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= 047048
(240 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3II6|A Chain A, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|B Chain B, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|C Chain C, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|D Chain D, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv
Length = 203
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/187 (25%), Positives = 83/187 (44%), Gaps = 26/187 (13%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A + +Y+ +L + L
Sbjct: 19 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMEMEKGKYVGELRKALLSGA 78
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNSKKVPAGILDFLMDANI 132
P VY F + + C + FEK + +R + N +V ++ + +D
Sbjct: 79 GPADVYTFNFSKESC---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTTA 135
Query: 133 RLSAEKCLAQSE-------------RFK---NEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
A+ Q E RF+ + K E+ +Y +F+ VLN KK+K+R L
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLH 195
Query: 177 DKLSKQA 183
+KL A
Sbjct: 196 NKLLNAA 202
>pdb|1FU1|A Chain A, Crystal Structure Of Human Xrcc4
pdb|1FU1|B Chain B, Crystal Structure Of Human Xrcc4
Length = 203
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 46/187 (24%), Positives = 81/187 (43%), Gaps = 26/187 (13%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 19 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNSKKVPAGILDFLMDANI 132
P VY F + + + FEK + +R + N +V ++ + +D
Sbjct: 79 GPADVYTFNFSKESX---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIXYXLDTTA 135
Query: 133 RLSAEKCLAQSE-------------RFK---NEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
A+ Q E RF+ + K E+ +Y +F+ VLN KK+K+R L
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKXVSAKEALETDLYKRFILVLNEKKTKIRSLH 195
Query: 177 DKLSKQA 183
+KL A
Sbjct: 196 NKLLNAA 202
>pdb|1IK9|A Chain A, Crystal Structure Of A Xrcc4-Dna Ligase Iv Complex
pdb|1IK9|B Chain B, Crystal Structure Of A Xrcc4-Dna Ligase Iv Complex
Length = 213
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 83/183 (45%), Gaps = 26/183 (14%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 19 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKC-------GPAPNSKKVPAGILDFLM 128
P VY F + + + FEK + +R PA +++ A LD +
Sbjct: 79 GPADVYTFNFSKESA---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIA 135
Query: 129 -----DANIRLSAEKCL-------AQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
+ +++ E+ L + E+ + K E+ +Y +F+ VLN KK+K+R L
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLH 195
Query: 177 DKL 179
+KL
Sbjct: 196 NKL 198
>pdb|3MUD|A Chain A, Structure Of The Tropomyosin Overlap Complex From Chicken
Smooth Muscle
pdb|3MUD|B Chain B, Structure Of The Tropomyosin Overlap Complex From Chicken
Smooth Muscle
Length = 175
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 22 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 81
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR 107
P VY F + + C + FEK + +R
Sbjct: 82 GPADVYTFNFSKESCY---FFFEKNLKDVSFR 110
>pdb|3SR2|A Chain A, Crystal Structure Of Human Xlf-Xrcc4 Complex
pdb|3SR2|B Chain B, Crystal Structure Of Human Xlf-Xrcc4 Complex
pdb|3SR2|E Chain E, Crystal Structure Of Human Xlf-Xrcc4 Complex
pdb|3SR2|F Chain F, Crystal Structure Of Human Xlf-Xrcc4 Complex
Length = 145
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 24 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 83
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR 107
P VY F + + C + FEK + +R
Sbjct: 84 GPADVYTFNFSKESCY---FFFEKNLKDVSFR 112
>pdb|3W03|C Chain C, Xlf-Xrcc4 Complex
pdb|3W03|D Chain D, Xlf-Xrcc4 Complex
Length = 184
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 39 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 98
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR 107
P VY F + + C + FEK + +R
Sbjct: 99 GPADVYTFNFSKESC---YFFFEKNLKDVSFR 127
>pdb|3RWR|A Chain A, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|B Chain B, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|F Chain F, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|G Chain G, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|J Chain J, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|K Chain K, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|N Chain N, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|P Chain P, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|R Chain R, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|V Chain V, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|U Chain U, Crystal Structure Of The Human Xrcc4-Xlf Complex
pdb|3RWR|Y Chain Y, Crystal Structure Of The Human Xrcc4-Xlf Complex
Length = 163
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 19 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR 107
P VY F + + C + FEK + +R
Sbjct: 79 GPADVYTFNFSKESCY---FFFEKNLKDVSFR 107
>pdb|3Q4F|C Chain C, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
pdb|3Q4F|D Chain D, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
pdb|3Q4F|G Chain G, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
