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= 032449
(140 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EH2|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24c
pdb|3EH2|B Chain B, Crystal Structure Of The Human Copii-Coat Protein Sec24c
pdb|3EH2|C Chain C, Crystal Structure Of The Human Copii-Coat Protein Sec24c
Length = 766
Score = 96.7 bits (239), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 45/94 (47%), Positives = 62/94 (65%)
Query: 23 VTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVD 82
VT+ ++VKD GN SPRYIRC+ IPCT ++ K + +P A +++ LA P E VVD
Sbjct: 29 VTTNFLVKDQGNASPRYIRCTSYNIPCTSDMAKQAQVPLAAVIKPLARLPPEEASPYVVD 88
Query: 83 FGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFC 116
GESG +RC C+ Y PFM+F++ G+ F C FC
Sbjct: 89 HGESGPLRCNRCKAYMCPFMQFIEGGRRFQCCFC 122
>pdb|3EFO|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
SYNTAXIN 5
pdb|3EG9|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
MEMBRIN
Length = 770
Score = 87.4 bits (215), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 38/94 (40%), Positives = 61/94 (64%)
Query: 23 VTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVD 82
VT+ +++D GN SPR+IRC+ PCT ++ K + +P A +++ A +E P+ +V+
Sbjct: 33 VTTDCMIQDQGNASPRFIRCTTYCFPCTSDMAKQAQIPLAAVIKPFATIPSNESPLYLVN 92
Query: 83 FGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFC 116
GESG VRC C+ Y PFM+F++ G+ + C FC
Sbjct: 93 HGESGPVRCNRCKAYMCPFMQFIEGGRRYQCGFC 126
>pdb|1PCX|A Chain A, Crystal Structure Of The Copii Coat Subunit, Sec24,
Complexed With A Peptide From The Snare Protein Bet1
pdb|1PD0|A Chain A, Crystal Structure Of The Copii Coat Subunit, Sec24,
Complexed With A Peptide From The Snare Protein Sed5
(Yeast Syntaxin-5)
pdb|1PD1|A Chain A, Crystal Structure Of The Copii Coat Subunit, Sec24,
Complexed With A Peptide Containing The Dxe Cargo
Sorting Signal Of Yeast Sys1 Protein
Length = 810
Score = 69.3 bits (168), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 36/87 (41%), Positives = 50/87 (57%), Gaps = 4/87 (4%)
Query: 31 DTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGL-V 89
+ N SP YIR +LN +P +LLK S +P L+++ DP P+ E GL V
Sbjct: 57 ELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPL---NEDGLIV 113
Query: 90 RCCCCRGYRNPFMEFVDNGKSFVCNFC 116
RC CR Y NPF+ F++ G+ + CNFC
Sbjct: 114 RCRRCRSYMNPFVTFIEQGRRWRCNFC 140
>pdb|1M2V|B Chain B, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 926
Score = 69.3 bits (168), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 36/87 (41%), Positives = 50/87 (57%), Gaps = 4/87 (4%)
Query: 31 DTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGL-V 89
+ N SP YIR +LN +P +LLK S +P L+++ DP P+ E GL V
Sbjct: 173 ELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPL---NEDGLIV 229
Query: 90 RCCCCRGYRNPFMEFVDNGKSFVCNFC 116
RC CR Y NPF+ F++ G+ + CNFC
Sbjct: 230 RCRRCRSYMNPFVTFIEQGRRWRCNFC 256
>pdb|3EGD|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND
BOUND To The Transport Signal Sequence Of Vesicular
Stomatitis Virus Glycoprotein
pdb|3EGX|B Chain B, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22B AND
Bound To The Transport Signal Sequence Of The Snare
Protein Bet1
Length = 748
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NC+P RC+L IP T+ LL + +P L++ P +D + + S +VRC
Sbjct: 35 NCNPELFRCTLTSIPQTQALLNKAKLPLGLLLH------PFKDLVQLPVVTSSTIVRCRS 88
Query: 94 CRGYRNPFMEFVDNGKSFVCNFC 116
CR Y NPF+ F+D + + CN C
Sbjct: 89 CRTYINPFVSFLDQ-RRWKCNLC 110
>pdb|2NUP|B Chain B, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|B Chain B, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 753
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NC+P RC+L IP T+ LL + +P L++ P +D + + S +VRC
Sbjct: 40 NCNPELFRCTLTSIPQTQALLNKAKLPLGLLLH------PFKDLVQLPVVTSSTIVRCRS 93
Query: 94 CRGYRNPFMEFVDNGKSFVCNFC 116
CR Y NPF+ F+D + + CN C
Sbjct: 94 CRTYINPFVSFLDQ-RRWKCNLC 115
>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
Length = 751
Score = 57.0 bits (136), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NCSP RC+L IP T+ LL + +P L++ P D + + +VRC
Sbjct: 37 NCSPDSFRCTLTNIPQTQALLNKAKLPLGLLLH------PFRDLTQLPVITSNTIVRCRS 90
Query: 94 CRGYRNPFMEFVDNGKSFVCNFC 116
CR Y NPF+ F+D + + CN C
Sbjct: 91 CRTYINPFVSFIDQ-RRWKCNLC 112
>pdb|2JRI|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3 In
Complex With Ubiquitin Molecule.
