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= 039311
(909 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 = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 39/113 (34%), Positives = 52/113 (46%), Gaps = 1/113 (0%)
Query: 363 NLVSLEMPHSSIKQLWKGVQRLVNLKHINLSHSEHLTKIPDLSLATNLESLNFQGCTCLL 422
NL SL + + I+ L + L NLK + + +S P + LE L+ +GCT L
Sbjct: 184 NLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALR 243
Query: 423 ETHSSIQYLNKLVVLNLKHCRSLTSLSTSIH-LGSLKKLILSGCSNLMSFPEL 474
L L LK C +L +L IH L L+KL L GC NL P L
Sbjct: 244 NYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSL 296
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 48/112 (42%), Gaps = 10/112 (8%)
Query: 544 IREVPSSIACLKNLGRLSFESFMCHEQMGLLLPISF--------GLTSLTYLRLTDCGII 595
+R +P+SIA L L LS + C E L P++ GL +L LRL GI
Sbjct: 139 LRALPASIASLNRLRELSIRA--CPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIR 196
Query: 596 ELPECLGQLSSRSILLLEKNNFERIPESIIQLSHLFSLGISHCERLHSLPEL 647
LP + L + L + + + +I L L L + C L + P +
Sbjct: 197 SLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPI 248
>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 = 38.1 bits (87), Expect = 0.024, Method: Composition-based stats.
Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 42/189 (22%)
Query: 240 KIMMHDLLQEMGREIVRQESIKDPGKRSRLWHHEDIYNVLTNNTGTEAIEGISLDMSKVK 299
+I D E + ++++S+ D ++ L I ++ NN+ ++++GI + V+
Sbjct: 11 QIFPDDAFAETIKANLKKKSVTDAVTQNEL---NSIDQIIANNSDIKSVQGIQY-LPNVR 66
Query: 300 EIHLNAGSFTNMHKLRFFKFYSSHYGENVNKVHNFRGL-ESTELRYLQWHGCPLKSLSSK 358
+ L NK+H+ L E T L YL G L+SL +
Sbjct: 67 YLALGG-----------------------NKLHDISALKELTNLTYLILTGNQLQSLPNG 103
Query: 359 IPPE--NLVSLEMPHSSIKQLWKGV-QRLVNLKHINLSHSE----------HLTKIPDLS 405
+ + NL L + + ++ L GV +L NL ++NL+H++ LT + +L
Sbjct: 104 VFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELD 163
Query: 406 LATN-LESL 413
L+ N L+SL
Sbjct: 164 LSYNQLQSL 172
>pdb|4FS7|A Chain A, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Bacova_04585) From Bacteroides Ovatus Atcc 8483
At 1.19 A Resolution
Length = 394
Score = 34.3 bits (77), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 68/159 (42%), Gaps = 19/159 (11%)
Query: 542 IAIREVPSSIACLKNLGRLSFESFMCHEQMGLLLPISFGLTSLTYLRLTDCGIIELPECL 601
+ I +P S+ K +GR +F C+ +LLP+ + + D I +PE +
Sbjct: 96 LEIINIPDSV---KXIGRCTFSG--CYALKSILLPLXLKSIGVEAFKGCDFKEITIPEGV 150
Query: 602 GQLSSRSILLLEKNNFERIPESIIQLSH-LFSLGISHCERLHSLPELPCDLSDIEAHCCS 660
+ + E + +P+S L + LF S C +L S+ +LP +L I +C +
Sbjct: 151 TVIGDEAFATCESLEYVSLPDSXETLHNGLF----SGCGKLKSI-KLPRNLKIIRDYCFA 205
Query: 661 SLEALSGLSILFTQTSWNSQFFYFVNCFKLDKNELKEII 699
IL + + +Y + F L K +K II
Sbjct: 206 E-------CILLENXEFPNSLYYLGD-FALSKTGVKNII 236
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 33.5 bits (75), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 45/90 (50%), Gaps = 3/90 (3%)
Query: 384 LVNLKHINLSHSEHLTKIPDLSLATNLESLNFQGCTCLLETHSSIQYLNKLVVLNLKHCR 443
LVNL+++NL +L IP+L+ LE L G L S Q L L L L H +
Sbjct: 155 LVNLRYLNLGMC-NLKDIPNLTALVRLEELELSGNRLDLIRPGSFQGLTSLRKLWLMHAQ 213
Query: 444 SLTSLSTSI-HLGSLKKLILSGCSNLMSFP 472
T + L SL++L LS +NLMS P
Sbjct: 214 VATIERNAFDDLKSLEELNLSH-NNLMSLP 242
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 32.7 bits (73), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 45/90 (50%), Gaps = 3/90 (3%)
Query: 384 LVNLKHINLSHSEHLTKIPDLSLATNLESLNFQGCTCLLETHSSIQYLNKLVVLNLKHCR 443
LVNL+++NL +L IP+L+ LE L G L S Q L L L L H +
Sbjct: 155 LVNLRYLNLGMC-NLKDIPNLTALVRLEELELSGNRLDLIRPGSFQGLTSLRKLWLMHAQ 213
