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= 012602
(460 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RZU|A Chain A, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|B Chain B, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|C Chain C, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|D Chain D, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|E Chain E, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|F Chain F, The Crystal Structure Of The Catalytic Domain Of Amsh
pdb|3RZU|G Chain G, The Crystal Structure Of The Catalytic Domain Of Amsh
Length = 187
Score = 121 bits (303), Expect = 8e-28, Method: Compositional matrix adjust.
Identities = 57/110 (51%), Positives = 78/110 (70%), Gaps = 3/110 (2%)
Query: 345 FMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKR 404
F++LA +NT + +ETCGIL G L +F IT ++IPKQ + SD C NEEE+F +QD++
Sbjct: 30 FLQLASANTARGVETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQ 89
Query: 405 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPD--ARSCWKKRGEIG 452
L LGWIHTHPTQ+ F+SS+D+HTH SYQ+ ++P+ A C K E G
Sbjct: 90 GLITLGWIHTHPTQTAFLSSVDLHTHCSYQM-MLPESVAIVCSPKFQETG 138
>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp
Length = 178
Score = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 57/117 (48%), Positives = 80/117 (68%), Gaps = 3/117 (2%)
Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV 400
+ F++LA+SNT + +ETCGIL G L + +F IT +I+PKQ + D C N EE+F V
Sbjct: 17 LCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNV 76
Query: 401 QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARS--CWKKRGEIGRKR 455
QD+ L LGWIHTHPTQ+ F+SS+D+HTH SYQ+ ++P+A + C K + G R
Sbjct: 77 QDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQL-MLPEAIAIVCSPKHKDTGIFR 132
>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic
Domain Of Amsh
Length = 211
Score = 119 bits (298), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 56/114 (49%), Positives = 78/114 (68%), Gaps = 3/114 (2%)
Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV 400
+ F++LA +NT + + TCGIL G L +F IT ++IPKQ + SD C NEEE+F +
Sbjct: 50 LCPQFLQLASANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLI 109
Query: 401 QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPD--ARSCWKKRGEIG 452
QD++ L LGWIHTHPTQ+ F+SS+D+HTH SYQ+ ++P+ A C K E G
Sbjct: 110 QDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQM-MLPESVAIVCSPKFQETG 162
>pdb|2ZNV|A Chain A, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
With Lys63-Linked Ubiquitin Dimer
pdb|2ZNV|D Chain D, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
With Lys63-Linked Ubiquitin Dimer
Length = 178
Score = 118 bits (296), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 56/117 (47%), Positives = 79/117 (67%), Gaps = 3/117 (2%)
Query: 341 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV 400
+ F++LA+SNT + + TCGIL G L + +F IT +I+PKQ + D C N EE+F V
Sbjct: 17 LCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNV 76
Query: 401 QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQVNVVPDARS--CWKKRGEIGRKR 455
QD+ L LGWIHTHPTQ+ F+SS+D+HTH SYQ+ ++P+A + C K + G R
Sbjct: 77 QDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQL-MLPEAIAIVCSPKHKDTGIFR 132
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 306
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 10/86 (11%)
Query: 357 LETCGILAGS-LKNRKFYITALIIPKQESTSDSCQATNEEEIFEV-------QDKRSLFP 408
+E G++ G + + + + Q T S +A +++F+ Q R
Sbjct: 47 MEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAV--DDVFQAKMMDMLKQTGRDQMV 104
Query: 409 LGWIHTHPTQSCFMSSIDVHTHYSYQ 434
+GW H+HP C++SS+DV+T S++
Sbjct: 105 VGWYHSHPGFGCWLSSVDVNTQKSFE 130
>pdb|2XZE|A Chain A, Structural Basis For Amsh-Escrt-Iii Chmp3 Interaction
pdb|2XZE|B Chain B, Structural Basis For Amsh-Escrt-Iii Chmp3 Interaction
Length = 146
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 17 LDVDNRIALRYYYRIADNILKQADIFREEKNIIDLYVMLLRFSSLVTETIPCHRDY 72
++V+ I R Y+R I++ A I+ EE NI +++ ++ +L E +P HRDY
Sbjct: 25 VEVNEDIPPRRYFRSGVEIIRMASIYSEEGNIEHAFILYNKYITLFIEKLPKHRDY 80
>pdb|4I43|B Chain B, Crystal Structure Of Prp8:aar2 Complex
Length = 1564
Score = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 375 TALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTH 430
T +++P Q S Q +N +I ++ D L LGWIHT + FM++ +V TH
Sbjct: 1374 TVVLVP-QLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATH 1428
>pdb|3SBG|A Chain A, Crystal Structure Of A Prp8 C-Terminal Fragment
Length = 565
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 375 TALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTH 430
T +++P Q S Q +N +I ++ D L LGWIHT + FM++ +V TH
Sbjct: 391 TVVLVP-QLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATH 445
>pdb|3ZEF|B Chain B, Crystal Structure Of Prp8:aar2 Complex: Second Crystal Form
At 3.1 Angstrom Resolution
pdb|3ZEF|E Chain E, Crystal Structure Of Prp8:aar2 Complex: Second Crystal Form
At 3.1 Angstrom Resolution
Length = 1531
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 375 TALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTH 430
T +++P Q S Q +N +I ++ D L LGWIHT + FM++ +V TH
Sbjct: 1341 TVVLVP-QLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATH 1395
>pdb|2OG4|A Chain A, Structure Of An Expanded Jab1-mpn-like Domain Of Splicing
Factor Prp8p From Yeast
Length = 254
