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= 047135
(134 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|N Chain N, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 134
Score = 233 bits (595), Expect = 2e-62, Method: Compositional matrix adjust.
Identities = 115/133 (86%), Positives = 126/133 (94%)
Query: 2 PFKRYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAPDMVRGQMNFKRLSLTDIKID 61
PFKR+VEIGRVALVNYGK+YGRLVVIVDV+DQNRALVDAPDMVR Q+NFKRLSLTDIKID
Sbjct: 2 PFKRFVEIGRVALVNYGKDYGRLVVIVDVVDQNRALVDAPDMVRCQINFKRLSLTDIKID 61
Query: 62 IPRVPKKKTLIDAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLV 121
I RVPKK TLI AME+ADVKNKWE+SSWG+KLIVQK+RASLNDFDRFK+MLAKIK+GG +
Sbjct: 62 IKRVPKKTTLIKAMEEADVKNKWENSSWGKKLIVQKRRASLNDFDRFKVMLAKIKRGGAI 121
Query: 122 RQELAKLKKENAA 134
RQELAKLKK AA
Sbjct: 122 RQELAKLKKTAAA 134
>pdb|4A18|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2.
pdb|4ADX|7 Chain 7, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 126
Score = 92.0 bits (227), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 43/115 (37%), Positives = 76/115 (66%), Gaps = 1/115 (0%)
Query: 1 MPFKRYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAPDMVRGQMNFKRLSLTDIKI 60
M F ++V++GRV +NYG + G+L VIV++++QNR L+D +VR + +R+ LT +I
Sbjct: 1 MVFNKFVQVGRVVYINYGADKGKLAVIVNIINQNRILIDGEHIVRQVIPIRRVHLTKFQI 60
Query: 61 DIPRVPKKKTLI-DAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAK 114
D + ++ L+ + K D+ K+ +S+ +K ++ KRA+L DFDRF++M+ K
Sbjct: 61 DNVELNQRTVLLKKKIAKFDLTKKYAETSFAKKQAIKTKRANLGDFDRFRVMVLK 115
>pdb|3IZS|N Chain N, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|N Chain N, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|N Chain N, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|M Chain M, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|M Chain M, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|M Chain M, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 138
Score = 90.9 bits (224), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 45/125 (36%), Positives = 77/125 (61%), Gaps = 2/125 (1%)
Query: 5 RYVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP--DMVRGQMNFKRLSLTDIKIDI 62
R VE+GRV L+ G+ G+L IV+++DQ + L+D P + R +N ++ LT + +
Sbjct: 13 RLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINLGQVVLTPLTFAL 72
Query: 63 PRVPKKKTLIDAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVR 122
PR + T+ A V KW +SSW +K+ +++RA+L DF+RF++M+ + +K V+
Sbjct: 73 PRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQVMVLRKQKRYTVK 132
Query: 123 QELAK 127
+ LAK
Sbjct: 133 KALAK 137
>pdb|3ZF7|P Chain P, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 189
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 58/121 (47%), Gaps = 3/121 (2%)
Query: 6 YVEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAP---DMVRGQMNFKRLSLTDIKIDI 62
Y+ GR+ + G R+ VIVD++D NR LV+ P M R N K + + I
Sbjct: 6 YIRAGRLVRILRGPRQNRVGVIVDIVDANRVLVENPCEQKMWRHVQNLKNVEPLKFCVSI 65
Query: 63 PRVPKKKTLIDAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVR 122
R K L +A+E V K+ ++ R +K A DF+R++L +AK + R
Sbjct: 66 SRNCSTKALKEALESKKVLEKYAATKVRRPHRAKKAFAESTDFERYQLRVAKRSRAYWAR 125
Query: 123 Q 123
+
Sbjct: 126 K 126
>pdb|3J21|5 Chain 5, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|K Chain K, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 83
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 3/77 (3%)
Query: 7 VEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAPDMV---RGQMNFKRLSLTDIKIDIP 63
+++GR+A+V G+ G+ VV+VD++D+N LV + R +MN K + KIDIP
Sbjct: 4 IDVGRIAVVIAGRRAGQKVVVVDIIDKNFVLVTGAGLNKVKRRRMNIKHIEPLPQKIDIP 63
Query: 64 RVPKKKTLIDAMEKADV 80
R + + A+EKA +
Sbjct: 64 RGASDEEVRAALEKAGI 80
