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= psy5109
(145 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JK4|A Chain A, Structure Of The Human Voltage-Dependent Anion Channel
Length = 294
Score = 133 bits (334), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 68/144 (47%), Positives = 94/144 (65%), Gaps = 3/144 (2%)
Query: 3 PPLYGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYK 62
PP Y DLGK ARD+F+KGY +IK+DLKTK+++G+EF S G+A E+ K+ G+LE+KY+
Sbjct: 7 PPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYR 66
Query: 63 AKNYAGLTFSEKWNTDNVLTTEVS--SNIIDGARLAANTSFAPQTGDKTVKLSGEYKNSL 120
Y GLTF+EKWNTDN L TE++ + G +L ++SF+P TG K K+ YK
Sbjct: 67 WTEY-GLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREH 125
Query: 121 AAVNLESEFKSLNPVISAAGVLGY 144
+ + +F P I A VLGY
Sbjct: 126 INLGCDMDFDIAGPSIRGALVLGY 149
>pdb|2K4T|A Chain A, Solution Structure Of Human Vdac-1 In Ldao Micelles
Length = 291
Score = 133 bits (334), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 68/144 (47%), Positives = 94/144 (65%), Gaps = 3/144 (2%)
Query: 3 PPLYGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYK 62
PP Y DLGK ARD+F+KGY +IK+DLKTK+++G+EF S G+A E+ K+ G+LE+KY+
Sbjct: 4 PPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYR 63
Query: 63 AKNYAGLTFSEKWNTDNVLTTEVS--SNIIDGARLAANTSFAPQTGDKTVKLSGEYKNSL 120
Y GLTF+EKWNTDN L TE++ + G +L ++SF+P TG K K+ YK
Sbjct: 64 WTEY-GLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREH 122
Query: 121 AAVNLESEFKSLNPVISAAGVLGY 144
+ + +F P I A VLGY
Sbjct: 123 INLGCDMDFDIAGPSIRGALVLGY 146
>pdb|3EMN|X Chain X, The Crystal Structure Of Mouse Vdac1 At 2.3 A Resolution
Length = 295
Score = 132 bits (332), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 68/144 (47%), Positives = 94/144 (65%), Gaps = 3/144 (2%)
Query: 3 PPLYGDLGKHARDLFSKGYNIDVIKIDLKTKTDSGVEFNSGGTAQLESGKIFGTLESKYK 62
PP Y DLGK ARD+F+KGY +IK+DLKTK+++G+EF S G+A E+ K+ G+LE+KY+
Sbjct: 16 PPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVNGSLETKYR 75
Query: 63 AKNYAGLTFSEKWNTDNVLTTEVS--SNIIDGARLAANTSFAPQTGDKTVKLSGEYKNSL 120
Y GLTF+EKWNTDN L TE++ + G +L ++SF+P TG K K+ YK
Sbjct: 76 WTEY-GLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREH 134
Query: 121 AAVNLESEFKSLNPVISAAGVLGY 144
+ + +F P I A VLGY
Sbjct: 135 INLGCDVDFDIAGPSIRGALVLGY 158
>pdb|3GZN|B Chain B, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
pdb|3GZN|D Chain D, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
Length = 463
Score = 28.1 bits (61), Expect = 1.6, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 389 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 448
Query: 100 SFAPQT 105
PQT
Sbjct: 449 VTTPQT 454
>pdb|1YOV|B Chain B, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
pdb|1YOV|D Chain D, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
Length = 444
Score = 28.1 bits (61), Expect = 1.6, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 370 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 429
Query: 100 SFAPQT 105
PQT
Sbjct: 430 VTTPQT 435
>pdb|2WFP|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase (Apo
Form) From Salmonella Typhimurium
Length = 394
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 68 GLTFSEKWNTDNVLTTEVSSNIIDGARLAANTSFAPQTG 106
G+ N+DNVL ++ ID L AN F P+
Sbjct: 263 GVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPA 301
>pdb|3H1M|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase (Holo;
Zinc Bound)
pdb|3H1W|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase Bound
With Zinc And Yttrium
pdb|3H1Y|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase From
Salmonella Typhimurium Bound To Substrate (F6p)and Metal
Atom (Zn)
Length = 393
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 68 GLTFSEKWNTDNVLTTEVSSNIIDGARLAANTSFAPQTG 106
G+ N+DNVL ++ ID L AN F P+
Sbjct: 262 GVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPA 300
>pdb|1L2Q|A Chain A, Crystal Structure Of The Methanosarcina Barkeri
Monomethylamine Methyltransferase (Mtmb)
pdb|1NTH|A Chain A, Crystal Structure Of The Methanosarcina Barkeri
Monomethylamine Methyltransferase (Mtmb)
pdb|1TV2|A Chain A, Crystal Structure Of The Hydroxylamine Mtmb Complex
pdb|1TV3|A Chain A, Crystal Structure Of The N-Methyl-Hydroxylamine Mtmb
Complex
pdb|1TV4|A Chain A, Crystal Structure Of The Sulfite Mtmb Complex
Length = 458
Score = 26.9 bits (58), Expect = 4.5, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 42 SGGTAQLESGKIFGTLESKYKAKNYA----GLTFSEKWNTDNVLTTEVSSNIIDGAR 94
+ G E I L S Y+ KNYA G TF E ++ V TE + DGAR
Sbjct: 393 TAGVEISEVNVILDKLVSLYE-KNYASAPAGKTFQECYDVKTVTPTEEYMQVYDGAR 448
