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= 000962
(1208 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 47.4 bits (111), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 46/88 (52%), Gaps = 12/88 (13%)
Query: 616 LRYLDLSRTEIKVLPNSICNLYNLQTLKLIGCIWIMELPKDLAN---------LVKLRNL 666
L L L+R ++ LP SI +L L+ L + C + ELP+ LA+ LV L++L
Sbjct: 129 LETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSL 188
Query: 667 ELEEMFWFKCSTLPAGIGKLTNLHNLHV 694
LE W +LPA I L NL +L +
Sbjct: 189 RLE---WTGIRSLPASIANLQNLKSLKI 213
Score = 38.9 bits (89), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 52/185 (28%), Positives = 77/185 (41%), Gaps = 35/185 (18%)
Query: 907 LRVIPTSDNGQGQHLLLHSFQTLLEMKAINCPKLRGLPQIFAPQ---------------K 951
LR +P S + S L E+ CP+L LP+ A +
Sbjct: 139 LRALPAS---------IASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLR 189
Query: 952 LEISGCDLLSTLPNSEFS-QRLQLLALEGCPDGTLVRAIPETSSLNFLILSKISNLDSFP 1010
LE +G + +LP S + Q L+ L + P L AI L L L + L ++P
Sbjct: 190 LEWTG---IRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYP 246
Query: 1011 RWPNLPG---LKALYIRDCKDLVSLSGEGALQSLTSLNLLSIRGCPKLETLPDEGLPTSL 1067
P G LK L ++DC +L++L + + LT L L +RGC L LP
Sbjct: 247 --PIFGGRAPLKRLILKDCSNLLTLPLD--IHRLTQLEKLDLRGCVNLSRLPSLIAQLPA 302
Query: 1068 KCLII 1072
C+I+
Sbjct: 303 NCIIL 307
Score = 30.8 bits (68), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 43/151 (28%), Positives = 63/151 (41%), Gaps = 32/151 (21%)
Query: 847 LGRLKISNCPRLNELPECMP------------NLTVMKIKKCCSLKALPVTPFLQFLILV 894
L L I CP L ELPE + NL +++ + +++LP + +
Sbjct: 152 LRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL-EWTGIRSLPAS--------I 202
Query: 895 DNLELENWNERCLRVIPTSDNGQGQHLLLHSFQTLLEMKAINCPKLRGLPQIF---AP-Q 950
N L+N +R P S G +H L E+ C LR P IF AP +
Sbjct: 203 AN--LQNLKSLKIRNSPLSALGPA----IHHLPKLEELDLRGCTALRNYPPIFGGRAPLK 256
Query: 951 KLEISGCDLLSTLP-NSEFSQRLQLLALEGC 980
+L + C L TLP + +L+ L L GC
Sbjct: 257 RLILKDCSNLLTLPLDIHRLTQLEKLDLRGC 287
Score = 29.6 bits (65), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 48/100 (48%), Gaps = 15/100 (15%)
Query: 1036 GALQSLTSLNLLSIRGCPKLETLPD-----------EGLPTSLKCLIIASCSGLKSLGPR 1084
++ SL L LSIR CP+L LP+ +GL +L+ L + +G++SL
Sbjct: 144 ASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGL-VNLQSLRL-EWTGIRSLP-- 199
Query: 1085 GTLKSLNSLKDFYIEDCPLLQSFPEDGLPENLQHLVIQNC 1124
++ +L +LK I + PL P L+ L ++ C
Sbjct: 200 ASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGC 239
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 47.0 bits (110), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 58/217 (26%), Positives = 90/217 (41%), Gaps = 41/217 (18%)
Query: 201 IPIIGMPGLGKTTLAQLLFNEERVREH------FESRM-WVCVTVDYDLPRILKGMIEFH 253
+ I GM G GK+ LA E VR+H F + WV V D +L +
Sbjct: 150 VTIHGMAGCGKSVLA-----AEAVRDHSLLEGCFPGGVHWVSVG-KQDKSGLLMKLQNLC 203
Query: 254 SKMEQSTSSISLL---------ETRLLEFLTGQRFLLVLDDVWNEDYRKWEPLQQLLKQG 304
++++Q S L R+L R LL+LDDVW+ W +LK
Sbjct: 204 TRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----W-----VLKAF 254
