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= 033474
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QGV|A Chain A, Human Spliceosomal Protein U5-15kd
pdb|1SYX|A Chain A, The Crystal Structure Of A Binary U5 Snrnp Complex
pdb|1SYX|C Chain C, The Crystal Structure Of A Binary U5 Snrnp Complex
pdb|1SYX|E Chain E, The Crystal Structure Of A Binary U5 Snrnp Complex
Length = 142
Score = 194 bits (493), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 88/104 (84%), Positives = 99/104 (95%)
Query: 15 LEMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYELYDPSTVMFFFRNKHIMIDLGTGN 74
++MDEVL S+AE +KNFAVIYLVDI+EVPDFN MYELYDP TVMFFFRNKHIMIDLGTGN
Sbjct: 39 MKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGN 98
Query: 75 NNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYSTKYRY 118
NNKINWA++DKQE +DI+ETVYRGARKGRGLV++PKDYSTKYRY
Sbjct: 99 NNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY 142
>pdb|2AV4|A Chain A, Crystal Structure Of Plasmodium Yoelii Thioredoxin-like
Protein 4a (dim1)
Length = 160
Score = 182 bits (463), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 83/104 (79%), Positives = 97/104 (93%)
Query: 15 LEMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYELYDPSTVMFFFRNKHIMIDLGTGN 74
++MDE+L VA+ IKNF VIYLVDI+EVPDFNTMYELYDP +VMFF+RNKH+MIDLGTGN
Sbjct: 57 MKMDELLYKVADDIKNFCVIYLVDITEVPDFNTMYELYDPVSVMFFYRNKHMMIDLGTGN 116
Query: 75 NNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYSTKYRY 118
NNKINW + +KQEFIDIVET++RGARKGRGLVI+PKDYSTKY+Y
Sbjct: 117 NNKINWPMNNKQEFIDIVETIFRGARKGRGLVISPKDYSTKYKY 160
>pdb|1PQN|A Chain A, Dominant Negative Human Hdim1 (Hdim1 1-128)
Length = 127
Score = 167 bits (424), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 76/90 (84%), Positives = 85/90 (94%)
Query: 15 LEMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYELYDPSTVMFFFRNKHIMIDLGTGN 74
++MDEVL S+AE +KNFAVIYLVDI+EVPDFN MYELYDP TVMFFFRNKHIMIDLGTGN
Sbjct: 38 MKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGN 97
Query: 75 NNKINWALKDKQEFIDIVETVYRGARKGRG 104
NNKINWA++DKQE +DI+ETVYRGARKGRG
Sbjct: 98 NNKINWAMEDKQEMVDIIETVYRGARKGRG 127
>pdb|1XBS|A Chain A, Crystal Structure Of Human Dim2: A Dim1-Like Protein
Length = 149
Score = 80.1 bits (196), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 37/98 (37%), Positives = 64/98 (65%), Gaps = 2/98 (2%)
Query: 15 LEMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYEL-YDPSTVMFFFRNKHIMIDLGTG 73
L++D++LS + + A IYLVD+ + + +++ Y PSTV FFF +H+ +D G+
Sbjct: 39 LQLDDILSKTSSDLSKMAAIYLVDVDQTAVYTQYFDISYIPSTV-FFFNGQHMKVDYGSP 97
Query: 74 NNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKD 111
++ K + K KQ+FID++E +YRGA +G+ +V +P D
Sbjct: 98 DHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPID 135
>pdb|3GIX|A Chain A, Crystal Structure Of Human Splicing Factor Dim2
pdb|3GIX|B Chain B, Crystal Structure Of Human Splicing Factor Dim2
Length = 149
Score = 80.1 bits (196), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 37/98 (37%), Positives = 64/98 (65%), Gaps = 2/98 (2%)
Query: 15 LEMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYEL-YDPSTVMFFFRNKHIMIDLGTG 73
L++D++LS + + A IYLVD+ + + +++ Y PSTV FFF +H+ +D G+
Sbjct: 39 LQLDDILSKTSSDLSKMAAIYLVDVDQTAVYTQYFDISYIPSTV-FFFNGQHMKVDYGSP 97
Query: 74 NNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKD 111
++ K + K KQ+FID++E +YRGA +G+ +V +P D
Sbjct: 98 DHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPID 135
>pdb|1ECR|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
Complexed With Dna
pdb|2EWJ|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
Complexed With Dna- Locked Form
pdb|2I05|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
Complexed With Tera Dna
pdb|2I06|A Chain A, Escherichia Coli Replication Terminator Protein (tus)
Complexed With Dna- Locked Form
Length = 309
Score = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 45 FNTMYELYDPSTVMFFFRNKHIMIDL 70
+ T+ L+DP+T+ F + NKHI+ +L
Sbjct: 156 YRTLTVLHDPATLRFGWANKHIIKNL 181
>pdb|3DPT|A Chain A, Cor Domain Of Rab Family Protein (Roco)
pdb|3DPT|B Chain B, Cor Domain Of Rab Family Protein (Roco)
Length = 332
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 55 STVMFFFRNKHIMID-LGTGNNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYS 113
S + + + I D NNK + L +++ +DI++ +G+GL I P +
Sbjct: 108 SALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLP 167
Query: 114 TK 115
T+
Sbjct: 168 TQ 169
>pdb|4F6V|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Bph-1034, Mg2+ And Fmp.
