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= psy6065
(316 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LXL|A Chain A, Lip5(mit)2
Length = 183
Score = 164 bits (414), Expect = 8e-41, Method: Compositional matrix adjust.
Identities = 75/144 (52%), Positives = 103/144 (71%)
Query: 12 LKAIQHFLNVASEHDNRDLTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKT 71
K+IQH L A EHD RD V+Y+CRL+A+Q +KID + + L KLMD LE KK
Sbjct: 14 FKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEALKKQ 73
Query: 72 HRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNKNVVKAFYTASILMDVLQTFGE 131
DN+ I E A++ENYALK+F +AD+ DRA F+KN++K+FYTAS+L+DV+ FGE
Sbjct: 74 LGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLLIDVITVFGE 133
Query: 132 TSEDIEQNKKYAKWKAAYIHNCLK 155
+++ +++KYA+WKA YIHNCLK
Sbjct: 134 LTDENVKHRKYARWKATYIHNCLK 157
>pdb|2LXM|A Chain A, Lip5-chmp5
Length = 168
Score = 163 bits (413), Expect = 9e-41, Method: Compositional matrix adjust.
Identities = 75/144 (52%), Positives = 103/144 (71%)
Query: 12 LKAIQHFLNVASEHDNRDLTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKT 71
K+IQH L A EHD RD V+Y+CRL+A+Q +KID + + L KLMD LE KK
Sbjct: 14 FKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEALKKQ 73
Query: 72 HRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNKNVVKAFYTASILMDVLQTFGE 131
DN+ I E A++ENYALK+F +AD+ DRA F+KN++K+FYTAS+L+DV+ FGE
Sbjct: 74 LGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLLIDVITVFGE 133
Query: 132 TSEDIEQNKKYAKWKAAYIHNCLK 155
+++ +++KYA+WKA YIHNCLK
Sbjct: 134 LTDENVKHRKYARWKATYIHNCLK 157
>pdb|2RKL|A Chain A, Crystal Structure Of S.cerevisiae Vta1 C-terminal Domain
pdb|2RKL|B Chain B, Crystal Structure Of S.cerevisiae Vta1 C-terminal Domain
pdb|2RKL|C Chain C, Crystal Structure Of S.cerevisiae Vta1 C-terminal Domain
pdb|2RKL|D Chain D, Crystal Structure Of S.cerevisiae Vta1 C-terminal Domain
pdb|2RKL|E Chain E, Crystal Structure Of S.cerevisiae Vta1 C-terminal Domain
pdb|2RKL|F Chain F, Crystal Structure Of S.cerevisiae Vta1 C-terminal Domain
Length = 53
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%)
Query: 277 INKCQKYIKFASSALNYDDYKEAKSNLIKVLNILNT 312
I + QK K+A SALNY+D AK L K L++LN+
Sbjct: 17 IEQIQKLAKYAISALNYEDLPTAKDELTKALDLLNS 52
>pdb|3MHV|A Chain A, Crystal Structure Of Vps4 And Vta1
Length = 42
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%)
Query: 277 INKCQKYIKFASSALNYDDYKEAKSNLIKVLNILNT 312
I + QK K+A SALNY+D AK L K L++LN+
Sbjct: 6 IEQIQKLAKYAISALNYEDLPTAKDELTKALDLLNS 41
>pdb|1VH6|A Chain A, Crystal Structure Of A Flagellar Protein
pdb|1VH6|B Chain B, Crystal Structure Of A Flagellar Protein
Length = 145
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 276 LINKCQKYIKFASSALNYDDYKEAKSNLIKVLNIL 310
L N C K+I+ A+ A+ DD + NLIK NI+
Sbjct: 29 LYNGCLKFIRLAAQAIENDDXERKNENLIKAQNII 63
>pdb|4HOQ|A Chain A, Crystal Structure Of Full-length Human Ifit5
Length = 482
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 38 LHALQKALKIDKSSDGAKMLL-LKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLF 96
L L+KA+ ++ + K+ L LKL D + E + + + I+++ ++Q Y+ YA K +
Sbjct: 201 LGPLRKAVTLNPDNSYIKVFLALKLQD-VHAEAEGEKYIEEILDQISSQPYVLRYAAKFY 259
Query: 97 QWADSMDRASTFNKNVVKAFYTASIL 122
+ +S ++A K ++ T+S L
Sbjct: 260 RRKNSWNKALELLKKALEVTPTSSFL 285
>pdb|3ZGQ|A Chain A, Crystal Structure Of Human Interferon-induced Protein
Ifit5
pdb|4HOR|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligocytidine
pdb|4HOS|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligouridine
