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= 005761
(678 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii
pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii Complexed With Rna-Analog
Length = 651
Score = 45.8 bits (107), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 35/162 (21%), Positives = 75/162 (46%), Gaps = 13/162 (8%)
Query: 310 EEMEKLAFICSCAIDSVKAGGSVLIPINRVGVFLQLLEQIAIFMECSSLKIPIYIISSVA 369
EE EK + +++K GG VLIP VG +++ + + +++PIY+ +
Sbjct: 406 EEAEKR--LIEVIHNTIKRGGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLDGMIW 463
Query: 370 EELLAYTNTIPEWLCKQRQEKLFSG--DPLFAHVKLIKEKKIHVFPAVHSPKLLMNWQEP 427
E +T PE+L ++ +E++F +P + + H + +++ EP
Sbjct: 464 EATAIHT-AYPEYLSRRLREQIFKEGYNPFLSEI-------FHPVANSRERQDIIDSNEP 515
Query: 428 CIVFSPHWSLRLGPTIHLLRRWSGD-HNSLLVLENEVDAELA 468
I+ + L GP++ ++ + D NS++ + + + L
Sbjct: 516 AIIIASSGMLVGGPSVEYFKQLAPDPKNSIIFVSYQAEGTLG 557
>pdb|2I7X|A Chain A, Structure Of Yeast Cpsf-100 (Ydh1p)
Length = 717
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 9/69 (13%)
Query: 324 DSVKAG----GSVLIPINRVGVFLQLLEQI-AIFMECSSL----KIPIYIISSVAEELLA 374
D++K G GSV+IP++ G FL L Q+ + E + + ++P+ I+S L
Sbjct: 232 DTLKKGLSSDGSVIIPVDMSGKFLDLFTQVHELLFESTKINAHTQVPVLILSYARGRTLT 291
Query: 375 YTNTIPEWL 383
Y ++ EWL
Sbjct: 292 YAKSMLEWL 300
>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
Length = 459
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 48/225 (21%), Positives = 90/225 (40%), Gaps = 33/225 (14%)
Query: 303 SNYDESVEEM--EKLAFICSCAIDSVKAGGSVLIPINRVGVFLQLLEQIAIFMECSS--L 358
S Y + E E+ A C+ D V GG LIP+ +G +LL + + +
Sbjct: 205 STYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELH 264
Query: 359 KIPIYIISSVAEELLAYTNTIPEWLCKQRQEKLFSGDPLFAHVKLIKEKKIHVFPAVHSP 418
IPIY SS+A++ +A T + + ++++ +P VF + +
Sbjct: 265 DIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININNPF-------------VFKHISNL 311
Query: 419 KLLMNWQE--PCIVFSPHWSLRLGPTIHLLRRWSGD-HNSLLVLENEVDAELAVLPFK-- 473
K + ++ + P +V + ++ G + L W D N +++ V+ LA
Sbjct: 312 KSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSEP 371
Query: 474 -----------PISMKVLQCSFLSGKKLQKVQPLLKILQPKLVLF 507
P+ M V SF + Q+ ++ L+P V+
Sbjct: 372 EEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVIL 416
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 325 SVKAGGSVLIPINRVGVFLQLLEQIAIFMECSSL-KIPIYIISSVAEELLAYTNTIPEWL 383
+++ GG +LIP+ VG +L+ + ++ + ++P+YI + E +T PE+L
Sbjct: 404 TLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTAR-PEYL 462
Query: 384 CKQRQEKLF 392
K ++++F
Sbjct: 463 SKDLRDQIF 471
>pdb|2VFJ|A Chain A, Structure Of The A20 Ovarian Tumour (Otu) Domain
pdb|2VFJ|B Chain B, Structure Of The A20 Ovarian Tumour (Otu) Domain
pdb|2VFJ|C Chain C, Structure Of The A20 Ovarian Tumour (Otu) Domain
pdb|2VFJ|D Chain D, Structure Of The A20 Ovarian Tumour (Otu) Domain
Length = 366
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 324 DSVKAGGSVLIPINRVGVFLQLLEQIAIFMECSSLKIPIYIISS 367
D++ S P+ R G+ LE+I IF+ C+ L+ PI +IS
Sbjct: 169 DNLIKMASTDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISD 212
>pdb|3DKB|A Chain A, Crystal Structure Of A20, 2.5 Angstrom
pdb|3DKB|B Chain B, Crystal Structure Of A20, 2.5 Angstrom
pdb|3DKB|C Chain C, Crystal Structure Of A20, 2.5 Angstrom
