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= psy2302
(292 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GUC|A Chain A, Human Ubiquitin-Activating Enzyme 5 In Complex With Amppnp
pdb|3GUC|B Chain B, Human Ubiquitin-Activating Enzyme 5 In Complex With Amppnp
pdb|3H8V|A Chain A, Human Ubiquitin-Activating Enzyme 5 In Complex With Atp
pdb|3H8V|B Chain B, Human Ubiquitin-Activating Enzyme 5 In Complex With Atp
Length = 292
Score = 384 bits (985), Expect = e-107, Method: Compositional matrix adjust.
Identities = 191/279 (68%), Positives = 215/279 (77%), Gaps = 10/279 (3%)
Query: 1 MALKRMGIVENYEHIRTLTXXXXXXXXXXXXTAEMLTRCGIGKLILFDYDKVELANMNRL 60
MALKRMGIV +YE IRT TAEMLTRCGIGKL+LFDYDKVELANMNRL
Sbjct: 20 MALKRMGIVSDYEKIRTFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYDKVELANMNRL 79
Query: 61 FFQPDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALA---VQGSLTEG-PVD 116
FFQP Q GLSKV+AA TL+NINPDV EVHN+NIT + G L EG PVD
Sbjct: 80 FFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVENFQHFMDRISNGGLEEGKPVD 139
Query: 117 LVLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSGHIQLIIPGESACFACAPPLIVA 176
LVLSCVDNFEARMTIN ACN+LGQTW ESGVSENAVSGHIQLIIPGESACFACAPPL+VA
Sbjct: 140 LVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQLIIPGESACFACAPPLVVA 199
Query: 177 SSIDEKTLKKDGVCAASLPTTMGIVAGFLVQNALKKLLKFGEVSWYLGYSALTDFFPKMK 236
++IDEKTLK++GVCAASLPTTMG+VAG LVQN LK LL FG VS+YLGY+A+ DFFP M
Sbjct: 200 ANIDEKTLKREGVCAASLPTTMGVVAGILVQNVLKFLLNFGTVSFYLGYNAMQDFFPTMS 259
Query: 237 LKPNPSCDDSYCVQRQKEFNARPVEVKLEAAKPEAQVVH 275
+KPNP CDD C ++Q+E+ K AA P+ +V+
Sbjct: 260 MKPNPQCDDRNCRKQQEEYK------KKVAALPKQEVIQ 292
>pdb|1JWB|B Chain B, Structure Of The Covalent Acyl-Adenylate Form Of The
Moeb-Moad Protein Complex
pdb|1JWA|B Chain B, Structure Of The Atp-Bound Moeb-Moad Protein Complex
pdb|1JW9|B Chain B, Structure Of The Native Moeb-Moad Protein Complex
Length = 249
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 63/217 (29%), Positives = 94/217 (43%), Gaps = 23/217 (10%)
Query: 33 AEMLTRCGIGKLILFDYDKVELANMNRLFFQPD-QCGLSKVEAARITLQNINPDVTIEVH 91
++ L G+G L L D+D V L+N+ R D G KVE+AR L INP + I
Sbjct: 47 SQYLASAGVGNLTLLDFDTVSLSNLQRQTLHSDATVGQPKVESARDALTRINPHIAITPV 106
Query: 92 NFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGVSENA 151
N + +A DLVL C DN R +N C + SG +
Sbjct: 107 NALLDDAELAALIAEH--------DLVLDCTDNVAVRNQLNAGCFA-AKVPLVSGAAIR- 156
Query: 152 VSGHIQLII--PGESACFACAPPLIVASSIDEKTLKKDGVCAASLPTTMGIVAGFLVQNA 209
+ G I + GE C+ C L +++ T + GV A +G++ A
Sbjct: 157 MEGQITVFTYQDGEP-CYRCLSRLFGENAL---TCVEAGVMA----PLIGVIGSLQAMEA 208
Query: 210 LKKLLKFGEVSW--YLGYSALTDFFPKMKLKPNPSCD 244
+K L +G+ + + Y A+T F +MKL NP C+
Sbjct: 209 IKMLAGYGKPASGKIVMYDAMTCQFREMKLMRNPGCE 245
>pdb|1ZFN|A Chain A, Structural Analysis Of Escherichia Coli Thif
pdb|1ZFN|B Chain B, Structural Analysis Of Escherichia Coli Thif
pdb|1ZFN|C Chain C, Structural Analysis Of Escherichia Coli Thif
pdb|1ZFN|D Chain D, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|A Chain A, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|B Chain B, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|C Chain C, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|D Chain D, Structural Analysis Of Escherichia Coli Thif
Length = 253
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/141 (28%), Positives = 66/141 (46%), Gaps = 16/141 (11%)
Query: 36 LTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNFN 94
L G+G L+L D D V L+N+ R + F + K + ++ L +NPD+ +
Sbjct: 49 LAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQL------ 102
Query: 95 ITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSG 154
L +++ A++ ++ D+VL C DN R IN AC L ++ +AV
Sbjct: 103 TALQQRLTGEALKDAVAR--ADVVLDCTDNMATRQEINAACVALNTPL----ITASAVGF 156
Query: 155 HIQLII---PGESACFACAPP 172
QL++ P E C+ C P
Sbjct: 157 GGQLMVLTPPWEQGCYRCLWP 177
