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= 044156
(288 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SNH|A Chain A, Crystal Structure Of Nucleotide-Free Human Dynamin1
Length = 743
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/176 (21%), Positives = 71/176 (40%), Gaps = 16/176 (9%)
Query: 105 QMVQSVEGTRSLSLELCREFEDKFLQLITTGEGSGWKIVASFEGNFPNRIKQLPLDRRFD 164
QMVQ +++ + E Q+ T G +I F FP + ++ D +
Sbjct: 328 QMVQQ------FAVDFEKRIEGSGDQIDTYELSGGARINRIFHERFPFELVKMEFDEKEL 381
Query: 165 INNVQRIVLEADGYQPYLISPEKGLRSLIKGVLELAKEPSRLSVDEVIEPLKHVHRVLVG 224
+ + A L +P+ +++K ++ +EP VD VI L
Sbjct: 382 RREISYAIKNAAAAATGLFTPDMAFETIVKKQVKKIREPCLKCVDMVISEL--------- 432
Query: 225 MVSAAANATPGLGRYPLFKREVVAIASAALDGFKNEARKMVVALVDMERAFVPPQH 280
+S T L +YP + E+ I + + + ++ V+ L+D+E A++ H
Sbjct: 433 -ISTVRQCTKKLQQYPRLREEMERIVTTHIREREGRTKEQVMLLIDIELAYMNTNH 487
>pdb|3ZVR|A Chain A, Crystal Structure Of Dynamin
Length = 772
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/183 (21%), Positives = 73/183 (39%), Gaps = 30/183 (16%)
Query: 105 QMVQSVEGTRSLSLELCREFEDKFLQLITTGEGSGWKIVASFEGNFPNRIKQLPLDRR-- 162
QMVQ +++ + E Q+ T G +I F FP + ++ D +
Sbjct: 351 QMVQQ------FAVDFEKRIEGSGDQIDTYELSGGARINRIFHERFPFELVKMEFDEKEL 404
Query: 163 -----FDINNVQRIVLEADGYQPYLISPEKGLRSLIKGVLELAKEPSRLSVDEVIEPLKH 217
+ I N+ I + L +P+ + +K ++ KEPS VD V+ L
Sbjct: 405 RREISYAIKNIHDI-------RTGLFTPDLAFEATVKKQVQKLKEPSIKCVDMVVSEL-- 455
Query: 218 VHRVLVGMVSAAANATPGLGRYPLFKREVVAIASAALDGFKNEARKMVVALVDMERAFVP 277
S + L +YP + E+ I + + + ++ V+ L+D+E A++
Sbjct: 456 --------TSTIRKCSEKLQQYPRLREEMERIVTTHIREREGRTKEQVMLLIDIELAYMN 507
Query: 278 PQH 280
H
Sbjct: 508 TNH 510
>pdb|1MSK|A Chain A, Methionine Synthase (Activation Domain)
Length = 331
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 52/124 (41%), Gaps = 16/124 (12%)
Query: 25 SIATTQSGSEISLETAWTAESESLKSILIGAPQSQLGRIALADDLAQLIRKRMKVRVPNL 84
+ A T E +L A+ A+ + I++ A LAD LA+ + + RV +
Sbjct: 164 AFAVTGGLEEDALADAFEAQHDDYNKIMVKA---------LADRLAEAFAEYLHERVRKV 214
Query: 85 LSGLQGKSQIVQDELVRLGEQMVQSVEGTRSLSLELCREFEDK--FLQLITTGEGSGWKI 142
G + +EL+R Q ++ G + C E +K +L+ + +G K+
Sbjct: 215 YWGYAPNENLSNEELIRENYQGIRPAPGYPA-----CPEHTEKATIWELLEVEKHTGMKL 269
Query: 143 VASF 146
SF
Sbjct: 270 TESF 273
>pdb|1K7Y|A Chain A, E. Coli Meth C-Terminal Fragment (649-1227)
pdb|1K98|A Chain A, Adomet Complex Of Meth C-Terminal Fragment
Length = 577
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 52/124 (41%), Gaps = 16/124 (12%)
Query: 25 SIATTQSGSEISLETAWTAESESLKSILIGAPQSQLGRIALADDLAQLIRKRMKVRVPNL 84
+ A T E +L A+ A+ + I++ A LAD LA+ + + RV +
Sbjct: 410 AFAVTGGLEEDALADAFEAQHDDYNKIMVKA---------LADRLAEAFAEYLHERVRKV 460
Query: 85 LSGLQGKSQIVQDELVRLGEQMVQSVEGTRSLSLELCREFEDK--FLQLITTGEGSGWKI 142
G + +EL+R Q ++ G + C E +K +L+ + +G K+
Sbjct: 461 YWGYAPNENLSNEELIRENYQGIRPAPGYPA-----CPEHTEKATIWELLEVEKHTGMKL 515
Query: 143 VASF 146
SF
Sbjct: 516 TESF 519
>pdb|3BUL|A Chain A, E. Coli I690cG743C METH C-Terminal Fragment (649-1227)
pdb|3IV9|A Chain A, Structure Of The B12-Dependent Methionine Synthase (Meth)
C-Teminal Half In A "his-On" Conformation
pdb|3IVA|A Chain A, Structure Of The B12-Dependent Methionine Synthase (Meth)
C-Teminal Half With Adohcy Bound
Length = 579
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 52/124 (41%), Gaps = 16/124 (12%)
Query: 25 SIATTQSGSEISLETAWTAESESLKSILIGAPQSQLGRIALADDLAQLIRKRMKVRVPNL 84
+ A T E +L A+ A+ + I++ A LAD LA+ + + RV +
Sbjct: 412 AFAVTGGLEEDALADAFEAQHDDYNKIMVKA---------LADRLAEAFAEYLHERVRKV 462
Query: 85 LSGLQGKSQIVQDELVRLGEQMVQSVEGTRSLSLELCREFEDK--FLQLITTGEGSGWKI 142
G + +EL+R Q ++ G + C E +K +L+ + +G K+
Sbjct: 463 YWGYAPNENLSNEELIRENYQGIRPAPGYPA-----CPEHTEKATIWELLEVEKHTGMKL 517
Query: 143 VASF 146
SF
Sbjct: 518 TESF 521
>pdb|4GMR|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or266.
