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= 027525
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NUP|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
pdb|2NUT|C Chain C, Crystal Structure Of The Human Sec23a24A HETERODIMER,
Complexed With The Snare Protein Sec22b
Length = 196
Score = 111 bits (278), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 51/162 (31%), Positives = 100/162 (61%), Gaps = 3/162 (1%)
Query: 1 MVKMTIVGRVSDGLPLARGPRYLNQEHDSFSFYKQQAEFILKEISRGALAPSKMTIRVDH 60
MV +T++ RV+DGLPLA + Q Y+ QA+ + ++++ + P++ T+
Sbjct: 2 MVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQS--PTRCTLEAGA 59
Query: 61 HSFHYLMENGIGCFITLCDSSYPRKLAFHYLQDLQKEFQKFDISLIDKITRPYSCVKFES 120
+FHY++E G+ C++ LC++++P+KLAF YL+DL EF + + ++RPYS ++F++
Sbjct: 60 MTFHYIIEQGV-CYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDT 118
Query: 121 IIGNIRKQYVDTRTQANLSKLNANRGQDLDIVIEHMYQIVER 162
I +K Y+D+R + NL +N I++ ++ ++++R
Sbjct: 119 FIQKTKKLYIDSRARRNLGSINTELQDVQRIMVANIEEVLQR 160
>pdb|3EGD|C Chain C, 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|C Chain C, 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 = 157
Score = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 49/142 (34%), Positives = 90/142 (63%), Gaps = 3/142 (2%)
Query: 1 MVKMTIVGRVSDGLPLARGPRYLNQEHDSFSFYKQQAEFILKEISRGALAPSKMTIRVDH 60
MV +T++ RV+DGLPLA + Q Y+ QA+ + ++++ + P++ T+
Sbjct: 1 MVLLTMIARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQS--PTRCTLEAGA 58
Query: 61 HSFHYLMENGIGCFITLCDSSYPRKLAFHYLQDLQKEFQKFDISLIDKITRPYSCVKFES 120
+FHY++E G+ C++ LC++++P+KLAF YL+DL EF + + ++RPYS ++F++
Sbjct: 59 MTFHYIIEQGV-CYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDT 117
Query: 121 IIGNIRKQYVDTRTQANLSKLN 142
I +K Y+D+R + NL +N
Sbjct: 118 FIQKTKKLYIDSRARRNLGSIN 139
>pdb|1IFQ|A Chain A, Sec22b N-Terminal Domain
pdb|1IFQ|B Chain B, Sec22b N-Terminal Domain
Length = 138
Score = 94.0 bits (232), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 43/129 (33%), Positives = 80/129 (62%), Gaps = 3/129 (2%)
Query: 2 VKMTIVGRVSDGLPLARGPRYLNQEHDSFSFYKQQAEFILKEISRGALAPSKMTIRVDHH 61
V +T + RV+DGLPLA + Q Y+ QA+ + ++++ + P++ T+
Sbjct: 13 VLLTXIARVADGLPLAASXQEDEQSGRDLQQYQSQAKQLFRKLNEQS--PTRCTLEAGAX 70
Query: 62 SFHYLMENGIGCFITLCDSSYPRKLAFHYLQDLQKEFQKFDISLIDKITRPYSCVKFESI 121
+FHY++E G+ C++ LC++++P+KLAF YL+DL EF + + ++RPYS ++F++
Sbjct: 71 TFHYIIEQGV-CYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTF 129
Query: 122 IGNIRKQYV 130
I +K Y+
Sbjct: 130 IQKTKKLYI 138
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 33.9 bits (76), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 27/129 (20%), Positives = 63/129 (48%), Gaps = 12/129 (9%)
Query: 37 AEFILKEISRGALAPSKMTIRVDHHSFHYLMENGIGCFITLCDSSYPRKLAFHYLQDLQK 96
++ I++ ++G S+ +++ + H + + + + DS YP ++AF L+ +
Sbjct: 45 SQLIVERSAKG----SRASVKEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLD 100
Query: 97 EFQKFDISLIDKITRPY---SCVKFESIIGNIRKQYVDTRTQANLSKLNANRGQDLDIVI 153
EF K +D+I P + + + ++ G++ + Y + R +SK+ A + I+
Sbjct: 101 EFSK----QVDRIDWPVGSPATIHYTALDGHLSR-YQNPREADPMSKVQAELDETKIILH 155
Query: 154 EHMYQIVER 162
M ++ER
Sbjct: 156 NTMESLLER 164
