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= 013360
(444 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3S84|A Chain A, Dimeric Apoa-Iv
pdb|3S84|B Chain B, Dimeric Apoa-Iv
Length = 273
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 33/69 (47%)
Query: 288 LKTKTIEACEATKTAVTPHIIRVQEVVDPYFQEAKKFSKPYIDQVATVAKPHVDNVRVAL 347
LK + + E + + PH V + + +E ++ +PY DQ+ T + +R L
Sbjct: 16 LKEEIGKELEELRARLLPHANEVSQKIGDNLRELQQRLEPYADQLRTQVNTQAEQLRRQL 75
Query: 348 KPYTKKVVR 356
PY +++ R
Sbjct: 76 TPYAQRMER 84
Score = 33.5 bits (75), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/100 (19%), Positives = 45/100 (45%), Gaps = 4/100 (4%)
Query: 253 KWVQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQE 312
+ ++P+ + ++ + V Q + P+ Q ++ E ++ + ++ PH ++
Sbjct: 51 QRLEPYADQLRTQ----VNTQAEQLRRQLTPYAQRMERVLRENADSLQASLRPHADELKA 106
Query: 313 VVDPYFQEAKKFSKPYIDQVATVAKPHVDNVRVALKPYTK 352
+D +E K PY D+ V+ +R +L PY +
Sbjct: 107 KIDQNVEELKGRLTPYADEFKVKIDQTVEELRRSLAPYAQ 146
>pdb|1AV1|A Chain A, Crystal Structure Of Human Apolipoprotein A-I
pdb|1AV1|B Chain B, Crystal Structure Of Human Apolipoprotein A-I
pdb|1AV1|C Chain C, Crystal Structure Of Human Apolipoprotein A-I
pdb|1AV1|D Chain D, Crystal Structure Of Human Apolipoprotein A-I
Length = 201
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 281 VEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQEAKKFSKPYIDQVATVAKPHV 340
V+P++ + K E E + V P +QE E ++ P +++ A+ HV
Sbjct: 55 VQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHV 114
Query: 341 DNVRVALKPYTKKV 354
D +R L PY+ ++
Sbjct: 115 DALRTHLAPYSDEL 128
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 15/93 (16%)
Query: 255 VQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVV 314
VQP+++ + KW +E+ ++ VEP L+ + E + +QE +
Sbjct: 55 VQPYLDDFQKKW----QEEMELYRQKVEP----LRAELQEGARQK-------LHELQEKL 99
Query: 315 DPYFQEAKKFSKPYIDQVATVAKPHVDNVRVAL 347
P +E + ++ ++D + T P+ D +R L
Sbjct: 100 SPLGEEMRDRARAHVDALRTHLAPYSDELRQRL 132
>pdb|3J00|0 Chain 0, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3J00|1 Chain 1, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
Length = 200
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 281 VEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQEAKKFSKPYIDQVATVAKPHV 340
V+P++ + K E E + V P +QE E ++ P +++ A+ HV
Sbjct: 54 VQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHV 113
Query: 341 DNVRVALKPYTKKV 354
D +R L PY+ ++
Sbjct: 114 DALRTHLAPYSDEL 127
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 15/93 (16%)
Query: 255 VQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVV 314
VQP+++ + KW +E+ ++ VEP L+ + E + +QE +
Sbjct: 54 VQPYLDDFQKKW----QEEMELYRQKVEP----LRAELQEGARQK-------LHELQEKL 98
Query: 315 DPYFQEAKKFSKPYIDQVATVAKPHVDNVRVAL 347
P +E + ++ ++D + T P+ D +R L
Sbjct: 99 SPLGEEMRDRARAHVDALRTHLAPYSDELRQRL 131
>pdb|2LEM|A Chain A, Monomeric Mouse Apoai(1-216)
Length = 216
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 50/108 (46%), Gaps = 6/108 (5%)
Query: 281 VEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQEAKKFSKPYIDQVATVAKPHV 340
V+P++ + K E E + +P +QE QE + P ++ + HV
Sbjct: 96 VQPYLDEFQKKWKEDVELYRQKASPQGAELQESARQKLQELQGRLSPVAEEFRDRMRTHV 155
Query: 341 DNVRVALKPYTKKVVRAYGKF---LKSATT---YHHQVQASVQEMLKK 382
D++R L P+++++ + + LKS T YH ++ ++ + +K
Sbjct: 156 DSLRTQLAPHSEQMRESLAQRLAELKSNPTLNEYHSSAKSHLKSLGEK 203
>pdb|3R2P|A Chain A, 2.2 Angstrom Crystal Structure Of C Terminal Truncated
Human Apolipoprotein A-I Reveals The Assembly Of Hdl By
Dimerization
Length = 185
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 281 VEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQEAKKFSKPYIDQVATVAKPHV 340
V+P++ + K E E + V P +QE E ++ P +++ A+ HV
Sbjct: 98 VQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHV 157
Query: 341 DNVRVALKPYTKKV 354
D +R L PY+ ++
Sbjct: 158 DALRTHLAPYSDEL 171
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 15/93 (16%)
