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= psy12736
(567 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 69/226 (30%), Positives = 116/226 (51%), Gaps = 16/226 (7%)
Query: 299 HYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRLNTDEDLSLMSGHI 357
HYI++ R+LSR + L A + + T E VR W +E R DRL E+ I
Sbjct: 1508 HYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKEWTDKKI 1567
Query: 358 ADSVKRNFPQDVNV-VMRDPLLFGDFRNALKETEPRYYEDLLDY-SAVGHLFTEILEEYN 415
+ ++FP VN+ ++ P+L+ ++ K+ +P DL +Y A +F E EE +
Sbjct: 1568 DEVALKHFP-SVNLDALKRPILYSNWLT--KDYQPVNRSDLREYVKARLKVFYE--EELD 1622
Query: 416 ESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLVRLASFAAGYQV 475
+ LVLF + +H+ RI R R +GH +++GV GGGK L R ++ G +
Sbjct: 1623 --------VPLVLFNEVLDHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSI 1674
Query: 476 FTIQLSRGYNEASFKEDLKSLYNLLGVKNQATVFLFTAAEIVEEGY 521
+TI+++ Y + F +DL+ L G K + F+F + ++E +
Sbjct: 1675 YTIKVNNNYKSSDFDDDLRMLLKRAGCKEEKICFIFDESNVLESSF 1720
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 2/92 (2%)
Query: 130 TQIPTAESSWYHYTLDRSKNAWVPWRHLVRSYVHDGDK-SFGDILVPTTDSTKLTWILSL 188
T +P Y++ W W++ V S + K + D+++PT D+T+ +L
Sbjct: 1240 TPVPANTIPLLDYSVSIDDANWSLWKNKVPSVEVETHKVASPDVVIPTVDTTRHVDVLHA 1299
Query: 189 MNEIKRPCIVVGDTGTSKTATMMNFLRSLSPD 220
RP I+ G G+ KT T+ + LR+ PD
Sbjct: 1300 WLSEHRPLILCGPPGSGKTMTLTSTLRAF-PD 1330
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 236 HYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRL 281
HYI++ R+LSR + L A + + T E VR W +E R DRL
Sbjct: 1508 HYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRL 1554
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 69/226 (30%), Positives = 116/226 (51%), Gaps = 16/226 (7%)
Query: 299 HYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRLNTDEDLSLMSGHI 357
HYI++ R+LSR + L A + + T E VR W +E R DRL E+ I
Sbjct: 1508 HYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKEWTDKKI 1567
Query: 358 ADSVKRNFPQDVNV-VMRDPLLFGDFRNALKETEPRYYEDLLDY-SAVGHLFTEILEEYN 415
+ ++FP VN+ ++ P+L+ ++ K+ +P DL +Y A +F E EE +
Sbjct: 1568 DEVALKHFP-SVNLDALKRPILYSNWLT--KDYQPVNRSDLREYVKARLKVFYE--EELD 1622
Query: 416 ESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLVRLASFAAGYQV 475
+ LVLF + +H+ RI R R +GH +++GV GGGK L R ++ G +
Sbjct: 1623 --------VPLVLFNEVLDHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSI 1674
Query: 476 FTIQLSRGYNEASFKEDLKSLYNLLGVKNQATVFLFTAAEIVEEGY 521
+TI+++ Y + F +DL+ L G K + F+F + ++E +
Sbjct: 1675 YTIKVNNNYKSSDFDDDLRMLLKRAGCKEEKICFIFDESNVLESSF 1720
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 2/92 (2%)
Query: 130 TQIPTAESSWYHYTLDRSKNAWVPWRHLVRSYVHDGDK-SFGDILVPTTDSTKLTWILSL 188
T +P Y++ W W++ V S + K + D+++PT D+T+ +L
Sbjct: 1240 TPVPANTIPLLDYSVSIDDANWSLWKNKVPSVEVETHKVASPDVVIPTVDTTRHVDVLHA 1299
Query: 189 MNEIKRPCIVVGDTGTSKTATMMNFLRSLSPD 220
RP I+ G G+ KT T+ + LR+ PD
Sbjct: 1300 WLSEHRPLILCGPPGSGKTMTLTSTLRAF-PD 1330
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 236 HYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRL 281
HYI++ R+LSR + L A + + T E VR W +E R DRL
Sbjct: 1508 HYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRL 1554
>pdb|4AI6|A Chain A, Dynein Motor Domain - Adp Complex
pdb|4AI6|B Chain B, Dynein Motor Domain - Adp Complex
pdb|4AKG|A Chain A, Dynein Motor Domain - Atp Complex
pdb|4AKG|B Chain B, Dynein Motor Domain - Atp Complex
pdb|4AKH|A Chain A, Dynein Motor Domain - Amppnp Complex
pdb|4AKH|B Chain B, Dynein Motor Domain - Amppnp Complex
pdb|4AKI|A Chain A, Dynein Motor Domain - Luac Derivative
pdb|4AKI|B Chain B, Dynein Motor Domain - Luac Derivative
Length = 2695
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 54/231 (23%), Positives = 97/231 (41%), Gaps = 15/231 (6%)
Query: 294 TPAKFHYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRLNTDEDLSL 352
T + HY+F+ R+L+R+++G+ TA T +R W E R DRL ++ +
Sbjct: 1465 TGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNS 1524
