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= 003753
(798 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 37.0 bits (84), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 536 FKSMYALRVLDSSQNAKLSKLHVGEGELIDLQYLNLSNTNICELPIGIKSCTHLRTLLLD 595
F S+ L VLD N L+ L+ L + + ELP GI+ THL L LD
Sbjct: 84 FDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALD 143
Query: 596 GTENLKAIPVGMLSSLLSL 614
+ LK+IP G L SL
Sbjct: 144 QNQ-LKSIPHGAFDRLSSL 161
>pdb|3M19|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
pdb|3M19|B Chain B, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
Length = 251
Score = 36.2 bits (82), Expect = 0.078, Method: Composition-based stats.
Identities = 33/114 (28%), Positives = 53/114 (46%), Gaps = 6/114 (5%)
Query: 504 SIDSLSPTPPCSPRLLTLLVRYTMIKEFENKFFKSMYALRVLDSSQNAKLSKLHVGE-GE 562
S+DS+ P L L + T + + F+ + L L+ N +L L G +
Sbjct: 25 SLDSVPSGIPADTEKLDL--QSTGLATLSDATFRGLTKLTWLNLDYN-QLQTLSAGVFDD 81
Query: 563 LIDLQYLNLSNTNICELPIGI-KSCTHLRTLLLDGTENLKAIPVGMLSSLLSLR 615
L +L L L+N + LP+G+ T L L L G + LK++P G+ L L+
Sbjct: 82 LTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQ-LKSLPSGVFDRLTKLK 134
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 36.2 bits (82), Expect = 0.078, Method: Composition-based stats.
Identities = 33/114 (28%), Positives = 53/114 (46%), Gaps = 6/114 (5%)
Query: 504 SIDSLSPTPPCSPRLLTLLVRYTMIKEFENKFFKSMYALRVLDSSQNAKLSKLHVGE-GE 562
S+DS+ P L L + T + + F+ + L L+ N +L L G +
Sbjct: 25 SLDSVPSGIPADTEKLDL--QSTGLATLSDATFRGLTKLTWLNLDYN-QLQTLSAGVFDD 81
Query: 563 LIDLQYLNLSNTNICELPIGI-KSCTHLRTLLLDGTENLKAIPVGMLSSLLSLR 615
L +L L L+N + LP+G+ T L L L G + LK++P G+ L L+
Sbjct: 82 LTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQ-LKSLPSGVFDRLTKLK 134
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 30/90 (33%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 528 IKEFENKFFKSMYALRVLDSSQNAKLSKLHVGE-GELIDLQYLNLSNTNICELPIGI-KS 585
+K N F + +L L N KL L G +L L YLNLS + LP G+
Sbjct: 40 LKSLPNGVFDELTSLTQLYLGGN-KLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDK 98
Query: 586 CTHLRTLLLDGTENLKAIPVGMLSSLLSLR 615
T L+ L L+ T L+++P G+ L L+
Sbjct: 99 LTQLKELALN-TNQLQSLPDGVFDKLTQLK 127
>pdb|2QM8|A Chain A, Meab, A Bacterial Homolog Of Mmaa, In The Nucleotide Free
Form
pdb|2QM8|B Chain B, Meab, A Bacterial Homolog Of Mmaa, In The Nucleotide Free
Form
Length = 337
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 135 IESRLSEVWRYIEDDGVKIIGLYGVRGVGKSTLLKQLNDTFSDMSHKFGAVIMVKASTEL 194
I++ L + R I +G+ GV GVGKST + L + HK + + +ST
Sbjct: 45 IDAVLPQTGRAIR------VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRT 98
Query: 195 NIEKIQDVIR-SRLGID 210
+ D R +RL ID
Sbjct: 99 GGSILGDKTRXARLAID 115
>pdb|2QM7|A Chain A, Meab, A Bacterial Homolog Of Mmaa, Bound To Gdp
pdb|2QM7|B Chain B, Meab, A Bacterial Homolog Of Mmaa, Bound To Gdp
Length = 337
