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= 041379
(85 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|AA Chain a, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 136
Score = 102 bits (255), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 55/112 (49%), Positives = 66/112 (58%), Gaps = 32/112 (28%)
Query: 6 IVKSFDDRTRERPNGHCL-------------------------------LVSYQHLMPTR 34
IV+ F++ TR+RP GHCL LV++ HLMPTR
Sbjct: 25 IVRVFEEGTRDRPYGHCLVAGLAKYPKKVIRKDSAKKTAKKSRVKCFLKLVNFTHLMPTR 84
Query: 35 YTLDVDLKVVVTA-DSLQSKDKKMIACKETKKRLEERFKTSKNRWFFTKLRF 85
YTLDVDLK V D+L ++DKK+ ACK K RLE+RFKT KNRWFFTKLRF
Sbjct: 85 YTLDVDLKEVAAGPDALATRDKKVAACKSAKARLEDRFKTGKNRWFFTKLRF 136
>pdb|3IZS|AA Chain a, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|Z Chain Z, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 136
Score = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 39/112 (34%), Positives = 55/112 (49%), Gaps = 32/112 (28%)
Query: 6 IVKSFDDRTRERPNGHCLL-------------------------------VSYQHLMPTR 34
IVK D+ ++ P GH L+ V+Y HL+PTR
Sbjct: 25 IVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAKKVAKRTKIKPFIKVVNYNHLLPTR 84
Query: 35 YTLDVD-LKVVVTADSLQSKDKKMIACKETKKRLEERFKTSKNRWFFTKLRF 85
YTLDV+ K VV+ ++ + ++ A K KK EER + KN+WFF+KLRF
Sbjct: 85 YTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF 136
>pdb|3ZF7|AA Chain a, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 133
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/115 (27%), Positives = 53/115 (46%), Gaps = 40/115 (34%)
Query: 6 IVKSFDDRTRERPNGHCLL-------------------------------VSYQHLMPTR 34
IV++ D R +ERP GH LL V+++H +PTR
Sbjct: 24 IVQNTDTRNKERPYGHSLLAGIKKYPRKVVRGMSKRSITRRSQVGVFLRVVNHKHFLPTR 83
Query: 35 YTLDVD----LKVVVTADSLQSKDKKMIACKETKKRLEERFKTSKNRWFFTKLRF 85
Y +D+ ++ V+ S ++K K+++ K+ + R+ NRWFF +LRF
Sbjct: 84 YNMDLSRELRGRINVSDASKKAKSKQLV-----KRLFQARYNAGNNRWFFQRLRF 133
>pdb|4A18|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|N Chain N, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 144
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 44/122 (36%)
Query: 6 IVKSFDDRTRERPNGHCLL-------------------------------VSYQHLMPTR 34
IVKS +D T++R GH L+ V+ H+MPTR
Sbjct: 25 IVKSSEDGTKDRKFGHVLVAGVERSPKKVTKRMGSKKIQKRTSVKPFIKYVNLNHIMPTR 84
Query: 35 YTLD--VDLKVVVTADSLQSKDKKMIACKET-KKRLEERFKT--------SKNRWFFTKL 83
Y++ D K +V D +++ K + ++T KK E+++T S ++FF+KL
Sbjct: 85 YSVKELCDFKELVKEDKIKNNAKSEV--RDTLKKVFVEKYRTINPEEKSASHTKFFFSKL 142
Query: 84 RF 85
RF
Sbjct: 143 RF 144
>pdb|2E55|A Chain A, Structure Of Aq2163 Protein From Aquifex Aeolicus
pdb|2E55|B Chain B, Structure Of Aq2163 Protein From Aquifex Aeolicus
pdb|2E55|C Chain C, Structure Of Aq2163 Protein From Aquifex Aeolicus
pdb|2E55|D Chain D, Structure Of Aq2163 Protein From Aquifex Aeolicus
Length = 208
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 23 LLVSYQHLMPTRYTLDVDLKVVVTADSLQSKDKKMIACKETKKRLEERFK 72
++V ++ T TL+V L+ ++ L+ K IA E KR+EE+FK
Sbjct: 123 IVVILDPMLATGGTLEVALREILKHSPLKVKSVHAIAAPEGLKRIEEKFK 172
>pdb|2DCN|A Chain A, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|B Chain B, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|C Chain C, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|D Chain D, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|E Chain E, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|F Chain F, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|G Chain G, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|H Chain H, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|I Chain I, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|J Chain J, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|K Chain K, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|2DCN|L Chain L, Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From
Sulfolobus Tokodaii Complexed With
2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
pdb|1WYE|A Chain A, Crystal Structure Of 2-keto-3-deoxygluconate Kinase (form
1) From Sulfolobus Tokodaii
pdb|1WYE|B Chain B, Crystal Structure Of 2-keto-3-deoxygluconate Kinase (form
1) From Sulfolobus Tokodaii
pdb|1WYE|C Chain C, Crystal Structure Of 2-keto-3-deoxygluconate Kinase (form
1) From Sulfolobus Tokodaii
pdb|1WYE|D Chain D, Crystal Structure Of 2-keto-3-deoxygluconate Kinase (form
1) From Sulfolobus Tokodaii
pdb|1WYE|E Chain E, Crystal Structure Of 2-keto-3-deoxygluconate Kinase (form
1) From Sulfolobus Tokodaii
pdb|1WYE|F Chain F, Crystal Structure Of 2-keto-3-deoxygluconate Kinase (form
1) From Sulfolobus Tokodaii
Length = 311
Score = 26.2 bits (56), Expect = 4.5, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 24/48 (50%)
Query: 38 DVDLKVVVTADSLQSKDKKMIACKETKKRLEERFKTSKNRWFFTKLRF 85
DVD + V +AD + S + K+ + + F+ + NR F T +R
Sbjct: 120 DVDEEYVKSADLVHSSGITLAISSTAKEAVYKAFEIASNRSFDTNIRL 167
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
0.324 0.136 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,298,064
Number of Sequences: 62578
Number of extensions: 70779
Number of successful extensions: 234
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 221
Number of HSP's gapped (non-prelim): 12
length of query: 85
length of database: 14,973,337
effective HSP length: 53
effective length of query: 32
effective length of database: 11,656,703
effective search space: 373014496
effective search space used: 373014496
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)