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= 022965
(289 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 = 113 bits (282), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 54/173 (31%), Positives = 88/173 (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 HIDDPSSLPECRFMGSDPMVNSLRKTWQRNSKRWNKDKPFVENVANLLETQLP 198
P+ LPEC F+G+D +V L RN W+ + ++N+ ++LE P
Sbjct: 133 DPRHPTMLPECFFLGADHVVKPLGIKLSRNIHLWDPENSVLQNLKDVLEIDFP 185
>pdb|3K1L|B Chain B, Crystal Structure Of Fancl
pdb|3K1L|A Chain A, Crystal Structure Of Fancl
Length = 381
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 48/208 (23%), Positives = 88/208 (42%), Gaps = 20/208 (9%)
Query: 88 LKDLLQQFREHLEKLQEIWNILDEIDKSLWVIDLKNPSRANVCRQINLGYNCIIMLSIHI 147
L++ L FR+ LE L+ ++ +ID+ V+ S + R L + L + I
Sbjct: 179 LEEALNLFRKLLEDLRPFYDNFMDIDELCHVLQPSPISSKHKTRLFPLKDR--VYLKLTI 236
Query: 148 DDPSSL---PECRFMGSDPMVNSLRKTWQRNSKRWNKDKPFVENVANLLET-QLPRP--- 200
DP + + +G V LR W+ + +N+ + + P P
Sbjct: 237 ADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCYFPMPDWS 296
Query: 201 --PE-HENNYQQVECGICYAQFLPIDEELGAKSGGGTDYTCDNSSCSKAFHSVCLGDWLR 257
P+ E + +++ C IC+A L G +CDN+ C H+VCL +W +
Sbjct: 297 DGPKLDEEDNEELRCNICFAYRL--------DGGEVPLVSCDNAKCVLKCHAVCLEEWFK 348
Query: 258 SITTTRQSYDVLFGNCPYCSEPVAVKIS 285
++ + +V FG CP+C ++ +
Sbjct: 349 TLMDGKTFLEVSFGQCPFCKAKLSTSFA 376
>pdb|2BG9|A Chain A, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution.
pdb|2BG9|D Chain D, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 189 VANLLET--QLPRPPEHENNYQQVECGICYAQFLPIDE 224
VANLLE ++ RP EH ++ + G+ Q + +DE
Sbjct: 8 VANLLENYNKVIRPVEHHTHFVDITVGLQLIQLINVDE 45
>pdb|4AQ5|A Chain A, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ5|D Chain D, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|A Chain A, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
pdb|4AQ9|D Chain D, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 461
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 189 VANLLET--QLPRPPEHENNYQQVECGICYAQFLPIDE 224
VANLLE ++ RP EH ++ + G+ Q + +DE
Sbjct: 32 VANLLENYNKVIRPVEHHTHFVDITVGLQLIQLINVDE 69
>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 = 28.9 bits (63), Expect = 3.3, 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|2LGV|A Chain A, Rbx1
Length = 100
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 212 CGICYAQFLPIDEELGAKSGGGTDYTCDNS--SCSKAFHSVCLGDWLRS 258
C IC + + E A T C + C+ AFH C+ WL++
Sbjct: 34 CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT 82
>pdb|2Q0V|A Chain A, Crystal Structure Of Ubiquitin Conjugating Enzyme E2,
Putative, From Plasmodium Falciparum
Length = 156
Score = 28.1 bits (61), Expect = 5.8, 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 = 5.8, 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|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr-
Ring (Triad) Motif
Length = 60
Score = 28.1 bits (61), Expect = 6.4, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 229 KSGGGTDYTCDNSSCSKAFHSVCLGDW 255
K GG C N +C F VCLG W
Sbjct: 18 KDGGCNHMVCRNQNCKAEFCWVCLGPW 44
>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 = 27.3 bits (59), Expect = 9.2, 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
0.320 0.136 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,581,838
Number of Sequences: 62578
Number of extensions: 355531
Number of successful extensions: 880
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 874
Number of HSP's gapped (non-prelim): 21
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
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: 51 (24.3 bits)