pdb|3Q4F|H Chain H, Crystal Structure Of Xrcc4XLF-Cernunnos Complex
Length = 186
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
F++ +W +S F +++TDG +AW SE ++ A +Y+ +L + L
Sbjct: 48 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 107
Query: 76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR 107
P VY F + + C + FEK + +R
Sbjct: 108 GPADVYTFNFSKESCY---FFFEKNLKDVSFR 136
>pdb|1G9N|G Chain G, Hiv-1 Yu2 Gp120 Envelope Glycoprotein Complexed With Cd4
And Induced Neutralizing Antibody 17b
pdb|1RZK|G Chain G, Hiv-1 Yu2 Gp120 Envelope Glycoprotein Complexed With Cd4
And Induced Neutralizing Antibody 17b
pdb|1YYL|G Chain G, Crystal Structure Of Cd4m33, A Scorpion-Toxin Mimic Of
Cd4, In Complex With Hiv-1 Yu2 Gp120 Envelope
Glycoprotein And Anti-Hiv-1 Antibody 17b
pdb|1YYL|P Chain P, Crystal Structure Of Cd4m33, A Scorpion-Toxin Mimic Of
Cd4, In Complex With Hiv-1 Yu2 Gp120 Envelope
Glycoprotein And Anti-Hiv-1 Antibody 17b
pdb|1YYM|G Chain G, Crystal Structure Of F23, A Scorpion-Toxin Mimic Of Cd4,
In Complex With Hiv-1 Yu2 Gp120 Envelope Glycoprotein
And Anti-Hiv-1 Antibody 17b
pdb|1YYM|P Chain P, Crystal Structure Of F23, A Scorpion-Toxin Mimic Of Cd4,
In Complex With Hiv-1 Yu2 Gp120 Envelope Glycoprotein
And Anti-Hiv-1 Antibody 17b
pdb|2I5Y|G Chain G, Crystal Structure Of Cd4m47, A Scorpion-Toxin Mimic Of
Cd4, In Complex With Hiv-1 Yu2 Gp120 Envelope
Glycoprotein And Anti-Hiv-1 Antibody 17b
pdb|2I5Y|P Chain P, Crystal Structure Of Cd4m47, A Scorpion-Toxin Mimic Of
Cd4, In Complex With Hiv-1 Yu2 Gp120 Envelope
Glycoprotein And Anti-Hiv-1 Antibody 17b
pdb|2I60|G Chain G, Crystal Structure Of [phe23]m47, A Scorpion-Toxin Mimic
Of Cd4, In Complex With Hiv-1 Yu2 Gp120 Envelope
Glycoprotein And Anti-Hiv-1 Antibody 17b
pdb|2I60|P Chain P, Crystal Structure Of [phe23]m47, A Scorpion-Toxin Mimic
Of Cd4, In Complex With Hiv-1 Yu2 Gp120 Envelope
Glycoprotein And Anti-Hiv-1 Antibody 17b
Length = 313
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
++T+ N W N E+ +D +LWDQ + +KL +G
Sbjct: 10 NVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVG 50
>pdb|4DVR|G Chain G, Crystal Structure Of Yu2 Gp120 Core In Complex With Fab
48d And Nbd- 557
Length = 313
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
++T+ N W N E+ +D +LWDQ + +KL
Sbjct: 6 NVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLT 41
>pdb|2NY1|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (I109c, T257s, S334a,
S375w, Q428c) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 5 VNVTENFNMWKNDMVEQMHEDICSLWDQSLKPCVKLTPLCVG 46
>pdb|3NGB|G Chain G, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|A Chain A, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|D Chain D, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|I Chain I, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3SE8|G Chain G, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc03 In Complex With Hiv-1 Gp120
pdb|3SE9|G Chain G, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc- Pg04 In Complex With Hiv-1 Gp120
pdb|3TGT|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade AE STRAIN
93TH057 GP120 Core
Length = 353
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
++T+ N W N E+ +D +LWDQ + +KL
Sbjct: 45 NVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLT 80
>pdb|3VQI|A Chain A, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|B Chain B, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|C Chain C, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|D Chain D, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|E Chain E, Crystal Structure Of Kluyveromyces Marxianus Atg5
Length = 274
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 65 IKLAERYLGFQQPGCVYGFTDAADG---CKRLSWTFEKEGTKLEWRWKCG 111
+ L + YLGF P V D +W FE G + W + CG
Sbjct: 41 VMLRDAYLGFYLPTVVRKLADTIKVPYESDYRNWWFEYNGEGVPWEYPCG 90
>pdb|4DKO|A Chain A, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Ts-Ii-224
pdb|4DKO|C Chain C, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Ts-Ii-224
pdb|4DKP|A Chain A, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Aws-I-50
pdb|4DKP|C Chain C, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Aws-I-50
pdb|4DKQ|A Chain A, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Dmj-I-228
pdb|4DKR|A Chain A, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Aws-I-169
pdb|4DKR|C Chain C, Crystal Structure Of Clade AE 93TH057 HIV-1 Gp120 Core
In Complex With Aws-I-169
pdb|4DVS|A Chain A, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With Nbd-557
pdb|4DVS|B Chain B, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With Nbd-557
pdb|4DVT|A Chain A, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With As-ii-37
pdb|4DVT|B Chain B, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With As-ii-37
pdb|4DVV|A Chain A, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With As-i-261
pdb|4DVV|B Chain B, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With As-i-261
pdb|4DVW|A Chain A, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With Mae-ii-167
