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= psy130
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KYQ|A Chain A, Lipid-Induced Conformational Switch Controls Fusion
Activity Of Longin Domain Snare Ykt6
Length = 199
Score = 254 bits (650), Expect = 2e-68, Method: Compositional matrix adjust.
Identities = 125/198 (63%), Positives = 160/198 (80%)
Query: 1 MVKLFALNILYKAPTSAVMLKSSYDLQSFSFFQRGSVQEFMTFVSKTMVERSQTASRQSI 60
++KL++L++ YK AV+LK++YD+ SFSFFQR SVQEFMTF S+ +VERS SR S+
Sbjct: 1 LMKLYSLSVFYKGEPKAVLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSAKGSRASV 60
Query: 61 KEGEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEASIS 120
KE EY+CHV+VR D+LAG++++D EYP RVA TL+ VL+EFSK V WP G+ A+I
Sbjct: 61 KEQEYLCHVYVRSDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIH 120
Query: 121 FPQLPQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSM 180
+ L +L+RYQNPREAD M+K+Q ELDETKIILHNT+E++L+RGEKLDDLVSKSE L
Sbjct: 121 YTALDGHLSRYQNPREADPMSKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGT 180
Query: 181 QSKAFYKTARKTNSCCSL 198
QSKAFYKTARK NSCC++
Sbjct: 181 QSKAFYKTARKQNSCCAI 198
>pdb|3BW6|A Chain A, Crystal Structure Of The Longin Domain Of Yeast Ykt6
Length = 144
Score = 118 bits (295), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 52/140 (37%), Positives = 86/140 (61%), Gaps = 2/140 (1%)
Query: 2 VKLFALNILYKAPTSAVMLKSSYDLQSFSFFQRGSVQEFMTFVSKTMVERSQTASRQSIK 61
++++ + + A+ L DL F FF+R SV +FMTF ++T+ R+ RQSI+
Sbjct: 5 MRIYYIGVFRSGGEKALELSEVKDLSQFGFFERSSVGQFMTFFAETVASRTGAGQRQSIE 64
Query: 62 EGEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEA--SI 119
EG Y+ HV+ R + + G+L++D+EYP R A+TL+ +L+E+ A P W TE ++
Sbjct: 65 EGNYIGHVYARSEGICGVLITDKEYPVRPAYTLLNKILDEYLVAHPKEEWADVTETNDAL 124
Query: 120 SFPQLPQYLARYQNPREADA 139
QL Y+++YQ+P +ADA
Sbjct: 125 KMKQLDTYISKYQDPSQADA 144
>pdb|1IOU|A Chain A, Solution Structure Of Ykt6p (1-140)
pdb|1H8M|A Chain A, Solution Structure Of Ykt6
Length = 140
Score = 116 bits (291), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 51/140 (36%), Positives = 86/140 (61%), Gaps = 2/140 (1%)
Query: 2 VKLFALNILYKAPTSAVMLKSSYDLQSFSFFQRGSVQEFMTFVSKTMVERSQTASRQSIK 61
++++ + + A+ L DL F FF+R SV +FMTF ++T+ R+ RQSI+
Sbjct: 1 MRIYYIGVFRSGGEKALELSEVKDLSQFGFFERSSVGQFMTFFAETVASRTGAGERQSIE 60
Query: 62 EGEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEA--SI 119
EG Y+ HV+ R + + G+L++D++YP R A+TL+ +L+E+ A P W TE ++
Sbjct: 61 EGNYIGHVYARSEGICGVLITDKQYPVRPAYTLLNKILDEYLVAHPKEEWADVTETNDAL 120
Query: 120 SFPQLPQYLARYQNPREADA 139
QL Y+++YQ+P +ADA
Sbjct: 121 KMKQLDTYISKYQDPSQADA 140
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 40/145 (27%), Positives = 69/145 (47%), Gaps = 7/145 (4%)
Query: 53 QTASRQSIKEGEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEF----SKAVPP 108
Q+ +R +++ G H + + +++ + +P ++A + ++ +EF K VP
Sbjct: 48 QSPTRCTLEAGAMTFHYIIE-QGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPT 106
Query: 109 SSWPTGTEASISFPQLPQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKL 168
S P +F Q + L Y + R + I EL + + I+ IE VLQRGE L
Sbjct: 107 VSRPYSFIEFDTFIQKTKKL--YIDSRARRNLGSINTELQDVQRIMVANIEEVLQRGEAL 164
Query: 169 DDLVSKSEGLSMQSKAFYKTARKTN 193
L SK+ LS SK + + A+ N
Sbjct: 165 SALDSKANNLSSLSKKYRQDAKYLN 189
>pdb|4B93|A Chain A, Complex Of Vamp7 Cytoplasmic Domain With 2nd Ankyrin
Repeat Domain Of Varp
Length = 189