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 135 IESRLSEVWRYIEDDGVKIIGLYGVRGVGKSTLLKQLNDTFSDMSHKFGAVIMVKASTEL 194
I++ L + R I +G+ GV GVGKST + L + HK + + +ST
Sbjct: 45 IDAVLPQTGRAIR------VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRT 98
Query: 195 NIEKIQDVIR-SRLGID 210
+ D R +RL ID
Sbjct: 99 GGSILGDKTRMARLAID 115
>pdb|3NXS|A Chain A, Crystal Structure Of LaoAO TRANSPORT SYSTEM FROM
MYCOBACTERIUM Smegmatis Bound To Gdp
Length = 329
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 154 IGLYGVRGVGKSTLLKQLNDTFSDMSHKFGAVIMVKASTELNIEKIQDVIR-SRLGIDPD 212
+G+ GV GVGKST ++ L + H+ + + +ST + D R +RL + PD
Sbjct: 60 VGITGVPGVGKSTTIEALGMHLIEAGHRVAVLAVDPSSTRTGGSILGDKTRMARLAVHPD 119
>pdb|3TWI|D Chain D, Variable Lymphocyte Receptor Recognition Of The
Immunodominant Glycoprotein Of Bacillus Anthracis Spores
pdb|3TWI|E Chain E, Variable Lymphocyte Receptor Recognition Of The
Immunodominant Glycoprotein Of Bacillus Anthracis Spores
pdb|3TWI|F Chain F, Variable Lymphocyte Receptor Recognition Of The
Immunodominant Glycoprotein Of Bacillus Anthracis Spores
Length = 179
Score = 33.5 bits (75), Expect = 0.46, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 552 KLSKLHVGE-GELIDLQYLNLSNTNICELPIGI-KSCTHLRTLLLDGTENLKAIPVGMLS 609
+++KL G L L YLNL+ + LP+G+ T L L L LK+IP+G+
Sbjct: 51 QITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFDKLTKLTHLALH-INQLKSIPMGVFD 109
Query: 610 SLLSL 614
+L SL
Sbjct: 110 NLKSL 114
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/100 (32%), Positives = 50/100 (50%), Gaps = 3/100 (3%)
Query: 517 RLLTLLVRYTMIKEFENKFFKSMYALRVLDSSQNAKLSKLHVGEGE-LIDLQYLNLSNTN 575
+L L +R I+ + F + +LR LD + +LS + G E L +L+YLNL+ N
Sbjct: 137 KLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCN 196
Query: 576 ICELPIGIKSCTHLRTLLLDGTENLKAIPVGMLSSLLSLR 615
+ E+P + L L L G +L AI G L+ L+
Sbjct: 197 LREIP-NLTPLIKLDELDLSG-NHLSAIRPGSFQGLMHLQ 234
>pdb|3MD0|A Chain A, Crystal Structure Of ArginineORNITHINE TRANSPORT SYSTEM
ATPASE FROM Mycobacterium Tuberculosis Bound To Gdp (A
Ras-Like Gtpase Superfamily Protein)
pdb|3P32|A Chain A, Hydrolysis Of Gtp To Gdp By An Mcm-Associated And Meab-
And Mmaa-Like G-Protein From Mycobacterium Tuberculosis
pdb|4GT1|A Chain A, Crystal Structure Of A Meab- And Mmaa-Like Gtpase From
Mycobacterium Tuberculosis Bound To 2'-Deoxyguanosine
Diphosphate
Length = 355
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 154 IGLYGVRGVGKSTLLKQLNDTFSDMSHKFGAVIMVKASTELNIEKIQDVIR-SRLGIDPD 212
+G+ GV GVGKST ++ L + H+ + + +ST + D R +RL + P+
Sbjct: 82 VGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGGSILGDKTRMARLAVHPN 141
>pdb|2V66|B Chain B, Crystal Structure Of The Coiled-Coil Domain Of Ndel1 (A.A.
58 To 169)c
pdb|2V66|C Chain C, Crystal Structure Of The Coiled-Coil Domain Of Ndel1 (A.A.
58 To 169)c
pdb|2V66|D Chain D, Crystal Structure Of The Coiled-Coil Domain Of Ndel1 (A.A.
58 To 169)c
pdb|2V66|E Chain E, Crystal Structure Of The Coiled-Coil Domain Of Ndel1 (A.A.
