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= 031054
(166 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase
pdb|1VIO|B Chain B, Crystal Structure Of Pseudouridylate Synthase
Length = 243
Score = 68.9 bits (167), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 42/141 (29%), Positives = 72/141 (51%), Gaps = 8/141 (5%)
Query: 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV 81
+L + GRLDV TTGL+++T+DG ++ ++ P +K Y+ T+ V + + A +EG +
Sbjct: 96 KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGIL 155
Query: 82 IEGTH--CTPDVVELLXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKLYSLKRLRIGG 139
+ G P +E+L + EGR H+V+ + G K+ L R +IG
Sbjct: 156 LRGEKEPTKPAKLEIL------DDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGD 209
Query: 140 FRLPSDLGIGMHVELKQSDLK 160
L L G + L QS+++
Sbjct: 210 VVLDESLEEGEYRPLTQSEIE 230
>pdb|1KSK|A Chain A, Structure Of Rsua
pdb|1KSL|A Chain A, Structure Of Rsua
pdb|1KSV|A Chain A, Structure Of Rsua
Length = 234
Score = 63.5 bits (153), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 67/140 (47%), Gaps = 8/140 (5%)
Query: 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV 81
+L GRLD+ TTGL++ T+DG ++ ++ P +K Y+ T++ V ++G
Sbjct: 97 KLHAAGRLDIDTTGLVLXTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQ 156
Query: 82 I--EGTHCTPDVVELLXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKLYSLKRLRIGG 139
+ E P V+E++ + EGR H+V+ G + L R RIGG
Sbjct: 157 LHNEKDLTKPAVLEVI------TPTQVRLTISEGRYHQVKRXFAAVGNHVVELHRERIGG 210
Query: 140 FRLPSDLGIGMHVELKQSDL 159
L +DL G + L + ++
Sbjct: 211 ITLDADLAPGEYRPLTEEEI 230
>pdb|3DH3|A Chain A, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
Rna Substrate
pdb|3DH3|B Chain B, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
Rna Substrate
pdb|3DH3|C Chain C, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
Rna Substrate
pdb|3DH3|D Chain D, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
Rna Substrate
Length = 290
Score = 49.7 bits (117), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 54/116 (46%), Gaps = 6/116 (5%)
Query: 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV 81
R+F +GRLD + GLI +TN GD + + +KEY+ T+D + + + +S G
Sbjct: 99 RVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVP 158
Query: 82 IEGTHCTPDVVELLXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKLYSLKRLRI 137
I GT + +G N ++R + ++ G ++ L+R RI
Sbjct: 159 ILGTVTK------KCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRI 208
>pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
Length = 189
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 53/133 (39%), Gaps = 13/133 (9%)
Query: 23 LFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVI 82
++ GRLD + GL+++TN+G ++ P + K Y ++G + L A+ G +
Sbjct: 44 VYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTL 103
Query: 83 EGTHCTPDVVEL-------------LXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKL 129
P EL + ++EGRN +VR + + G
Sbjct: 104 NDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPT 163
Query: 130 YSLKRLRIGGFRL 142
L R +G + L
Sbjct: 164 LRLIRYAMGDYSL 176
>pdb|2OLW|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
pdb|2OLW|B Chain B, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
Length = 217
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 53/133 (39%), Gaps = 13/133 (9%)
Query: 23 LFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVI 82
++ GRLD + GL+++TN+G ++ P + K Y ++G + L A+ G +
Sbjct: 72 VYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTL 131
Query: 83 EGTHCTPDVVEL-------------LXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKL 129
P EL + ++EGRN +VR + + G
Sbjct: 132 NDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPT 191
Query: 130 YSLKRLRIGGFRL 142
L R +G + L
Sbjct: 192 LRLIRYAMGDYSL 204
>pdb|2GML|A Chain A, Crystal Structure Of Catalytic Domain Of E.Coli Rluf
pdb|2GML|B Chain B, Crystal Structure Of Catalytic Domain Of E.Coli Rluf
Length = 237
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 52/116 (44%), Gaps = 6/116 (5%)
Query: 22 RLFTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV 81
R+F +GRLD + GLI +TN GD + + +KEY+ T+D + + + S G
Sbjct: 46 RVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGXSAGVP 105
Query: 82 IEGTHCTPDVVELLXXXXXXXXXXXXXVVHEGRNHEVRELVKNAGLKLYSLKRLRI 137
I GT + +G N ++R ++ G ++ L+R RI
Sbjct: 106 ILGTVTK------KCKVKKEAPFVFRITLVQGLNRQIRRXCEHFGYEVKKLERTRI 155
>pdb|1D2F|A Chain A, X-Ray Structure Of Maly From Escherichia Coli: A
Pyridoxal-5'- Phosphate-Dependent Enzyme Acting As A
Modulator In Mal Gene Expression
pdb|1D2F|B Chain B, X-Ray Structure Of Maly From Escherichia Coli: A
Pyridoxal-5'- Phosphate-Dependent Enzyme Acting As A
Modulator In Mal Gene Expression
Length = 390
Score = 30.8 bits (68), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 30/72 (41%)
Query: 24 FTVGRLDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTVIE 83
FT+ +D AT II + V S E++A I + +H AI TV+
Sbjct: 33 FTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVY 92
Query: 84 GTHCTPDVVELL 95
G V EL+
Sbjct: 93 GPSVIYMVSELI 104
>pdb|1FFU|A Chain A, Carbon Monoxide Dehydrogenase From Hydrogenophaga
Pseudoflava Which Lacks The Mo-Pyranopterin Moiety Of
The Molybdenum Cofactor
pdb|1FFU|D Chain D, Carbon Monoxide Dehydrogenase From Hydrogenophaga
Pseudoflava Which Lacks The Mo-Pyranopterin Moiety Of
The Molybdenum Cofactor
pdb|1FFV|A Chain A, Carbon Monoxide Dehydrogenase From Hydrogenophaga
Pseudoflava
pdb|1FFV|D Chain D, Carbon Monoxide Dehydrogenase From Hydrogenophaga
Pseudoflava
Length = 163
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 29 LDVATTGLIIVTNDGDFAQAVSHPSSKLQKEYIATIDGAVNKRHLIAISEGTV----IEG 84
+ + G V DG ++ +H + + + T++G NK L A+ EG ++
Sbjct: 42 CETSHCGACTVDIDGRSVKSCTHLAVQCDGSEVLTVEGLANKGVLHAVQEGFYKEHGLQC 101
Query: 85 THCTPDVV 92
CTP ++
Sbjct: 102 GFCTPGML 109
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 0.139 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,701,574
Number of Sequences: 62578
Number of extensions: 169489
Number of successful extensions: 436
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 425
Number of HSP's gapped (non-prelim): 8
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
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: 47 (22.7 bits)