pdb|4HOT|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligoadenine
pdb|4J0U|A Chain A, Crystal Structure Of Ifit5/isg58
Length = 482
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 38 LHALQKALKIDKSSDGAKMLL-LKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLF 96
L L+KA+ ++ + K+ L LKL D + E + + + I+++ ++Q Y+ YA K +
Sbjct: 201 LGPLRKAVTLNPDNSYIKVFLALKLQD-VHAEAEGEKYIEEILDQISSQPYVLRYAAKFY 259
Query: 97 QWADSMDRASTFNKNVVKAFYTASIL 122
+ +S ++A K ++ T+S L
Sbjct: 260 RRKNSWNKALELLKKALEVTPTSSFL 285
>pdb|3GHG|B Chain B, Crystal Structure Of Human Fibrinogen
pdb|3GHG|E Chain E, Crystal Structure Of Human Fibrinogen
pdb|3GHG|H Chain H, Crystal Structure Of Human Fibrinogen
pdb|3GHG|K Chain K, Crystal Structure Of Human Fibrinogen
Length = 461
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 271 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 325
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 326 YGGFTVQNE 334
>pdb|3H32|B Chain B, Crystal Structure Of D-Dimer From Human Fibrin Complexed
With Gly-His- Arg-Pro-Tyr-Amide
pdb|3H32|E Chain E, Crystal Structure Of D-Dimer From Human Fibrin Complexed
With Gly-His- Arg-Pro-Tyr-Amide
Length = 458
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 271 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 325
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 326 YGGFTVQNE 334
>pdb|3E1I|B Chain B, Crystal Structure Of Bbetad432a Variant Fibrinogen
Fragment D With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|3E1I|E Chain E, Crystal Structure Of Bbetad432a Variant Fibrinogen
Fragment D With The Peptide Ligand Gly-His-Arg-Pro-Amide
Length = 328
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 138 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 192
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 193 YGGFTVQNE 201
>pdb|2Z4E|B Chain B, Crystal Structure Of D-dimer From Human Fibrin Complexed
With Gly-his- Arg-pro-tyr-amide
pdb|2Z4E|E Chain E, Crystal Structure Of D-dimer From Human Fibrin Complexed
With Gly-his- Arg-pro-tyr-amide
Length = 326
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 138 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 192
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 193 YGGFTVQNE 201
>pdb|1FZA|B Chain B, Crystal Structure Of Fibrinogen Fragment D
pdb|1FZA|E Chain E, Crystal Structure Of Fibrinogen Fragment D
pdb|1FZB|B Chain B, Crystal Structure Of Crosslinked Fragment D
pdb|1FZB|E Chain E, Crystal Structure Of Crosslinked Fragment D
pdb|1FZC|B Chain B, Crystal Structure Of Fragment Double-d From Human Fibrin
With Two Different Bound Ligands
pdb|1FZC|E Chain E, Crystal Structure Of Fragment Double-d From Human Fibrin
With Two Different Bound Ligands
pdb|1FZE|B Chain B, Crystal Structure Of Fragment Double-D From Human Fibrin
pdb|1FZE|E Chain E, Crystal Structure Of Fragment Double-D From Human Fibrin
pdb|1FZF|B Chain B, Crystal Structure Of Fragment Double-D From Human Fibrin
With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|1FZF|E Chain E, Crystal Structure Of Fragment Double-D From Human Fibrin
With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|1FZG|B Chain B, Crystal Structure Of Fragment D From Human Fibrinogen With
The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|1FZG|E Chain E, Crystal Structure Of Fragment D From Human Fibrinogen With
The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|1N86|B Chain B, Crystal Structure Of Human D-Dimer From Cross-Linked
Fibrin Complexed With Gpr And Ghrpldk Peptide Ligands.