>pdb|1ZUD|1 Chain 1, Structure Of This-Thif Protein Complex
pdb|1ZUD|3 Chain 3, Structure Of This-Thif Protein Complex
Length = 251
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 40/141 (28%), Positives = 66/141 (46%), Gaps = 16/141 (11%)
Query: 36 LTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNFN 94
L G+G L+L D D V L+N+ R + F + K + ++ L +NPD+ +
Sbjct: 47 LAGAGVGTLVLADDDDVHLSNLQRQILFTTEDIDRPKSQVSQQRLTQLNPDIQL------ 100
Query: 95 ITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSG 154
L +++ A++ ++ D+VL C DN R IN AC L ++ +AV
Sbjct: 101 TALQQRLTGEALKDAVAR--ADVVLDCTDNMATRQEINAACVALNTPL----ITASAVGF 154
Query: 155 HIQLII---PGESACFACAPP 172
QL++ P E C+ C P
Sbjct: 155 GGQLMVLTPPWEQGCYRCLWP 175
>pdb|4II2|A Chain A, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1)
In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg
pdb|4II3|A Chain A, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
pdb|4II3|C Chain C, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
Length = 1001
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 66/136 (48%), Gaps = 11/136 (8%)
Query: 42 GKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRK 100
G + + D D +E +N+NR F F+P G K E A + +NP +T ++ ++ +
Sbjct: 446 GHISVTDMDSIEKSNLNRQFLFRPRDVGKLKSECASTAVSIMNPSLTGKITSYQ----ER 501
Query: 101 VG--ALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSGHIQL 158
VG + + G + LV + +DN EARM ++ C + ESG G+ Q+
Sbjct: 502 VGPESEGIFGDEFFEKLSLVTNALDNVEARMYVDRRCVFFEKPLLESGTL--GTKGNTQV 559
Query: 159 IIPGESACFACA--PP 172
++P + + + PP
Sbjct: 560 VVPHLTESYGSSQDPP 575
>pdb|3CMM|A Chain A, Crystal Structure Of The Uba1-Ubiquitin Complex
pdb|3CMM|C Chain C, Crystal Structure Of The Uba1-Ubiquitin Complex
Length = 1015
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 68/137 (49%), Gaps = 13/137 (9%)
Query: 42 GKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRK 100
G +++ D D +E +N+NR F F+P G +K E A + +NPD+ +++ + K
Sbjct: 455 GYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKIN----AKIDK 510
Query: 101 VGALAVQ---GSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSGHIQ 157
VG + S E +D V + +DN +AR ++ C + ESG G+ Q
Sbjct: 511 VGPETEEIFNDSFWES-LDFVTNALDNVDARTYVDRRCVFYRKPLLESGTL--GTKGNTQ 567
Query: 158 LIIPGESACFACA--PP 172
+IIP + ++ + PP
Sbjct: 568 VIIPRLTESYSSSRDPP 584
>pdb|3H5N|A Chain A, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|B Chain B, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|C Chain C, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|D Chain D, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5R|A Chain A, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|B Chain B, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|C Chain C, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|D Chain D, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H9G|A Chain A, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|B Chain B, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|C Chain C, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|D Chain D, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9J|A Chain A, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|B Chain B, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|C Chain C, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|D Chain D, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9Q|A Chain A, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|B Chain B, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|C Chain C, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|D Chain D, Crystal Structure Of E. Coli Mccb + Semet Mcca
Length = 353
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 66/140 (47%), Gaps = 17/140 (12%)
Query: 35 MLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNF 93
+L GIG++IL D D++E N+ R + F D G +K E + L N ++++
Sbjct: 136 ILATSGIGEIILIDNDQIENTNLTRQVLFSEDDVGKNKTEVIKRELLKRNSEISVSEIAL 195