Query: 353 MSGHIADSVKRNFPQDVNVVMRDPLLFGDFRNALKETEPRYYEDLLDYSAVGH--LFTEI 410
+ ++V + P D N + LD+ V L I
Sbjct: 1525 FEQLLYETVDKYLPNQ------------DLGNISSTSLLFSGLLSLDFKEVNKTDLVNFI 1572
Query: 411 LEEYNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLVRLASFA 470
E + + + +V+ E +H+ RI RAL+ +GH M++G GK L R ++
Sbjct: 1573 EERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWL 1632
Query: 471 AGYQVFTIQLSRGYNEASFKEDLKSLYNLLGVKNQATVFLFTAAEIVEEGY 521
G ++ ++ R N + F LK + +K T + + I+E +
Sbjct: 1633 NGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAF 1683
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 171 DILVPTTDSTKLTWILSLMNEIKRPCIVVGDTGTSKTATMMNFLRSLS 218
DI++PT D+ K I + KR I+ G G+ KT M N LR+ S
Sbjct: 1245 DIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSS 1292
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 231 TPAKFHYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRL 281
T + HY+F+ R+L+R+++G+ TA T +R W E R DRL
Sbjct: 1465 TGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRL 1516
>pdb|3QMZ|A Chain A, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
pdb|3QMZ|B Chain B, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
Length = 2486
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 54/231 (23%), Positives = 97/231 (41%), Gaps = 15/231 (6%)
Query: 294 TPAKFHYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRLNTDEDLSL 352
T + HY+F+ R+L+R+++G+ TA T +R W E R DRL ++ +
Sbjct: 1246 TGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNS 1305
Query: 353 MSGHIADSVKRNFPQDVNVVMRDPLLFGDFRNALKETEPRYYEDLLDYSAVGH--LFTEI 410
+ ++V + P D N + LD+ V L I
Sbjct: 1306 FEQLLYETVDKYLPNQ------------DLGNISSTSLLFSGLLSLDFKEVNKTDLVNFI 1353
Query: 411 LEEYNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHCMVVGVEGGGKRSLVRLASFA 470
E + + + +V+ E +H+ RI RAL+ +GH M++G GK L R ++
Sbjct: 1354 EERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWL 1413
Query: 471 AGYQVFTIQLSRGYNEASFKEDLKSLYNLLGVKNQATVFLFTAAEIVEEGY 521
G ++ ++ R N + F LK + +K T + + I+E +
Sbjct: 1414 NGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAF 1464
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 171 DILVPTTDSTKLTWILSLMNEIKRPCIVVGDTGTSKTATMMNFLRSLS 218
DI++PT D+ K I + KR I+ G G+ KT M N LR+ S
Sbjct: 1026 DIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSS 1073
Score = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 231 TPAKFHYIFNLRDLSRIIQGL-TATEKIIFNTKEMFVRAWRNEFTRTICDRL 281
T + HY+F+ R+L+R+++G+ TA T +R W E R DRL
Sbjct: 1246 TGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRL 1297
>pdb|2R7A|A Chain A, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|B Chain B, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|C Chain C, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2R7A|D Chain D, Crystal Structure Of A Periplasmic Heme Binding Protein
From Shigella Dysenteriae
pdb|2RG7|A Chain A, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|B Chain B, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|C Chain C, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
pdb|2RG7|D Chain D, Apo- Crystal Structure Of A Periplasmic Heme Binding
Protein From Shigella Dysenteriae
Length = 256
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/107 (20%), Positives = 46/107 (42%), Gaps = 10/107 (9%)
Query: 229 PPTPAKFHYIFNLRDLSRIIQGLTATEKIIFNTKEMFVRAWRNEFTRTICDRLNTDELVI 288
PP AK +I + LS + I + + V W++ + + D+L ++ +
Sbjct: 35 PPETAKLPHIGYWKQLS---------SEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNV 85
Query: 289 AELPPTPAKFHYIF-NLRDLSRIIQGLTATEKIIFNTKEMFVRAWRN 334
LP PA ++ N+R L++ +Q + ++ + R +N
Sbjct: 86 VTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQN 132
>pdb|3GUJ|A Chain A, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Benzene Binding
pdb|3GUK|A Chain A, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Toluene Binding
pdb|3GUK|B Chain B, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Toluene Binding
pdb|3GUL|A Chain A, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Ethylbenzene Binding