Query: 444 SLTSLSTSI-HLGSLKKLILSGCSNLMSFP 472
T + L SL++L LS +NLMS P
Sbjct: 214 VATIERNAFDDLKSLEELNLSH-NNLMSLP 242
>pdb|2W9M|A Chain A, Structure Of Family X Dna Polymerase From Deinococcus
Radiodurans
pdb|2W9M|B Chain B, Structure Of Family X Dna Polymerase From Deinococcus
Radiodurans
Length = 578
Score = 32.7 bits (73), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 11/99 (11%)
Query: 800 VAVGHLTG-------WSDGYRGPRYIGSDHVFLGFDFYMFSDGFDEYYYSDEVFIQFY-- 850
V VG L G WSDG R + + LG +F +D YY++ + I+
Sbjct: 322 VTVGDLRGMIHTHSTWSDGGASIREMAEATLTLGHEFLGTADHSRAAYYANGLTIERLRE 381
Query: 851 -LEDCCEVTKCGIHLLYAQDFSDSTEDSVWNFSSDEQGE 888
L++ E+ + G+ ++ + D +D +F D GE
Sbjct: 382 QLKEIRELQRAGLPIVAGSEV-DILDDGSLDFPDDVLGE 419
>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 606
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 46/147 (31%), Positives = 59/147 (40%), Gaps = 23/147 (15%)
Query: 582 TSLTYLRLTDCGIIELPECLGQLSSRSILLLEKNNFERI----PESIIQLSHL------- 630
+ L L LT + ELP L LS+ L+L N FE + + L+HL
Sbjct: 278 SGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTK 337
Query: 631 -FSLGISHCERLHSLPELPCDLSDIE-AHCCS-SLEALSGLSILFTQTSWNSQFFYFVNC 687
LG E L +L EL DIE + CC+ L LS L L S+N
Sbjct: 338 RLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSL--NLSYNEPLSLKTEA 395
Query: 688 FK-------LDKNELKEIIKDAQRKMQ 707
FK LD + +KDAQ Q
Sbjct: 396 FKECPQLELLDLAFTRLKVKDAQSPFQ 422
>pdb|1G8S|A Chain A, Methanococcus Jannaschii Fibrillarin Pre-Rrna Processing
Protein
Length = 230
Score = 32.0 bits (71), Expect = 1.7, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 50 KKVLIVFDDVSTSEQMEFLIGNQGWLMQGSRLIITARDKQVLKNCGVDTIYEVKELFDDD 109
+KV ++++DV+ Q E LI N W ++ + A +K +D + KE+F +
Sbjct: 142 EKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGMIA-----IKARSIDVTKDPKEIFKEQ 196
Query: 110 ARML 113
+L
Sbjct: 197 KEIL 200
>pdb|1FBN|A Chain A, Crystal Structure Of A Fibrillarin Homologue From
Methanococcus Jannaschii, A Hyperthermophile, At 1.6 A
Length = 230
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 11/67 (16%)
Query: 50 KKVLIVFDDVSTSEQMEFLIGNQGWLMQG---SRLIITARDKQVLKNCGVDTIYEVKELF 106
+KV ++++DV+ Q E LI N W ++ + I AR +D + KE+F
Sbjct: 142 EKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGXIAIKARS--------IDVTKDPKEIF 193
Query: 107 DDDARML 113
+ +L
Sbjct: 194 KEQKEIL 200
>pdb|2F8L|A Chain A, Crystal Structure Of A Putative Class I
S-Adenosylmethionine-Dependent Methyltransferase
(Lmo1582) From Listeria Monocytogenes At 2.20 A
Resolution
Length = 344
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 593 GIIELPECL--GQLSSRSILLLEKNNFERIPESIIQLSHLFSL 633
GII+LPE L + + +SIL+LEK + + P + L++L SL
Sbjct: 281 GIIKLPETLFKSEQARKSILILEKADVDVKPPKEVLLANLSSL 323
>pdb|1XEU|A Chain A, Crystal Structure Of Internalin C From Listeria
Monocytogenes
Length = 263
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 56/108 (51%), Gaps = 23/108 (21%)
Query: 371 HSSIKQLWKGVQRLVNLKHINLSHSE--------HLTKIPDLSLATN-LESLNFQGCTCL 421
+S+I+ L G+Q NLK ++LSH++ LTK+ +LS+ N L++LN CL
Sbjct: 50 NSNIQSL-AGMQFFTNLKELHLSHNQISDLSPLKDLTKLEELSVNRNRLKNLNGIPSACL 108
Query: 422 ---------LETHSSIQYLNKLVVLNLKHCRSLTSLSTSIHLGSLKKL 460
L S+ +L L +L++++ + L + + LG L KL
Sbjct: 109 SRLFLDNNELRDTDSLIHLKNLEILSIRNNK----LKSIVMLGFLSKL 152
>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 = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 64/146 (43%), Gaps = 23/146 (15%)
Query: 51 KVLIVFDDVSTSEQMEFLIGNQGWLMQG----SRLIITARDKQVLKNC-GVDTIYEVKE- 104