Query: 94 NI---TLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESG-VSE 149
NI T L KV + + P +L+ +N C + Q + +G V++
Sbjct: 196 NINDYTDLHKVPEADIWVVSADHPFNLI----------NWVNKYCVRANQPYINAGYVND 245
Query: 150 NAVSGHIQLIIPGESACFAC 169
AV G L +PG++ C+ C
Sbjct: 246 IAVFG--PLYVPGKTGCYEC 263
>pdb|3H5A|A Chain A, Crystal Structure Of E. Coli Mccb
pdb|3H5A|B Chain B, Crystal Structure Of E. Coli Mccb
pdb|3H5A|C Chain C, Crystal Structure Of E. Coli Mccb
pdb|3H5A|D Chain D, Crystal Structure Of E. Coli Mccb
Length = 358
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 66/140 (47%), Gaps = 17/140 (12%)
Query: 35 MLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNF 93
+L GIG++IL D D++E N+ R + F D G +K E + L N ++++
Sbjct: 133 ILATSGIGEIILIDNDQIENTNLTRQVLFSEDDVGKNKTEVIKRELLKRNSEISVSEIAL 192
Query: 94 NI---TLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESG-VSE 149
NI T L KV + + P +L+ +N C + Q + +G V++
Sbjct: 193 NINDYTDLHKVPEADIWVVSADHPFNLI----------NWVNKYCVRANQPYINAGYVND 242
Query: 150 NAVSGHIQLIIPGESACFAC 169
AV G L +PG++ C+ C
Sbjct: 243 IAVFG--PLYVPGKTGCYEC 260
>pdb|1Y8Q|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8Q|D Chain D, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8R|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|1Y8R|E Chain E, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
Length = 640
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTIEVH--- 91
L G + L D D ++++N+NR F FQ G SK + A+ ++ P I +
Sbjct: 36 LVLTGFSHIDLIDLDTIDVSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDS 95
Query: 92 ----NFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGV 147
++N+ R+ LV++ +DN AR +N C ESG
Sbjct: 96 IMNPDYNVEFFRQFI--------------LVMNALDNRAARNHVNRMCLAADVPLIESGT 141
Query: 148 SENAVSGHIQLIIPGESACFACAP 171
+ G + I G + C+ C P
Sbjct: 142 A--GYLGQVTTIKKGVTECYECHP 163
>pdb|3KYC|B Chain B, Human Sumo E1 Complex With A Sumo1-Amp Mimic
Length = 660
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTIEVH--- 91
L G + L D D ++++N+NR F FQ G SK + A+ ++ P I +
Sbjct: 56 LVLTGFSHIDLIDLDTIDVSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDS 115
Query: 92 ----NFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGV 147
++N+ R+ LV++ +DN AR +N C ESG
Sbjct: 116 IMNPDYNVEFFRQFI--------------LVMNALDNRAARNHVNRMCLAADVPLIESGT 161
Query: 148 SENAVSGHIQLIIPGESACFACAP 171
+ G + I G + C+ C P
Sbjct: 162 A--GYLGQVTTIKKGVTECYECHP 183
>pdb|3KYD|B Chain B, Human Sumo E1~sumo1-amp Tetrahedral Intermediate Mimic
Length = 551
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTIEVH--- 91
L G + L D D ++++N+NR F FQ G SK + A+ ++ P I +
Sbjct: 38 LVLTGFSHIDLIDLDTIDVSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDS 97
Query: 92 ----NFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLGQTWFESGV 147
++N+ R+ LV++ +DN AR +N C ESG
Sbjct: 98 IMNPDYNVEFFRQFI--------------LVMNALDNRAARNHVNRMCLAADVPLIESGT 143
Query: 148 SENAVSGHIQLIIPGESACFACAP 171
+ G + I G + C+ C P
Sbjct: 144 A--GYLGQVTTIKKGVTECYECHP 165
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/154 (24%), Positives = 66/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 59 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 118
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 119 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 161
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ Q+I+PG +AC C
Sbjct: 162 DPSSIVPLIDGGTEGFKGNAQVILPGMTACIECT 195
>pdb|2NVU|B Chain B, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 805
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 37/153 (24%), Positives = 66/153 (43%), Gaps = 36/153 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 430 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 489
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 490 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 532
Query: 149 E------------NAVSGHIQLIIPGESACFAC 169