pdb|1N86|E Chain E, Crystal Structure Of Human D-Dimer From Cross-Linked
Fibrin Complexed With Gpr And Ghrpldk Peptide Ligands.
pdb|1N8E|B Chain B, Fragment Double-D From Human Fibrin
pdb|1N8E|E Chain E, Fragment Double-D From Human Fibrin
pdb|2H43|B Chain B, Crystal Structure Of Human Fragment D Complexed With
Ala-His-Arg-Pro- Amide
pdb|2H43|E Chain E, Crystal Structure Of Human Fragment D Complexed With
Ala-His-Arg-Pro- Amide
pdb|2HOD|B Chain B, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-hydroxypro-arg-pro-amide
pdb|2HOD|E Chain E, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-hydroxypro-arg-pro-amide
pdb|2HOD|H Chain H, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-hydroxypro-arg-pro-amide
pdb|2HOD|K Chain K, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-hydroxypro-arg-pro-amide
pdb|2HPC|B Chain B, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-Pro-Arg-Pro-Amide.
pdb|2HPC|E Chain E, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-Pro-Arg-Pro-Amide.
pdb|2HPC|H Chain H, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-Pro-Arg-Pro-Amide.
pdb|2HPC|K Chain K, Crystal Structure Of Fragment D From Human Fibrinogen
Complexed With Gly-Pro-Arg-Pro-Amide.
pdb|2HLO|B Chain B, Crystal Structure Of Fragment D-Dimer From Human Fibrin
Complexed With Gly-Hydroxypro-Arg-Pro-Amide
pdb|2HLO|E Chain E, Crystal Structure Of Fragment D-Dimer From Human Fibrin
Complexed With Gly-Hydroxypro-Arg-Pro-Amide
pdb|2Q9I|B Chain B, Crystal Structure Of D-dimer From Human Fibrin Complexed
With Met-his- Arg-pro-tyr-amide.
pdb|2Q9I|E Chain E, Crystal Structure Of D-dimer From Human Fibrin Complexed
With Met-his- Arg-pro-tyr-amide.
pdb|2XNX|B Chain B, Bc1 Fragment Of Streptococcal M1 Protein In Complex With
Human Fibrinogen
pdb|2XNX|E Chain E, Bc1 Fragment Of Streptococcal M1 Protein In Complex With
Human Fibrinogen
pdb|2XNX|H Chain H, Bc1 Fragment Of Streptococcal M1 Protein In Complex With
Human Fibrinogen
pdb|2XNX|K Chain K, Bc1 Fragment Of Streptococcal M1 Protein In Complex With
Human Fibrinogen
pdb|2XNY|B Chain B, A Fragment Of Streptococcal M1 Protein In Complex With
Human Fibrinogen
pdb|2XNY|E Chain E, A Fragment Of Streptococcal M1 Protein In Complex With
Human Fibrinogen
Length = 328
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 138 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 192
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 193 YGGFTVQNE 201
>pdb|1RE3|B Chain B, Crystal Structure Of Fragment D Of Bbetad398a Fibrinogen
With The Peptide Ligand Gly-his-arg-pro-amide
pdb|1RE3|E Chain E, Crystal Structure Of Fragment D Of Bbetad398a Fibrinogen
With The Peptide Ligand Gly-his-arg-pro-amide
pdb|1RE4|B Chain B, Crystal Structure Of Fragment D Of Bbetad398a Fibrinogen
pdb|1RE4|E Chain E, Crystal Structure Of Fragment D Of Bbetad398a Fibrinogen
Length = 313
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 123 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 177
