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= 027117
(228 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZQS|A Chain A, Human Fancl Central Domain
pdb|3ZQS|B Chain B, Human Fancl Central Domain
Length = 186
Score = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 49/150 (32%), Positives = 76/150 (50%)
Query: 26 VGWEHLVRLSEDLKFLSFRVIDKKGRVHCMEIQLDKNYPRSPPSISADVPYIFNLKWSRK 85
+GW+ LV + + D GR H + ++L YP P D P F W+ +
Sbjct: 13 LGWDKLVYADTCFSTIKLKAEDASGREHLITLKLKAKYPAESPDYFVDFPVPFCASWTPQ 72
Query: 86 SRLKDLLQQFREHLEKLQEIWNILDEIDKSLWVIDLKNPSRANVCRQINLGYNCIIMLSI 145
S L + QF +E L+ W+++DEID+ WV++ + P R+ R+I LG N I + +
Sbjct: 73 SSLISIYSQFLAAIESLKAFWDVMDEIDEKTWVLEPEKPPRSATARRIALGNNVSINIEV 132
Query: 146 HIDDPSSLPECRFMGSDPMVNSLRKTWQRN 175
P+ LPEC F+G+D +V L RN
Sbjct: 133 DPRHPTMLPECFFLGADHVVKPLGIKLSRN 162
>pdb|1F2H|A Chain A, Solution Structure Of The N-Terminal Domain Of The Tnfr1
Associated Protein, Tradd
Length = 169
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 138 NCIIMLSIHIDDPSSLPECRFMGSDP---MVNSLRKTWQRNSKRCASSSSFCLLRVPIGL 194
+ + ML IH DP + + RF G P + + R+ R + + + +++ VP+ L
Sbjct: 57 DVLQMLKIHRSDPQLIVQLRFCGRQPCGRFLRAYREGALRAALQRSLAAALAQHSVPLQL 116
Query: 195 RLRC 198
LR
Sbjct: 117 ELRA 120
>pdb|1WF3|A Chain A, Crystal Structure Of Gtp-Binding Protein Tt1341 From
Thermus Thermophilus Hb8
Length = 301
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 5/35 (14%)
Query: 90 DLLQQFREHLEKLQEIWNILDEIDKSLWVIDLKNP 124
D L +F + QE++ L +++ +WV+DL++P
Sbjct: 70 DALGEFMD-----QEVYEALADVNAVVWVVDLRHP 99
>pdb|2Q0V|A Chain A, Crystal Structure Of Ubiquitin Conjugating Enzyme E2,
Putative, From Plasmodium Falciparum
Length = 156
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 49 KGRVHCMEIQLDKNYPRSPPSISADV 74
+ R++ + I D NYP SPP++ D
Sbjct: 70 ENRIYSLTIFCDDNYPDSPPTVKFDT 95
>pdb|3E95|C Chain C, Crystal Structure Of The Plasmodium Falciparum Ubiquitin
Conjugating Enzyme Complex, Pfubc13-Pfuev1a
Length = 158
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 49 KGRVHCMEIQLDKNYPRSPPSISADV 74
+ R++ + I D NYP SPP++ D
Sbjct: 74 ENRIYSLTIFCDDNYPDSPPTVKFDT 99
>pdb|1F3V|A Chain A, Crystal Structure Of The Complex Between The N-Terminal
Domain Of Tradd And The Traf Domain Of Traf2
Length = 179
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 138 NCIIMLSIHIDDPSSLPECRFMGSDP---MVNSLRKTWQRNSKRCASSSSFCLLRVPIGL 194
+ + ML IH DP + + RF G P + + R+ R + + + +++ VP+ L
Sbjct: 57 DVLQMLKIHRSDPQLIVQLRFCGRQPCGRFLRAYREGALRAALQRSLAAALAQHSVPLQL 116
Query: 195 RLRC 198
LR
Sbjct: 117 ELRA 120
>pdb|1DKG|A Chain A, Crystal Structure Of The Nucleotide Exchange Factor Grpe
Bound To The Atpase Domain Of The Molecular Chaperone
Dnak
pdb|1DKG|B Chain B, Crystal Structure Of The Nucleotide Exchange Factor Grpe
Bound To The Atpase Domain Of The Molecular Chaperone
Dnak
Length = 197
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 51 RVHCMEIQLDKNYPRSPPSISADVPYIFNLKWSRKSRLKDLLQQFREHLEK-LQEIWNIL 109
+V +E QL + R I + NL+ R++ L D+ + + LEK + E+ ++
Sbjct: 43 KVANLEAQLAEAQTRERDGILRVKAEMENLR--RRTEL-DIEKAHKFALEKFINELLPVI 99
Query: 110 DEIDKSLWVIDLKNPSRANVCRQINLGYNCII 141
D +D++L V D NP + + I L ++
Sbjct: 100 DSLDRALEVADKANPDMSAMVEDIELTLKSML 131
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 27.7 bits (60), Expect = 5.3, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 61 KNYPRSPPSISADVPYIFNLK-WS-RKSRLKDLLQQFREHLEKLQEIWNILDEIDKSLWV 118
+N P + Y+ ++ WS K R + LL+Q +E K E+ N+L K +W
Sbjct: 692 ENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQE---KETELENLLKLSAKDIWN 748
Query: 119 IDLK 122
DLK
Sbjct: 749 TDLK 752
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 27.7 bits (60), Expect = 5.8, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 61 KNYPRSPPSISADVPYIFNLK-WS-RKSRLKDLLQQFREHLEKLQEIWNILDEIDKSLWV 118
+N P + Y+ ++ WS K R + LL+Q +E K E+ N+L K +W
Sbjct: 682 ENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQE---KETELENLLKLSAKDIWN 738
Query: 119 IDLK 122
DLK
Sbjct: 739 TDLK 742
>pdb|3E1B|Z Chain Z, Structure Of The 50s Subunit Of E. Coli Ribosome In
Pre-Accommodation State
pdb|3E1D|Z Chain Z, Structure Of The 50s Subunit Of E. Coli Ribosome In
Post-Accommodation State
Length = 213
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 40 FLSFRVIDKKGRVHCMEIQLDKNYPRSPPSISADVPYIFNLKWSRKSRLKDLLQQFREHL 99
L+F+ IDKKG + EI P + VP L++++K+ K ++ RE L
Sbjct: 33 ILTFKGIDKKGDLKLREIVPLPKQPSKAKRVLV-VPSSEQLEYAKKASPKVVIT--REEL 89
Query: 100 EKLQ 103
+KLQ
Sbjct: 90 QKLQ 93
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
0.323 0.138 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,218,565
Number of Sequences: 62578
Number of extensions: 230845
Number of successful extensions: 611
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: 607
Number of HSP's gapped (non-prelim): 10
length of query: 228
length of database: 14,973,337
effective HSP length: 95
effective length of query: 133
effective length of database: 9,028,427
effective search space: 1200780791
effective search space used: 1200780791
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)