+ G+ ++I+PG +AC C
Sbjct: 533 DPSSIVPLIDGGTEGFKGNARVILPGMTACIEC 565
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 66/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 59 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 118
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 119 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 161
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ ++I+PG +AC C
Sbjct: 162 DPSSIVPLIDGGTEGFKGNARVILPGMTACIECT 195
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 66/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 88 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 147
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 148 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 190
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ ++I+PG +AC C
Sbjct: 191 DPSSIVPLIDGGTEGFKGNARVILPGMTACIECT 224
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 66/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 56 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 115
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 116 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 158
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ ++I+PG +AC C
Sbjct: 159 DPSSIVPLIDGGTEGFKGNARVILPGMTACIECT 192
>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 = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 66/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 59 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 118
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 119 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 161
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ ++I+PG +AC C
Sbjct: 162 DPSSIVPLIDGGTEGFKGNARVILPGMTACIECT 195
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 66/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 69 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 128
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 129 IQDFNDTFYRQF--------------HIIVCGLDSIIARRWINGMLISLLN---YEDGVL 171
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ ++I+PG +AC C
Sbjct: 172 DPSSIVPLIDGGTEGFKGNARVILPGMTACIECT 205
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 65/154 (42%), Gaps = 36/154 (23%)
Query: 36 LTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARITLQNINPDVTI-----E 89
L G ++ + D D ++++N+NR F F+P G K E A L + P+ + +
Sbjct: 59 LALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNK 118
Query: 90 VHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN-MACNQLGQTWFESGVS 148
+ +FN T R+ +++ +D+ AR IN M + L +E GV
Sbjct: 119 IQDFNDTFYRQ--------------FHIIVCGLDSIIARRWINGMLISLLN---YEDGVL 161
Query: 149 E------------NAVSGHIQLIIPGESACFACA 170
+ G+ +I+PG +AC C
Sbjct: 162 DPSSIVPLIDGGTEGFKGNAAVILPGMTACIECT 195
>pdb|2NVU|A Chain A, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 536
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 40 GIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARITLQNINPDVT 87
GIG + D ++V + N F Q G ++ EAA LQ +N DV+
Sbjct: 55 GIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVS 103
>pdb|1YOV|A Chain A, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
pdb|1YOV|C Chain C, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
Length = 537
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 40 GIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARITLQNINPDVT 87
GIG + D ++V + N F Q G ++ EAA LQ +N DV+
Sbjct: 56 GIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVS 104
>pdb|3GZN|A Chain A, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
pdb|3GZN|C Chain C, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
Length = 534
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 40 GIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARITLQNINPDVT 87
GIG + D ++V + N F Q G ++ EAA LQ +N DV+
Sbjct: 53 GIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVS 101
