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= 000248
(1789 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 38.5 bits (88), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 34/108 (31%), Positives = 38/108 (35%), Gaps = 55/108 (50%)
Query: 1474 LSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQD 1533
LSLIQGPPGTGKT T IV
Sbjct: 196 LSLIQGPPGTGKTVTSATIVY--------------------------------------- 216
Query: 1534 AALARQINXXXXXXXXXXXXXVRARVLICAQSNAAVDELVSRISKEGL 1581
LARQ N VL+CA SN AVD+L +I + GL
Sbjct: 217 -HLARQGN---------------GPVLVCAPSNIAVDQLTEKIHQTGL 248
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 38.5 bits (88), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 34/108 (31%), Positives = 38/108 (35%), Gaps = 55/108 (50%)
Query: 1474 LSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQD 1533
LSLIQGPPGTGKT T IV
Sbjct: 197 LSLIQGPPGTGKTVTSATIVY--------------------------------------- 217
Query: 1534 AALARQINXXXXXXXXXXXXXVRARVLICAQSNAAVDELVSRISKEGL 1581
LARQ N VL+CA SN AVD+L +I + GL
Sbjct: 218 -HLARQGN---------------GPVLVCAPSNIAVDQLTEKIHQTGL 249
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 38.5 bits (88), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 34/108 (31%), Positives = 38/108 (35%), Gaps = 55/108 (50%)
Query: 1474 LSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQD 1533
LSLIQGPPGTGKT T IV
Sbjct: 373 LSLIQGPPGTGKTVTSATIVY--------------------------------------- 393
Query: 1534 AALARQINXXXXXXXXXXXXXVRARVLICAQSNAAVDELVSRISKEGL 1581
LARQ N VL+CA SN AVD+L +I + GL
Sbjct: 394 -HLARQGN---------------GPVLVCAPSNIAVDQLTEKIHQTGL 425
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 37.4 bits (85), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 7/46 (15%)
Query: 1448 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIV 1493
T + SQ +A+ A+ S K EL++I GPPGTGKT T+V I+
Sbjct: 188 TCLDTSQKEAVLFAL----SQK---ELAIIHGPPGTGKTTTVVEII 226
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 37.4 bits (85), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 7/46 (15%)
Query: 1448 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIV 1493
T + SQ +A+ A+ S K EL++I GPPGTGKT T+V I+
Sbjct: 188 TCLDTSQKEAVLFAL----SQK---ELAIIHGPPGTGKTTTVVEII 226
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 35.4 bits (80), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/23 (73%), Positives = 17/23 (73%)
Query: 1474 LSLIQGPPGTGKTRTIVAIVSAL 1496
LSLIQGPPGTGKT T IV L
Sbjct: 377 LSLIQGPPGTGKTVTSATIVYHL 399
>pdb|4A17|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 157
Score = 32.7 bits (73), Expect = 1.8, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 6/87 (6%)
Query: 1586 GKTYKPYLVRVGNVKTVHPNSLPFFIDTLVDHRLAEERMHL----TDPKNEFCTRSSTLR 1641
G YK Y R G V V+P S+ + +V+ R E+R+H+ P N S +
Sbjct: 51 GMPYKLYHGRTGKVFNVNPRSIGVIVHRIVNGRYIEKRLHVKIEHVRPSNVKTALSKRYQ 110
Query: 1642 SNLEKLVDRIRFFEAKRANTKDGNSDP 1668
+N + + + KR +TK P
Sbjct: 111 ANDQAKAEGNK--AGKRVSTKRNPGQP 135
>pdb|2XSZ|A Chain A, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|B Chain B, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|C Chain C, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
Length = 367
Score = 32.0 bits (71), Expect = 3.0, Method: Composition-based stats.
Identities = 29/99 (29%), Positives = 38/99 (38%), Gaps = 18/99 (18%)
Query: 1452 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIV--------------SALL 1497
E+ +A V + L S K L+ GPPGTGKT +AI S +
Sbjct: 57 ENAREACGVIVELIKSKKXAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPXVGSEVY 116
Query: 1498 ATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAAL 1536
+T L +N+ I R K G I QD L
Sbjct: 117 STEIKKTEVLXENFRRAIGLRIKEGPPGII----QDVTL 151
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 32.0 bits (71), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/18 (72%), Positives = 14/18 (77%)
Query: 1476 LIQGPPGTGKTRTIVAIV 1493
L GPPGTGKT TIVA+
Sbjct: 50 LFYGPPGTGKTSTIVALA 67
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 31.6 bits (70), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 1476 LIQGPPGTGKTRTIVAIVSAL 1496
L GPPGTGKT TI+A+ L
Sbjct: 62 LFYGPPGTGKTSTILALTKEL 82
>pdb|2C9O|A Chain A, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
pdb|2C9O|B Chain B, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
pdb|2C9O|C Chain C, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
Length = 456
Score = 31.6 bits (70), Expect = 4.4, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 23/45 (51%)
Query: 1452 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1496
E+ +A V + L S K L+ GPPGTGKT +AI L
Sbjct: 43 ENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQEL 87
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 0.135 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 49,526,085
Number of Sequences: 62578
Number of extensions: 1970275
Number of successful extensions: 4625
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 4596
Number of HSP's gapped (non-prelim): 33
length of query: 1789
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1676
effective length of database: 7,902,023
effective search space: 13243790548
effective search space used: 13243790548
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: 59 (27.3 bits)