+ L++ DDV S W+++ ++++T RDK V + G + V+
Sbjct: 243 RSLLILDDVWDS-----------WVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESS 291
Query: 105 LFDDDARMLFSRYAFGKNYPNVGYMELSNKIIKYAKGVPLAIKVLGRFLCGRRIKD-WES 163
L + + S + N E ++ IIK KG PL + ++G L R + WE
Sbjct: 292 LGKEKGLEILSLFV---NMKKADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEY 346
Query: 164 TIKKIKRIPHVDIQKVLKVSFDGLDD 189
+K+++ I+K ++ LD+
Sbjct: 347 YLKQLQNKQFKRIRKSSSYDYEALDE 372
>pdb|3B2D|A Chain A, Crystal Structure Of Human Rp105MD-1 Complex
pdb|3B2D|B Chain B, Crystal Structure Of Human Rp105MD-1 Complex
Length = 603
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 43/138 (31%), Positives = 63/138 (45%), Gaps = 15/138 (10%)
Query: 550 SIACLKNLGRLSFESFMCHE-QMGLLLPISFG-LTSLTYLRLTDCGIIELPECLGQLSSR 607
S A LK L +S ES E + + +F T L L LT + LP + L+
Sbjct: 241 SSAMLKGLCEMSVESLNLQEHRFSDISSTTFQCFTQLQELDLTATHLKGLPSGMKGLNLL 300
Query: 608 SILLLEKNNFERI----PESIIQLSHLF--------SLGISHCERLHSLPELPCDLSDIE 655
L+L N+F+++ + L+HL+ LG+ E+L +L L +DIE
Sbjct: 301 KKLVLSVNHFDQLCQISAANFPSLTHLYIRGNVKKLHLGVGCLEKLGNLQTLDLSHNDIE 360
Query: 656 AHCCSSLEALSGLSILFT 673
A C SL+ L LS L T
Sbjct: 361 ASDCCSLQ-LKNLSHLQT 377
>pdb|1Y5E|A Chain A, Crystal Structure Of Molybdenum Cofactor Biosynthesis
Protein B
pdb|1Y5E|B Chain B, Crystal Structure Of Molybdenum Cofactor Biosynthesis
Protein B
pdb|1Y5E|C Chain C, Crystal Structure Of Molybdenum Cofactor Biosynthesis
Protein B
Length = 169
Score = 30.0 bits (66), Expect = 5.9, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 242 MMHDLLQEMGREIVRQESIKDPGKRSRL-----WHHEDIYNVLTN 281
++H+LL+E G ++ E +KD + + +H ED+ VLTN
Sbjct: 35 LLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTN 79
>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 = 29.6 bits (65), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 64/146 (43%), Gaps = 23/146 (15%)
Query: 51 KVLIVFDDVSTSEQMEFLIGNQGWLMQG----SRLIITARDKQVLKNC-GVDTIYEVKE- 104
+ L++ DDV S W+++ ++++T RDK V + G + V+
Sbjct: 237 RSLLILDDVWDS-----------WVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESS 285
Query: 105 LFDDDARMLFSRYAFGKNYPNVGYMELSNKIIKYAKGVPLAIKVLGRFLCGRRIKD-WES 163
L + + S + N E ++ IIK KG PL + ++G L R + WE
Sbjct: 286 LGKEKGLEILSLFV---NMKKADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEY 340
Query: 164 TIKKIKRIPHVDIQKVLKVSFDGLDD 189
+K+++ I+K ++ LD+
Sbjct: 341 YLKQLQNKQFKRIRKSSSYDYEALDE 366
>pdb|3K8P|D Chain D, Structural Basis For Vesicle Tethering By The Dsl1 Complex
Length = 709
Score = 29.3 bits (64), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 11/95 (11%)
Query: 269 LWHHEDIYNVLTNNTGTEAIEGISLDMSKVKEIHLNAGSFTNMHKLRFFKFYS---SHYG 325
WH +N +N E + ++ + H + + TN+ KL S SHY
Sbjct: 442 FWH---FFNNASNGLRKEPEXKKASQTLQIIQKHXSQRAGTNLTKLEVLLEISDKLSHYS 498
Query: 326 ENVNKVHNFRGLESTELR---YLQWHGCPLKSLSS 357
N+NK HN G T + L++ CPL +S+
Sbjct: 499 INLNKSHN--GARDTAFKPSNILEYRDCPLDIISN 531
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
0.322 0.138 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,210,756
Number of Sequences: 62578
Number of extensions: 1028625
Number of successful extensions: 2424
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 2409
Number of HSP's gapped (non-prelim): 30
length of query: 909
length of database: 14,973,337
effective HSP length: 108
effective length of query: 801
effective length of database: 8,214,913
effective search space: 6580145313
effective search space used: 6580145313
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)