNSNGFVVSNQAMDREIDALAAAGVEAV---RIPERFTAVGNLVLANDNGAVASPL 115
Query: 121 LDRETEEIIADVLGVEVFRQTIAGNILVGSYCSFSNRGGLVRHRISS 167
L + ++I DVL V+V T+AG +VGS + +NRG L+ + SS
Sbjct: 116 LSDDALQVIGDVLEVDVKVSTLAGLNIVGSMGAATNRGALLNPQASS 162
>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 = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 56/164 (34%), Positives = 86/164 (52%), Gaps = 12/164 (7%)
Query: 1 MATRLMFENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEA-ELADVIPV--VKTSIGGNR 57
M R F +GV + T L+ I F + E+++V+ ++T+IGG+
Sbjct: 3 MIIRKYFSGIPTIGVLALTTEEITLLPI-----FLDKDDVNEVSEVLETKCLQTNIGGSS 57
Query: 58 IIGRLCVGNKNGLLLPHTTTDQELQHLRNSLPD---QVVVQRIEERLSALGNCIACNDHV 114
++G L V NK GLLLP D+EL ++N L + + V+ I+ + +ALGN I ND
Sbjct: 58 LVGSLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKG 117
Query: 115 ALAHTDLDRETEEIIADVLGVEVFRQTIAGNILVGSYCSFSNRG 158
AL +L ++ ++ I D L VEV TIA VGS +N+G
Sbjct: 118 ALISPEL-KDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKG 160
>pdb|3C2W|A Chain A, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|B Chain B, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|C Chain C, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|D Chain D, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|E Chain E, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|F Chain F, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|G Chain G, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3C2W|H Chain H, Crystal Structure Of The Photosensory Core Domain Of P.
Aeruginosa Bacteriophytochrome Pabphp In The Pfr State
pdb|3NHQ|A Chain A, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|B Chain B, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|C Chain C, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|D Chain D, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|E Chain E, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|F Chain F, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|G Chain G, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NHQ|H Chain H, The Dark Pfr Structure Of The Photosensory Core Module Of
P. Aeruginosa Bacteriophytochrome
pdb|3NOP|C Chain C, Light-Induced Intermediate Structure L1 Of Pseudomonas
Aeruginosa Bacteriophytochrome
pdb|3NOT|C Chain C, Light-Induced Intermediate Structure L2 Of P. Aeruginosa
Bacteriophytochrome
pdb|3NOU|C Chain C, Light-Induced Intermediate Structure L3 Of P. Aeruginosa
Bacteriophytochrome
Length = 505
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 57/138 (41%), Gaps = 17/138 (12%)
Query: 7 FENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIGRLCVGN 66
+ NS E + L F ++ E FY FE AD + + ++ RII ++ + N
Sbjct: 82 WSNSVETRIGEHL---FDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHN 138
Query: 67 KNGLLLPHTTTDQELQHL-----------RNSLPDQVVVQ-RIEERLSALGNCIACNDHV 114
LL + T EL+ + R+ +VV + R E+ S LG +D
Sbjct: 139 DTASLLSNVT--DELRRMTGYDRVMAYRFRHDDSGEVVAESRREDLESYLGQRYPASDIP 196
Query: 115 ALAHTDLDRETEEIIADV 132
A A + +IADV
Sbjct: 197 AQARRLYIQNPIRLIADV 214
>pdb|3G6O|A Chain A, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Pabphp Photosensory Core Domain Mutant Q188l
pdb|3G6O|B Chain B, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Pabphp Photosensory Core Domain Mutant Q188l
Length = 505
Score = 30.0 bits (66), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 7 FENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIGRLCVGN 66
+ NS E + L F ++ E FY FE AD + + ++ RII ++ + N
Sbjct: 82 WSNSVETRIGEHL---FDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHN 138
Query: 67 KNGLLLPHTTTD 78
LL + T +
Sbjct: 139 DTASLLSNVTDE 150
>pdb|3IBR|A Chain A, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Photosensory Core Module Mutant Q188l In The Mixed PrPFR
STATE
pdb|3IBR|B Chain B, Crystal Structure Of P. Aeruginosa Bacteriophytochrome
Photosensory Core Module Mutant Q188l In The Mixed PrPFR
STATE
Length = 505
Score = 29.6 bits (65), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 7 FENSCEVGVFSKLTNAFCLVAIGGSESFYSTFEAELADVIPVVKTSIGGNRIIGRLCVGN 66
+ NS E + L F ++ E FY FE AD + + ++ RII ++ + N
Sbjct: 82 WSNSVETRIGEHL---FDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHN 138
Query: 67 KNGLLLPHTTTD 78
LL + T +
Sbjct: 139 DTASLLSNVTDE 150
>pdb|4DVY|P Chain P, Crystal Structure Of The Helicobacter Pylori Caga
Oncoprotein
Length = 876
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 67 KNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTDLDRETE 126
KNG + Q L NS+ D ++ Q++ +++ L ++ VA A D R E
Sbjct: 755 KNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVS----VAKAMGDFSR-VE 809
Query: 127 EIIADV 132
+++AD+
Sbjct: 810 QVLADL 815
>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
Pylori Caga Protein
Length = 916
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 67 KNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTDLDRETE 126
KNG + Q L NS+ D ++ Q++ +++ L ++ VA A D R E
Sbjct: 755 KNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVS----VAKAMGDFSR-VE 809
Query: 127 EIIADV 132
+++AD+
Sbjct: 810 QVLADL 815
>pdb|4DVZ|A Chain A, Crystal Structure Of The Helicobacter Pylori Caga
Oncoprotein
Length = 569
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 67 KNGLLLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAHTDLDRETE 126
KNG + Q L NS+ D ++ Q++ +++ L ++ VA A D R E
Sbjct: 495 KNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVS----VAKAMGDFSR-VE 549
Query: 127 EIIADV 132
+++AD+
Sbjct: 550 QVLADL 555
>pdb|2X3E|A Chain A, Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein)
Synthase Iii, Fabh From Pseudomonas Aeruginosa Pao1
pdb|2X3E|B Chain B, Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein)
Synthase Iii, Fabh From Pseudomonas Aeruginosa Pao1
Length = 331
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 71 LLPHTTTDQELQHLRNSLPDQVVVQRIEERLSALGNCIACNDHVALAH 118
L+PH + L + + L + V+R+ ++ +GN +A + +ALAH
Sbjct: 247 LVPHQANTRILAAVADQL--DLPVERVVSNIAEVGNTVAASIPLALAH 292
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 0.138 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,089,814
Number of Sequences: 62578
Number of extensions: 193322
Number of successful extensions: 395
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 372
Number of HSP's gapped (non-prelim): 20
length of query: 183
length of database: 14,973,337
effective HSP length: 93
effective length of query: 90
effective length of database: 9,153,583
effective search space: 823822470
effective search space used: 823822470
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)