>pdb|1TT5|B Chain B, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
pdb|1TT5|D Chain D, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
Length = 434
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 360 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 419
Query: 100 SFAPQT 105
PQT
Sbjct: 420 VTTPQT 425
>pdb|3DBL|B Chain B, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|D Chain D, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|F Chain F, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|H Chain H, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
Length = 434
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 360 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 419
Query: 100 SFAPQT 105
PQT
Sbjct: 420 VTTPQT 425
>pdb|3DBH|B Chain B, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|D Chain D, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|F Chain F, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|H Chain H, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
Length = 434
Score = 26.6 bits (57), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 360 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 419
Query: 100 SFAPQT 105
PQT
Sbjct: 420 VTTPQT 425
>pdb|1R4M|B Chain B, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|D Chain D, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|F Chain F, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|H Chain H, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4N|B Chain B, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|D Chain D, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|F Chain F, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|H Chain H, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
Length = 431
Score = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 357 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 416
Query: 100 SFAPQT 105
PQT
Sbjct: 417 VTTPQT 422
>pdb|3DBR|B Chain B, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|D Chain D, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|F Chain F, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|H Chain H, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
Length = 434
Score = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 360 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 419
Query: 100 SFAPQT 105
PQT
Sbjct: 420 VTTPQT 425
>pdb|2LQ7|A Chain A, E2 Binding Surface On Uba3 Beta-Grasp Domain Undergoes A
Conformational Transition
Length = 97
Score = 26.6 bits (57), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%)
Query: 40 FNSGGTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANT 99
+ + Q++S I TLE K + +T E+ N+ T ++DG LA
Sbjct: 23 LTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVAD 82
Query: 100 SFAPQT 105
PQT
Sbjct: 83 VTTPQT 88
>pdb|2NVU|B Chain B, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 805
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 27/62 (43%)
Query: 44 GTAQLESGKIFGTLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNIIDGARLAANTSFAP 103
+ Q++S I TLE K + +T E+ N+ T ++DG LA P
Sbjct: 735 ASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTP 794
Query: 104 QT 105
QT
Sbjct: 795 QT 796
>pdb|1B30|A Chain A, Xylanase From Penicillium Simplicissimum, Complex With
1,2- (4-Deoxy-Beta-L-Threo-Hex-4-Enopyranosyluronic
Acid)-Beta- 1,4-Xylotriose)
pdb|1B31|A Chain A, Xylanase From Penicillium Simplicissimum, Native With
Peg200 As Cryoprotectant
pdb|1B3V|A Chain A, Xylanase From Penicillium Simplicissimum, Complex With
Xylose
pdb|1B3W|A Chain A, Xylanase From Penicillium Simplicissimum, Complex With
Xylobiose
pdb|1B3X|A Chain A, Xylanase From Penicillium Simplicissimum, Complex With
Xylotriose
pdb|1B3Y|A Chain A, Xylanase From Penicillium Simplicissimum, Complex With
Xylotetraose
pdb|1B3Z|A Chain A, Xylanase From Penicillium Simplicissimum, Complex With
Xylopentaose
pdb|1BG4|A Chain A, Xylanase From Penicillium Simplicissimum
Length = 302
Score = 26.2 bits (56), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 56 TLESKYKAKNYAGLTFSEKWNTDNVLTTEVSSNII--DGARLAANTS 100
T+ ++YK K YA +E +N D L V N+I D R+A T+
Sbjct: 115 TVMTRYKGKIYAWDVLNEIFNEDGSLRNSVFYNVIGEDYVRIAFETA 161
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
0.310 0.129 0.357
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,414,825
Number of Sequences: 62578
Number of extensions: 175972
Number of successful extensions: 339
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 313
Number of HSP's gapped (non-prelim): 37
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 47 (22.7 bits)