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 375 TALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTH 430
T +++P Q S Q +N +I ++ D L LGWIHT + FM++ +V TH
Sbjct: 80 TVVLVP-QLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATH 134
>pdb|4F7O|A Chain A, Crystal Structure Of Csn5
pdb|4F7O|B Chain B, Crystal Structure Of Csn5
Length = 257
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 351 SNTDKNLETCGILAGSLKNRKFYIT---ALIIPKQESTSDSCQATNEEEIFEVQDKRSLF 407
+ + NLE G+ G + I AL + E+ ++ A E +++ + +
Sbjct: 69 ARSGGNLEVXGLXLGKVDGETXIIXDSFALPVEGTETRVNAQAAAYEYXAAYIENAKQVG 128
Query: 408 PL----GWIHTHPTQSCFMSSIDVHT 429
L GW H+HP C++S IDV T
Sbjct: 129 RLENAIGWYHSHPGYGCWLSGIDVST 154
>pdb|2I1W|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes
pdb|2I1W|B Chain B, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes
pdb|2I1W|C Chain C, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes
pdb|2I1W|D Chain D, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes
pdb|2I29|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes
pdb|2I2A|A Chain A, Crystal Structure Of Lmnadk1 From Listeria Monocytogenes
pdb|2I2B|A Chain A, Crystal Structure Of Lmnadk1 From Listeria Monocytogenes
pdb|2I2C|A Chain A, Crystal Structure Of Lmnadk1
pdb|2I2D|A Chain A, Crystal Structure Of Lmnadk1
pdb|4DY6|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With 2'-Phosphate
Bis(Adenosine)-5'-Diphosphate
pdb|3V7U|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With Mta
pdb|3V7W|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With 5'-Azido-5'-Deoxyadenosine
pdb|3V7Y|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With
5'-N-Propargylamino-5'-Deoxyadenosine
pdb|3V80|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With
5'-O-Propargylamino-5'-Deoxyadenosine
pdb|3V8M|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complexe With
5'-Azido-8-Bromo-5'-Deoxyadenosine
pdb|3V8N|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With
8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted With A
Citrate Molecule In N Site
pdb|3V8P|A Chain A, Crystal Structure Of Nad Kinase 1 From Listeria
Monocytogenes In Complex With A New Di-Adenosine
Inhibitor Formed In Situ
Length = 272
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 196 GPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQS 255
G G Y W+P ++DKLVK + + P L+ + I K +++ + +S+V+S
Sbjct: 70 GHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIG-KKEATYLALNESTVKS 128
Query: 256 ISTP 259
P
Sbjct: 129 SGGP 132
>pdb|2Q5F|A Chain A, Crystal Structure Of Lmnadk1 From Listeria Monocytogenes
pdb|3V8Q|A Chain A, Crystal Structure Of Nad Kinase 1 H223e Mutant From
Listeria Monocytogenes In Complex With
5'-Amino-5'-Deoxyadenosine
pdb|3V8R|A Chain A, Crystal Structure Of Nad Kinase 1 H223e Mutant From
Listeria Monocytogenes In Complex With
5'-Amino-8-Bromo-5'-Deoxyadenosine
Length = 272
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 196 GPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQS 255
G G Y W+P ++DKLVK + + P L+ + I K +++ + +S+V+S
Sbjct: 70 GHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIG-KKEATYLALNESTVKS 128
Query: 256 ISTP 259
P
Sbjct: 129 SGGP 132
>pdb|2I2F|A Chain A, Crystal Structure Of Lmnadk1
Length = 272
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 196 GPNGLYGHWQPPKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQS 255
G G Y W+P ++DKLVK + + P L+ + I K +++ + +S+V+S
Sbjct: 70 GHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIG-KKEATYLALNESTVKS 128
Query: 256 ISTP 259
P
Sbjct: 129 SGGP 132
>pdb|2P8R|A Chain A, Crystal Structure Of The C-Terminal Domain Of C. Elegans
Pre-Mrna Splicing Factor Prp8 Carrying R2303k Mutant
Length = 273
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 404 RSLFPLGWIHTHPTQSCFMSSIDVHTH 430
R PLGW+HT P + +S DV TH
Sbjct: 107 RDFEPLGWMHTQPNELPQLSPQDVTTH 133
>pdb|2P87|A Chain A, Crystal Structure Of The C-Terminal Domain Of C. Elegans
Pre-Mrna Splicing Factor Prp8
Length = 273
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 404 RSLFPLGWIHTHPTQSCFMSSIDVHTH 430
R PLGW+HT P + +S DV TH
Sbjct: 107 RDFEPLGWMHTQPNELPQLSPQDVTTH 133
>pdb|2DLC|X Chain X, Crystal Structure Of The Ternary Complex Of Yeast
Tyrosyl-Trna Synthetase
Length = 394
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 49/107 (45%), Gaps = 13/107 (12%)
Query: 222 TPIEIPSLR-QPSESSIKIKTDSSNVEPEK------SSVQSISTPNDEIEIHRTEEPCSM 274
P+E+ + R + E +IK S NV EK SS Q TP+ ++I R S
Sbjct: 89 APLEVVNYRAKYYELTIKAILRSINVPIEKLKFVVGSSYQL--TPDYTMDIFR----LSN 142
Query: 275 ISFETSEAPNSADVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGN 321
I + ADV++Q + P + + L+ A+ Q + +CQ G
Sbjct: 143 IVSQNDAKRAGADVVKQVANPLLSGLIYPLMQALDEQFLDVDCQFGG 189
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
0.314 0.129 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,366,755
Number of Sequences: 62578
Number of extensions: 477471
Number of successful extensions: 756
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 743
Number of HSP's gapped (non-prelim): 19
length of query: 460
length of database: 14,973,337
effective HSP length: 102
effective length of query: 358
effective length of database: 8,590,381
effective search space: 3075356398
effective search space used: 3075356398
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)