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= 048834
(1108 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/129 (26%), Positives = 55/129 (42%), Gaps = 7/129 (5%)
Query: 737 KRMGDKPADEVGNLLNKMI----NRRGYRLLRVLDLEGVYKPVLPETVGKLQLLRYFGLR 792
K++ DE ++ N+M+ ++ +L LDL + + + K L L
Sbjct: 196 KKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLN 255
Query: 793 WTFLDSIPESVGDLPCLETLDLKHTNITSLPKSIWKVKTLRHLYMNDIYLQMSVQKPFVK 852
L +P + +L L LDL H +TSLP + L++ Y D M P+
Sbjct: 256 GNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFD---NMVTTLPWEF 312
Query: 853 YSLTNLQTL 861
+L NLQ L
Sbjct: 313 GNLCNLQFL 321
>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 = 37.0 bits (84), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 52/215 (24%), Positives = 99/215 (46%), Gaps = 27/215 (12%)
Query: 389 ISVVGVAGSGKTTLV-ETIYNSSYIRQNFEYHA-WANVDVSHDFDLRKVFINILEQVTRV 446
+++ G+AG GK+ L E + + S + F W +V L N+ ++ +
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 209
Query: 447 K-IAEELALNELES----RLIRLFQSKRYLIVLDDVHLPGAWYELQRIFSPNTSSSGSRV 501
+ ++ L LN E+ R++ L + R L++LDDV +W + + F S ++
Sbjct: 210 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW--DSW--VLKAFD-----SQCQI 260
Query: 502 ILLTREAFVARA-FSPSIILLQLRPLNVDESWELFLKKVGREKRASELLNLKEKIWKKCG 560
+L TR+ V + P ++ L ++ E+ V +K ++L I K+C
Sbjct: 261 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK--ADLPEQAHSIIKECK 318
Query: 561 GLPLAICVLGGLLST--NR------QIQNSDWEKV 587
G PL + ++G LL NR Q+QN ++++
Sbjct: 319 GSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRI 353
>pdb|2EWV|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
Bound Adp
Length = 372
Score = 36.6 bits (83), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 42/84 (50%), Gaps = 11/84 (13%)
Query: 356 AEILGPEAELVGLKDQLLRLAQLTMSSSSKYFLISVVGVAGSGKTTLVETIYNSSYIRQN 415
AEI PE + +GL D++L L M LI V G GSGK+T + ++ + YI Q
Sbjct: 114 AEI--PEFKKLGLPDKVLELCHRKMG------LILVTGPTGSGKSTTIASMID--YINQT 163
Query: 416 FEYHAWANVD-VSHDFDLRKVFIN 438
YH D + + F +K +N
Sbjct: 164 KSYHIITIEDPIEYVFKHKKSIVN 187
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 36.2 bits (82), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 55/128 (42%), Gaps = 8/128 (6%)
Query: 765 VLDLEGVYKPVLPETVGKLQLLRYFGLRWTFLDSIPESVGDLPCLETLDLKHTNITSLPK 824
L+L V P P+ +L L++ + L +P++ LETL L + +LP
Sbjct: 85 ALELRSVPLPQFPDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLARNPLRALPA 144
Query: 825 SIWKVKTLRHLYMNDIYLQMSVQKPFVK-------YSLTNLQTLWSLLIGNKSPPLNWLE 877
SI + LR L + + +P L NLQ+L G +S P + +
Sbjct: 145 SIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPAS-IA 203
Query: 878 SLRGLKKL 885
+L+ LK L
Sbjct: 204 NLQNLKSL 211
>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 = 35.0 bits (79), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 53/218 (24%), Positives = 99/218 (45%), Gaps = 33/218 (15%)
Query: 389 ISVVGVAGSGKTTLV-ETIYNSSYIRQNFEYHA-WANVDVSHDFDLRKVFINILEQVTRV 446
+++ G+AG GK+ L E + + S + F W +V D + + + TR+
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ---DKSGLLMKLQNLCTRL 212
Query: 447 ----KIAEELALNELES----RLIRLFQSKRYLIVLDDVHLPGAWYELQRIFSPNTSSSG 498
++ L LN E+ R++ L + R L++LDDV +W + + F S
Sbjct: 213 DQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW--DSW--VLKAFD-----SQ 263
Query: 499 SRVILLTREAFVARA-FSPSIILLQLRPLNVDESWELFLKKVGREKRASELLNLKEKIWK 557
+++L TR+ V + P ++ L ++ E+ V +K ++L I K
Sbjct: 264 CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK--ADLPEQAHSIIK 321
Query: 558 KCGGLPLAICVLGGLLST--NR------QIQNSDWEKV 587
+C G PL + ++G LL NR Q+QN ++++
Sbjct: 322 ECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRI 359
>pdb|2EWW|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
Bound Atp
Length = 372