>pdb|2JOY|A Chain A, Nmr Structure Of 50s Ribosomal Protein L14e From
Sulfolobus Solfataricus: Northeast Structural Genomics
Consortium Target Ssr105
Length = 96
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 7 VEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAPDMVRG----QMNFKRLSLTDIKIDI 62
+E+GR+ + G+E G VIVD++D N LV P + G ++N L TD KIDI
Sbjct: 4 IEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKIDI 63
>pdb|2KDS|A Chain A, Structure Of Ribosomal Protein L14e From Sulfolobus
Solfataricus
Length = 95
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 7 VEIGRVALVNYGKEYGRLVVIVDVLDQNRALVDAPDMVRG----QMNFKRLSLTDIKIDI 62
+E+GR+ + G+E G VIVD++D N LV P + G ++N L TD KIDI
Sbjct: 3 IEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKIDI 62
>pdb|2HJR|A Chain A, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|B Chain B, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|C Chain C, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|D Chain D, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|E Chain E, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|F Chain F, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|G Chain G, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|H Chain H, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|I Chain I, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|J Chain J, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|K Chain K, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
pdb|2HJR|L Chain L, Crystal Structure Of Cryptosporidium Parvum Malate
Dehydrogenase
Length = 328
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 31 LDQNRALVDAPDMVRGQMNFKRLSLTDIKIDIPRVPKKKTL 71
L+ AL+ +P + G+ N++ L +D+ I VP+K +
Sbjct: 58 LNHCMALIGSPAKIFGENNYEYLQNSDVVIITAGVPRKPNM 98
>pdb|3LJK|A Chain A, Glucose-6-Phosphate Isomerase From Francisella Tularensis.
pdb|3M5P|A Chain A, Glucose-6-Phosphate Isomerase From Francisella Tularensis
Complexed With Fructose-6-Phosphate
Length = 543
Score = 26.9 bits (58), Expect = 3.4, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%)
Query: 69 KTLIDAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVRQELAKL 128
K+L+++ EK+ +K+K + G K+ + RA L+ R I G +RQE+ K
Sbjct: 57 KSLLESAEKSSLKDKIKQXFNGAKINSTEHRAVLHTALRDLSSTPLIVDGQDIRQEVTKE 116
Query: 129 KK 130
K+
Sbjct: 117 KQ 118
>pdb|3P8C|B Chain B, Structure And Control Of The Actin Regulatory Wave Complex
Length = 1128
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 19/39 (48%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 20 EYGRLVVI-VDVLDQNRALVDAPDMVRGQMNFKRLSLTD 57
E +LVV VDVL Q R D PD + FKRLS D
Sbjct: 865 ELKKLVVENVDVLTQMRTSFDKPDQMAAL--FKRLSSVD 901
>pdb|3Q88|A Chain A, Glucose-6-Phosphate Isomerase From Francisella Tularensis
Complexed With Ribose 1,5-Bisphosphate.
pdb|3Q7I|A Chain A, Glucose-6-Phosphate Isomerase From Francisella Tularensis
Complexed With 6-Phosphogluconic Acid
Length = 543
Score = 26.6 bits (57), Expect = 4.5, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%)
Query: 69 KTLIDAMEKADVKNKWESSSWGRKLIVQKKRASLNDFDRFKLMLAKIKKGGLVRQELAKL 128
K+L+++ EK+ +K+K + G K+ + RA L+ R I G +RQE+ K
Sbjct: 57 KSLLESAEKSSLKDKIKQMFNGAKINSTEHRAVLHTALRDLSSTPLIVDGQDIRQEVTKE 116
Query: 129 KK 130
K+
Sbjct: 117 KQ 118
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
0.320 0.137 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,655,214
Number of Sequences: 62578
Number of extensions: 127932
Number of successful extensions: 272
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 258
Number of HSP's gapped (non-prelim): 11
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
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: 46 (22.3 bits)