pdb|3GUL|B Chain B, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Ethylbenzene Binding
pdb|3GUM|A Chain A, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY--P- Xylene Binding
pdb|3GUM|B Chain B, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY--P- Xylene Binding
pdb|3GUN|A Chain A, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Aniline Binding
pdb|3GUN|B Chain B, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY-- Aniline Binding
pdb|3GUO|A Chain A, T4 Lysozyme M102e/l99a Mutant With Buried Charge In Apolar
Cavity-- Phenol Binding
pdb|3GUO|B Chain B, T4 Lysozyme M102e/l99a Mutant With Buried Charge In Apolar
Cavity-- Phenol Binding
pdb|3GUP|A Chain A, T4 Lysozyme M102e/l99a Mutant With Buried Charge In Apolar
Cavity-- Pyridine Binding
pdb|3GUP|B Chain B, T4 Lysozyme M102e/l99a Mutant With Buried Charge In Apolar
Cavity-- Pyridine Binding
Length = 164
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA---NL-GSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A N G ++ +E E +F Q V A+
Sbjct: 16 KIYKDCEGYYTIGIGHLLTKSPDL-NAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF V + GF NV+ + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRXAAINEVFQMGVTGVAGFTNVLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ DR+K
Sbjct: 135 KSRWYNQCPDRAK 147
>pdb|3GUI|A Chain A, T4 Lysozyme M102eL99A MUTANT WITH BURIED CHARGE IN APOLAR
CAVITY--Apo Structure
Length = 164
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDCEGYYTIGIGHLLTKSPDL-NAAKSELDKAIGRNXNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF V + GF NV+ + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRXAAINEVFQMGVTGVAGFTNVLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ DR+K
Sbjct: 135 KSRWYNQCPDRAK 147
>pdb|4E97|A Chain A, T4 Lysozyme L99aM102H WITH 2-Mercaptoethanol Bound
pdb|4E97|B Chain B, T4 Lysozyme L99aM102H WITH 2-Mercaptoethanol Bound
pdb|4EKP|A Chain A, T4 Lysozyme L99aM102H WITH NITROBENZENE BOUND
pdb|4EKP|B Chain B, T4 Lysozyme L99aM102H WITH NITROBENZENE BOUND
pdb|4EKQ|A Chain A, T4 Lysozyme L99aM102H WITH 4-Nitrophenol Bound
pdb|4EKQ|B Chain B, T4 Lysozyme L99aM102H WITH 4-Nitrophenol Bound
pdb|4EKR|A Chain A, T4 Lysozyme L99aM102H WITH 2-Cyanophenol Bound
pdb|4EKR|B Chain B, T4 Lysozyme L99aM102H WITH 2-Cyanophenol Bound
pdb|4EKS|A Chain A, T4 Lysozyme L99aM102H WITH ISOXAZOLE BOUND
pdb|4EKS|B Chain B, T4 Lysozyme L99aM102H WITH ISOXAZOLE BOUND
Length = 187
Score = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 58/140 (41%), Gaps = 25/140 (17%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA---NL-GSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A N G ++ +E E +F Q V A+
Sbjct: 39 KIYKDCEGYYTIGIGHLLTKSPDL-NAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAA 97
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF V + GF NV+ + + + A
Sbjct: 98 VRGILRNAKLKPVYDSLDAVRRCAAINHVFQMGVTGVAGFTNVLRMLQQKRWDEAAVNLA 157
Query: 136 ESSWYHYTLDRSKNAWVPWR 155
+S WY+ DR+K +R
Sbjct: 158 KSRWYNQCPDRAKRVITTFR 177
>pdb|3R9A|A Chain A, Human Alanine-Glyoxylate Aminotransferase In Complex With
The Tpr Domain Of Human Pex5p
pdb|3R9A|C Chain C, Human Alanine-Glyoxylate Aminotransferase In Complex With
The Tpr Domain Of Human Pex5p
Length = 394
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 394 YEDLLDYSAVGHLFTEILEEYNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHC 450
+ D++ Y + H EI+ S G R+ L+ RE++ R+ ALR + HC
Sbjct: 334 WRDIVSY-VIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHC 389
>pdb|1H0C|A Chain A, The Crystal Structure Of Human Alanine:glyoxylate
Aminotransferase
Length = 392
Score = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 394 YEDLLDYSAVGHLFTEILEEYNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHC 450
+ D++ Y + H EI+ S G R+ L+ RE++ R+ ALR + HC
Sbjct: 332 WRDIVSY-VIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHC 387
>pdb|1J04|A Chain A, Structural Mechanism Of Enzyme Mistargeting In Hereditary