Query: 305 HKGSRVLVTSRTARVS-QIMGIRSPYLLEYLPEDQCWSIFKKIAFNQGNFSSRMQQQNLE 363
++L+T+R V+ +MG + +E S+ K+ + M++ +L
Sbjct: 255 DSQCQILLTTRDKSVTDSVMGPKYVVPVES-------SLGKEKGLEILSLFVNMKKADLP 307
Query: 364 AIGREIVGKCKGLPLAVKAIAGFLRKYDDVNKWRKIL 400
I+ +CKG PL V I LR + N+W L
Sbjct: 308 EQAHSIIKECKGSPLVVSLIGALLRDFP--NRWEYYL 342
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 58/217 (26%), Positives = 90/217 (41%), Gaps = 41/217 (18%)
Query: 201 IPIIGMPGLGKTTLAQLLFNEERVREH------FESRM-WVCVTVDYDLPRILKGMIEFH 253
+ I GM G GK+ LA E VR+H F + WV V D +L +
Sbjct: 156 VTIHGMAGCGKSVLAA-----EAVRDHSLLEGCFPGGVHWVSVG-KQDKSGLLMKLQNLC 209
Query: 254 SKMEQSTSSISLL---------ETRLLEFLTGQRFLLVLDDVWNEDYRKWEPLQQLLKQG 304
++++Q S L R+L R LL+LDDVW+ W +LK
Sbjct: 210 TRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----W-----VLKAF 260
Query: 305 HKGSRVLVTSRTARVS-QIMGIRSPYLLEYLPEDQCWSIFKKIAFNQGNFSSRMQQQNLE 363
++L+T+R V+ +MG + +E S+ K+ + M++ +L
Sbjct: 261 DSQCQILLTTRDKSVTDSVMGPKYVVPVES-------SLGKEKGLEILSLFVNMKKADLP 313
Query: 364 AIGREIVGKCKGLPLAVKAIAGFLRKYDDVNKWRKIL 400
I+ +CKG PL V I LR + N+W L
Sbjct: 314 EQAHSIIKECKGSPLVVSLIGALLRDFP--NRWEYYL 348
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 56/217 (25%), Positives = 90/217 (41%), Gaps = 41/217 (18%)
Query: 201 IPIIGMPGLGKTTLAQLLFNEERVREH------FESRM-WVCVTVDYDLPRILKGMIEFH 253
+ I GM G GK+ LA E VR+H F + WV + D +L +
Sbjct: 150 VTIYGMAGCGKSVLAA-----EAVRDHSLLEGCFSGGVHWVSIG-KQDKSGLLMKLQNLC 203
Query: 254 SKMEQSTSSISLL---------ETRLLEFLTGQRFLLVLDDVWNEDYRKWEPLQQLLKQG 304
+++Q S L R+L R LL+LDDVW+ W +LK
Sbjct: 204 MRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD----PW-----VLKAF 254
Query: 305 HKGSRVLVTSRTARVS-QIMGIRSPYLLEYLPEDQCWSIFKKIAFNQGNFSSRMQQQNLE 363
++L+T+R V+ +MG + +E + ++ + M++++L
Sbjct: 255 DNQCQILLTTRDKSVTDSVMGPKHVVPVES-------GLGREKGLEILSLFVNMKKEDLP 307
Query: 364 AIGREIVGKCKGLPLAVKAIAGFLRKYDDVNKWRKIL 400
A I+ +CKG PL V I LR + N+W L
Sbjct: 308 AEAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYL 342
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 55/217 (25%), Positives = 89/217 (41%), Gaps = 41/217 (18%)
Query: 201 IPIIGMPGLGKTTLAQLLFNEERVREH------FESRM-WVCVTVDYDLPRILKGMIEFH 253
+ I GM G GK+ LA E VR+H F + WV + D +L +
Sbjct: 157 VTIYGMAGCGKSVLAA-----EAVRDHSLLEGCFSGGVHWVSIG-KQDKSGLLMKLQNLC 210
Query: 254 SKMEQSTSSISLL---------ETRLLEFLTGQRFLLVLDDVWNEDYRKWEPLQQLLKQG 304
+++Q S L R+L R LL+LDDVW+ W +LK
Sbjct: 211 MRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD----PW-----VLKAF 261
Query: 305 HKGSRVLVTSRTARVS-QIMGIRSPYLLEYLPEDQCWSIFKKIAFNQGNFSSRMQQQNLE 363
++L+T+ V+ +MG + +E + ++ + M++++L
Sbjct: 262 DNQCQILLTTSDKSVTDSVMGPKHVVPVES-------GLGREKGLEILSLFVNMKKEDLP 314
Query: 364 AIGREIVGKCKGLPLAVKAIAGFLRKYDDVNKWRKIL 400
A I+ +CKG PL V I LR + N+W L
Sbjct: 315 AEAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYL 349
>pdb|3LHA|A Chain A, Crystal Structure Of Mouse Vps26b(R240sG241AE242S) IN
SPACEGROUP P41 21 2
pdb|3LHA|B Chain B, Crystal Structure Of Mouse Vps26b(R240sG241AE242S) IN