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 178 YGGFTVQNE 186
>pdb|1LT9|B Chain B, Crystal Structure Of Recombinant Human Fibrinogen Fragment
D
pdb|1LT9|E Chain E, Crystal Structure Of Recombinant Human Fibrinogen Fragment
D
pdb|1LTJ|B Chain B, Crystal Structure Of Recombinant Human Fibrinogen Fragment
D With The Peptide Ligands Gly-Pro-Arg-Pro-Amide And
Gly-His-Arg-Pro-Amide
pdb|1LTJ|E Chain E, Crystal Structure Of Recombinant Human Fibrinogen Fragment
D With The Peptide Ligands Gly-Pro-Arg-Pro-Amide And
Gly-His-Arg-Pro-Amide
pdb|1RF0|B Chain B, Crystal Structure Of Fragment D Of Gammae132a Fibrinogen
pdb|1RF0|E Chain E, Crystal Structure Of Fragment D Of Gammae132a Fibrinogen
pdb|1RF1|B Chain B, Crystal Structure Of Fragment D Of Gammae132a Fibrinogen
With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|1RF1|E Chain E, Crystal Structure Of Fragment D Of Gammae132a Fibrinogen
With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|2FFD|B Chain B, Fibrinogen Fragment D With "a" Knob Peptide Mimic Gprvve
pdb|2FFD|E Chain E, Fibrinogen Fragment D With "a" Knob Peptide Mimic Gprvve
pdb|2OYH|B Chain B, Crystal Structure Of Fragment D Of Gammad298,301a
Fibrinogen With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|2OYH|E Chain E, Crystal Structure Of Fragment D Of Gammad298,301a
Fibrinogen With The Peptide Ligand Gly-His-Arg-Pro-Amide
pdb|2OYI|B Chain B, Crystal Structure Of Fragment D Of Gammad298,301a
Fibrinogen With The Peptide Ligand Gly-Pro-Arg-Pro-Amide
pdb|2OYI|E Chain E, Crystal Structure Of Fragment D Of Gammad298,301a
Fibrinogen With The Peptide Ligand Gly-Pro-Arg-Pro-Amide
pdb|3HUS|B Chain B, Crystal Structure Of Recombinant Gamma N308k Fibrinogen
Fragment D With The Peptide Ligand Gly-Pro-Arg-Pro-Amide
pdb|3HUS|E Chain E, Crystal Structure Of Recombinant Gamma N308k Fibrinogen
Fragment D With The Peptide Ligand Gly-Pro-Arg-Pro-Amide
Length = 313
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 123 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 177
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 178 YGGFTVQNE 186
>pdb|3BVH|B Chain B, Crystal Structure Of Recombinant Gammad364a Fibrinogen
Fragment D With The Peptide Ligand Gly-Pro-Arg-Pro-Amide
pdb|3BVH|E Chain E, Crystal Structure Of Recombinant Gammad364a Fibrinogen
Fragment D With The Peptide Ligand Gly-Pro-Arg-Pro-Amide
Length = 298
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 16 QHFLNVASEHDNRD---LTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKKTH 72
Q F NVA+ D ++ L YW + + ++ G LL+++ DW + K H
Sbjct: 111 QGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRM-----GPTELLIEMEDWKGDKVKAH 165
Query: 73 RDNDTIMNE 81
T+ NE
Sbjct: 166 YGGFTVQNE 174
>pdb|3VRI|A Chain A, Hla-B57:01-Rvaqlenvyi In Complex With Abacavir
pdb|3VRJ|A Chain A, Hla-B57:01-Lttkltntni In Complex With Abacavir
Length = 276