Kidney Stone Disease In Vitro
Length = 392
Score = 32.0 bits (71), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 394 YEDLLDYSAVGHLFTEILEEYNESAGAKARLDLVLFEDAREHLTRIHRALRLSRGHC 450
+ D++ Y + H EI+ S G R+ L+ RE++ R+ ALR + HC
Sbjct: 332 WRDIVSY-VIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHC 387
>pdb|1QUO|A Chain A, L99aE108V MUTANT OF T4 LYSOZYME
Length = 162
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 57/133 (42%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVF------- 86
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 87 ---------IQSVYASLGASLVAEA-QTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
++ VY SL A A A VF V + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAAAINMVFQMGVTGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|102L|A Chain A, How Amino-Acid Insertions Are Allowed In An Alpha-Helix Of
T4 Lysozyme
Length = 165
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 32/133 (24%), Positives = 54/133 (40%), Gaps = 24/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 75
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF + GF N + + + + A
Sbjct: 76 VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLA 135
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 136 KSRWYNQTPNRAK 148
>pdb|144L|A Chain A, Role Of Backbone Flexibility In The Accommodation Of
Variants That Repack The Core Of T4 Lysozyme
Length = 164
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 61/144 (42%), Gaps = 33/144 (22%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASLV-AEAQTVFDA-------------------HVKNLTGFLNVVDSD--DRLANYTQ 131
+ L A+ + V+D+ V T L ++ D LA
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMIQQKRWDELA---- 130
Query: 132 IPTAESSWYHYTLDRSKNAWVPWR 155
+ A+S WY+ T +R+K WR
Sbjct: 131 VNMAKSRWYNQTPNRAKRVITTWR 154
>pdb|1QUH|A Chain A, L99gE108V MUTANT OF T4 LYSOZYME
Length = 162
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF V + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAAGINMVFQMGVTGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|1L56|A Chain A, Analysis Of The Interaction Between Charged Side Chains
And The Alpha-helix Dipole Using Designed Thermostable
Mutants Of Phage T4 Lysozyme
Length = 164
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 56/133 (42%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA---NL-GSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A N G ++P+E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNCNGVITPDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|1AJE|A Chain A, Cdc42 From Human, Nmr, 20 Structures
Length = 194
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 185 ILSLMNEIKRPCIVVGDTGTSKTATMMNFLRSLSPDKYL 223
I+S M IK C+VVGD KT ++++ + P +Y+
Sbjct: 4 IISAMQTIK--CVVVGDGAVGKTCLLISYTTNKFPSEYV 40
>pdb|3AHM|A Chain A, Pz Peptidase A
pdb|3AHM|B Chain B, Pz Peptidase A
pdb|3AHN|A Chain A, Pz Peptidase A With Inhibitor 1
pdb|3AHN|B Chain B, Pz Peptidase A With Inhibitor 1
pdb|3AHO|A Chain A, Pz Peptidase A With Inhibitor 2
pdb|3AHO|B Chain B, Pz Peptidase A With Inhibitor 2
Length = 564
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 68 SLDEANLGSMSPEELEAVFIQSVYASLGASLVAEAQTVFDAHVKNLTGFLNVVDSDDR 125
+L EA L + SP+ +E + +++ S LVA A+ F+ + L V+S DR
Sbjct: 114 ALAEAELKTYSPDIVEDLQLENKLTSEYTKLVASAKIFFEGEERTLAQLQPFVESPDR 171
>pdb|146L|A Chain A, Role Of Backbone Flexibility In The Accommodation Of
Variants That Repack The Core Of T4 Lysozyme
Length = 164
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 56/140 (40%), Gaps = 25/140 (17%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMMQQKRWDELAVNMA 134
Query: 136 ESSWYHYTLDRSKNAWVPWR 155
+S WY+ T +R+K WR
Sbjct: 135 KSRWYNQTPNRAKRIITTWR 154
>pdb|1QUG|A Chain A, E108v Mutant Of T4 Lysozyme
Length = 162
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF V + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGVTGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|252L|A Chain A, Generating Ligand Binding Sites In T4 Lysozyme Using