pdb|4F6X|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Bph-1112
Length = 292
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 2 NATYDTPRRLILNLEMDEVLSSVAETIKNFAVI--------YLVDISEV 42
+ TYD RRL +L++ +L V E +N + Y VDI+EV
Sbjct: 156 HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEV 204
>pdb|2ZCO|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus
pdb|2ZCP|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Farnesyl Thiopyrophosphate
pdb|2ZCP|B Chain B, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Farnesyl Thiopyrophosphate
pdb|2ZCQ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-652
pdb|2ZCR|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-698
pdb|2ZCS|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-700
pdb|2ZY1|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bisphosphonate Bph-830
pdb|3ACW|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bph-651
pdb|3ACX|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bph-673
pdb|3ACY|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Bph-702
pdb|3NPR|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From S. Aureus Complexed With Presqualene
Diphosphate (Pspp)
pdb|3NRI|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From S. Aureus Complexed With Dehydrosqualene
(Dhs)
pdb|3TFN|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Bph-1183
pdb|3TFP|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Bph-1162
pdb|3TFV|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Bph-1154
Length = 293
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 2 NATYDTPRRLILNLEMDEVLSSVAETIKNFAVI--------YLVDISEV 42
+ TYD RRL +L++ +L V E +N + Y VDI+EV
Sbjct: 157 HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEV 205
>pdb|4E9U|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With A Thiocyanate Inhibitor
pdb|4E9Z|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Quinuclidine Bph-651 In The S1
Site
pdb|4EA0|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Diphosphate And Quinuclidine
Bph-651
pdb|4EA0|B Chain B, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From
S. Aureus Complexed With Diphosphate And Quinuclidine
Bph-651
pdb|4EA1|A Chain A, Co-Crystal Structure Of Dehydrosqualene Synthase (Crtm)
From S. Aureus With Sq-109
pdb|4EA2|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm)
Aureus Complexed With Sq-109
Length = 287
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 2 NATYDTPRRLILNLEMDEVLSSVAETIKNFAVI--------YLVDISEV 42
+ TYD RRL +L++ +L V E +N + Y VDI+EV
Sbjct: 151 HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEV 199
>pdb|3VJD|A Chain A, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid
Dehydrosqualene Synthase From Staphylococcus Aureus
pdb|3VJE|A Chain A, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid
Dehydrosqualene Synthase From Staphylococcus Aureus In
Complex With Zaragozic Acid A
pdb|3VJE|B Chain B, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid
Dehydrosqualene Synthase From Staphylococcus Aureus In
Complex With Zaragozic Acid A
Length = 293
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 2 NATYDTPRRLILNLEMDEVLSSVAETIKNFAVI--------YLVDISEV 42
+ TYD RRL +L++ +L V E +N + Y VDI+EV
Sbjct: 157 HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEV 205
>pdb|3ADZ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Intermediate Pspp
pdb|3LGZ|B Chain B, Crystal Structure Of Dehydrosqualene Synthase Y129a From
S. Aureus Complexed With Presqualene Pyrophosphate
Length = 293
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 2 NATYDTPRRLILNLEMDEVLSSVAETIKNFAVI--------YLVDISEV 42
+ TYD RRL +L++ +L V E +N + Y VDI+EV
Sbjct: 157 HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEV 205
>pdb|3AE0|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Geranylgeranyl Thiopyrophosphate
pdb|3AE0|B Chain B, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene
Synthase From Staphylococcus Aureus Complexed With
Geranylgeranyl Thiopyrophosphate
Length = 293
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 2 NATYDTPRRLILNLEMDEVLSSVAETIKNFAVI--------YLVDISEV 42
+ TYD RRL +L++ +L V E +N + Y VDI+EV
Sbjct: 157 HQTYDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEV 205
>pdb|3DPU|A Chain A, Roccor Domain Tandem Of Rab Family Protein (Roco)
pdb|3DPU|B Chain B, Roccor Domain Tandem Of Rab Family Protein (Roco)
Length = 535
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 55 STVMFFFRNKHIMID-LGTGNNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYS 113
S + + + I D NNK + L +++ +DI++ +G+GL I P +
Sbjct: 311 SALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLP 370
Query: 114 TK 115
T+
Sbjct: 371 TQ 372
>pdb|1JBA|A Chain A, Unmyristoylated Gcap-2 With Three Calcium Ions Bound
Length = 204
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 10/32 (31%)
Query: 76 NKINWALK----------DKQEFIDIVETVYR 97
+K+ W K D+QE +DIVE++Y+
Sbjct: 95 HKLKWTFKIYDKDRNGCIDRQELLDIVESIYK 126
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
0.321 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,620,970
Number of Sequences: 62578
Number of extensions: 145052
Number of successful extensions: 338
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 324
Number of HSP's gapped (non-prelim): 28
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
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: 45 (21.9 bits)