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= 041360
(561 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 = 35.8 bits (81), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 276 LSLTGVRFSSLPSSLGRLFNLQTLCLGGCRLKDI-AIVGQLKKLEILSFRDSYIEELPHE 334
L L G + LP+ + L NL+ L L RL + A +G +L+ F D+ + LP E
Sbjct: 252 LYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWE 311
Query: 335 IGQLTRL 341
G L L
Sbjct: 312 FGNLCNL 318
>pdb|3AYX|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An H2-Reduced Condition
pdb|3AYX|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An H2-Reduced Condition
pdb|3AYY|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In A Ferricyanide-Oxidized
Condition
pdb|3AYY|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In A Ferricyanide-Oxidized
Condition
pdb|3AYZ|A Chain A, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An Air-Oxidized Condition
pdb|3AYZ|C Chain C, Membrane-Bound Respiratory [nife] Hydrogenase From
Hydrogenovibrio Marinus In An Air-Oxidized Condition
Length = 596
Score = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 132 GHAIQVASLLRYGMGWGLFKNVYTLEEARSRVHRLIDNLKSSCLLLDGDGKD 183
GHA++V L RY + +E +++VH ++ + C LLD + KD
Sbjct: 405 GHAVEVGPLARY-----ILAYAQGVEYVKTQVHTSLNRFNAVCRLLDPNHKD 451
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 51/123 (41%), Gaps = 26/123 (21%)
Query: 293 LFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELPHEIGQLTRLVVIAPNLISKF 352
LFNL+ L LG C +KD+ + L LE L ++ E I P
Sbjct: 195 LFNLKYLNLGMCNIKDMPNLTPLVGLEELEMSGNHFPE-------------IRPGSFHGL 241
Query: 353 SQLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIQVRDAQILPQDLV-----LV 407
S L++L++ + SQ +E + GL+ L L + + LP DL LV
Sbjct: 242 SSLKKLWVMN--SQVSLIERNA------FDGLASLVELNLAHNNLSSLPHDLFTPLRYLV 293
Query: 408 ELQ 410
EL
Sbjct: 294 ELH 296
>pdb|2OMV|A Chain A, Crystal Structure Of Inla S192n Y369s/hec1 Complex
pdb|2OMW|A Chain A, Crystal Structure Of Inla S192n Y369s/mec1 Complex
Length = 461
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 57/105 (54%), Gaps = 7/105 (6%)
Query: 290 LGRLFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELPHEIGQLTRLVVIAPNLI 349
L L L+ L + ++ DI+++ +L LE L ++ I ++ +G LT L ++ N
Sbjct: 168 LANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDI-TPLGILTNLDELSLN-- 224
Query: 350 SKFSQLEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEI 392
+QL+++ S + ++ +N ++LA L GL+KLT L++
Sbjct: 225 --GNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKL 267
>pdb|2OMY|A Chain A, Crystal Structure Of Inla S192n/hec1 Complex
Length = 461
Score = 32.3 bits (72), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 57/105 (54%), Gaps = 7/105 (6%)
Query: 290 LGRLFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELPHEIGQLTRLVVIAPNLI 349
L L L+ L + ++ DI+++ +L LE L ++ I ++ +G LT L ++ N
Sbjct: 168 LANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDI-TPLGILTNLDELSLN-- 224
Query: 350 SKFSQLEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEI 392
+QL+++ S + ++ +N ++LA L GL+KLT L++
Sbjct: 225 --GNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKL 267
>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 = 32.3 bits (72), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 58/121 (47%), Gaps = 18/121 (14%)
Query: 1 MILTSRNRDLLERDMNSQKNFLIEV-LSKE---EALQLFENILGDSTKTSTIQPIADEIV 56
++LT+R++ + + M + +E L KE E L LF N+ K + + A I+
Sbjct: 260 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSII 314
Query: 57 KRCGGLPVAVTTVANALKSKSLDIWKDALSQL--------RSSNPREIDGMDKNVYTSIE 108
K C G P+ V+ + L+ + W+ L QL R S+ + + +D+ + S+E
Sbjct: 315 KECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVE 373
Query: 109 L 109
+
Sbjct: 374 M 374
>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 = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 58/121 (47%), Gaps = 18/121 (14%)
Query: 1 MILTSRNRDLLERDMNSQKNFLIEV-LSKE---EALQLFENILGDSTKTSTIQPIADEIV 56
++LT+R++ + + M + +E L KE E L LF N+ K + + A I+
Sbjct: 266 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSII 320
Query: 57 KRCGGLPVAVTTVANALKSKSLDIWKDALSQL--------RSSNPREIDGMDKNVYTSIE 108
K C G P+ V+ + L+ + W+ L QL R S+ + + +D+ + S+E
Sbjct: 321 KECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVE 379
Query: 109 L 109
+
Sbjct: 380 M 380
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 32/119 (26%), Positives = 55/119 (46%), Gaps = 15/119 (12%)
