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= 032184
(145 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 = 108 bits (269), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 58/136 (42%), Positives = 82/136 (60%), Gaps = 14/136 (10%)
Query: 23 VTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVD 82
VT+ ++VKD GN SPRYIRC+ IPCT ++ K + +P A +++ LA P E VVD
Sbjct: 29 VTTNFLVKDQGNASPRYIRCTSYNIPCTSDMAKQAQVPLAAVIKPLARLPPEEASPYVVD 88
Query: 83 FGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCG------------LD--GRCLDADER 128
GESG +RC C+ Y PFM+F++ G+ F C FC LD G+ +DA +R
Sbjct: 89 HGESGPLRCNRCKAYMCPFMQFIEGGRRFQCCFCSCINDVPPQYFQHLDHTGKRVDAYDR 148
Query: 129 PELCRGTVEFAASREF 144
PEL G+ EF A+ ++
Sbjct: 149 PELSLGSYEFLATVDY 164
>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 = 99.4 bits (246), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 51/136 (37%), Positives = 80/136 (58%), Gaps = 14/136 (10%)
Query: 23 VTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVD 82
VT+ +++D GN SPR+IRC+ PCT ++ K + +P A +++ A +E P+ +V+
Sbjct: 33 VTTDCMIQDQGNASPRFIRCTTYCFPCTSDMAKQAQIPLAAVIKPFATIPSNESPLYLVN 92
Query: 83 FGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCG------------LD--GRCLDADER 128
GESG VRC C+ Y PFM+F++ G+ + C FC LD GR LD E+
Sbjct: 93 HGESGPVRCNRCKAYMCPFMQFIEGGRRYQCGFCNCVNDVPPFYFQHLDHIGRRLDHYEK 152
Query: 129 PELCRGTVEFAASREF 144
PEL G+ E+ A+ ++
Sbjct: 153 PELSLGSYEYVATLDY 168
>pdb|1M2V|B Chain B, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 926
Score = 70.5 bits (171), Expect = 3e-13, Method: Composition-based stats.
Identities = 37/86 (43%), Positives = 50/86 (58%), Gaps = 4/86 (4%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGL-VRCC 92
N SP YIR +LN +P +LLK S +P L+++ DP P+ E GL VRC
Sbjct: 176 NASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPL---NEDGLIVRCR 232
Query: 93 CCRGYRNPFMEFVDNGKSFVCNFCGL 118
CR Y NPF+ F++ G+ + CNFC L
Sbjct: 233 RCRSYMNPFVTFIEQGRRWRCNFCRL 258
>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 = 37/89 (41%), Positives = 51/89 (57%), Gaps = 4/89 (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 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118
RC CR Y NPF+ F++ G+ + CNFC L
Sbjct: 114 RCRRCRSYMNPFVTFIEQGRRWRCNFCRL 142
>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 = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 42/128 (32%), Positives = 60/128 (46%), Gaps = 26/128 (20%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NC+P RC+L IP T+ LL + +P L++ P +D + + S +VRC
Sbjct: 35 NCNPELFRCTLTSIPQTQALLNKAKLPLGLLLH------PFKDLVQLPVVTSSTIVRCRS 88
Query: 94 CRGYRNPFMEFVDNGKSFVCNFCGLDGRCLDADE----------------RPELCRGTVE 137
CR Y NPF+ F+D + + CN C R D E RPE+ T+E
Sbjct: 89 CRTYINPFVSFLDQ-RRWKCNLC---YRVNDVPEEFLYNPLTRVYGEPHRRPEVQNATIE 144
Query: 138 FAASREFM 145
F A E+M
Sbjct: 145 FMAPSEYM 152
>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 = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 42/128 (32%), Positives = 60/128 (46%), Gaps = 26/128 (20%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NC+P RC+L IP T+ LL + +P L++ P +D + + S +VRC
Sbjct: 40 NCNPELFRCTLTSIPQTQALLNKAKLPLGLLLH------PFKDLVQLPVVTSSTIVRCRS 93
Query: 94 CRGYRNPFMEFVDNGKSFVCNFCGLDGRCLDADE----------------RPELCRGTVE 137
CR Y NPF+ F+D + + CN C R D E RPE+ T+E
Sbjct: 94 CRTYINPFVSFLDQ-RRWKCNLC---YRVNDVPEEFLYNPLTRVYGEPHRRPEVQNATIE 149
Query: 138 FAASREFM 145
F A E+M
Sbjct: 150 FMAPSEYM 157
>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
Length = 751
Score = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 42/125 (33%), Positives = 61/125 (48%), Gaps = 20/125 (16%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NCSP RC+L IP T+ LL + +P L++ P +PV+ + +VRC
Sbjct: 37 NCSPDSFRCTLTNIPQTQALLNKAKLPLGLLLH----PFRDLTQLPVI--TSNTIVRCRS 90
Query: 94 CRGYRNPFMEFVDNGKSFVCNFC-------------GLDGRCLDADERPELCRGTVEFAA 140
CR Y NPF+ F+D + + CN C L + +RPE+ TVEF A
Sbjct: 91 CRTYINPFVSFIDQ-RRWKCNLCYRVNDVPEEFMYNPLTRSYGEPHKRPEVQNSTVEFIA 149
Query: 141 SREFM 145
S ++M
Sbjct: 150 SSDYM 154
>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 = 26.9 bits (58), Expect = 4.5, 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 = 4.5, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 63 LMVQVLALPDP-SEDP-IPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFC 116
++V V AL P E P +P + + E L CR NP + K + CNFC
Sbjct: 38 MVVPVAALFTPLKERPDLPPIQY-EPVLCSRTTCRAVLNPLCQVDYRAKLWACNFC 92
>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 = 4.6, 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 = 6.6, 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
0.323 0.138 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,096,646
Number of Sequences: 62578
Number of extensions: 157308
Number of successful extensions: 231
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 212
Number of HSP's gapped (non-prelim): 13
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)