SPACEGROUP P41 21 2
Length = 340
Score = 31.6 bits (70), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 549 HVEKPALSVVENSKKLRTFLVPSFGEHLKDFGRALDKIFHQL 590
HVEKP S + KLR FL + L D + +D + H L
Sbjct: 115 HVEKPYESYTGQNVKLRYFLRATISRRLNDVVKEMDIVVHTL 156
>pdb|3LH8|A Chain A, Crystal Structure Of Mouse Vps26b In Spacegroup P41 21 2
pdb|3LH8|B Chain B, Crystal Structure Of Mouse Vps26b In Spacegroup P41 21 2
pdb|3LH9|A Chain A, Crystal Structure Of Mouse Vps26b(L197sR199E) IN
SPACEGROUP P41 21 2
pdb|3LH9|B Chain B, Crystal Structure Of Mouse Vps26b(L197sR199E) IN
SPACEGROUP P41 21 2
Length = 340
Score = 31.6 bits (70), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 549 HVEKPALSVVENSKKLRTFLVPSFGEHLKDFGRALDKIFHQL 590
HVEKP S + KLR FL + L D + +D + H L
Sbjct: 115 HVEKPYESYTGQNVKLRYFLRATISRRLNDVVKEMDIVVHTL 156
>pdb|1MKY|A Chain A, Structural Analysis Of The Domain Interactions In Der, A
Switch Protein Containing Two Gtpase Domains
Length = 439
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 197 DAFVIPIIGMPGLGKTTLAQLLFNEER 223
DA + I+G P +GK+TL + N+ER
Sbjct: 179 DAIKVAIVGRPNVGKSTLFNAILNKER 205
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 30.0 bits (66), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 200 VIPIIGMPGLGKTTLAQLLFNEERVREHFESRMWVCVTVDYDLPRILKG-----MIEFHS 254
VI I+G G+GKTT ++L V E E ++ +TV Y P+ +K + E S
Sbjct: 384 VIGIVGPNGIGKTTFVKMLAG---VEEPTEGKVEWDLTVAYK-PQYIKAEYEGTVYELLS 439
Query: 255 KMEQSTSSISLLETRLLE 272
K++ S + + +T LL+
Sbjct: 440 KIDSSKLNSNFYKTELLK 457
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 30.0 bits (66), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 200 VIPIIGMPGLGKTTLAQLLFNEERVREHFESRMWVCVTVDYDLPRILKG-----MIEFHS 254
VI I+G G+GKTT ++L V E E ++ +TV Y P+ +K + E S
Sbjct: 370 VIGIVGPNGIGKTTFVKMLAG---VEEPTEGKVEWDLTVAYK-PQYIKAEYEGTVYELLS 425
Query: 255 KMEQSTSSISLLETRLLE 272
K++ S + + +T LL+
Sbjct: 426 KIDSSKLNSNFYKTELLK 443
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 30.0 bits (66), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 49/87 (56%), Gaps = 6/87 (6%)
Query: 611 EELKLLRYLDLSRTEIKVLPNSICN-LYNLQTLKLIGCIWIMELPKDLANLVKLRNLELE 669
+ L L LDL ++ VLP+++ + L +L+ L + C + ELP+ + L L +L L+
Sbjct: 85 DSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKEL-FMCCNKLTELPRGIERLTHLTHLALD 143
Query: 670 EMFWFKCSTLPAG-IGKLTNLHNLHVF 695
+ + ++P G +L++L + ++F
Sbjct: 144 QN---QLKSIPHGAFDRLSSLTHAYLF 167
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
0.320 0.138 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,959,777
Number of Sequences: 62578
Number of extensions: 1382348
Number of successful extensions: 3566
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 3538
Number of HSP's gapped (non-prelim): 40
length of query: 1208
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1098
effective length of database: 8,089,757
effective search space: 8882553186
effective search space used: 8882553186
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)