pdb|4DVW|B Chain B, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With Mae-ii-167
pdb|4DVX|A Chain A, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With Mae-ii-188
pdb|4DVX|B Chain B, Crystal Structure Of Clade A/e 93th057 Hiv-1 Gp120 Core
In Complex With Mae-ii-188
Length = 353
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
++T+ N W N E+ +D +LWDQ + +KL
Sbjct: 45 NVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLT 80
>pdb|3TGQ|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
pdb|3TGQ|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
pdb|3TGQ|C Chain C, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
pdb|3TGQ|D Chain D, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
Length = 352
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
++T+ N W N E+ +D +LWDQ + +KL
Sbjct: 45 NVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLT 80
>pdb|2QAD|A Chain A, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
With Hiv-1 Yu2 Gp120 And Cd4
pdb|2QAD|E Chain E, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
With Hiv-1 Yu2 Gp120 And Cd4
Length = 322
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 34 ITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
+T+ N W N E+ +D +LWDQ + +KL
Sbjct: 1 VTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLT 35
>pdb|2NY2|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (T123c, T257s, S334a,
S375w, G431c) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 5 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLCPLCVG 46
>pdb|1GC1|G Chain G, Hiv-1 Gp120 Core Complexed With Cd4 And A Neutralizing
Human Antibody
Length = 321
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 9 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVG 50
>pdb|2NY4|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E268c,
S334a, S375w) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 5 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVG 46
>pdb|2NXY|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein(S334a) Complexed With
Cd4 And Antibody 17b
Length = 317
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 5 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVG 46
>pdb|2NY3|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E267c,
S334a, S375w) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 5 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVG 46
>pdb|1G9M|G Chain G, Hiv-1 Hxbc2 Gp120 Envelope Glycoprotein Complexed With
Cd4 And Induced Neutralizing Antibody 17b
pdb|1RZJ|G Chain G, Hiv-1 Hxbc2 Gp120 Envelope Glycoprotein Complexed With
Cd4 And Induced Neutralizing Antibody 17b
Length = 321
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 9 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVG 50
>pdb|2NXZ|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (t257s, S334a, S375w)
Complexed With Cd4 And Antibody 17b
Length = 317
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
+++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 5 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVG 46
>pdb|3U7Y|G Chain G, Structure Of Nih45-46 Fab In Complex With Gp120 Of
93th057 Hiv
Length = 361
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
++T+ N W N E+ +D +LWDQ + +KL
Sbjct: 45 NVTENFNMWKNNMVEQMQEDVISLWDQCLQPCVKLT 80
>pdb|3HI1|G Chain G, Structure Of Hiv-1 Gp120 (Core With V3) In Complex With
Cd4-Binding- Site Antibody F105
pdb|3HI1|J Chain J, Structure Of Hiv-1 Gp120 (Core With V3) In Complex With
Cd4-Binding- Site Antibody F105
Length = 321
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 35 TDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
T+ N W N E+ +D +LWDQ + +KL
Sbjct: 1 TENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLT 34
>pdb|2B4C|G Chain G, Crystal Structure Of Hiv-1 Jr-fl Gp120 Core Protein
Containing The Third Variable Region (v3) Complexed
With Cd4 And The X5 Antibody
Length = 344
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 33 SITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG 73
++T+ N W + E+ +D +LWDQ + +KL +G
Sbjct: 10 NVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVG 50
>pdb|3JWD|A Chain A, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWD|B Chain B, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 379
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
+++T+ N W + E+ +D +LWDQ + +KL
Sbjct: 57 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLT 93
>pdb|3JWO|A Chain A, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 357
Score = 27.7 bits (60), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 32 LSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLA 68
+++T+ N W + E+ +D +LWDQ + +KL
Sbjct: 54 VNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLT 90
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 0.132 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,507,020
Number of Sequences: 62578
Number of extensions: 250654
Number of successful extensions: 628
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 37
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
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: 50 (23.9 bits)