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 11/104 (10%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNK 110
SD A + W+EQE + D +T + +AQ Y EN + L + S
Sbjct: 38 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIALRYY-----NQSEAGS 92
Query: 111 NVVKAFYTASILMD--VLQTFGETSED----IEQNKKYAKWKAA 148
++++ Y + D +L+ +++ D I N+ + W AA
Sbjct: 93 HIIQVMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAA 136
>pdb|3UPR|A Chain A, Hla-B57:01 Complexed To Pep-V And Abacavir
pdb|3UPR|C Chain C, Hla-B57:01 Complexed To Pep-V And Abacavir
Length = 277
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 11/104 (10%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNK 110
SD A + W+EQE + D +T + +AQ Y EN + L + S
Sbjct: 39 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIALRYY-----NQSEAGS 93
Query: 111 NVVKAFYTASILMD--VLQTFGETSED----IEQNKKYAKWKAA 148
++++ Y + D +L+ +++ D I N+ + W AA
Sbjct: 94 HIIQVMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAA 137
>pdb|2HJK|A Chain A, Crystal Structure Of Hla-B5703 And Hiv-1 Peptide
pdb|2HJL|A Chain A, Crystal Structure Of Hla-B5703 And Hiv-1 Peptide
Length = 274
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 11/104 (10%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNK 110
SD A + W+EQE + D +T + +AQ Y EN + L + S
Sbjct: 38 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIALRYY-----NQSEAGS 92
Query: 111 NVVKAFYTASILMD--VLQTFGETSED----IEQNKKYAKWKAA 148
++++ Y + D +L+ +++ D I N+ + W AA
Sbjct: 93 HIIQVMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAA 136
>pdb|2BVO|A Chain A, Structures Of Three Hiv-1 Hla-B5703-Peptide Complexes
And Identification Of Related Hlas Potentially
Associated With Long-Term Non-Progression
pdb|2BVP|A Chain A, Structures Of Three Hiv-1 Hla-B5703-Peptide Complexes
And Identification Of Related Hlas Potentially
Associated With Long-Term Non-Progression
pdb|2BVQ|A Chain A, Structures Of Three Hiv-1 Hla-B5703-Peptide Complexes
And Identification Of Related Hlas Potentially
Associated With Long-Term Non-Progression
Length = 276
Score = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKL 95
SD A + W+EQE + D +T + +AQ Y EN + L
Sbjct: 38 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIAL 82
>pdb|2YPK|A Chain A, Structural Features Underlying T-cell Receptor Sensitivity
To Concealed Mhc Class I Micropolymorphisms
Length = 274
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 11/104 (10%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNK 110
SD A + W+EQE + D +T + +AQ Y EN + L + S
Sbjct: 38 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIALRYY-----NQSEAGS 92
Query: 111 NVVKAFYTASILMD--VLQTFGETSED----IEQNKKYAKWKAA 148
++++ Y + D +L+ +++ D I N+ + W AA
Sbjct: 93 HIIQVMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAA 136
>pdb|2RFX|A Chain A, Crystal Structure Of Hla-B5701, Presenting The Self
Peptide, Lsspvtksf
pdb|3VH8|A Chain A, Kir3dl1 In Complex With Hla-B5701
pdb|3VH8|D Chain D, Kir3dl1 In Complex With Hla-B5701
