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= 011999
(473 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3T5O|A Chain A, Crystal Structure Of Human Complement Component C6
pdb|4A5W|B Chain B, Crystal Structure Of C5b6
pdb|4E0S|B Chain B, Crystal Structure Of C5b-6
Length = 913
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 37/181 (20%), Positives = 81/181 (44%), Gaps = 40/181 (22%)
Query: 69 VPYSWDPPLLASFIENYGTHIVTSITIGG-RDVVY---IRQHQSSPLSMMDIENYVKDIG 124
+P ++ L + +++GTH TS ++GG D++Y + ++S L+ + ++ V+
Sbjct: 324 LPLEYNSALYSRIFDDFGTHYFTSGSLGGVYDLLYQFSSEELKNSGLTEEEAKHCVRIET 383
Query: 125 DERFMDSK--------------SQSSAAPLKYKDKDVTVIFRRRGGDDL----------- 159
+R + +K + + ++ +K +++I RGG
Sbjct: 384 KKRVLFAKKTKVEHRCTTNKLSEKHEGSFIQGAEKSISLI---RGGRSEYGAALAWEKGS 440
Query: 160 ----EQSHAKWAETVQLAPDVINMTFTPIVSLLEGVPGI----KHLARAIELYLEYKPPI 211
E++ ++W E+V+ P VI+ PIV L+ +P +L +A++ Y P
Sbjct: 441 SGLEEKTFSEWLESVKENPAVIDFELAPIVDLVRNIPCAVTKRNNLRKALQEYAAKFDPC 500
Query: 212 E 212
+
Sbjct: 501 Q 501
>pdb|3OJY|A Chain A, Crystal Structure Of Human Complement Component C8
Length = 554
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 31/48 (64%), Gaps = 3/48 (6%)
Query: 53 KLAKLNLVLREEIRRAV---PYSWDPPLLASFIENYGTHIVTSITIGG 97
K+ K +++L E + +++ P ++ + A FI +YGTH +TS ++GG
Sbjct: 272 KMRKDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGG 319
>pdb|3NSJ|A Chain A, The X-Ray Crystal Structure Of Lymphocyte Perforin
Length = 540
Score = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 47/222 (21%), Positives = 99/222 (44%), Gaps = 56/222 (25%)
Query: 32 ADAAATKSLAMVGNFIS------LYKVKLAK---LNLVLREEIRRAVPYSWDPPLLASF- 81
A+ AA K+ NF S +Y +L + L+L ++ +R A+P +++ ++
Sbjct: 134 ANFAAEKTYQDQYNFNSDTVECRMYSFRLVQKPPLHLDFKKALR-ALPRNFNSSTEHAYH 192
Query: 82 --IENYGTHIVTSITIGGRDVVYIRQHQSSPLSM-----------MDIENYVKDIGDERF 128
I +YGTH +T++ +GGR + + ++ L++ +++E V IG +
Sbjct: 193 ELISSYGTHFITAVDLGGR-ISVLTALRTCQLTLNGLTADEVGDCLNVEAQVS-IGAQAS 250
Query: 129 MDSKSQSSAAPLK-----------YKDKDVTVIFRRRGGDDLEQSH-------------A 164
+ S+ ++ K Y+++ V V+ G L+ +H +
Sbjct: 251 VSSEYKACEEKKKQHKMATSFHQTYRERHVEVL-----GGPLDSTHDLLFGNQATPEQFS 305
Query: 165 KWAETVQLAPDVINMTFTPIVSLLEGV-PGIKHLARAIELYL 205
W ++ P +++ + P+ +LLE P + L +AI Y+
Sbjct: 306 TWTASLPSNPGLVDYSLEPLHTLLEEQNPKREALRQAISHYI 347
>pdb|2RD7|A Chain A, Human Complement Membrane Attack Proteins Share A Common
Fold With Bacterial Cytolysins
Length = 367
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 31/48 (64%), Gaps = 3/48 (6%)
Query: 53 KLAKLNLVLREEIRRAV---PYSWDPPLLASFIENYGTHIVTSITIGG 97
K+ K +++L E + +++ P ++ + A FI +YGTH +TS ++GG
Sbjct: 177 KMRKDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGG 224
>pdb|2QQH|A Chain A, Structure Of C8a-Macpf Reveals Mechanism Of Membrane
Attack In Complement Immune Defense
Length = 334
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 31/48 (64%), Gaps = 3/48 (6%)
Query: 53 KLAKLNLVLREEIRRAV---PYSWDPPLLASFIENYGTHIVTSITIGG 97
K+ K +++L E + +++ P ++ + A FI +YGTH +TS ++GG
Sbjct: 172 KMRKDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGG 219