pdb|4GMR|B Chain B, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or266
Length = 169
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 52/111 (46%), Gaps = 14/111 (12%)
Query: 139 GWKIVASFEGNFPNRIKQLPLDRRFDINNVQRIVLEADGYQPYLISPEKGLRSLIKGVLE 198
G +++ + E +R+K L L+ D+N ++DG P ++ E G + ++K +L
Sbjct: 5 GKRLIEAAENGNKDRVKDL-LENGADVN-----ASDSDGKTPLHLAAENGHKEVVKLLLS 58
Query: 199 LAKEPSRLSVDEVIEPL----KHVHRVLVGMV---SAAANATPGLGRYPLF 242
+P+ D PL ++ H+ +V ++ A NA G+ PL
Sbjct: 59 QGADPNAKDSDGKT-PLHLAAENGHKEVVKLLLSQGADPNAKDSDGKTPLH 108
>pdb|1ZTP|A Chain A, X-Ray Structure Of Gene Product From Homo Sapiens
Hs.433573
pdb|1ZTP|B Chain B, X-Ray Structure Of Gene Product From Homo Sapiens
Hs.433573
pdb|1ZTP|C Chain C, X-Ray Structure Of Gene Product From Homo Sapiens
Hs.433573
pdb|2Q4K|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Homo Sapiens Hs.433573
pdb|2Q4K|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Homo Sapiens Hs.433573
pdb|2Q4K|C Chain C, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Homo Sapiens Hs.433573
Length = 251
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 5 NQGSPKTADIPWVALIGQSVSIATTQSGSEISLETAWTAESESLKSILIG 54
+ GSP + + W+A+ GQ S SG L+ AW A S + I G
Sbjct: 67 DPGSPNSEPVGWIAVYGQGYS---PNSGDVQGLQAAWEALQTSGRPITPG 113
>pdb|1Z3D|A Chain A, Protein Crystal Growth Improvement Leading To The 2.5a
Crystallographic Structure Of Ubiquitin-Conjugating
Enzyme (Ubc-1) From Caenorhabditis Elegans
Length = 157
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 75 KRMKVRVPNLLSGLQGKSQIVQDELVRLGEQMVQSVEGTRSLSLELCREFEDK 127
K+++ P +SG + I+ E + G Q +GT LSLE E+ +K
Sbjct: 17 KKLQEDPPAGVSGAPTEDNILTWEAIIFGPQETPFEDGTFKLSLEFTEEYPNK 69
>pdb|3K60|A Chain A, Crystal Structure Of N-Terminal Domain Of Plasmodium
Falciparum Hsp90 (Pf07_0029) Bound To Adp
pdb|3K60|B Chain B, Crystal Structure Of N-Terminal Domain Of Plasmodium
Falciparum Hsp90 (Pf07_0029) Bound To Adp
Length = 223
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 6/45 (13%)
Query: 241 LFKREVVAIASAALDGFKNEARKMVVALVDMERAFVPPQHFIRLV 285
+F RE+++ AS ALD + E ++ D ++ P+ FIR++
Sbjct: 29 IFLRELISNASDALDKIRYE------SITDTQKLSAEPEFFIRII 67
>pdb|1Q34|A Chain A, Crystal Structures Of Two Ubc (E2) Enzymes Of The
Ubiquitin- Conjugating System In Caenorhabditis Elegans
pdb|1Q34|B Chain B, Crystal Structures Of Two Ubc (E2) Enzymes Of The
Ubiquitin- Conjugating System In Caenorhabditis Elegans
pdb|1Q34|C Chain C, Crystal Structures Of Two Ubc (E2) Enzymes Of The
Ubiquitin- Conjugating System In Caenorhabditis Elegans
Length = 163
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 75 KRMKVRVPNLLSGLQGKSQIVQDELVRLGEQMVQSVEGTRSLSLELCREFEDK 127
K+++ P +SG + I+ E + G Q +GT LSLE E+ +K
Sbjct: 14 KKLQEDPPAGVSGAPTEDNILTWEAIIFGPQETPFEDGTFKLSLEFTEEYPNK 66
>pdb|3KXP|A Chain A, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|B Chain B, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|C Chain C, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|D Chain D, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|E Chain E, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|F Chain F, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|G Chain G, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|H Chain H, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|I Chain I, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|J Chain J, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|K Chain K, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
pdb|3KXP|L Chain L, Crystal Structure Of E-2-(Acetamidomethylene)succinate
Hydrolase
Length = 314
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 211 VIEPLKHVHRVLVGMVSAAANATPGLGRYPLFKREVVAI 249
+I L H +LVG A N+ +YP R VVAI
Sbjct: 127 LIRTLARGHAILVGHSLGARNSVTAAAKYPDLVRSVVAI 165
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
0.318 0.135 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,531,546
Number of Sequences: 62578
Number of extensions: 285664
Number of successful extensions: 837
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 827
Number of HSP's gapped (non-prelim): 31
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
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: 51 (24.3 bits)