Length = 275
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 11/104 (10%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKLFQWADSMDRASTFNK 110
SD A + W+EQE + D +T + +AQ Y EN + L + S
Sbjct: 38 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIALRYY-----NQSEAGS 92
Query: 111 NVVKAFYTASILMD--VLQTFGETSED----IEQNKKYAKWKAA 148
++++ Y + D +L+ +++ D I N+ + W AA
Sbjct: 93 HIIQVMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAA 136
>pdb|2YPL|A Chain A, Structural Features Underlying T-cell Receptor
Sensitivity To Concealed Mhc Class I Micropolymorphisms
Length = 274
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKL 95
SD A + W+EQE + D +T + +AQ Y EN + L
Sbjct: 38 SDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIAL 82
>pdb|3W39|A Chain A, Crystal Structure Of Hla-b*5201 In Complexed With Hiv
Immunodominant Epitope (taftipsi)
pdb|3W39|D Chain D, Crystal Structure Of Hla-b*5201 In Complexed With Hiv
Immunodominant Epitope (taftipsi)
Length = 277
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 51 SDGAKMLLLKLMDWLEQEKKTHRDNDTIMNETAAQAYIENYALKL 95
SD A W+EQE + D +T +++T Q Y EN + L
Sbjct: 39 SDAASPRTEPRAPWIEQEGPEYWDRETQISKTNTQTYRENLRIAL 83
>pdb|1M6O|A Chain A, Crystal Structure Of Hla B4402 In Complex With Hla Dpa0201
Peptide
pdb|3DX6|A Chain A, Crystal Structure Of B4402 Presenting A 10mer Ebv Epitope
pdb|3KPL|A Chain A, Crystal Structure Of Hla B4402 In Complex With Eeylqafty A
Self Peptide From The Abcd3 Protein
pdb|3KPM|A Chain A, Crystal Structure Of Hla B4402 In Complex With Eeylkawtf,
A Mimotope
pdb|3L3D|A Chain A, Crystal Structure Of Hla-B4402 In Complex With The F3a
Mutant Of A Self-Peptide Derived From Dpa0201
pdb|3L3G|A Chain A, Crystal Structure Of Hla-B4402 In Complex With The R5a
Mutant Of A Self-Peptide Derived From Dpa0201
pdb|3L3I|A Chain A, Crystal Structure Of Hla-B4402 In Complex With The F7a
Mutant Of A Self-Peptide Derived From Dpa0201
pdb|3L3J|A Chain A, Crystal Structure Of Hla-B4402 In Complex With The F3aR5A
DOUBLE Mutant Of A Self-Peptide Derived From Dpa0201
pdb|3L3K|A Chain A, Crystal Structure Of Hla-b*4402 In Complex With The
R5a/f7a Double Mutant Of A Self-peptide Derived From
Dpa*0201
Length = 276
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 31/146 (21%), Positives = 59/146 (40%), Gaps = 21/146 (14%)
Query: 11 SLKAIQHFLNVASEHDNRDLTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKK 70
S++ ++ + R +TV Y + L + SD W+EQE
Sbjct: 4 SMRYFYTAMSRPGRGEPRFITVGY------VDDTLFVRFDSDATSPRKEPRAPWIEQEGP 57
Query: 71 THRDNDTIMNETAAQAYIENY--ALKLFQWADSMDRASTFNKNVVKAFYTASILMD--VL 126
+ D +T +++T Q Y EN AL+ + S ++++ Y + D +L
Sbjct: 58 EYWDRETQISKTNTQTYRENLRTALRYYN-------QSEAGSHIIQRMYGCDVGPDGRLL 110
Query: 127 QTFGETSED----IEQNKKYAKWKAA 148
+ + + + D I N+ + W AA
Sbjct: 111 RGYDQDAYDGKDYIALNEDLSSWTAA 136
>pdb|1N2R|A Chain A, A Natural Selected Dimorphism In Hla B44 Alters Self,
Peptide Reportoire And T Cell Recognition.
