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= 015600
(404 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XJV|A Chain A, Crystal Structure Of Human Pot1 Bound To Telomeric Single-
Stranded Dna (Ttagggttag)
Length = 294
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 56/178 (31%), Positives = 91/178 (51%), Gaps = 12/178 (6%)
Query: 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83
VN+ GVV F P S+GTDY V+ IVD Q + +L +F+ + + LP + D++
Sbjct: 18 VNVYGVVKFFKPPYLSKGTDYCSVVTIVD--QTNVKLTCLLFSGNYEALPIIYKNGDIVR 75
Query: 84 LKNVMIKKHQAELSAVFYKDSSSFA--LFDGNSGSNLLPYQSSPQRFEITEAEERRINVL 141
+ I+ ++ E + SS FA F+G G+ ++P ++S + F T + + + L
Sbjct: 76 FHRLKIQVYKKETQGI---TSSGFASLTFEGTLGAPIIP-RTSSKYFNFTTEDHKMVEAL 131
Query: 142 RQWCVGFEFSSGSNDYLLSLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVP 199
R W S + LL L D+ +YFDL C++ + D ++L VWDGT P
Sbjct: 132 RVWASTHMSPSWT---LLKLCDVQPMQYFDLTCQLLGKAEVDGAS-FLLKVWDGTRTP 185
>pdb|3KJO|A Chain A, Crystal Structure Of Hpot1v2-Dtrud(Agggttag)
pdb|3KJP|A Chain A, Crystal Structure Of Hpot1v2-Ggttagggttag
Length = 299
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 56/178 (31%), Positives = 91/178 (51%), Gaps = 12/178 (6%)
Query: 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83
VN+ GVV F P S+GTDY V+ IVD Q + +L +F+ + + LP + D++
Sbjct: 23 VNVYGVVKFFKPPYLSKGTDYCSVVTIVD--QTNVKLTCLLFSGNYEALPIIYKNGDIVR 80
Query: 84 LKNVMIKKHQAELSAVFYKDSSSFA--LFDGNSGSNLLPYQSSPQRFEITEAEERRINVL 141
+ I+ ++ E + SS FA F+G G+ ++P ++S + F T + + + L
Sbjct: 81 FHRLKIQVYKKETQGI---TSSGFASLTFEGTLGAPIIP-RTSSKYFNFTTEDHKMVEAL 136
Query: 142 RQWCVGFEFSSGSNDYLLSLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVP 199
R W S + LL L D+ +YFDL C++ + D ++L VWDGT P
Sbjct: 137 RVWASTHMSPSWT---LLKLCDVQPMQYFDLTCQLLGKAEVDGAS-FLLKVWDGTRTP 190
>pdb|1K8G|A Chain A, Crystal Structure Of The N-Terminal Domain Of Oxytricha
Nova Telomere End Binding Protein Alpha Subunit Both
Uncomplexed And Complexed With Telomeric Ssdna
pdb|1K8G|B Chain B, Crystal Structure Of The N-Terminal Domain Of Oxytricha
Nova Telomere End Binding Protein Alpha Subunit Both
Uncomplexed And Complexed With Telomeric Ssdna
pdb|1K8G|C Chain C, Crystal Structure Of The N-Terminal Domain Of Oxytricha
Nova Telomere End Binding Protein Alpha Subunit Both
Uncomplexed And Complexed With Telomeric Ssdna
Length = 320
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 84/183 (45%), Gaps = 30/183 (16%)
Query: 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDS----QQ------SPELLVNIFTSSIDQLPR 74
+ VV++ + P K+ Y+C LKIVD + QQ S + ++ + LP
Sbjct: 53 HFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPI 112
Query: 75 VLSPRDLILLKNVMIKKH--QAELSA-VFYKDSSSFALF------------DGNSGSNLL 119
+ D+I + ++ + Q + +A VFY SSS+ALF + ++ S+
Sbjct: 113 IHRAGDIIRVHRATLRLYNGQRQFNANVFY--SSSWALFSTDKRSVTQEINNQDAVSDTT 170
Query: 120 PYQSSPQRFEITEAEERRINVLRQWCVGF--EFSSGSNDYLLSL-KDISEHRYFDLVCKV 176
P+ S + I + E + LR+W + +S S+D +L K ++ FD+V K+
Sbjct: 171 PFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKI 230
Query: 177 FHV 179
V
Sbjct: 231 LQV 233
>pdb|1PA6|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttgagg
pdb|1PH3|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttggtg
pdb|1PH4|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttggcg
pdb|1PH7|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttgigg
pdb|1PH8|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttgcgg
pdb|1PH9|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere
End-Binding Protein Complexed With Noncognate Ssdna
Ggggttttgagg
Length = 460
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 83/180 (46%), Gaps = 30/180 (16%)
Query: 28 GVVLEFSIPRKSQGTDYVCVLKIVDDS----QQ------SPELLVNIFTSSIDQLPRVLS 77
VV++ + P K+ Y+C LKIVD + QQ S + ++ + LP +
Sbjct: 21 AVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHR 80
Query: 78 PRDLILLKNVMIKKH--QAELSA-VFYKDSSSFALF------------DGNSGSNLLPYQ 122
D+I + ++ + Q + +A VFY SSS+ALF + ++ S+ P+
Sbjct: 81 AGDIIRVHRATLRLYNGQRQFNANVFY--SSSWALFSTDKRSVTQEINNQDAVSDTTPFS 138
Query: 123 SSPQRFEITEAEERRINVLRQWCVGF--EFSSGSNDYLLSL-KDISEHRYFDLVCKVFHV 179
S + I + E + LR+W + +S S+D +L K ++ FD+V K+ V
Sbjct: 139 FSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQV 198
>pdb|1OTC|A Chain A, The O. Nova Telomere End Binding Protein Complexed With