Score = 34.7 bits (78), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 11/84 (13%)
Query: 356 AEILGPEAELVGLKDQLLRLAQLTMSSSSKYFLISVVGVAGSGKTTLVETIYNSSYIRQN 415
AEI PE + +GL D++L L K LI V G GSGK+T + + + YI Q
Sbjct: 114 AEI--PEFKKLGLPDKVLELCH------RKXGLILVTGPTGSGKSTTIASXID--YINQT 163
Query: 416 FEYHAWANVD-VSHDFDLRKVFIN 438
YH D + + F +K +N
Sbjct: 164 KSYHIITIEDPIEYVFKHKKSIVN 187
>pdb|2GSZ|A Chain A, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|B Chain B, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|C Chain C, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|D Chain D, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|E Chain E, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|F Chain F, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
Length = 363
Score = 34.3 bits (77), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 11/84 (13%)
Query: 356 AEILGPEAELVGLKDQLLRLAQLTMSSSSKYFLISVVGVAGSGKTTLVETIYNSSYIRQN 415
AEI PE + +GL D++L L K LI V G GSGK+T + + + YI Q
Sbjct: 103 AEI--PEFKKLGLPDKVLELCH------RKXGLILVTGPTGSGKSTTIASXID--YINQT 152
Query: 416 FEYHAWANVD-VSHDFDLRKVFIN 438
YH D + + F +K +N
Sbjct: 153 KSYHIITIEDPIEYVFKHKKSIVN 176
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 33.5 bits (75), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 50/215 (23%), Positives = 96/215 (44%), Gaps = 27/215 (12%)
Query: 389 ISVVGVAGSGKTTLV-ETIYNSSYIRQNFEYHA-WANVDVSHDFDLRKVFINILEQVTRV 446
+++ G+AG GK+ L E + + S + F W ++ L N+ ++ +
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 209
Query: 447 K-IAEELALNELES----RLIRLFQSKRYLIVLDDVHLPGAWYELQRIFSPNTSSSGSRV 501
+ ++ L LN E+ R++ L + R L++LDDV P W + + F ++
Sbjct: 210 ESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP--W--VLKAFDNQC-----QI 260
Query: 502 ILLTREAFVARA-FSPSIILLQLRPLNVDESWELFLKKVGREKRASELLNLKEKIWKKCG 560
+L TR+ V + P ++ L ++ E+ V +K +L I K+C
Sbjct: 261 LLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE--DLPAEAHSIIKECK 318
Query: 561 GLPLAICVLGGLLSTN--------RQIQNSDWEKV 587
G PL + ++G LL RQ+QN ++++
Sbjct: 319 GSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRI 353
>pdb|2EYU|A Chain A, The Crystal Structure Of The C-Terminal Domain Of Aquifex
Aeolicus Pilt
pdb|2EYU|B Chain B, The Crystal Structure Of The C-Terminal Domain Of Aquifex
Aeolicus Pilt
Length = 261
Score = 33.5 bits (75), Expect = 0.68, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 11/84 (13%)
Query: 356 AEILGPEAELVGLKDQLLRLAQLTMSSSSKYFLISVVGVAGSGKTTLVETIYNSSYIRQN 415
AEI PE + +GL D++L L K LI V G GSGK+T + + + YI Q
Sbjct: 3 AEI--PEFKKLGLPDKVLELCH------RKXGLILVTGPTGSGKSTTIASXID--YINQT 52
Query: 416 FEYHAWANVD-VSHDFDLRKVFIN 438
YH D + + F +K +N
Sbjct: 53 KSYHIITIEDPIEYVFKHKKSIVN 76
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 31.2 bits (69), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 49/215 (22%), Positives = 95/215 (44%), Gaps = 27/215 (12%)
Query: 389 ISVVGVAGSGKTTLV-ETIYNSSYIRQNFEYHA-WANVDVSHDFDLRKVFINILEQVTRV 446
+++ G+AG GK+ L E + + S + F W ++ L N+ ++ +
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 216
Query: 447 K-IAEELALNELES----RLIRLFQSKRYLIVLDDVHLPGAWYELQRIFSPNTSSSGSRV 501
+ ++ L LN E+ R++ L + R L++LDDV P W + + F ++
Sbjct: 217 ESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP--W--VLKAFDNQC-----QI 267
Query: 502 ILLTREAFVARA-FSPSIILLQLRPLNVDESWELFLKKVGREKRASELLNLKEKIWKKCG 560
+L T + V + P ++ L ++ E+ V +K +L I K+C
Sbjct: 268 LLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE--DLPAEAHSIIKECK 325
Query: 561 GLPLAICVLGGLLSTN--------RQIQNSDWEKV 587
G PL + ++G LL RQ+QN ++++
Sbjct: 326 GSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRI 360
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 31.2 bits (69), Expect = 3.6, Method: Composition-based stats.