Deficiency-Creating Substitutions
Length = 164
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF A + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALINAVFQAGETGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|244L|A Chain A, The Response Of T4 Lysozyme To Large-To-Small
Substitutions Within The Core And Its Relation To The
Hydrophobic Effect
Length = 164
Score = 29.3 bits (64), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A A VF + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALANMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|1QSQ|A Chain A, Cavity Creating Mutation
Length = 164
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF A + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALINMVFQAGETGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|2ATX|A Chain A, Crystal Structure Of The Tc10 Gppnhp Complex
pdb|2ATX|B Chain B, Crystal Structure Of The Tc10 Gppnhp Complex
Length = 194
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 196 CIVVGDTGTSKTATMMNFLRSLSPDKYL 223
C+VVGD KT +M++ P++Y+
Sbjct: 21 CVVVGDGAVGKTCLLMSYANDAFPEEYV 48
>pdb|3JR6|A Chain A, Sequential Reorganization Of Beta-Sheet Topology By
Insertion Of A Single Strand
pdb|3JR6|B Chain B, Sequential Reorganization Of Beta-Sheet Topology By
Insertion Of A Single Strand
pdb|3JR6|C Chain C, Sequential Reorganization Of Beta-Sheet Topology By
Insertion Of A Single Strand
pdb|3JR6|D Chain D, Sequential Reorganization Of Beta-Sheet Topology By
Insertion Of A Single Strand
Length = 170
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 23/136 (16%)
Query: 35 KETEPRYYEDLLDYSAVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSV 90
K+TE Y + +GHL T+ L ++ LD+A G ++ +E E +F Q V
Sbjct: 19 KDTEGYYTIGIGHLLGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDV 77
Query: 91 YASLGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQI 132
A++ L A VF + GF N + + + +
Sbjct: 78 DAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAV 137
Query: 133 PTAESSWYHYTLDRSK 148
A+S WY+ T +R+K
Sbjct: 138 NLAKSRWYNQTPNRAK 153
>pdb|1D3F|A Chain A, N-Terminal Domain Core Methionine Mutation
Length = 164
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 33/133 (24%), Positives = 54/133 (40%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G M+ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVMTKDEAEKLFNQDVDAA 74
Query: 94 LGASL-----------------VAEAQTVFDAHVKNLTGFLNVVDS-DDRLANYTQIPTA 135
+ L A VF + GF N + + + + A
Sbjct: 75 VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
>pdb|247L|A Chain A, The Response Of T4 Lysozyme To Large-To-Small
Substitutions Within The Core And Its Relation To The
Hydrophobic Effect
Length = 164
Score = 28.9 bits (63), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 61/133 (45%), Gaps = 25/133 (18%)
Query: 40 RYYEDLLDYS--AVGHLFTEIVQLCQMLQASLDEA----NLGSMSPEELEAVFIQSVYAS 93
+ Y+D Y +GHL T+ L ++ LD+A G ++ +E E +F Q V A+
Sbjct: 16 KIYKDTEGYYTIGIGHLLTKSPSL-NAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAA 74
Query: 94 LGASLV-AEAQTVFD-------AHVKNL------TGFLNVVDS----DDRLANYTQIPTA 135
+ L A+A+ V+D A + N+ TG +S + + + A
Sbjct: 75 VRGILRNAKAKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLA 134
Query: 136 ESSWYHYTLDRSK 148
+S WY+ T +R+K
Sbjct: 135 KSRWYNQTPNRAK 147
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 0.136 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,992,138
Number of Sequences: 62578
Number of extensions: 648119
Number of successful extensions: 2094
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 2069
Number of HSP's gapped (non-prelim): 53
length of query: 567
length of database: 14,973,337
effective HSP length: 104
effective length of query: 463
effective length of database: 8,465,225
effective search space: 3919399175
effective search space used: 3919399175
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: 54 (25.4 bits)