58 To 169)c
Length = 111
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 24 YIRHLEANVDALSQAERELDSSCKDVSGRIEQAIEADFVPREQRGEKE 71
Y+R LE D L +A+R S +D R+ QAIE + + EKE
Sbjct: 57 YVRELEQANDDLERAKRATIVSLEDFEQRLNQAIERNAFLESELDEKE 104
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 310 EIRELAETVANMCGGLPLALVTIGSAMASRRDPDNWRYAIEELQ 353
++ E A ++ C G PL + IG+ + R P+ W Y +++LQ
Sbjct: 305 DLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYLKQLQ 346
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 31.2 bits (69), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 310 EIRELAETVANMCGGLPLALVTIGSAMASRRDPDNWRYAIEELQ 353
++ E A ++ C G PL + IG+ + R P+ W Y +++LQ
Sbjct: 311 DLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYLKQLQ 352
>pdb|3TK1|A Chain A, Crystal Structure Of A Meab And Rv1496 Ortholog From
Mycobacterium Thermoresistible Bound To Gdp
pdb|3TK1|B Chain B, Crystal Structure Of A Meab And Rv1496 Ortholog From
Mycobacterium Thermoresistible Bound To Gdp
Length = 330
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 154 IGLYGVRGVGKSTLLKQLNDTFSDMSHKFGAVIMVKASTELNIEKIQDVIR-SRLGIDPD 212
+G+ GV GVGKST ++ L + H+ + + +S + D R +RL + PD
Sbjct: 59 VGITGVPGVGKSTSIEALGMHLIEQGHRVAVLAVDPSSVRSGGSILGDKTRMARLAVHPD 118
>pdb|4A9A|A Chain A, Structure Of Rbg1 In Complex With Tma46 Dfrp Domain
pdb|4A9A|B Chain B, Structure Of Rbg1 In Complex With Tma46 Dfrp Domain
Length = 376
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 150 GVKIIGLYGVRGVGKSTLLKQLNDTFSDMS-HKFGAVIMVKASTELNIEKIQDVIRSRLG 208
GV +G G VGKSTLL +L T S+ + ++F ++ V KIQ
Sbjct: 71 GVASVGFVGFPSVGKSTLLSKLTGTESEAAEYEFTTLVTVPGVIRYKGAKIQ-------M 123
Query: 209 IDPDGDKWKNRDDQGRAAEIF 229
+D G +D +GR ++
Sbjct: 124 LDLPGIIDGAKDGRGRGKQVI 144
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 3/100 (3%)
Query: 517 RLLTLLVRYTMIKEFENKFFKSMYALRVLDSSQNAKLSKLHVGEGE-LIDLQYLNLSNTN 575
+L L +R I+ + F + +LR LD + +L + E L++L+YLNL N
Sbjct: 108 KLRELWLRNNPIESIPSYAFNRVPSLRRLDLGELKRLEYISEAAFEGLVNLRYLNLGMCN 167
Query: 576 ICELPIGIKSCTHLRTLLLDGTENLKAIPVGMLSSLLSLR 615
+ ++P + + L L L G L I G L SLR
Sbjct: 168 LKDIP-NLTALVRLEELELSGNR-LDLIRPGSFQGLTSLR 205
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 3/100 (3%)
Query: 517 RLLTLLVRYTMIKEFENKFFKSMYALRVLDSSQNAKLSKLHVGEGE-LIDLQYLNLSNTN 575
+L L +R I+ + F + +LR LD + +L + E L++L+YLNL N
Sbjct: 108 KLRELWLRNNPIESIPSYAFNRVPSLRRLDLGELKRLEYISEAAFEGLVNLRYLNLGMCN 167
Query: 576 ICELPIGIKSCTHLRTLLLDGTENLKAIPVGMLSSLLSLR 615
+ ++P + + L L L G L I G L SLR
Sbjct: 168 LKDIP-NLTALVRLEELELSGNR-LDLIRPGSFQGLTSLR 205
>pdb|2YNM|A Chain A, Structure Of The Adpxalf3-stabilized Transition State Of
The Nitrogenase-like Dark-operative Protochlorophyllide
Oxidoreductase Complex From Prochlorococcus Marinus With
Its Substrate Protochlorophyllide A
pdb|2YNM|B Chain B, Structure Of The Adpxalf3-stabilized Transition State Of
The Nitrogenase-like Dark-operative Protochlorophyllide
Oxidoreductase Complex From Prochlorococcus Marinus With
Its Substrate Protochlorophyllide A
Length = 301
Score = 29.6 bits (65), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 148 DDGVKIIGLYGVRGVGKSTLLKQLNDTFSDMSHK 181
++G +I +YG G+GKST L+ FS + K
Sbjct: 31 EEGALVIAVYGKGGIGKSTTSSNLSAAFSKLGKK 64
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
0.320 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,854,589
Number of Sequences: 62578
Number of extensions: 783364
Number of successful extensions: 1963
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 1939
Number of HSP's gapped (non-prelim): 53
length of query: 798
length of database: 14,973,337
effective HSP length: 107
effective length of query: 691
effective length of database: 8,277,491
effective search space: 5719746281
effective search space used: 5719746281
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)