Query: 255 VQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVV 314
VQP+++ + KW +E+ ++ VEP L+ + E + +QE +
Sbjct: 98 VQPYLDDFQKKW----QEEMELYRQKVEP----LRAELQEGARQK-------LHELQEKL 142
Query: 315 DPYFQEAKKFSKPYIDQVATVAKPHVDNVRVAL 347
P +E + ++ ++D + T P+ D +R L
Sbjct: 143 SPLGEEMRDRARAHVDALRTHLAPYSDELRQRL 175
>pdb|2A01|A Chain A, Crystal Structure Of Lipid-Free Human Apolipoprotein A-I
pdb|2A01|B Chain B, Crystal Structure Of Lipid-Free Human Apolipoprotein A-I
pdb|2A01|C Chain C, Crystal Structure Of Lipid-Free Human Apolipoprotein A-I
pdb|3K2S|A Chain A, Solution Structure Of Double Super Helix Model
pdb|3K2S|B Chain B, Solution Structure Of Double Super Helix Model
Length = 243
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 281 VEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVVDPYFQEAKKFSKPYIDQVATVAKPHV 340
V+P++ + K E E + V P +QE E ++ P +++ A+ HV
Sbjct: 97 VQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHV 156
Query: 341 DNVRVALKPYTKKV 354
D +R L PY+ ++
Sbjct: 157 DALRTHLAPYSDEL 170
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 15/93 (16%)
Query: 255 VQPHVETIKAKWIPAVKEQWVVFTTNVEPHVQTLKTKTIEACEATKTAVTPHIIRVQEVV 314
VQP+++ + KW +E+ ++ VEP L+ + E + +QE +
Sbjct: 97 VQPYLDDFQKKW----QEEMELYRQKVEP----LRAELQEGARQK-------LHELQEKL 141
Query: 315 DPYFQEAKKFSKPYIDQVATVAKPHVDNVRVAL 347
P +E + ++ ++D + T P+ D +R L
Sbjct: 142 SPLGEEMRDRARAHVDALRTHLAPYSDELRQRL 174
>pdb|1YNY|A Chain A, Molecular Structure Of D-Hydantoinase From A Bacillus Sp.
Ar9: Evidence For Mercury Inhibition
pdb|1YNY|B Chain B, Molecular Structure Of D-Hydantoinase From A Bacillus Sp.
Ar9: Evidence For Mercury Inhibition
Length = 461
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 28/96 (29%)
Query: 191 AKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLI-------ETHWNAHGKP-----AMD 238
A+ EAT R+ LT + + L VH+ C S + E WN +G+ A+D
Sbjct: 216 AEGEATGRAIALTALAGSQL---YVVHV-SCASAVQRIAEAREKGWNVYGETCPQYLALD 271
Query: 239 VAIQKALEKKAQAGKWVQPHVETIKAKWIPAVKEQW 274
V+I QP E K W P ++E+W
Sbjct: 272 VSIMD------------QPDFEGAKYVWSPPLREKW 295
>pdb|3SFW|A Chain A, Crystal Structure Of Dihydropyrimidinase From
Brevibacillus Agri Nchu1002
pdb|3SFW|B Chain B, Crystal Structure Of Dihydropyrimidinase From
Brevibacillus Agri Nchu1002
Length = 461
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 39/93 (41%), Gaps = 22/93 (23%)
Query: 191 AKFEATSRSKELTEVHSAWLPPWLAVHLLQCQSLI-------ETHWNAHGK--PAMDVAI 241
A+ EAT R+ LT + A L VH+ C + E WN +G+ P V
Sbjct: 216 AEGEATGRAIALTALADAQL---YVVHV-SCADAVRRIAEAREKGWNVYGETCPQYLVLD 271
Query: 242 QKALEKKAQAGKWVQPHVETIKAKWIPAVKEQW 274
ALEK P E K W P ++E+W
Sbjct: 272 ITALEK---------PDFEGAKYVWSPPLREKW 295
>pdb|2ZYG|A Chain A, Apo-Form Of Dimeric 6-Phosphogluconate Dehydrogenase
pdb|2ZYG|B Chain B, Apo-Form Of Dimeric 6-Phosphogluconate Dehydrogenase
Length = 480
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 13/88 (14%)
Query: 199 SKELTEVHSAWLPPWLAVHLLQCQSLIETHWNAHGKPAMDVAIQKALEKKAQAGKWVQPH 258
++EL + + W L+ +L+ I T + GK +DV + +A K GKW
Sbjct: 224 NEELAQTFTEWNEGELSSYLIDITKDIFTKKDEEGKYLVDVILDEAANKG--TGKWTSQS 281
Query: 259 -----------VETIKAKWIPAVKEQWV 275
E++ A++I ++K+Q V
Sbjct: 282 SLDLGEPLSLITESVFARYISSLKDQRV 309
>pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment.
pdb|1I84|V Chain V, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment
Length = 1184
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 53 KIRSLESHIDEKTQELKGKDEVVAQKEKAIQDKSERIVSLQKEL 96
KIR LESHI + ++L+ + + EK +D SE + +L+ EL
Sbjct: 1117 KIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTEL 1160
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 0.127 0.351
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,292,226
Number of Sequences: 62578
Number of extensions: 353187
Number of successful extensions: 1046
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 979
Number of HSP's gapped (non-prelim): 89
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)