pdb|3DKB|D Chain D, Crystal Structure Of A20, 2.5 Angstrom
pdb|3DKB|E Chain E, Crystal Structure Of A20, 2.5 Angstrom
pdb|3DKB|F Chain F, Crystal Structure Of A20, 2.5 Angstrom
Length = 390
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 324 DSVKAGGSVLIPINRVGVFLQLLEQIAIFMECSSLKIPIYIISS 367
D++ S P+ R G+ LE+I IF+ C+ L+ PI +IS
Sbjct: 189 DNLIKMASTDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISD 232
>pdb|1J79|A Chain A, Molecular Structure Of Dihydroorotase: A Paradigm For
Catalysis Through The Use Of A Binuclear Metal Center
pdb|1J79|B Chain B, Molecular Structure Of Dihydroorotase: A Paradigm For
Catalysis Through The Use Of A Binuclear Metal Center
Length = 347
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 48/102 (47%), Gaps = 9/102 (8%)
Query: 43 PLPNDFYKAICKENSDSQNRQKVEKPLDANDLIFAE----PWYKTVNNLHLWNVSFIDVV 98
P P+DF + +DS + ++E+ N+ +F P T N+ H V+ +D +
Sbjct: 67 PAPHDFTPLMTCYLTDSLDPNELERGF--NEGVFTAAXLYPANATTNSSH--GVTSVDAI 122
Query: 99 L-ISSPMGMLGLPFLTRMEGFSAKIYITEAAARIGQLMMEEL 139
+ + M +G+P L E A I I + AR + +ME L
Sbjct: 123 MPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPL 164
>pdb|3UTN|X Chain X, Crystal Structure Of Tum1 Protein From Saccharomyces
Cerevisiae
Length = 327
Score = 28.9 bits (63), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 21/47 (44%)
Query: 5 CLCQGGGFNFPPCHILNVSGFHVLFDCPLDLSALTVFSPLPNDFYKA 51
C G P ++LN + F PLD S + FSP P Y++
Sbjct: 130 CAWTLGVMGHPKVYLLNNFNQYREFKYPLDSSKVAAFSPYPKSHYES 176
>pdb|3RG2|A Chain A, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|B Chain B, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|C Chain C, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|D Chain D, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|E Chain E, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|F Chain F, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|G Chain G, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|H Chain H, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|I Chain I, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
pdb|3RG2|J Chain J, Structure Of A Two-Domain Nrps Fusion Protein Containing
The Ente Adenylation Domain And Entb Aryl-Carrier
Protein From Enterobactin Biosynthesis
Length = 617
Score = 28.9 bits (63), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 39/95 (41%), Gaps = 11/95 (11%)
Query: 304 NYDESVEEMEKLAFICSCAIDSVKAGGSVLIPINRVGVFLQLLEQIAIFMECSSLKIP-- 361
+Y E + + LA CS +K G + L+ + V E F L +
Sbjct: 52 SYRELNQAADNLA--CSLRRQGIKPGETALVQLGNVA------ELYITFFALLKLGVAPV 103
Query: 362 IYIISSVAEELLAYTNTI-PEWLCKQRQEKLFSGD 395
+ + S EL AY + I P L RQ LFSGD
Sbjct: 104 LALFSHQRSELNAYASQIEPALLIADRQHALFSGD 138
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 0.136 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,269,162
Number of Sequences: 62578
Number of extensions: 775553
Number of successful extensions: 1441
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1434
Number of HSP's gapped (non-prelim): 12
length of query: 678
length of database: 14,973,337
effective HSP length: 105
effective length of query: 573
effective length of database: 8,402,647
effective search space: 4814716731
effective search space used: 4814716731
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: 55 (25.8 bits)