pdb|1SYS|A Chain A, Crystal Structure Of Hla, B4403, And Peptide Eeptvikky
pdb|3DX7|A Chain A, Crystal Structure Of Hla-B4403 Presenting 10mer Ebv
Antigen
pdb|3KPN|A Chain A, Crystal Structure Of Hla B4403 In Complex With Eeylqafty A
Self Peptide From The Abcd3 Protein
pdb|3KPO|A Chain A, Crystal Structure Of Hla B*4403 In Complex With Eeylkawtf,
A Mimotope
Length = 276
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 31/146 (21%), Positives = 59/146 (40%), Gaps = 21/146 (14%)
Query: 11 SLKAIQHFLNVASEHDNRDLTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKK 70
S++ ++ + R +TV Y + L + SD W+EQE
Sbjct: 4 SMRYFYTAMSRPGRGEPRFITVGY------VDDTLFVRFDSDATSPRKEPRAPWIEQEGP 57
Query: 71 THRDNDTIMNETAAQAYIENY--ALKLFQWADSMDRASTFNKNVVKAFYTASILMD--VL 126
+ D +T +++T Q Y EN AL+ + S ++++ Y + D +L
Sbjct: 58 EYWDRETQISKTNTQTYRENLRTALRYYN-------QSEAGSHIIQRMYGCDVGPDGRLL 110
Query: 127 QTFGETSED----IEQNKKYAKWKAA 148
+ + + + D I N+ + W AA
Sbjct: 111 RGYDQDAYDGKDYIALNEDLSSWTAA 136
>pdb|1SYV|A Chain A, Hla-B4405 Complexed To The Dominant Self Ligand Eefgraygf
pdb|3DX8|A Chain A, Crystal Structure Of B4405 Presenting A 10mer Ebv Epitope
pdb|3DXA|A Chain A, Crystal Structure Of The Dm1 Tcr In Complex With Hla-B4405
And Decamer Ebv Antigen
pdb|3DXA|F Chain F, Crystal Structure Of The Dm1 Tcr In Complex With Hla-B4405
And Decamer Ebv Antigen
pdb|3DXA|K Chain K, Crystal Structure Of The Dm1 Tcr In Complex With Hla-B4405
And Decamer Ebv Antigen
pdb|3KPP|A Chain A, Crystal Structure Of Hla B4405 In Complex With Eeylqafty A
Self Peptide From The Abcd3 Protein
pdb|3KPQ|A Chain A, Crystal Structure Of Hla B*4405 In Complex With Eeylkawtf,
A Mimotope
pdb|3KPR|A Chain A, Crystal Structure Of The Lc13 Tcr In Complex With Hla
B4405 Bound To Eeylkawtf A Mimotope
pdb|3KPR|F Chain F, Crystal Structure Of The Lc13 Tcr In Complex With Hla
B4405 Bound To Eeylkawtf A Mimotope
pdb|3KPS|A Chain A, Crystal Structure Of The Lc13 Tcr In Complex With Hla
B4405 Bound To Eeylqafty A Self Peptide From The Abcd3
Protein
Length = 276
Score = 27.7 bits (60), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 31/146 (21%), Positives = 59/146 (40%), Gaps = 21/146 (14%)
Query: 11 SLKAIQHFLNVASEHDNRDLTVSYWCRLHALQKALKIDKSSDGAKMLLLKLMDWLEQEKK 70
S++ ++ + R +TV Y + L + SD W+EQE
Sbjct: 4 SMRYFYTAMSRPGRGEPRFITVGY------VDDTLFVRFDSDATSPRKEPRAPWIEQEGP 57
Query: 71 THRDNDTIMNETAAQAYIENY--ALKLFQWADSMDRASTFNKNVVKAFYTASILMD--VL 126
+ D +T +++T Q Y EN AL+ + S ++++ Y + D +L
Sbjct: 58 EYWDRETQISKTNTQTYRENLRTALRYYN-------QSEAGSHIIQRMYGCDVGPDGRLL 110
Query: 127 QTFGETSED----IEQNKKYAKWKAA 148
+ + + + D I N+ + W AA
Sbjct: 111 RGYDQYAYDGKDYIALNEDLSSWTAA 136
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
0.314 0.128 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,646,144
Number of Sequences: 62578
Number of extensions: 198925
Number of successful extensions: 608
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 588
Number of HSP's gapped (non-prelim): 38
length of query: 316
length of database: 14,973,337
effective HSP length: 99
effective length of query: 217
effective length of database: 8,778,115
effective search space: 1904850955
effective search space used: 1904850955
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)