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 62/133 (46%), Gaps = 9/133 (6%)
Query: 63 GEYMCHVFVRGDNLAGILVSDQEYPHRVAHTLITNVLNEF-----SKAVPPSSWPTGTEA 117
G Y+ H ++ D + + ++D ++ A + + V F S+A + +E
Sbjct: 49 GNYLFH-YICQDRIVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEF 107
Query: 118 SISFPQLPQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEG 177
S L L + + D + + Q ++DE K I+ I+ V QRGE+L+ L+ K+E
Sbjct: 108 S---SVLAAQLKHHSENKSLDKVMETQAQVDELKGIMVRNIDLVAQRGERLELLIDKTEN 164
Query: 178 LSMQSKAFYKTAR 190
L S F T+R
Sbjct: 165 LVDSSVTFKTTSR 177
>pdb|2NPS|A Chain A, Crystal Structure Of The Early Endosomal Snare Complex
Length = 74
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 134 PREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
PR D + +Q ++DE ++ I V++RGE+LD+L KSE LS + AF +++
Sbjct: 5 PRN-DKIKHVQNQVDEVIDVMQENITKVIERGERLDELQDKSESLSDNATAFSNRSKQ 61
>pdb|1GL2|A Chain A, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 38.9 bits (89), Expect = 0.002, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 138 DAMTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
D + +Q E++ K I+ +E +L RGE LD L +K+E L S+ F T++K
Sbjct: 9 DRVRNLQSEVEGVKNIMTQNVERILARGENLDHLRNKTEDLEATSEHFKTTSQK 62
>pdb|3B5N|A Chain A, Structure Of The Yeast Plasma Membrane Snare Complex
pdb|3B5N|E Chain E, Structure Of The Yeast Plasma Membrane Snare Complex
pdb|3B5N|I Chain I, Structure Of The Yeast Plasma Membrane Snare Complex
Length = 61
Score = 37.0 bits (84), Expect = 0.008, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 32/50 (64%)
Query: 142 KIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
++Q E+D+T I+ + I V +RGE+L + K++ L++ ++ F + A +
Sbjct: 6 ELQAEIDDTVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANR 55
>pdb|3SGA|E Chain E, Structures Of Product And Inhibitor Complexes Of
Streptomyces Griseus Protease A At 1.8 Angstroms
Resolution. A Model For Serine Protease Catalysis
pdb|4SGA|E Chain E, Structures Of Product And Inhibitor Complexes Of
Streptomyces Griseus Protease A At 1.8 Angstroms
Resolution. A Model For Serine Protease Catalysis
pdb|5SGA|E Chain E, Structures Of Product And Inhibitor Complexes Of
Streptomyces Griseus Protease A At 1.8 Angstroms
Resolution. A Model For Serine Protease Catalysis
pdb|1SGC|A Chain A, The 1.8 Angstroms Structure Of The Complex Between
Chymostatin And Streptomyces Griseus Protease A. A Model
For Serine Protease Catalytic Tetrahedral Intermediates
pdb|2SGA|A Chain A, Electron Density Calculations As An Extension Of Protein
Structure Refinement. Streptomyces Griseus Protease At
1.5 Angstroms Resolution
Length = 181
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 88 HRVAHTLITNVLNEFSKAVPPSSWPTGTEASISFPQLPQYLARYQNPREADA 139
+ VAH L S +SW GT SFP + R+ NP AD
Sbjct: 23 NGVAHALTAGHCTNIS-----ASWSIGTRTGTSFPNNDYGIIRHSNPAAADG 69
>pdb|1KIL|A Chain A, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 66
Score = 29.6 bits (65), Expect = 1.0, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 140 MTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 6 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 57
>pdb|1N7S|A Chain A, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 63
Score = 29.6 bits (65), Expect = 1.3, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 140 MTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 6 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 57
