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= 013815
(436 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QAI|A Chain A, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1QAI|B Chain B, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1MML|A Chain A, Mechanistic Implications From The Structure Of A Catalytic
Fragment Of Mmlv Reverse Transcriptase
Length = 265
Score = 32.3 bits (72), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 122 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 174
>pdb|1NND|A Chain A, Arginine 116 Is Essential For Nucleic Acid Recognition By
The Fingers Domain Of Moloney Murine Leukemia Virus
Reverse Transcriptase
Length = 255
Score = 32.0 bits (71), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 108 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 160
>pdb|4HKQ|A Chain A, Protein Dna Complex
Length = 681
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 141 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 193
>pdb|1D1U|A Chain A, Use Of An N-Terminal Fragment From Moloney Murine Leukemia
Virus Reverse Transcriptase To Facilitate
Crystallization And Analysis Of A Pseudo-16-Mer Dna
Molecule Containing G- A Mispairs
pdb|1N4L|A Chain A, A Dna Analogue Of The Polypurine Tract Of Hiv-1
pdb|1ZTT|A Chain A, Netropsin Bound To D(cttaattcgaattaag) In Complex With
Mmlv Rt Catalytic Fragment
pdb|1ZTW|A Chain A, D(Cttaattcgaattaag) Complexed With Moloney Murine Leukemia
Virus Reverse Transcriptase Catalytic Fragment
pdb|2FJV|A Chain A, Rt29 Bound To D(Cttaattcgaattaag) In Complex With Mmlv Rt
Catalytic Fragment
pdb|2FJW|A Chain A, D(Cttgaatgcattcaag) In Complex With Mmlv Rt Catalytic
Fragment
pdb|2FJX|A Chain A, Rt29 Bound To D(Cttgaatgcattcaag) In Complex With Mmlv Rt
Catalytic Fragment
pdb|2FVP|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2FVQ|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2FVR|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2FVS|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2R2R|A Chain A, D(Attagttataactaat) Complexed With Mmlv Rt Catalytic
Fragment
pdb|2R2S|A Chain A, Co(Iii)bleomycinb2 Bound To D(Attagttataactaat) Complexed
With Mmlv Rt Catalytic Fragment
pdb|2R2T|A Chain A, D(Atttagttaactaaat) Complexed With Mmlv Rt Catalytic
Fragment
pdb|2R2U|A Chain A, Co(Iii)bleomycinb2 BithiazoleC-Terminal Tail Domain Bound
To D(Atttagttaactaaat) Complexed With Mmlv Rt Catalytic
Fragment
pdb|3FSI|A Chain A, Crystal Structure Of A Trypanocidal 4,4'-
Bis(Imidazolinylamino)diphenylamine Bound To Dna
Length = 255
Score = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 108 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 160
>pdb|1I6J|A Chain A, Crystal Structure Of A Pseudo-16-Mer Dna With Stacked
Guanines And Two G-A Mispairs Complexed With The N-
Terminal Fragment Of Moloney Murine Leukemia Virus
Reverse Transcriptase
Length = 256
Score = 32.0 bits (71), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 109 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 161
>pdb|1D0E|A Chain A, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1D0E|B Chain B, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1QAJ|A Chain A, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1QAJ|B Chain B, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
Length = 259
Score = 32.0 bits (71), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 112 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 164
>pdb|1RW3|A Chain A, The Crystal Structure Of The Monomeric Reverse
Transcriptase From Moloney Murine Leukemia Virus
Length = 455
Score = 31.6 bits (70), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 246 NPLRAIGGKPASQR--SIL----AFFAGRMHGYLRPILLHHWENKDPDMKIFGQM 294
NP + G P S + ++L AFF R+H +P+ W +DP+M I GQ+
Sbjct: 112 NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEW--RDPEMGISGQL 164
>pdb|2AGA|A Chain A, De-Ubiquitinating Function Of Ataxin-3: Insights From The
Solution Structure Of The Josephin Domain
Length = 190
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 348 PVIISDNFVPPFFEILNWESFAVFVLEKDIPNLK 381
P +ISD ++ F L E +++FV++ D+P+ +
Sbjct: 145 PELISDTYLALFLAQLQQEGYSIFVVKGDLPDCE 178
>pdb|2JRI|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3 In
Complex With Ubiquitin Molecule.
pdb|1YZB|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3
Length = 182
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 348 PVIISDNFVPPFFEILNWESFAVFVLEKDIPNLK 381
P +ISD ++ F L E +++FV++ D+P+ +
Sbjct: 140 PELISDTYLALFLAQLQQEGYSIFVVKGDLPDCE 173
>pdb|2DOS|A Chain A, Structural Basis For The Recognition Of Lys48-Linked
Polyubiquitin Chain By The Josephin Domain Of Ataxin-3,
A Putative Deubiquitinating Enzyme
Length = 176
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 348 PVIISDNFVPPFFEILNWESFAVFVLEKDIPN 379
P +ISD ++ F L E +++FV++ D+P+
Sbjct: 145 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 176
>pdb|3DWL|C Chain C, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
pdb|3DWL|H Chain H, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
Length = 377
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 12/72 (16%)
Query: 175 NYVNLISAKHNFWN--RTEGADHFLVACHDWAPAETRIIMANCIRALCNSDVKEGFVFGK 232
N V L N W RT +V C DWAP RI+ C+ D + +V+ K
Sbjct: 33 NQVELYEQDGNGWKHARTFSDHDKIVTCVDWAPKSNRIVT-------CSQD-RNAYVYEK 84
Query: 233 --DVALPETYVL 242
D +T VL
Sbjct: 85 RPDGTWKQTLVL 96
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
0.321 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,115,898
Number of Sequences: 62578
Number of extensions: 538985
Number of successful extensions: 1025
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1010
Number of HSP's gapped (non-prelim): 25
length of query: 436
length of database: 14,973,337
effective HSP length: 102
effective length of query: 334
effective length of database: 8,590,381
effective search space: 2869187254
effective search space used: 2869187254
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: 53 (25.0 bits)