Single Strand Dna
pdb|1JB7|A Chain A, Dna G-Quartets In A 1.86 A Resolution Structure Of An
Oxytricha Nova Telomeric Protein-Dna Complex
pdb|1KIX|A Chain A, Dimeric Structure Of The O. Nova Telomere End Binding
Protein Alpha Subunit With Bound Ssdna
pdb|2I0Q|A Chain A, Crystal Structure Of A Telomere Single-Strand Dna-Protein
Complex From O. Nova With Full-Length Alpha And Beta
Telomere Proteins
Length = 495
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 83/180 (46%), Gaps = 30/180 (16%)
Query: 28 GVVLEFSIPRKSQGTDYVCVLKIVDDS----QQ------SPELLVNIFTSSIDQLPRVLS 77
VV++ + P K+ Y+C LKIVD + QQ S + ++ + LP +
Sbjct: 56 AVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHR 115
Query: 78 PRDLILLKNVMIKKH--QAELSA-VFYKDSSSFALF------------DGNSGSNLLPYQ 122
D+I + ++ + Q + +A VFY SSS+ALF + ++ S+ P+
Sbjct: 116 AGDIIRVHRATLRLYNGQRQFNANVFY--SSSWALFSTDKRSVTQEINNQDAVSDTTPFS 173
Query: 123 SSPQRFEITEAEERRINVLRQWCVGF--EFSSGSNDYLLSL-KDISEHRYFDLVCKVFHV 179
S + I + E + LR+W + +S S+D +L K ++ FD+V K+ V
Sbjct: 174 FSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQV 233
>pdb|1PH2|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttg
pdb|1PH5|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttg(3dr)gg
Length = 459
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 83/180 (46%), Gaps = 30/180 (16%)
Query: 28 GVVLEFSIPRKSQGTDYVCVLKIVDDS----QQ------SPELLVNIFTSSIDQLPRVLS 77
VV++ + P K+ Y+C LKIVD + QQ S + ++ + LP +
Sbjct: 21 AVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHR 80
Query: 78 PRDLILLKNVMIKKH--QAELSA-VFYKDSSSFALF------------DGNSGSNLLPYQ 122
D+I + ++ + Q + +A VFY SSS+ALF + ++ S+ P+
Sbjct: 81 AGDIIRVHRATLRLYNGQRQFNANVFY--SSSWALFSTDKRSVTQEINNQDAVSDTTPFS 138
Query: 123 SSPQRFEITEAEERRINVLRQWCVGF--EFSSGSNDYLLSL-KDISEHRYFDLVCKVFHV 179
S + I + E + LR+W + +S S+D +L K ++ FD+V K+ V
Sbjct: 139 FSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQV 198
>pdb|1PH1|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttggggt
pdb|1PH6|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna
Ggggttttgtgg
pdb|1PHJ|A Chain A, Crystal Structure Of The Oxytricha Nova Telomere End-
Binding Protein Complexed With Noncognate Ssdna Gg(3dr)
Gttttgggg
Length = 461
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 83/180 (46%), Gaps = 30/180 (16%)
Query: 28 GVVLEFSIPRKSQGTDYVCVLKIVDDS----QQ------SPELLVNIFTSSIDQLPRVLS 77
VV++ + P K+ Y+C LKIVD + QQ S + ++ + LP +
Sbjct: 22 AVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHR 81
Query: 78 PRDLILLKNVMIKKH--QAELSA-VFYKDSSSFALF------------DGNSGSNLLPYQ 122
D+I + ++ + Q + +A VFY SSS+ALF + ++ S+ P+
Sbjct: 82 AGDIIRVHRATLRLYNGQRQFNANVFY--SSSWALFSTDKRSVTQEINNQDAVSDTTPFS 139
Query: 123 SSPQRFEITEAEERRINVLRQWCVGF--EFSSGSNDYLLSL-KDISEHRYFDLVCKVFHV 179
S + I + E + LR+W + +S S+D +L K ++ FD+V K+ V
Sbjct: 140 FSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQV 199
>pdb|1GKN|A Chain A, Structure Determination And Rational Mutagenesis Reveal
Binding Surface Of Immune Adherence Receptor, Cr1 (Cd35)
Length = 128
Score = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 208 EDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYENFGRYFTAT 257
E E H P H + L +T + FP+GT L+ Y +GR F+ T
Sbjct: 1 EAEAHCQAPDHFLFAKLKTQTTASDFPIGTSLKYECRPEY--YGRPFSIT 48
>pdb|4B28|A Chain A, Crystal Structure Of Dmsp Lyase Rddddp From Roseobacter
Denitrificans
Length = 470
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 256 ATGKWVRIRNMSCQVSSGMWHGLLQ-SSSKIRLFSDNDNV-VWDYMRRFRERISGGHGHM 313
A + R R ++ V + + GLL IR +D+ N+ +W+ FR + G+M
Sbjct: 76 AAMRRFRHRRLTDHVVARGYAGLLMFDPLNIRYATDSTNMQLWNTHNPFRATLLCADGYM 135
Query: 314 PIWTDPSSQFLTEVD 328
+W +S FL+E +
Sbjct: 136 VMWDYKNSPFLSEFN 150
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 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,116,154
Number of Sequences: 62578
Number of extensions: 487754
Number of successful extensions: 1069
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1063
Number of HSP's gapped (non-prelim): 9
length of query: 404
length of database: 14,973,337
effective HSP length: 101
effective length of query: 303
effective length of database: 8,652,959
effective search space: 2621846577
effective search space used: 2621846577
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)