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 8/99 (8%)
Query: 766 LDLEGVYKPV---LPETVGKLQLLR--YFGLRWTFLDSIPESVGDLPCLETLDLKHTNIT 820
LDL G+ P +P ++ L L Y G + IP ++ L L L + HTN++
Sbjct: 55 LDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVS 114
Query: 821 -SLPKSIWKVKTLRHLYMNDIYLQMSVQKPFVKYSLTNL 858
++P + ++KTL L + Y +S P SL NL
Sbjct: 115 GAIPDFLSQIKTLVTLDFS--YNALSGTLPPSISSLPNL 151
>pdb|1GAX|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1GAX|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IVS|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
Synthetase Complexed With Trna(Val) And Valyl-Adenylate
Analogue
pdb|1IYW|A Chain A, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
pdb|1IYW|B Chain B, Preliminary Structure Of Thermus Thermophilus Ligand-Free
Valyl-Trna Synthetase
Length = 862
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 476 DVHLPGAWYELQRIFSPNTSSSGSRVILLTREAFVARAFSPSI 518
D+ L W E+ R F+ N + +R +LL+RE F A+ +P++
Sbjct: 564 DIRLDLRWLEMARNFA-NKLYNAARFVLLSREGFQAKEDTPTL 605
>pdb|3NAP|B Chain B, Structure Of Triatoma Virus (Trv)
Length = 255
Score = 30.8 bits (68), Expect = 4.5, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 806 LPCLETLDLKHTNITSLPKSIWKVKTLRHLYMN-----DIYLQMSVQKPFVKYSLTNLQT 860
+P + L L N+ S S V TL H+ ++ ++ L++ PFV+Y L T
Sbjct: 154 VPVPDILPLHRLNMLSFDVS--NVITLPHVQLDISKETEVLLKIPYVSPFVQYDLVTKFT 211
Query: 861 LWSLLIGNKSPPLN 874
W+ + + PLN
Sbjct: 212 PWAAFLAHVYAPLN 225
>pdb|1ZY7|A Chain A, Crystal Structure Of The Catalytic Domain Of An Adenosine
Deaminase That Acts On Rna (hadar2) Bound To Inositol
Hexakisphosphate (ihp)
pdb|1ZY7|B Chain B, Crystal Structure Of The Catalytic Domain Of An Adenosine
Deaminase That Acts On Rna (hadar2) Bound To Inositol
Hexakisphosphate (ihp)
Length = 403
Score = 30.4 bits (67), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 378 LTMSSSSKYFLISVVGVAGSGKTTLVETIYNSSYIRQNFEYHA 420
LTMS S K +VVG+ GS + VE IY SS I + YH
Sbjct: 214 LTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSL-YHG 255
>pdb|3SOP|A Chain A, Crystal Structure Of Human Septin 3 Gtpase Domain
pdb|3SOP|B Chain B, Crystal Structure Of Human Septin 3 Gtpase Domain
Length = 270
Score = 29.6 bits (65), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 387 FLISVVGVAGSGKTTLVETIYNSSYIRQ 414
F I VVG +G GK+TLV T++ S R+
Sbjct: 3 FNIMVVGQSGLGKSTLVNTLFKSQVSRK 30
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
0.319 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,417,356
Number of Sequences: 62578
Number of extensions: 1292968
Number of successful extensions: 3358
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 3348
Number of HSP's gapped (non-prelim): 23
length of query: 1108
length of database: 14,973,337
effective HSP length: 109
effective length of query: 999
effective length of database: 8,152,335
effective search space: 8144182665
effective search space used: 8144182665
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)