>pdb|2KOG|A Chain A, Lipid-Bound Synaptobrevin Solution Nmr Structure
Length = 119
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 140 MTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 35 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 86
>pdb|3OEK|A Chain A, Crystal Structure Of Glun2d Ligand-Binding Core In Complex
With L- Aspartate
pdb|3OEL|A Chain A, Crystal Structure Of Glun2d Ligand-Binding Core In Complex
With D- Glutamate
pdb|3OEM|A Chain A, Crystal Structure Of Glun2d Ligand-Binding Core In Complex
With N- Methyl-D-Aspartate
pdb|3OEN|A Chain A, Crystal Structure Of Glun2d Ligand-Binding Core In Complex
With L- Glutamate
Length = 286
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 3/36 (8%)
Query: 112 PTG-TEASI--SFPQLPQYLARYQNPREADAMTKIQ 144
P G TE +I ++P + Y+ RY PR +A+T+++
Sbjct: 170 PNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQLK 205
>pdb|3HD7|A Chain A, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3HD7|E Chain E, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3IPD|A Chain A, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
pdb|3IPD|E Chain E, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
Length = 91
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 140 MTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 7 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 58
>pdb|1SFC|A Chain A, Neuronal Synaptic Fusion Complex
pdb|1SFC|E Chain E, Neuronal Synaptic Fusion Complex
pdb|1SFC|I Chain I, Neuronal Synaptic Fusion Complex
Length = 96
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 140 MTKIQEELDETKIILHNTIEAVLQRGEKLDDLVSKSEGLSMQSKAFYKTARK 191
+ + Q ++DE I+ ++ VL+R +KL +L +++ L + F +A K
Sbjct: 32 LQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK 83
>pdb|2BDT|A Chain A, Crystal Structure Of The Putative Gluconate Kinase From
Bacillus Halodurans, Northeast Structural Genomics
Target Bhr61
Length = 189
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 16/96 (16%)
Query: 110 SWPTGTEASISF--PQLPQYLARYQNPREADAMTK-IQEELDETKI---ILHNTIEAVLQ 163
+W T+ +++F Q L P EA+A+ + +Q ++D+ +I IL E +L+
Sbjct: 58 TWKNITDLTVNFLLAQNDVVLDYIAFPDEAEALAQTVQAKVDDVEIRFIILWTNREELLR 117
Query: 164 R----------GEKLDDLVSKSEGLSMQSKAFYKTA 189
R GE+ +LV + E + + FY T+
Sbjct: 118 RDALRKKDEQXGERCLELVEEFESKGIDERYFYNTS 153
>pdb|1JXH|A Chain A, 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine Phosphate
Kinase From Salmonella Typhimurium
pdb|1JXH|B Chain B, 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine Phosphate
Kinase From Salmonella Typhimurium
pdb|1JXI|A Chain A, 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine Phosphate
Kinase From Salmonella Typhimurium Complexed With
4-Amino-5- Hydroxymethyl-2-Methylpyrimidine
pdb|1JXI|B Chain B, 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine Phosphate
Kinase From Salmonella Typhimurium Complexed With
4-Amino-5- Hydroxymethyl-2-Methylpyrimidine
Length = 288
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 116 EASISFPQLPQYLARYQNPREADAMTKIQEELDETKIILHNTIEAVLQRGEKLDD 170
+ S+ P LP+ A P A T+ QE L + + +L EAVL +G L+D
Sbjct: 154 QVSLITPNLPEAAALLDAPH---ARTE-QEMLAQGRALLAMGCEAVLMKGGHLED 204
>pdb|1W0O|A Chain A, Vibrio Cholerae Sialidase
pdb|1W0P|A Chain A, Vibrio Cholerae Sialidase With Alpha-2,6-Sialyllactose
Length = 781
Score = 26.9 bits (58), Expect = 8.2, Method: Composition-based stats.