pdb|1YZB|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3
Length = 182
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 107 NGKSFVCNFCGVWMLMRGLSSVEGQLNLLLQG 138
N +SF+CN+ W +R L LN LL G
Sbjct: 108 NERSFICNYKEHWFTVRKLGKQWFNLNSLLTG 139
>pdb|2DOS|A Chain A, Structural Basis For The Recognition Of Lys48-Linked
Polyubiquitin Chain By The Josephin Domain Of Ataxin-3,
A Putative Deubiquitinating Enzyme
Length = 176
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 107 NGKSFVCNFCGVWMLMRGLSSVEGQLNLLLQG 138
N +SF+CN+ W +R L LN LL G
Sbjct: 113 NERSFICNYKEHWFTVRKLGKQWFNLNSLLTG 144
>pdb|2AGA|A Chain A, De-Ubiquitinating Function Of Ataxin-3: Insights From The
Solution Structure Of The Josephin Domain
Length = 190
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 107 NGKSFVCNFCGVWMLMRGLSSVEGQLNLLLQG 138
N +SF+CN+ W +R L LN LL G
Sbjct: 113 NERSFICNYKEHWFTVRKLGKQWFNLNSLLTG 144
>pdb|3O65|A Chain A, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|C Chain C, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|E Chain E, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
pdb|3O65|G Chain G, Crystal Structure Of A Josephin-Ubiquitin Complex:
Evolutionary Restraints On Ataxin-3 Deubiquitinating
Activity
Length = 191
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 107 NGKSFVCNFCGVWMLMRGLSSVEGQLNLLLQG 138
N +SF+CN+ W +R LN LL G
Sbjct: 109 NERSFICNYKQHWFTIRKFGKHWFNLNSLLAG 140
>pdb|3EFO|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
SYNTAXIN 5
Length = 765
Score = 26.9 bits (58), Expect = 4.2, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 40 IRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRN 99
+R S N P + +L + + V L P +P + + E L CR N
Sbjct: 17 VRFSWNVWPSS----RLEATRMVVPVAALFTPLKERPDLPPIQY-EPVLCSRTTCRAVLN 71
Query: 100 PFMEFVDNGKSFVCNFC 116
P + K + CNFC
Sbjct: 72 PLCQVDYRAKLWACNFC 88
>pdb|2NUP|A Chain A, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|A Chain A, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 769
Score = 26.9 bits (58), Expect = 4.2, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 40 IRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRN 99
+R S N P + +L + + V L P +P + + E L CR N
Sbjct: 21 VRFSWNVWPSS----RLEATRMVVPVAALFTPLKERPDLPPIQY-EPVLCSRTTCRAVLN 75
Query: 100 PFMEFVDNGKSFVCNFC 116
P + K + CNFC
Sbjct: 76 PLCQVDYRAKLWACNFC 92
>pdb|3EG9|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec2324 BOUND TO THE TRANSPORT SIGNAL SEQUENCE OF
MEMBRIN
pdb|3EGD|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22 AND
BOUND To The Transport Signal Sequence Of Vesicular
Stomatitis Virus Glycoprotein
pdb|3EGX|A Chain A, Crystal Structure Of The Mammalian Copii-Coat Protein
Sec23a24A COMPLEXED WITH THE SNARE PROTEIN SEC22B AND
Bound To The Transport Signal Sequence Of The Snare
Protein Bet1
Length = 764
Score = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 40 IRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRN 99
+R S N P + +L + + V L P +P + + E L CR N
Sbjct: 17 VRFSWNVWPSS----RLEATRMVVPVAALFTPLKERPDLPPIQY-EPVLCSRTTCRAVLN 71
Query: 100 PFMEFVDNGKSFVCNFC 116
P + K + CNFC
Sbjct: 72 PLCQVDYRAKLWACNFC 88
>pdb|2Z7E|A Chain A, Crystal Structure Of Aquifex Aeolicus Iscu With Bound
[2fe- 2s] Cluster
pdb|2Z7E|B Chain B, Crystal Structure Of Aquifex Aeolicus Iscu With Bound
[2fe- 2s] Cluster
pdb|2Z7E|C Chain C, Crystal Structure Of Aquifex Aeolicus Iscu With Bound
[2fe- 2s] Cluster
Length = 157
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 30/68 (44%)
Query: 5 SVILYETRQGKSVKXXXXVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALM 64
S +L E +GK ++ +T K I ++ G P+ I C+ + +K M +
Sbjct: 70 SSMLTEMVKGKPIQYALNLTYKDIFEELGGLPPQKIHCTNLGLETLHVAIKDYLMKQGRV 129
Query: 65 VQVLALPD 72
+ +PD
Sbjct: 130 EEASKIPD 137
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
0.322 0.137 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,884,848
Number of Sequences: 62578
Number of extensions: 142734
Number of successful extensions: 248
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 229
Number of HSP's gapped (non-prelim): 17
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)