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= 028291
(211 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 = 132 bits (332), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 72/179 (40%), Positives = 104/179 (58%), Gaps = 16/179 (8%)
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 PELCRGTVEFAASREFMMRNVM--PPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185
PEL G+ EF A+ ++ N PP + F+IDVS +A++TG C + ++ LP
Sbjct: 149 PELSLGSYEFLATVDYCKNNKFPSPPAFIFMIDVSYNAIRTGLVRLLCEELKSLLDFLP 207
>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 = 118 bits (295), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 61/179 (34%), Positives = 100/179 (55%), Gaps = 16/179 (8%)
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 PELCRGTVEFAASREFMMRNV--MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185
PEL G+ E+ A+ ++ ++ PP + F+IDVS ++ G C + ++ +P
Sbjct: 153 PELSLGSYEYVATLDYCRKSKPPNPPAFIFMIDVSYSNIKNGLVKLICEELKTMLEKIP 211
>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 = 100 bits (249), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 59/170 (34%), Positives = 86/170 (50%), Gaps = 26/170 (15%)
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-RRWKCNLCY---RVNDVPEEFLYNPLTRVYGEPHRRPEVQNATIE 144
Query: 138 FAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN 187
F A E+M+R PPVY F+ DVS +AV+TG + C +++ + LP N
Sbjct: 145 FMAPSEYMLRPPQPPVYLFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGN 194
>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 = 100 bits (249), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 59/170 (34%), Positives = 86/170 (50%), Gaps = 26/170 (15%)
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-RRWKCNLCY---RVNDVPEEFLYNPLTRVYGEPHRRPEVQNATIE 149
Query: 138 FAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPIN 187
F A E+M+R PPVY F+ DVS +AV+TG + C +++ + LP N
Sbjct: 150 FMAPSEYMLRPPQPPVYLFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGN 199
>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
Length = 751
Score = 96.7 bits (239), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 55/165 (33%), Positives = 83/165 (50%), Gaps = 20/165 (12%)
Query: 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC 93
NCSP RC+L IP T+ LL + +P L++ P D + + +VRC
Sbjct: 37 NCSPDSFRCTLTNIPQTQALLNKAKLPLGLLLH------PFRDLTQLPVITSNTIVRCRS 90
Query: 94 CRGYRNPFMEFVDNGKSFVCNFC-------------GLDGRCLDADERPELCRGTVEFAA 140
CR Y NPF+ F+D + + CN C L + +RPE+ TVEF A
Sbjct: 91 CRTYINPFVSFIDQ-RRWKCNLCYRVNDVPEEFMYNPLTRSYGEPHKRPEVQNSTVEFIA 149
Query: 141 SREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185
S ++M+R P VY F++DVS +AV+ G C ++++ + LP
Sbjct: 150 SSDYMLRPPQPAVYLFVLDVSHNAVEAGYLTILCQSLLENLDKLP 194
>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 = 95.5 bits (236), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 56/168 (33%), Positives = 87/168 (51%), Gaps = 16/168 (9%)
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 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRC-LDADE-----------RPELCRGTVE 137
RC CR Y NPF+ F++ G+ + CNFC L + D+ R E+ +E
Sbjct: 114 RCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVME 173
Query: 138 FAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185
+ A +E+ +R P Y FLIDVS ++++G A + ++Q + +P
Sbjct: 174 YMAPKEYTLRQPPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIP 221
>pdb|1M2V|B Chain B, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 926
Score = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 56/171 (32%), Positives = 88/171 (51%), Gaps = 16/171 (9%)
Query: 28 IVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESG 87
+ + N SP YIR +LN +P +LLK S +P L+++ DP P+ E G
Sbjct: 170 VPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPL---NEDG 226
Query: 88 L-VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRC-LDADE-----------RPELCRG 134
L VRC CR Y NPF+ F++ G+ + CNFC L + D+ R E+
Sbjct: 227 LIVRCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCA 286
Query: 135 TVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185
+E+ A +E+ +R P Y FLIDVS ++++G A + ++Q + +P
Sbjct: 287 VMEYMAPKEYTLRQPPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIP 337
>pdb|1M2O|A Chain A, Crystal Structure Of The Sec23-Sar1 Complex
pdb|1M2O|C Chain C, Crystal Structure Of The Sec23-Sar1 Complex
pdb|1M2V|A Chain A, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 768
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 52/121 (42%), Gaps = 24/121 (19%)
Query: 94 CRGYRNPFMEFVDNGKSFVCNFCGLDGRC------LDADERP-ELCRGTVEFAASREFMM 146
C+ NP+ S+ C C L + P EL T+E+ ++
Sbjct: 61 CKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPV-- 118
Query: 147 RNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMCILYG 206
+PP++FF++D+++ +T + +I+ +S LP N ++GL I YG
Sbjct: 119 --TVPPIFFFVVDLTS---ETENLDSLKESIITSLSLLPPNA-LIGL---------ITYG 163
Query: 207 N 207
N
Sbjct: 164 N 164
>pdb|2QTV|A Chain A, Structure Of Sec23-Sar1 Complexed With The Active Fragment
Of Sec31
Length = 772
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 52/121 (42%), Gaps = 24/121 (19%)
Query: 94 CRGYRNPFMEFVDNGKSFVCNFCGLDGRC------LDADERP-ELCRGTVEFAASREFMM 146
C+ NP+ S+ C C L + P EL T+E+ ++
Sbjct: 65 CKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPV-- 122
Query: 147 RNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPINIFVVGLLKLKIWWMCILYG 206
+PP++FF++D+++ +T + +I+ +S LP N ++GL I YG
Sbjct: 123 --TVPPIFFFVVDLTS---ETENLDSLKESIITSLSLLPPNA-LIGL---------ITYG 167
Query: 207 N 207
N
Sbjct: 168 N 168
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
0.325 0.139 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,840,947
Number of Sequences: 62578
Number of extensions: 221266
Number of successful extensions: 491
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 471
Number of HSP's gapped (non-prelim): 12
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)