>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 = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 240 CSSLQFSLMGPKLYISPDQVTVGRKPVTGLKLGLEGS-KQNRLEINLQHLVSLPKILQPH 298
C+ F+ GP +S Q T G KPV +L L GS + + I ++L + K + H
Sbjct: 112 CNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVH 171
Query: 299 WDAHVAIGAPK 309
+ V I +
Sbjct: 172 LNKSVEINCTR 182
>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 = 31.6 bits (70), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 240 CSSLQFSLMGPKLYISPDQVTVGRKPVTGLKLGLEGS-KQNRLEINLQHLVSLPKILQPH 298
C+ F+ GP +S Q T G KPV +L L GS + + I ++L + K + H
Sbjct: 112 CNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVH 171
Query: 299 WDAHVAIGAPK 309
+ V I +
Sbjct: 172 LNKSVEINCTR 182
>pdb|3U7Y|G Chain G, Structure Of Nih45-46 Fab In Complex With Gp120 Of 93th057
Hiv
Length = 361
Score = 31.6 bits (70), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 240 CSSLQFSLMGPKLYISPDQVTVGRKPVTGLKLGLEGS-KQNRLEINLQHLVSLPKILQPH 298
C+ F+ GP +S Q T G KPV +L L GS + + I ++L + K + H
Sbjct: 112 CNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVH 171
Query: 299 WDAHVAIGAPK 309
+ V I +
Sbjct: 172 LNKSVEINCTR 182
>pdb|3TGR|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade C Strain C1086
Gp120 Core
pdb|3TGR|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade C Strain C1086
Gp120 Core
pdb|3TGS|A Chain A, Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120 Core
In Complex With Nbd-556
pdb|3TGS|B Chain B, Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120 Core
In Complex With Nbd-556
Length = 358
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 240 CSSLQFSLMGPKLYISPDQVTVGRKPVTGLKLGLEGS-KQNRLEINLQHLVSLPKILQPH 298
C++ F+ GP +S Q T G KPV +L L GS + + I ++L + K + H
Sbjct: 112 CNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVH 171
Query: 299 WDAHVAI 305
+ V I
Sbjct: 172 LNESVNI 178
>pdb|3RJQ|A Chain A, Crystal Structure Of Anti-Hiv Llama Vhh Antibody A12 In
Complex With C186 Gp120
Length = 382
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 240 CSSLQFSLMGPKLYISPDQVTVGRKPVTGLKLGLEGS-KQNRLEINLQHLVSLPKILQPH 298
C++ F+ GP +S Q T G KPV +L L GS + + I ++L + K + H
Sbjct: 136 CNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVH 195
Query: 299 WDAHVAI 305
+ V I
Sbjct: 196 LNESVNI 202
>pdb|3TIH|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
pdb|3TIH|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
pdb|3TIH|C Chain C, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
pdb|3TIH|D Chain D, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
Zm109f.Pb4 Gp120 Core
Length = 345
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 240 CSSLQFSLMGPKLYISPDQVTVGRKPVTGLKLGLEGS-KQNRLEINLQHLVSLPKILQPH 298
C++ FS GP +S Q T G +PV +L L GS + + I ++L K + H
Sbjct: 112 CNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVH 171
Query: 299 WDAHVAI 305
+ V I
Sbjct: 172 LNKSVEI 178
>pdb|3J20|U Chain U, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 150