Query: 293 LFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELPH----EIGQLTRLVVIAPNL 348
L N++ L LGG +L DI+ + +L L L + ++ LP+ ++ L LV++ L
Sbjct: 62 LPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQL 121
Query: 349 IS----KFSQLEEL-YMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIQVRDAQILPQ 402
S F +L L Y+ + +Q + G L+ LT L++ Q LP+
Sbjct: 122 QSLPDGVFDKLTNLTYLNLAHNQLQSLPKGV------FDKLTNLTELDLSYNQLQSLPE 174
>pdb|2CDQ|A Chain A, Crystal Structure Of Arabidopsis Thaliana Aspartate Kinase
Complexed With Lysine And S-Adenosylmethionine
pdb|2CDQ|B Chain B, Crystal Structure Of Arabidopsis Thaliana Aspartate Kinase
Complexed With Lysine And S-Adenosylmethionine
Length = 510
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 7 NRDLLERDMNSQKNFLIEVLSKEEALQLFENILGDSTKTSTIQPIADEIVKRCGGLPVAV 66
N D+LE + L + + A+ + LG KT + + GG +
Sbjct: 184 NGDILEATYPAVAKRLYDDWMHDPAVPIVTGFLGKGWKTGAVTTLGR------GGSDLTA 237
Query: 67 TTVANALKSKSLDIWKD 83
TT+ AL K + +WKD
Sbjct: 238 TTIGKALGLKEIQVWKD 254
>pdb|1XEU|A Chain A, Crystal Structure Of Internalin C From Listeria
Monocytogenes
Length = 263
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 289 SLGRLFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELPHEIGQLTRL 341
SL L NL+ L + +LK I ++G L KLE+L + I G LTRL
Sbjct: 123 SLIHLKNLEILSIRNNKLKSIVMLGFLSKLEVLDLHGNEIT----NTGGLTRL 171
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 56/121 (46%), Gaps = 18/121 (14%)
Query: 1 MILTSRNRDLLERDMNSQKNFLIEV-LSKE---EALQLFENILGDSTKTSTIQPIADEIV 56
++LT+R++ + + M + +E L +E E L LF N+ K + A I+
Sbjct: 260 ILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNM-----KKEDLPAEAHSII 314
Query: 57 KRCGGLPVAVTTVANALKSKSLDIWKDALSQL--------RSSNPREIDGMDKNVYTSIE 108
K C G P+ V+ + L+ + W L QL R S+ + + +D+ + S+E
Sbjct: 315 KECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVE 373
Query: 109 L 109
+
Sbjct: 374 M 374
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 54/121 (44%), Gaps = 19/121 (15%)
Query: 293 LFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELPH----EIGQLTRLVVIAPNL 348
L N++ L LGG +L DI+ + +L L L + ++ LP+ ++ L LV++ L
Sbjct: 62 LPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQL 121
Query: 349 IS-------KFSQLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIQVRDAQILP 401
S K + L LY+ +Q + G L+ LT L++ Q LP
Sbjct: 122 QSLPDGVFDKLTNLTYLYL--YHNQLQSLPKGV------FDKLTNLTRLDLDNNQLQSLP 173
Query: 402 Q 402
+
Sbjct: 174 E 174
>pdb|4FMZ|A Chain A, Crystal Structure Of An Internalin (Inlf) From Listeria
Monocytogenes Str. 4b F2365 At 1.91 A Resolution
pdb|4FMZ|B Chain B, Crystal Structure Of An Internalin (Inlf) From Listeria
Monocytogenes Str. 4b F2365 At 1.91 A Resolution
Length = 347
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 59/133 (44%), Gaps = 28/133 (21%)
Query: 274 KVLSLTGVRFSSLPSSLGRLFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSYIEELP- 332
KV S+ G+ + L NL+ L L G ++ DI+ + L KL L + I ++
Sbjct: 55 KVASIQGIEY---------LTNLEYLNLNGNQITDISPLSNLVKLTNLYIGTNKITDISA 105
Query: 333 -HEIGQLTRLVVIAPNL--ISKFSQLEELYMGDSFSQWDKVEGGSNASLAELK------G 383
+ L L + N+ IS + L + Y + G+N +L++L G
Sbjct: 106 LQNLTNLRELYLNEDNISDISPLANLTKXY---------SLNLGANHNLSDLSPLSNXTG 156
Query: 384 LSKLTTLEIQVRD 396
L+ LT E +V+D
Sbjct: 157 LNYLTVTESKVKD 169
>pdb|2ELL|A Chain A, Solution Structure Of The Leucine Rich Repeat Of Human
Acidic Leucine- Rich Nuclear Phosphoprotein 32 Family
Member B
pdb|2RR6|A Chain A, Solution Structure Of The Leucine Rich Repeat Of Human
Acidic Leucine- Rich Nuclear Phosphoprotein 32 Family
Member B
Length = 168
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 22/36 (61%)
Query: 292 RLFNLQTLCLGGCRLKDIAIVGQLKKLEILSFRDSY 327
+L NL L L G +LKDI+ + LKKLE L D +
Sbjct: 93 KLPNLTHLNLSGNKLKDISTLEPLKKLECLKSLDLF 128
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 0.136 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,637,337
Number of Sequences: 62578
Number of extensions: 634820
Number of successful extensions: 1561
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 1537
Number of HSP's gapped (non-prelim): 54
length of query: 561
length of database: 14,973,337
effective HSP length: 104
effective length of query: 457
effective length of database: 8,465,225
effective search space: 3868607825
effective search space used: 3868607825
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: 54 (25.4 bits)