>pdb|2DMW|A Chain A, Solution Structure Of The Longin Domain Of
Synaptobrevin- Like Protein 1
Length = 131
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 52 SKMTIRVDHHSFHYLMENGIGCFITLCDSSYPRKLAFHYLQDLQKEFQ 99
+K+T ++ FHY+ ++ I ++ + D + R AF++L +++K FQ
Sbjct: 48 NKLTYSHGNYLFHYICQDRI-VYLCITDDDFERSRAFNFLNEIKKRFQ 94
>pdb|3V8I|A Chain A, Crystal Structure Of A Drosophila Melanogaster Dopamine N-
Acetyltransferase
pdb|3V8I|B Chain B, Crystal Structure Of A Drosophila Melanogaster Dopamine N-
Acetyltransferase
Length = 210
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 57 RVDHHSFHYLMENGIGCFITLCDSSYP----RKLAFHYLQDLQ 95
R+ ++ Y+ ENGI + LC S Y KL FH + +Q
Sbjct: 140 RLTERAYEYMRENGINVYHVLCSSHYSARVMEKLGFHEVFRMQ 182
>pdb|3TE4|A Chain A, Crystal Structure Of Dopamine N Acetyltransferase In
Complex With Acetyl-Coa From Drosophila Melanogaster
Length = 215
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 57 RVDHHSFHYLMENGIGCFITLCDSSYP----RKLAFHYLQDLQ 95
R+ ++ Y+ ENGI + LC S Y KL FH + +Q
Sbjct: 145 RLTERAYEYMRENGINVYHVLCSSHYSARVMEKLGFHEVFRMQ 187
>pdb|3P0S|A Chain A, Crystal Structure Of Bombyx Mori Densovirus 1 Capsid
Length = 494
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 24/111 (21%), Positives = 53/111 (47%), Gaps = 9/111 (8%)
Query: 42 KEISRGALAPSKMTIRVDHHSFHYLMENGIGCF--ITLCDSSYPRKLAFHYLQDLQKEFQ 99
++I GA P++ V S+H+ + NG+ F + +S Y + F ++ + E
Sbjct: 48 QDIFSGAPQPNQHHTLVYGKSYHFTITNGLPEFRHLATTNSGYYAQQRFKHIHGIPWERL 107
Query: 100 KFDISLID--KITRPYSCVKFESIIG-----NIRKQYVDTRTQANLSKLNA 143
+S + ++ R Y+ +K E ++ +R +V + T ++++ NA
Sbjct: 108 LMYVSEGELLRMFRDYTSLKVEEVVCEVYSLGVRLPFVTSATTSSVANANA 158
>pdb|1AF0|A Chain A, Serratia Protease In Complex With Inhibitor
Length = 471
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 87 AFHYLQDLQKEFQKFDISLIDKITRPYSCVKF-ESIIGNIRKQYVDTRTQANLSKLNANR 145
A +++D QK K D+S DK S + F + G + + +N++ L+ N
Sbjct: 388 ASDWIRDFQKGIDKIDLSFFDKEANSSSFIHFVDHFSGTAGEALLSYNASSNVTDLSVNI 447
Query: 146 G--QDLDIVIEHMYQI 159
G Q D +++ + Q+
Sbjct: 448 GGHQAPDFLVKIVGQV 463
>pdb|3ZEY|E Chain E, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 174
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 7/42 (16%)
Query: 142 NANRGQDLDIVIEH--MYQIVERKRQSEISEEILTATRKHVS 181
N R +D+ ++H YQ RQ+ ++E I TA++KHV+
Sbjct: 7 NYARTPTVDLTVQHEKAYQ-----RQTAVNENIRTASKKHVN 43
>pdb|1SAT|A Chain A, Crystal Structure Of The 50 Kda Metallo Protease From S.
Marcescens
Length = 471
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 87 AFHYLQDLQKEFQKFDISLIDKITRPYSCVKF-ESIIGNIRKQYVDTRTQANLSKLNANR 145
A +++D QK K D+S DK S + F + G + + +N++ L+ N
Sbjct: 388 ASDWIRDFQKGIDKIDLSFFDKEANSSSFIHFVDHFSGTAGEALLSYNASSNVTDLSVNI 447
Query: 146 G 146
G
Sbjct: 448 G 448
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 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,670,434
Number of Sequences: 62578
Number of extensions: 201039
Number of successful extensions: 523
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 510
Number of HSP's gapped (non-prelim): 13
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
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: 49 (23.5 bits)