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 39/102 (38%), Gaps = 17/102 (16%)
Query: 286 QHLVSLPKILQPHWDAHVAIGAPKWQGPEEQDSRWFEPIKWKNFSHVSTAPIEYTDTSIG 345
Q L +P+I P W V G K + PE++D W + S Y D +G
Sbjct: 18 QRLKEIPEIKPPEWAPFVKTGRHKERLPEQED--------WWYYRVASILRRVYLDGPVG 69
Query: 346 DLSGVHVVTGAQLGVWDFGAKNVLHLKLLFSKVPGCTIRRSV 387
+L + G KN H F K G IR+++
Sbjct: 70 I---------ERLRTYYGGRKNRGHAPEKFYKAGGSIIRKAL 102
>pdb|3BDV|A Chain A, Crystal Structure Of A Putative Yden-Like Hydrolase
(Eca3091) From Pectobacterium Atrosepticum Scri1043 At
1.66 A Resolution
pdb|3BDV|B Chain B, Crystal Structure Of A Putative Yden-Like Hydrolase
(Eca3091) From Pectobacterium Atrosepticum Scri1043 At
1.66 A Resolution
Length = 191
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 298 HWDAHVAIGAPKWQGPEEQD------SRWFEPIKWKNFSHVSTAPIEYTDTSIGDLSGVH 351
HW +H P WQ +++ RW I+ + S V T P+ S G L+ H
Sbjct: 33 HWQSHWERRFPHWQRIRQREWYQADLDRWVLAIR-RELS-VCTQPVILIGHSFGALAACH 90
Query: 352 VVTGAQLGV 360
VV Q G+
Sbjct: 91 VVQQGQEGI 99
>pdb|3ZQS|A Chain A, Human Fancl Central Domain
pdb|3ZQS|B Chain B, Human Fancl Central Domain
Length = 186
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 178 NMTFTPIVSLLEGVPGIKHLARAIELYLEYKPPIEDLQYFLDYQIPRV--WAPQHSNI 233
+ F+ I E G +HL I L L+ K P E YF+D+ +P W PQ S I
Sbjct: 22 DTCFSTIKLKAEDASGREHL---ITLKLKAKYPAESPDYFVDFPVPFCASWTPQSSLI 76
>pdb|1W07|A Chain A, Arabidopsis Thaliana Acyl-Coa Oxidase 1
pdb|1W07|B Chain B, Arabidopsis Thaliana Acyl-Coa Oxidase 1
Length = 659
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 285 LQHLVSLPKILQPHWDAHVAIGAPKWQGPEEQDSRWF 321
L+H + P + HW V A K QG EEQ +W
Sbjct: 89 LRHFIDQPAYVDLHWGMFVP--AIKGQGTEEQQKKWL 123
>pdb|3PWX|A Chain A, Structure Of Putative Flagellar Hook-Associated Protein
From Vibrio Parahaemolyticus
pdb|3PWX|B Chain B, Structure Of Putative Flagellar Hook-Associated Protein
From Vibrio Parahaemolyticus
Length = 239
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 419 EDSSGHIGKLAKIVDVTEMSKGPQDLPGHWLVTGAK 454
+D SG I +L D E S QD GH+L +G K
Sbjct: 69 QDRSGXITELKSYRDSIESSFNAQDEEGHFLFSGTK 104
>pdb|2V7F|A Chain A, Structure Of P. Abyssi Rps19 Protein
Length = 150
Score = 28.5 bits (62), Expect = 7.5, Method: Composition-based stats.
Identities = 27/102 (26%), Positives = 39/102 (38%), Gaps = 17/102 (16%)
Query: 286 QHLVSLPKILQPHWDAHVAIGAPKWQGPEEQDSRWFEPIKWKNFSHVSTAPIEYTDTSIG 345
Q L +P+I P W V G K + PE++D W + S Y D +G
Sbjct: 18 QRLKEIPEIKPPEWAPFVKTGRHKERLPEQED--------WWYYRVASILRRVYLDGPVG 69
Query: 346 DLSGVHVVTGAQLGVWDFGAKNVLHLKLLFSKVPGCTIRRSV 387
+L + G KN H F K G IR+++
Sbjct: 70 I---------ERLRTYYGGRKNRGHAPERFYKAGGSIIRKAL 102
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 0.135 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,752,421
Number of Sequences: 62578
Number of extensions: 622913
Number of successful extensions: 1139
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1133
Number of HSP's gapped (non-prelim): 18
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
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: 53 (25.0 bits)