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= 034084
(104 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 306
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGS-VLEVTNCFPFPIQEEDEEIEADGA 82
V I + +LK++KH + P V G +LG V + V + F P +EA
Sbjct: 26 TVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDD 85
Query: 83 NYQLEMMRCLREVNVDNNTVGW 104
+Q +MM L++ D VGW
Sbjct: 86 VFQAKMMDMLKQTGRDQMVVGW 107
>pdb|2O96|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-177)
pdb|2O96|B Chain B, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-177)
Length = 178
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 25 VQIEGLVMLKIIKHCKEFSPA----LVTGQLLGLDVGSVLEVTNCFPFPIQEEDEE--IE 78
V + LV+L ++ H V G LLG VL+V+N F P E+D++ +
Sbjct: 10 VVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVW 69
Query: 79 ADGANYQLEMMRCLREVNVDNNTVGW 104
+Y M ++VN VGW
Sbjct: 70 FLDHDYLENMYGMFKKVNARERIVGW 95
>pdb|2O95|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-186)
pdb|2O95|B Chain B, Crystal Structure Of The Metal-Free Dimeric Human Mov34
Mpn Domain (Residues 1-186)
Length = 187
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 25 VQIEGLVMLKIIKHCKEFSPA----LVTGQLLGLDVGSVLEVTNCFPFPIQEEDEE--IE 78
V + LV+L ++ H V G LLG VL+V+N F P E+D++ +
Sbjct: 10 VVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVW 69
Query: 79 ADGANYQLEMMRCLREVNVDNNTVGW 104
+Y M ++VN VGW
Sbjct: 70 FLDHDYLENMYGMFKKVNARERIVGW 95
>pdb|4B4T|U Chain U, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 338
Score = 31.2 bits (69), Expect = 0.17, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 5/85 (5%)
Query: 25 VQIEGLVMLKIIKHCKEFSPA---LVTGQLLGLDVGSVLEVTNCFPFPIQEEDE--EIEA 79
V I LV+L + H + G +LG S + VTN F P +E+++ ++
Sbjct: 8 VTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWF 67
Query: 80 DGANYQLEMMRCLREVNVDNNTVGW 104
NY M +++N +GW
Sbjct: 68 LDHNYIENMNEMCKKINAKEKLIGW 92
>pdb|3KRA|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium
pdb|3KRA|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium
pdb|3KRC|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Ipp
pdb|3KRC|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Ipp
pdb|3KRF|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (I)
pdb|3KRF|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (I)
pdb|3KRO|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (Ii)
pdb|3KRO|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (Ii)
pdb|3KRP|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium And Gpp
pdb|3KRP|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium And Gpp
pdb|3OAB|A Chain A, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAB|D Chain D, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAC|A Chain A, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAC|D Chain D, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
Length = 295
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 6/45 (13%)
Query: 8 SFLQVAAAEEVAPPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLL 52
+F VAAA + APP R+V++ G + + I S LV GQ++
Sbjct: 120 AFEHVAAATKGAPPERIVRVLGELAVSI------GSEGLVAGQVV 158
>pdb|4E0Q|A Chain A, Crystal Structure Of Mpn Domain From Cop9 Signalosome
pdb|4E0Q|B Chain B, Crystal Structure Of Mpn Domain From Cop9 Signalosome
Length = 141
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 6/86 (6%)
Query: 24 VVQIEGLVMLKIIKHCKEFS-----PALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIE 78
+ + LV+ I +H F P V G L+G G +E+ N F +E
Sbjct: 7 TISLHPLVIXNISEHWTRFRAQHGEPRQVYGALIGKQKGRNIEIXNSFELKTDVIGDETV 66
Query: 79 ADGANYQLEMMRCLREVNVDNNTVGW 104
+ +Y + + ++V D + +GW
Sbjct: 67 IN-KDYYNKKEQQYKQVFSDLDFIGW 91
>pdb|2Q71|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Enzyme
In Complex With Coproporphyrinogen-Iii
pdb|2Q6Z|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Apo-
Enzyme
Length = 356
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 74 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 133
>pdb|1JPI|A Chain A, Phe232leu Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 105 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 164
>pdb|1R3W|A Chain A, Uroporphyrinogen Decarboxylase Y164f Mutant In Complex
With Coproporphyrinogen-Iii
Length = 367
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|3GW3|A Chain A, Human Urod Mutant K297n
Length = 367
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|3GW0|A Chain A, Urod Mutant G318r
Length = 367
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|1URO|A Chain A, Uroporphyrinogen Decarboxylase
pdb|1R3Q|A Chain A, Uroporphyrinogen Decarboxylase In Complex With
Coproporphyrinogen-I
pdb|1R3Y|A Chain A, Uroporphyrinogen Decarboxylase In Complex With
Coproporphyrinogen-Iii
pdb|3GVQ|A Chain A, Urod Single-Chain Dimer
pdb|3GVR|A Chain A, Single-Chain Urod Y164g (Gy) Mutation
Length = 367
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|1JPK|A Chain A, Gly156asp Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 105 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 164
>pdb|1JPH|A Chain A, Ile260thr Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 105 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 164
>pdb|1R3V|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86e In
Complex With Coproporphyrinogen-I
Length = 367
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSEILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|3GVV|A Chain A, Single-Chain Urod Y164g (Gy) Mutation
pdb|3GVW|A Chain A, Single-Chain Urod F217y (Yf) Mutation
Length = 367
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|1R3S|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86g In
Complex With Coproporphyrinogen-I
pdb|1R3T|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86g In
Complex With Coproporphyrinogen-Iii
Length = 367
Score = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSGILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|1R3R|A Chain A, Uroporphyrinogen Decarboxylase With Mutation D86n
Length = 367
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 42 FSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE-------DEEIEADGANYQLEMMRCLRE 94
FS LV Q LG++V V FP P++EE D E+ A Y + + R+
Sbjct: 84 FSNILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQ 143
>pdb|4F7O|A Chain A, Crystal Structure Of Csn5
pdb|4F7O|B Chain B, Crystal Structure Of Csn5
Length = 257
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 21/50 (42%)
Query: 22 LRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQ 71
+ +I L +LK + H + V G LG G + + F P++
Sbjct: 52 FKYCKISALALLKXVXHARSGGNLEVXGLXLGKVDGETXIIXDSFALPVE 101
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 0.135 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,740,884
Number of Sequences: 62578
Number of extensions: 95194
Number of successful extensions: 262
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 20
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
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: 45 (21.9 bits)