Identities = 32/134 (23%), Positives = 53/134 (39%), Gaps = 9/134 (6%)
Query: 18 VMLKSSYDLQSFSFF----QRGSVQEFMTFVSKTMVERSQTAS---RQSIKEGEYMCHVF 70
V+ + ++L F F Q V++ + + T ++ T S S+ G
Sbjct: 495 VLTQQGHNLVEFDAFYLAQQTPEVEKDLEKLGWTKIKTGNTMSLYGNASVNPGPGHGITL 554
Query: 71 VRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEASISFPQLPQYLAR 130
R N++G YP V NV++ +S S+W TG+ I F +
Sbjct: 555 TRQQNISGSQNGRLIYPAIVLDRFFLNVMSIYSDD-GGSNWQTGSTLPIPFRWKSSSILE 613
Query: 131 YQNPREADAMTKIQ 144
P EAD M ++Q
Sbjct: 614 TLEPSEAD-MVELQ 626
>pdb|1KIT|A Chain A, Vibrio Cholerae Neuraminidase
Length = 757
Score = 26.6 bits (57), Expect = 8.5, Method: Composition-based stats.
Identities = 32/134 (23%), Positives = 53/134 (39%), Gaps = 9/134 (6%)
Query: 18 VMLKSSYDLQSFSFF----QRGSVQEFMTFVSKTMVERSQTAS---RQSIKEGEYMCHVF 70
V+ + ++L F F Q V++ + + T ++ T S S+ G
Sbjct: 471 VLTQQGHNLVEFDAFYLAQQTPEVEKDLEKLGWTKIKTGNTMSLYGNASVNPGPGHGITL 530
Query: 71 VRGDNLAGILVSDQEYPHRVAHTLITNVLNEFSKAVPPSSWPTGTEASISFPQLPQYLAR 130
R N++G YP V NV++ +S S+W TG+ I F +
Sbjct: 531 TRQQNISGSQNGRLIYPAIVLDRFFLNVMSIYSDD-GGSNWQTGSTLPIPFRWKSSSILE 589
Query: 131 YQNPREADAMTKIQ 144
P EAD M ++Q
Sbjct: 590 TLEPSEAD-MVELQ 602
>pdb|3TC8|A Chain A, Crystal Structure Of A Hypothetical Zn-Dependent
Exopeptidase (Bdi_3547) From Parabacteroides Distasonis
Atcc 8503 At 1.06 A Resolution
pdb|3TC8|B Chain B, Crystal Structure Of A Hypothetical Zn-Dependent
Exopeptidase (Bdi_3547) From Parabacteroides Distasonis
Atcc 8503 At 1.06 A Resolution
Length = 309
Score = 26.6 bits (57), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 101 EFSKAVPPSSWPTGTEASISFPQLPQYLARY 131
EF P SW GT+ P +P Y A Y
Sbjct: 165 EFVTDYTPDSWCLGTQFWAKNPHVPNYTAEY 195
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
0.317 0.129 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,930,902
Number of Sequences: 62578
Number of extensions: 175001
Number of successful extensions: 513
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 495
Number of HSP's gapped (non-prelim): 20
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)