>pdb|1TT5|A Chain A, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
pdb|1TT5|C Chain C, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
pdb|3DBH|A Chain A, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|C Chain C, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|E Chain E, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|G Chain G, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBL|A Chain A, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|C Chain C, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|E Chain E, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|G Chain G, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBR|A Chain A, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|C Chain C, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|E Chain E, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|G Chain G, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
Length = 531
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 40 GIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARITLQNINPDVT 87
GIG + D ++V + N F Q G ++ EAA LQ +N DV+
Sbjct: 55 GIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVS 103
>pdb|1R4M|A Chain A, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|C Chain C, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|E Chain E, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|G Chain G, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4N|A Chain A, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|C Chain C, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|E Chain E, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|G Chain G, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
Length = 529
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 40 GIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARITLQNINPDVT 87
GIG + D ++V + N F Q G ++ EAA LQ +N DV+
Sbjct: 53 GIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVS 101
>pdb|3MLY|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 3074 In Complex
With A Ur29 V3 Peptide
pdb|3MLY|I Chain I, Crystal Structure Of Anti-Hiv-1 V3 Fab 3074 In Complex
With A Ur29 V3 Peptide
pdb|3MLZ|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 3074 In Complex
With A Vi191 V3 Peptide
Length = 230
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 13/101 (12%)
Query: 189 VCAASLPTTMGIVAGFLVQNALKKLLKFGEVSWYLGYSALTDFFPKMKLKPNPSCDDSYC 248
C S + G ++ Q K L G Y+ YS T + P +K + + S D S
Sbjct: 21 TCTVSGGSISGFHWSWIRQPPGKGLEYIG----YIYYSGSTSYNPSLKSRVSMSVDTS-- 74
Query: 249 VQRQKEFNARPVEVKLEAAKPEAQVVHADNDWGEYHYQVQG 289
+ +F+ +E+ A A V + D+GEYHY +G
Sbjct: 75 ---RNQFS---LELSSVTAADTA-VYYCARDFGEYHYDGRG 108
>pdb|3MLX|H Chain H, Crystal Structure Of Anti-Hiv-1 V3 Fab 3074 In Complex
With An Mn V3 Peptide
pdb|3MLX|I Chain I, Crystal Structure Of Anti-Hiv-1 V3 Fab 3074 In Complex
With An Mn V3 Peptide
Length = 228
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 13/101 (12%)
Query: 189 VCAASLPTTMGIVAGFLVQNALKKLLKFGEVSWYLGYSALTDFFPKMKLKPNPSCDDSYC 248
C S + G ++ Q K L G Y+ YS T + P +K + + S D S
Sbjct: 21 TCTVSGGSISGFHWSWIRQPPGKGLEYIG----YIYYSGSTSYNPSLKSRVSMSVDTS-- 74
Query: 249 VQRQKEFNARPVEVKLEAAKPEAQVVHADNDWGEYHYQVQG 289
+ +F+ +E+ A A V + D+GEYHY +G
Sbjct: 75 ---RNQFS---LELSSVTAADTA-VYYCARDFGEYHYDGRG 108
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,927,154
Number of Sequences: 62578
Number of extensions: 293819
Number of successful extensions: 653
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 629
Number of HSP's gapped (non-prelim): 26
length of query: 292
length of database: 14,973,337
effective HSP length: 98
effective length of query: 194
effective length of database: 8,840,693
effective search space: 1715094442
effective search space used: 1715094442
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: 51 (24.3 bits)